# Generic rules
-*.c filter=uncrustify
-*.cpp filter=uncrustify
+*.c filter=uncrustify gmx-doxygen
+*.cpp filter=uncrustify gmx-doxygen
*.cu filter=uncrustify
-*.h filter=uncrustify
+*.h filter=uncrustify gmx-doxygen
*.cuh filter=uncrustify
CMakeLists.txt filter=copyright
*.cmake filter=copyright
*.cmakein filter=copyright
*.py filter=copyright
-*.l filter=copyright
-*.y filter=copyright
-*.pre filter=copyright
+*.l filter=includesort
+*.y filter=includesort
+*.pre filter=includesort
*.tex filter=copyright
*.bm filter=copyright
# Exceptions: extra files to include
cmake/FindLAPACK.cmake !filter
cmake/ThreadMPI.cmake !filter
cmake/Platform/BluegeneQ*.cmake !filter
-cmake/*.c !filter
+cmake/*.c -filter -gmx-doxygen
+cmake/*.cpp -filter -gmx-doxygen
cmake/*.c.cmakein !filter
docs/doxygen/Doxyfile-*.cmakein !filter
docs/doxygen/*.cpp !filter
docs/manual/UseLATEX.cmake !filter
scripts/GMXRC.* !filter
scripts/make_gromos_rtp.py !filter
-src/contrib/* !filter
-src/gromacs/gmxlib/gpu_utils/memtestG80_core.* !filter
+src/contrib/* -filter -gmx-doxygen
src/gromacs/gmxlib/nonbonded/preprocessor/gmxpreprocess.py !filter
src/gromacs/linearalgebra/gmx_blas/* !filter
src/gromacs/linearalgebra/gmx_lapack/* !filter
-src/gromacs/selection/parser.cpp !filter
-src/gromacs/selection/parser.h !filter
-src/gromacs/selection/scanner.cpp !filter
-src/gromacs/selection/scanner_flex.h !filter
-nb_kernel_Elec* filter=copyright
+src/gromacs/selection/parser.cpp -filter -gmx-doxygen
+src/gromacs/selection/parser.h -filter -gmx-doxygen
+src/gromacs/selection/scanner.cpp -filter -gmx-doxygen
+src/gromacs/selection/scanner_flex.h -filter
+nb_kernel_Elec* filter=copyright -gmx-doxygen
+nb_kernel*pre filter=copyright
+*.eps binary
+*.jpg binary
+*.svg binary
+*.png binary
+*.pdf binary
+*.ogl binary
+*.gif binary
+*.jpg binary
+*.tpr binary
+*.trr binary
+*.tng binary
+*.xtc binary
+*.edr binary
+*.cpt binary
.project
.cproject
CMakeLists.txt.user
+/VersionInfo*.cmake
--- /dev/null
+language: cpp
+
+before_install:
+ - echo "yes" | sudo add-apt-repository ppa:kalakris/cmake #https://github.com/travis-ci/travis-ci/issues/2212
+ - sudo apt-get update
+ - sudo apt-get install libfftw3-dev libopenmpi-dev libx11-dev zlib1g-dev libgsl0-dev libxml2-dev libblas-dev liblapack-dev libboost-dev cmake
+
+env:
+ matrix:
+ - GMX_DOUBLE=OFF GMX_MPI=OFF
+ - GMX_DOUBLE=OFF GMX_MPI=ON
+ - GMX_DOUBLE=ON GMX_MPI=OFF
+ - GMX_DOUBLE=ON GMX_MPI=ON
+
+script:
+ - mkdir build && pushd build && cmake -DGMX_DOUBLE=$GMX_DOUBLE -DGMX_MPI=$GMX_MPI .. && make -j4
+
+compiler:
+ - clang
+ - gcc
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
-# PROJECT_VERSION should have the following structure:
-# VERSION-dev[-SUFFIX] where the VERSION should have the for: vMajor.vMinor.vPatch
-#
-# The "-dev" suffix is important to keep because it makes possible to distinguish
-# between a build from official release and a build from git release branch on a
-# machine with no git.
-#
-# NOTE: when releasing the "-dev" suffix needs to be stripped off!
-# REGRESSIONTEST_VERSION and REGRESSIONTEST_BRANCH should always be
-# defined.
-set(PROJECT_VERSION "5.0.5-dev")
-# If this is a released tarball, "-dev" will not be present in
-# PROJECT_VERSION, and REGRESSIONTEST_VERSION specifies the version
-# number of the regressiontest tarball against which the code tarball
-# can be tested. This will be the version of the last patch release.
-set(REGRESSIONTEST_VERSION "5.0.5-dev")
-# The MD5 checksum of the regressiontest tarball. Only used if "-dev"
-# is not present in the PROJECT_VERSION
-set(REGRESSIONTEST_MD5SUM "81e8ff1600495ce2a57706dca9d73482")
-# If this is not a released tarball, "-dev" will be present in
-# PROJECT_VERSION, and REGRESSIONTEST_BRANCH specifies the name of the
-# gerrit.gromacs.org branch whose HEAD can test this code, *if* this
-# code contains all recent fixes from the corresponding code branch.
-set(REGRESSIONTEST_BRANCH "refs/heads/release-5-0")
-
-set(CUSTOM_VERSION_STRING ""
- CACHE STRING "Custom version string (if empty, use hard-coded default)")
-mark_as_advanced(CUSTOM_VERSION_STRING)
-if (CUSTOM_VERSION_STRING)
- set(PROJECT_VERSION ${CUSTOM_VERSION_STRING})
-endif()
-set(LIBRARY_SOVERSION 0)
-set(LIBRARY_VERSION ${LIBRARY_SOVERSION}.0.0)
-# It is a bit irritating, but this has to be set separately for now!
-SET(CPACK_PACKAGE_VERSION_MAJOR "5")
-SET(CPACK_PACKAGE_VERSION_MINOR "0")
-#SET(CPACK_PACKAGE_VERSION_PATCH "0")
-
-# The numerical gromacs version. It is 40600 for 4.6.0.
-# The #define GMX_VERSION in gromacs/version.h is set to this value.
-math(EXPR NUM_VERSION
- "${CPACK_PACKAGE_VERSION_MAJOR}*10000 + ${CPACK_PACKAGE_VERSION_MINOR}*100")
-if(CPACK_PACKAGE_VERSION_PATCH)
- math(EXPR NUM_VERSION
- "${NUM_VERSION} + ${CPACK_PACKAGE_VERSION_PATCH}")
-endif()
-
-# The API version tracks the numerical Gromacs version (for now).
-# It is potentially different from the Gromacs version in the future, if
-# the programs/libraries diverge from the presumably more stable API.
-# The #define GMX_API_VERSION in version.h is set to this value to
-# provide backward compatibility of software written against the Gromacs API.
-set(API_VERSION ${NUM_VERSION})
+# Set up common version variables, as well as general information about
+# the build tree (whether the build is from a source package or from a git
+# repository). Also declares a few functions that will be used for generating
+# version info files later.
+include(gmxVersionInfo)
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND UNIX)
set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
endif()
include(gmxBuildTypeReference)
+include(gmxBuildTypeProfile)
include(gmxBuildTypeTSAN)
include(gmxBuildTypeASAN)
include(gmxBuildTypeReleaseWithAssert)
if(NOT CMAKE_BUILD_TYPE)
- set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference RelWithAssert." FORCE)
+ set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference RelWithAssert Profile." FORCE)
# There's no need to offer a user the choice of ThreadSanitizer
# Set the possible values of build type for cmake-gui
set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
- "MinSizeRel" "RelWithDebInfo" "Reference" "RelWithAssert")
+ "MinSizeRel" "RelWithDebInfo" "Reference" "RelWithAssert" "Profile")
endif()
if(CMAKE_CONFIGURATION_TYPES)
# Add appropriate GROMACS-specific build types for the Visual
"List of configuration types"
FORCE)
endif()
-set(build_types_with_explicit_flags RELEASE DEBUG RELWITHDEBINFO RELWITHASSERT MINSIZEREL)
+set(build_types_with_explicit_flags RELEASE DEBUG RELWITHDEBINFO RELWITHASSERT MINSIZEREL PROFILE)
-enable_language(C)
-enable_language(CXX)
set_property(GLOBAL PROPERTY FIND_LIBRARY_USE_LIB64_PATHS ON)
-set(CPACK_PACKAGE_NAME "gromacs")
-set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION})
-set(CPACK_SOURCE_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}")
-set(CPACK_PACKAGE_VENDOR "gromacs.org")
-set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
-set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt")
-# Its GPL/LGPL, so they do not have to agree to a license for mere usage, but some installers require this...
-set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
-set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/admin/InstallInfo.txt")
-set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$;\\\\.gitattributes;")
-set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake")
-# CPack source archives include only the directories we list here.
-# This variable is a list of pairs of names of source and destination
-# directories. Most of these are used for content GROMACS generates as
-# part of the configuration or build.
-set(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/src/programs/completion;src/programs/completion;${CMAKE_BINARY_DIR}/docs/man/man1;docs/man/man1;${CMAKE_BINARY_DIR}/docs/man/man7;docs/man/man7;${CMAKE_BINARY_DIR}/docs/old-html/final;docs/old-html/final;${CMAKE_BINARY_DIR}/docs/install-guide/final;/")
-set(CPACK_PACKAGE_CONTACT "gmx-users@gromacs.org")
-set(CPACK_GMX_BUILD_HELP "${GMX_BUILD_HELP}") #Works even though GMX_BUILD_HELP is defined later because it is off by default.
-
-#must come after all cpack settings!
-include(CPack)
-
# Set a default valgrind suppression file.
# This unfortunately needs to duplicate information from CTest to work as
# expected...
"File that contains suppressions for the memory checker")
include(CTest)
-set(SOURCE_IS_GIT_REPOSITORY OFF)
-set(SOURCE_IS_SOURCE_DISTRIBUTION OFF)
-if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
- set(SOURCE_IS_GIT_REPOSITORY ON)
-endif()
-if(NOT EXISTS "${CMAKE_SOURCE_DIR}/admin/.isreposource")
- set(SOURCE_IS_SOURCE_DISTRIBUTION ON)
-endif()
+include(gmxCPackUtilities)
+gmx_cpack_init()
+
+# Variables that accumulate stuff influencing the installed headers
+set(INSTALLED_HEADER_INCLUDE_DIRS "")
+set(INSTALLED_HEADER_DEFINITIONS "")
########################################################################
# Check and warn if cache generated on a different host is being reused
set(REQUIRED_CUDA_COMPUTE_CAPABILITY 2.0)
include(gmxManageGPU)
-if(GMX_CPU_ACCELERATION)
- # Stay compatible with old Jenkins command line options for specific SIMD acceleration
- set(GMX_SIMD "${GMX_CPU_ACCELERATION}" CACHE STRING "SIMD instruction set level and compiler optimization" FORCE)
- message("You set GMX_CPU_ACCELERATION, which is deprecated, and will be removed in a later version of GROMACS. It is replaced by GMX_SIMD. For now, copying the value from GMX_CPU_ACCELERATION to GMX_SIMD.")
- # TODO remove all references to GMX_CPU_ACCELERATION in master branch
-endif()
-
-if(NOT GMX_TARGET_MIC)
- include(gmxDetectSimd)
- gmx_detect_simd(GMX_SUGGESTED_SIMD)
-else()
- set(GMX_SUGGESTED_SIMD "None")
-endif()
+include(gmxDetectSimd)
+gmx_detect_simd(GMX_SUGGESTED_SIMD)
gmx_option_multichoice(
GMX_SIMD
"SIMD instruction set for CPU kernels and compiler optimization"
"${GMX_SUGGESTED_SIMD}"
- None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 IBM_QPX Sparc64_HPC_ACE Reference)
+ None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 MIC ARM_NEON ARM_NEON_ASIMD IBM_QPX IBM_VMX IBM_VSX Sparc64_HPC_ACE Reference)
+
+if(GMX_TARGET_MIC)
+ set(GMX_FFT_LIBRARY_DEFAULT "mkl")
+else()
+ set(GMX_FFT_LIBRARY_DEFAULT "fftw3")
+endif()
gmx_option_multichoice(
GMX_FFT_LIBRARY
"FFT library"
- "fftw3"
+ "${GMX_FFT_LIBRARY_DEFAULT}"
fftw3 mkl "fftpack[built-in]")
gmx_dependent_option(
GMX_BUILD_OWN_FFTW
option(GMX_USE_TNG "Use the TNG library for trajectory I/O" ON)
-option(GMX_GIT_VERSION_INFO "Generate git version information" ${SOURCE_IS_GIT_REPOSITORY})
-mark_as_advanced(GMX_GIT_VERSION_INFO)
-
-if(UNIX)
- option(GMX_SYMLINK_OLD_BINARY_NAMES "Create symbolic links for pre-5.0 binary names" ON)
-endif()
option(GMX_BUILD_MDRUN_ONLY "Build and install only the mdrun binary" OFF)
option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
endif()
-
-set(PKG_CFLAGS "")
if(GMX_DOUBLE)
add_definitions(-DGMX_DOUBLE)
- set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
+ list(APPEND INSTALLED_HEADER_DEFINITIONS "-DGMX_DOUBLE")
if(GMX_RELAXED_DOUBLE_PRECISION)
add_definitions(-DGMX_RELAXED_DOUBLE_PRECISION)
endif()
endif()
if(GMX_SOFTWARE_INVSQRT)
- set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
+ list(APPEND INSTALLED_HEADER_DEFINITIONS "-DGMX_SOFTWARE_INVSQRT")
endif()
-if(WIN32 AND NOT CYGWIN)
+if(WIN32)
list(APPEND GMX_EXTRA_LIBRARIES "wsock32")
add_definitions(-DGMX_HAVE_WINSOCK)
endif()
check_function_exists(rsqrt HAVE_RSQRT)
check_function_exists(rsqrtf HAVE_RSQRTF)
check_function_exists(sqrtf HAVE_SQRTF)
+check_function_exists(nice HAVE_NICE)
include(CheckLibraryExists)
check_library_exists(m sqrt "" HAVE_LIBM)
check_library_exists(rt clock_gettime "" HAVE_CLOCK_GETTIME)
+check_library_exists(m feenableexcept "" HAVE_FEENABLEEXCEPT)
include(TestSchedAffinity)
test_sched_affinity(HAVE_SCHED_AFFINITY)
include(TestBigEndian)
test_big_endian(GMX_INTEGER_BIG_ENDIAN)
+set(GMX_USE_NICE 0)
+if (HAVE_UNISTD_H AND HAVE_NICE)
+ set(GMX_USE_NICE 1)
+endif()
+
# Management of GROMACS options for specific toolchains should go
# here. Because the initial settings for some of the main options have
# already happened, but things like library detection and MPI compiler
if(GMX_THREAD_MPI)
# enable MPI functions
tmpi_enable()
- set(GMX_MPI 1)
set(MPI_IN_PLACE_EXISTS 1)
endif()
# If atomics are manually disabled a define is needed because atomics.h doesn't depend on config.h
set(GMX_CYGWIN 1)
endif()
-if(WIN32 AND NOT CYGWIN)
+if(WIN32)
set(GMX_NATIVE_WINDOWS 1)
# This makes windows.h not declare min/max as macros that would break
# C++ code using std::min/std::max.
add_definitions(-DNOMINMAX)
endif()
-# only bother with finding git and using version.h if the source is a git repo
-if(GMX_GIT_VERSION_INFO)
- if (NOT SOURCE_IS_GIT_REPOSITORY)
- message(FATAL_ERROR
- "Cannot generate git version information from source tree not under git. "
- "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
- endif()
- # We need at least git v1.5.3 be able to parse git's date output. If not
- # found or the version is too small, we can't generate version information.
- find_package(Git)
-
- if(NOT GIT_FOUND OR GIT_VERSION_STRING VERSION_LESS "1.5.3")
- message(FATAL_ERROR
- "No compatible git version found (>= 1.5.3 required). "
- "Won't be able to generate development version information. "
- "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
- endif()
-endif()
-
# Detect boost unless GMX_EXTERNAL_BOOST is explicitly OFF
# Used for default if GMX_EXTERNAL_BOOST is not defined (first CMake pass)
if(NOT DEFINED GMX_EXTERNAL_BOOST OR GMX_EXTERNAL_BOOST)
+ if(DEFINED Boost_INCLUDE_DIR)
+ set(Boost_FIND_QUIETLY TRUE)
+ endif()
find_package(Boost 1.44.0)
if(Boost_FOUND AND Boost_VERSION VERSION_LESS "104400")
set(Boost_FOUND FALSE)
gmx_test_zlib(HAVE_ZLIB)
endif()
-########################################################################
-# Generate development version info for cache
-########################################################################
-# set(GEN_VERSION_INFO_INTERNAL "ON")
-# include(gmxGenerateVersionString)
-
########################################################################
# Our own GROMACS tests
########################################################################
include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include)
# Required for config.h, maybe should only be set in src/CMakeLists.txt
include_directories(BEFORE ${CMAKE_BINARY_DIR}/src)
-# Required for gmx_header_config_gen.h to be found before installation
-include_directories(BEFORE ${CMAKE_BINARY_DIR}/src/gromacs/utility)
-# Required for now to make old code compile
-include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
include(gmxTestInlineASM)
gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
set(GMX_USE_PLUGINS OFF)
if(GMX_LOAD_PLUGINS)
- if(CYGWIN OR NOT WIN32)
+ if(NOT WIN32)
# Native Windows does not have, nor need dlopen
- # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
include(gmxTestdlopen)
gmx_test_dlopen(HAVE_DLOPEN)
endif()
# so, should we use plug-ins?
- if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
+ if(WIN32 OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
if(NOT VMD_QUIETLY)
MESSAGE(STATUS "Using dynamic plugins (e.g VMD-supported file formats)")
endif()
if (GMX_NACL)
list(APPEND GMX_EXTRA_LIBRARIES nosys)
set(GMX_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lnosys")
- set(GMX_NO_NICE 1)
+ # TODO: Is this still necessary with the check for its presence?
+ set(GMX_USE_NICE 0)
set(GMX_NO_RENAME 1)
endif()
mark_as_advanced(GMX_NACL)
include_directories(${COREWRAP_INCLUDE_DIR})
endif()
-option(GMX_BUILD_HELP "Build man pages, HTML help, and completions automatically (requires that compiled binaries can be executed on the build host)" OFF)
+# Value of AUTO tries to generate things, but will only produce warnings if
+# that fails.
+set(build_help_default AUTO)
+if (SOURCE_IS_SOURCE_DISTRIBUTION)
+ set(build_help_default OFF)
+endif()
+gmx_option_trivalue(GMX_BUILD_HELP "Build man pages, HTML help, and completions automatically (requires that compiled binaries can be executed on the build host)" ${build_help_default})
mark_as_advanced(GMX_BUILD_HELP)
-if (GMX_BUILD_HELP AND SOURCE_IS_SOURCE_DISTRIBUTION AND
- "${CMAKE_CURRENT_SOURCE_DIR}" STREQUAL "${CMAKE_CURRENT_BINARY_DIR}")
-
+if (GMX_BUILD_HELP AND SOURCE_IS_SOURCE_DISTRIBUTION AND BUILD_IS_INSOURCE)
message(FATAL_ERROR
- "Rebuilding HTML and man pages is not supported for in-source "
- "builds from a source distribution. "
+ "Rebuilding HTML and man pages or shell completions is not supported "
+ "for in-source builds from a source distribution. "
"Set GMX_BUILD_HELP=OFF or do an out-of-source build to proceed.")
endif()
set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} ${OpenMP_LINKER_FLAGS})
set(GMX_SHARED_LINKER_FLAGS ${GMX_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS})
endif()
-set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
########################################################################
# Specify install locations
# These variables are used internally to provide a central location for
# customizing the install locations.
-set(LIB_INSTALL_DIR ${GMX_LIB_INSTALL_DIR})
-set(BIN_INSTALL_DIR bin)
-set(DATA_INSTALL_DIR share/${GMX_DATA_INSTALL_DIR})
-set(MAN_INSTALL_DIR share/man)
-set(INCL_INSTALL_DIR include)
-
-# These variables get written into config.h for use in finding the data
+set(LIB_INSTALL_DIR ${GMX_LIB_INSTALL_DIR})
+set(BIN_INSTALL_DIR bin)
+# This variable also gets written into config.h for use in finding the data
# directories.
-set(GMXLIB_SEARCH_DIR share/${GMX_DATA_INSTALL_DIR}/top)
-set(GMXLIB_FALLBACK ${CMAKE_INSTALL_PREFIX}/${DATA_INSTALL_DIR}/top)
+set(DATA_INSTALL_DIR share/${GMX_DATA_INSTALL_DIR})
+set(MAN_INSTALL_DIR share/man)
+# If the nesting level wrt. the installation root is changed,
+# gromacs-config.cmake.cmakein needs to be adapted.
+set(CMAKE_INSTALL_DIR share/cmake)
+# TODO: Make GMXRC adapt if this is changed
+set(PKGCONFIG_INSTALL_DIR ${LIB_INSTALL_DIR}/pkgconfig)
+set(INCL_INSTALL_DIR include)
+
+list(APPEND INSTALLED_HEADER_INCLUDE_DIRS ${INCL_INSTALL_DIR})
# Binary and library suffix options
include(gmxManageSuffixes)
if(GMX_EXTERNAL_BOOST)
include_directories(${Boost_INCLUDE_DIRS})
- set(PKG_CFLAGS "${PKG_CFLAGS} -I${Boost_INCLUDE_DIRS}")
+ list(APPEND INSTALLED_HEADER_INCLUDE_DIRS ${Boost_INCLUDE_DIRS})
else()
include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/boost)
+ list(APPEND INSTALLED_HEADER_INCLUDE_DIRS ${INCL_INSTALL_DIR}/gromacs/external/boost)
+ list(APPEND INSTALLED_HEADED_DEFINITIONS "-DBOOST_NO_TYPEID")
# typeid not supported for minimal internal version
# (would add significant amount of code)
add_definitions(-DBOOST_NO_TYPEID)
- # TODO: Propagate the above settings to the installed CMakeFiles.txt template
- # (from share/template/)
- set(PKG_CFLAGS "${PKG_CFLAGS} -DBOOST_NO_TYPEID -I${CMAKE_INSTALL_PREFIX}/${INCL_INSTALL_DIR}/gromacs/external/boost")
if (NOT GMX_BUILD_MDRUN_ONLY)
install(DIRECTORY ${CMAKE_SOURCE_DIR}/src/external/boost/boost
DESTINATION ${INCL_INSTALL_DIR}/gromacs/external/boost
add_subdirectory(tests)
endif()
+gmx_cpack_write_config()
+
# Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
# Don't bother the user after the first configure pass.
if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
1. GROMACS
2. Trajectory file reading using VMD plugins
3. Internal FFT (fftpack)
-4. The memtestG80 library
-5. thread_mpi
-6. Blas
-7. Lapack
-8. Subset of Boost C++ library
-9. Google Test and Google Mock
-10. Sun XDR implementation (External Data Representation)
-11. Sun FDLIBM (Freely Distributable Maths Library)
-12. Random123
-13. md5
+4. thread_mpi
+5. Blas
+6. Lapack
+7. Subset of Boost C++ library
+8. Google Test and Google Mock
+9. Sun XDR implementation (External Data Representation)
+10. Sun FDLIBM (Freely Distributable Maths Library)
+11. Random123
+12. md5
+13. lmfit
Our chosen method for packaging distributions (CPack) only permits a
package to have a single license file, so we are unfortunately forced
fftpack.c : A set of FFT routines in C.
Algorithmically based on Fortran-77 FFTPACK by Paul N. Swarztrauber (Version 4, 1985).
-4. The memtestG80 library
-=========================
-
- Files: src/gromacs/gmxlib/gpu_utils/memtestG80_core.*
-
-The memtestG80 library, written by Imran Haque, is Copyright 2009 Stanford University,
-covered by the LGPL license. It may be used under the following terms:
-
-IN NO EVENT SHALL STANFORD UNIVERSITY BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT,
-SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF
-THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF STANFORD UNIVERSITY HAS BEEN
-ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-STANFORD UNIVERSITY SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED
-TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-THE SOFTWARE AND ACCOMPANYING DOCUMENTATION PROVIDED HEREUNDER IS PROVIDED "AS IS".
-Folding@home HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS,
-OR MODIFICATIONS.
-
-Restrictions:
-
-You may use this software on a computer system only if you own the system or have the
-written permission of the owner.
-
-You may not alter the software or associated data files.
-
-Certain builds of this software incorporate by linkage code from the libintl
-and libiconv libraries, which are covered by the Library GNU Public License,
-available at http://www.gnu.org/licenses/lgpl-3.0.txt.
-
-5. thread_mpi
+4. thread_mpi
=============
Files: src/external/thread_mpi/
inclusion in the official distribution, but derived work should not
be called official thread_mpi.
-6. Blas
+5. Blas
=======
These files are semi-automatic translations by f2c from the original netlib BLAS library.
Erik Lindahl, 2008-10-07.
-7. Lapack
+6. Lapack
=========
These files are semi-automatic translations by f2c from the original netlib LAPACK library.
Erik Lindahl, 2008-10-07.
-8. Subset of Boost C++ library
+7. Subset of Boost C++ library
==============================
Files: src/external/boost/boost/*
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.
-9. Google Test and Google Mock
+8. Google Test and Google Mock
===============================
Files: src/external/gmock-1.7.0/*
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-10. Sun Extensible Data Representation routines (XDR)
+9. Sun Extensible Data Representation routines (XDR)
=====================================================
Files: src/gromacs/fileio/gmx_system_xdr.c
Mountain View, California 94043
-11. Sun FDLIBM (Freely Distributable Maths Library)
+10. Sun FDLIBM (Freely Distributable Maths Library)
===================================================
Files: src/gromacs/math/utilities.c
is preserved.
-12. Random123
+11. Random123
============================================
Copyright 2010-2012, D. E. Shaw Research.
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-13. md5
+12. md5
============================================
Copyright (C) 1999, 2002 Aladdin Enterprises. All rights reserved.
L. Peter Deutsch
ghost@aladdin.com
+
+13. lmfit
+============================================
+The package lmfit is distributed under the FreeBSD License:
+
+--
+ Copyright (c) 1980-1999 University of Chicago,
+ as operator of Argonne National Laboratory
+ Copyright (c) 2004-2013 Joachim Wuttke, Forschungszentrum Juelich GmbH
+
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+
+ - Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ - Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+
+ This software is provided by the copyright holders and contributors "as is"
+ and any express or implied warranties, including, but not limited to, the
+ implied warranties of merchantability and fitness for a particular purpose
+ are disclaimed. In no event shall the copyright holder or contributors
+ be liable for any direct, indirect, incidental, special, exemplary, or
+ consequential damages (including, but not limited to, procurement of
+ substitute goods or services; loss of use, data, or profits; or business
+ interruption) however caused and on any theory of liability, whether in
+ contract, strict liability, or tort (including negligence or otherwise)
+ arising in any way out of the use of this software, even if advised of the
+ possibility of such damage.
+--
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-#TODO: add check that source doesn't contain any untracked files
-if(NOT CPACK_INSTALL_CMAKE_PROJECTS) #building source package
+set(BUILDING_SOURCE_PACKAGE OFF)
+# The essential difference in building a source package is that install() rules
+# from the CMake project are not considered when deciding what to package.
+# Instead, only the listed directories are packaged (and the listed directories
+# contain the source tree).
+if (NOT CPACK_INSTALL_CMAKE_PROJECTS)
+ set(BUILDING_SOURCE_PACKAGE ON)
+endif()
+
+if (BUILDING_SOURCE_PACKAGE)
+ # TODO: add check that source doesn't contain any untracked files
get_filename_component(CMAKE_BINARY_DIR ${CPACK_OUTPUT_CONFIG_FILE} PATH)
+ # TODO: The list could be generated at the same time as the list of
+ # directories to include to keep the probe file names at the same place.
+ # And this does not detect if things have been built in the past, but are
+ # outdated.
if (NOT EXISTS "${CMAKE_BINARY_DIR}/docs/man/man1/gmx-view.1" OR
NOT EXISTS "${CMAKE_BINARY_DIR}/docs/install-guide/final/INSTALL" OR
NOT EXISTS "${CMAKE_BINARY_DIR}/docs/old-html/final/online.html" OR
"GMX_BUILD_HELP=ON to automatically build the HTML parts.")
endif()
else()
+ # TODO: If GMX_BUILD_HELP is AUTO, it may happen that the generation fails,
+ # and things are silently left out.
+ # Also, it is currently impossible to get these files into the binary
+ # package for cross-compilation. However, binary packages are not
+ # currently used much, either...
if (NOT CPACK_GMX_BUILD_HELP)
message(WARNING
"To create a complete binary package, bash completions, and "
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013, by the GROMACS development team, led by
+# Copyright (c) 2013,2014, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+"""Checks and/or updates copyright headers in GROMACS source files.
+
+It is used internally by several bash scripts to do copyright-relates tasks,
+but can also be invoked directly for some rare use cases.
+
+See docs/dev-manual/uncrustify.md for more details.
+"""
+
import datetime
import os.path
import re
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013, by the GROMACS development team, led by
+# Copyright (c) 2013,2014, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# changes through some formatting check. Currently, it runs uncrustify and
# checks copyright headers.
#
-# By default, it does nothing. To enable the script after copying it to
-# .git/hooks/pre-commit, you need to set
-# git config hooks.uncrustifymode check
+# It needs to be copied as .git/hooks/pre-commit and configured with
# git config hooks.uncrustifypath /path/to/uncrustify
-# With this configuration, all source files modified in the commit are run
-# through uncrustify and checked for correct copyright headers
-# (see admin/uncrustify.sh for how this set of files is determined).
-# If any file is changed by uncrustify or has other problems, the names of
-# those files are reported and the commit is prevented. The issues can be
-# fixed by running admin/uncrustify.sh manually.
+# git config hooks.uncrustifymode check
+# git config hooks.copyrightmode update
#
-# To disable the hook, you can set
-# git config hooks.uncrustifymode off
-# To disable it temporarily for a commit, set NO_FORMAT_CHECK environment
+# To disable the hook temporarily for a commit, set NO_FORMAT_CHECK environment
# variable. For example,
# NO_FORMAT_CHECK=1 git commit -a
# You can also run git commit --no-verify, but that also disables other hooks,
-# such as the Change-Id hook used by gerrit.
+# such as the Change-Id hook used by Gerrit.
#
-# The actual work is done by the admin/uncrustify.sh script, which gets
-# run with the 'check-index' action.
-# See the comments in that script for more information.
+# See docs/dev-manual/uncrustify.md for more details.
if [ ! -z "$NO_FORMAT_CHECK" ]
then
--- /dev/null
+[
+{ include: ["<boost/smart_ptr/shared_ptr.hpp>", "private", "<boost/shared_ptr.hpp>", "public"] },
+{ include: ["<xmmintrin.h>", "public", "<emmintrin.h>", "public"] },
+{ include: ["<emmintrin.h>", "public", "<pmmintrin.h>", "public"] },
+{ include: ["<pmmintrin.h>", "public", "<smmintrin.h>", "public"] },
+{ include: ["<smmintrin.h>", "public", "<immintrin.h>", "public"] },
+{ include: ["<avxintrin.h>", "private", "<immintrin.h>", "public"] },
+{ include: ['"mpi.h"', "private", '"gromacs/utility/gmxmpi.h"', "public"] },
+{ include: ['"thread_mpi/atomic/gcc_x86.h"', "private", '"thread_mpi/atomic.h"', "public"] },
+{ include: ['<immintrin.h>', "public", '"gromacs/simd/simd.h"', "public"] },
+{ include: ['"gromacs/simd/impl_x86_avx_256/impl_x86_avx_256.h"', "private", '"gromacs/simd/simd.h"', "public"] },
+{ symbol: ["M_SQRT2", "private", '"gromacs/math/utilities.h"', "public"] }
+]
\ No newline at end of file
--- /dev/null
+#!/bin/bash
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+# The build and source folder can be specified with -B and -S respectively.
+# By default it assume "-B. -S..".
+# include-what-you-use needs to be in the path. Add --apply if you want
+# changes to be applied. Any extra arguments are added as is to the
+# command (can be used for extra defines or include paths).
+
+filename=
+build_path=.
+src_path=..
+cmd="include-what-you-use -DHAVE_CONFIG_H -mavx"
+
+# Read all special arguments and add others to the command
+apply=0
+for arg in "$@"; do
+ if [ $arg == "--apply" ]; then
+ apply=1
+ elif [[ $arg == -[SB] ]]; then
+ echo -S and -B require an argument
+ exit 1
+ elif [[ $arg == -B* ]]; then
+ build_path=${arg:2}
+ elif [[ $arg == -S* ]]; then
+ src_path=${arg:2}
+ elif [[ $arg != -* ]]; then
+ if [ "$filename" == "" ]; then
+ filename=$arg
+ else
+ echo "This script can only be run on one file at a time"
+ exit 1
+ fi
+ else
+ cmd="$cmd $arg"
+ fi
+done
+
+if [ "$filename" == "" ]; then
+ echo "No file specified"
+ exit 1
+fi
+
+# We cannot detect wether it is a C++ or C header. Should be fine to always use C++
+if [ "${filename##*.}" == "h" ]; then
+ cmd="$cmd -x c++"
+fi
+
+cmd="$cmd $filename"
+
+# Always use C++11.
+if [ "${filename##*.}" == "cpp" -o "${filename##*.}" == "h" ]; then
+ cmd="$cmd -std=c++11"
+fi
+
+# keep gmxpre.h for source files
+if [ "${filename##*.}" == "cpp" -o "${filename##*.}" == "c" ]; then
+ cmd="$cmd -Xiwyu --pch_in_code -Xiwyu --prefix_header_includes=keep"
+fi
+
+if [ $src_path == "." ]; then
+ src_folder="src" # ./src confuses IWYU
+else
+ src_folder="$src_path/src"
+fi
+
+cmd="$cmd -I${src_folder} -I${src_folder}/external/thread_mpi/include
+ -I$build_path/src -I${src_folder}/external/boost
+ -Xiwyu --mapping_file=${src_path}/admin/iwyu.imp"
+
+if [ $apply -eq 1 ] ; then
+ cmd="$cmd 2>&1 | fix_includes.py --nosafe_headers ||
+ ${src_path}/docs/doxygen/includesorter.py $filename -B$build_path -S$src_path"
+fi
+
+eval $cmd
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# This script runs uncrustify, copyright header checks, or include sorter on
+# all applicable files in the source tree.
+#
+# See `reformat_all.sh -h` for a brief usage, and docs/dev-manual/uncrustify.md
+# for more details (docs/dev-manual/gmxtree.md for include sorter).
+
function usage() {
echo "usage: reformat_all.sh [-f|--force]"
- echo " [--filter=(uncrustify|copyright)] [<action>]"
- echo "<action>: (list-files|uncrustify*|copyright) (*=default)"
+ echo " [--filter=(uncrustify|copyright|includesort)]"
+ echo " [--pattern=<pattern>] [<action>] [-B=<build dir>]"
+ echo "<action>: (list-files|uncrustify*|copyright|includesort) (*=default)"
}
filter=default
force=
+patterns=()
action=uncrustify
for arg in "$@" ; do
if [[ "$arg" == "list-files" || "$arg" == "uncrustify" ||
- "$arg" == "copyright" ]] ; then
+ "$arg" == "copyright" || "$arg" == "includesort" ]] ; then
action=$arg
elif [[ "$arg" == --filter=* ]] ; then
filter=${arg#--filter=}
+ elif [[ "$arg" == --pattern=* ]] ; then
+ patterns[${#patterns[@]}]=${arg#--pattern=}
+ elif [[ "$arg" == -B=* ]] ; then
+ builddir=${arg#-B=}
elif [[ "$arg" == "-f" || "$arg" == "--force" ]] ; then
force=1
+ elif [[ "$arg" == "-h" || "$arg" == "--help" ]] ; then
+ usage
+ exit 0
else
echo "Unknown option: $arg"
echo
copyright)
command="xargs admin/copyright.py --check"
;;
+ includesort)
+ if [ -z "${builddir}" ] ; then
+ echo "Build directory must be set with -B for includesort."
+ exit 2
+ fi
+ command="docs/doxygen/includesorter.py -S . -B ${builddir} -F -"
+ ;;
*)
echo "Unknown action: $action"
exit 2
fi
case "$filter" in
+ includesort)
+ filter_re="(uncrustify|includesort)"
+ ;;
uncrustify)
filter_re="(uncrustify|uncrustify_only)"
;;
copyright)
- filter_re="(uncrustify|copyright)"
+ filter_re="(uncrustify|copyright|includesort)"
;;
*)
echo "Unknown filter mode: $filter"
cd `git rev-parse --show-toplevel`
-if ! git ls-tree -r --name-only HEAD | git check-attr --stdin filter | \
+if ! git ls-files "${patterns[@]}" | git check-attr --stdin filter | \
sed -nEe "/${filter_re}$/ {s/:.*//;p;}" | $command ; then
echo "The reformatting command failed! Please check the output."
exit 1
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-# This script runs uncrustify on modified files and reports/applies the
-# results. It also checks for outdated copyright years or headers.
-# By default, the current HEAD commit is compared to the work tree,
-# and files that
-# 1. are different between these two trees and
-# 2. change under uncrustify and/or have outdated copyright header
-# are reported. This behavior can be changed by
-# 1. Specifying an --rev=REV argument, which uses REV instead of HEAD as
-# the base of the comparison.
-# 2. Specifying an action:
-# check-*: reports the files that uncrustify changes
-# diff-*: prints the actual diff of what would change
-# update-*: applies the changes to the repository
-# *-workdir: operates on the working directory (files on disk)
-# *-index: operates on the index of the repository
-# For convenience, if you omit the workdir/index suffix, workdir is assumed
-# (i.e., diff equals diff-workdir).
-# 3. Specifying --uncrustify=off, which does not run uncrustify.
-# 4. Specifying --copyright=<mode>, which alters the level of copyright
-# checking is done:
-# off: does not check copyright headers at all
-# year: only update copyright year in new-format copyright headers
-# add: in addition to 'year', add copyright headers to files that
-# don't have any
-# update: in addition to 'year' and 'add', also update new-format
-# copyright headers if they are broken or outdated.
-# replace: replace any copyright header with a new-format copyright
-# header
-# full: do all of the above
-# By default, update-* refuses to update "dirty" files (i.e., that differ
-# between the disk and the index) to make it easy to revert the changes.
-# This can be overridden by adding a -f/--force option.
+# This script runs uncrustify and copyright header checks on modified files and
+# reports/applies the necessary changes.
#
-# The location of the uncrustify executable must be specified using an
-# environment variable UNCRUSTIFY. Note that to produce the indentation used
-# in the source tree, you need a custom version of uncrustify.
-# To get and configure the currently used version, you can do the following:
-# 1. Run
-# git clone -b gromacs git://github.com/rolandschulz/uncrustify.git
-# cd uncrustify
-# ./configure
-# make
-# 2. Copy the binary src/uncrustify into a directory of your choice.
-# 3. Set the UNCRUSTIFY environment variable to point to the copied binary.
-#
-# To identify which files to run through uncrustify, the script uses git
-# filters, specified in .gitattributes files. Only files that have the filter
-# set as "uncrustify" (or something ending in "uncrustify") are processed: if
-# other files have been changed, they are ignored by the script. Files passed
-# to uncrustify, as well as files with filter "copyright", get their copyright
-# header checked. To only run uncrustify for a file, set the filter to
-# "uncrustify_only".
-#
-# If you want to run uncrustify automatically for changes you make, there are
-# two options:
-# 1. Copy the git-pre-commit script in this directory to .git/hooks/pre-commit
-# and set
-# git config hooks.uncrustifymode check
-# git config hooks.uncrustifypath /path/to/uncrustify
-# See comments in the hook script for more information.
-# 2. Configure a git filter (doesn't require this script, only the
-# .gitattributes files):
-# git config filter.uncrustify.clean \
-# "/path/to/uncrustify -c admin/uncrustify.cfg -q -l cpp"
-# The pre-commit hook + manually running the script gives better/more intuitive
-# control (with the filter, it is possible to have a work tree that is
-# different from HEAD and still have an empty 'git diff') and provides better
-# performance for changes that modify many files. It is the only way that
-# currently also checks the copyright headers.
-# The filter allows one to transparently merge branches that have not been run
-# through uncrustify, and is applied more consistently (the pre-commit hook is
-# not run for every commit, e.g., during a rebase).
+# See `uncrustify.sh -h` for a brief usage, and docs/dev-manual/uncrustify.md
+# for more details.
# Parse command-line arguments
function usage() {
force=1
elif [[ "$arg" == --rev=* ]] ; then
baserev=${arg#--rev=}
- elif [[ "$arg" == "-h" ]] ; then
+ elif [[ "$arg" == "-h" || "$arg" == "--help" ]] ; then
usage
exit 0
else
then
if [ -z "$UNCRUSTIFY" ]
then
- echo "Please set the path to uncrustify using UNCRUSTIFY."
+ UNCRUSTIFY=`git config hooks.uncrustifypath`
+ fi
+ if [ -z "$UNCRUSTIFY" ]
+ then
+ echo "Please set the path to uncrustify using UNCRUSTIFY or"
+ echo "git config hooks.uncrustifypath."
echo "Note that you need a custom version of uncrustify."
- echo "See comments in the script file for how to get one."
+ echo "See docs/dev-manual/uncrustify.md for how to get one."
exit 2
fi
if ! which "$UNCRUSTIFY" 1>/dev/null
git check-attr --stdin filter | \
sed -e 's/.*: filter: //' | \
paste $tmpdir/difflist - | \
- grep -E '(uncrustify|uncrustify_only|copyright)$' >$tmpdir/filtered
+ grep -E '(uncrustify|uncrustify_only|copyright|includesort)$' >$tmpdir/filtered
cut -f2 <$tmpdir/filtered >$tmpdir/filelist_all
grep -E '(uncrustify|uncrustify_only)$' <$tmpdir/filtered | \
cut -f2 >$tmpdir/filelist_uncrustify
-grep -E '(uncrustify|copyright)$' <$tmpdir/filtered | \
+grep -E '(uncrustify|copyright|includesort)$' <$tmpdir/filtered | \
cut -f2 >$tmpdir/filelist_copyright
git diff-files --name-only | grep -Ff $tmpdir/filelist_all >$tmpdir/localmods
fi
# Find the changed files
+git diff --no-index --name-only --exit-code org/ new/ | \
+ sed -e 's#new/##' > $tmpdir/changed
changes=
-set -o pipefail
-if ! git diff --no-index --name-only --exit-code org/ new/ | \
- sed -e 's#new/##' > $tmpdir/changed
+if [[ -s $tmpdir/changed ]]
then
changes=1
fi
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+#.rst:
+# FindNVML
+# --------
+#
+# Find the NVIDIA Management Library (NVML) includes and library. NVML documentation
+# is available at: http://docs.nvidia.com/deploy/nvml-api/index.html
+#
+# NVML is part of the GPU Deployment Kit (GDK) and GPU_DEPLOYMENT_KIT_ROOT_DIR can
+# be specified if the GPU Deployment Kit is not installed in a default location.
+#
+# FindNVML defines the following variables:
+#
+# NVML_INCLUDE_DIR, where to find nvml.h, etc.
+# NVML_LIBRARY, the libraries needed to use NVML.
+# NVML_FOUND, If false, do not try to use NVML.
+#
+
+# Jiri Kraus, NVIDIA Corp (nvidia.com - jkraus)
+#
+# Copyright (c) 2008 - 2014 NVIDIA Corporation. All rights reserved.
+#
+# This code is licensed under the MIT License. See the FindNVML.cmake script
+# for the text of the license.
+
+# The MIT License
+#
+# License for the specific language governing rights and limitations under
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+#
+###############################################################################
+
+if( CMAKE_SYSTEM_NAME STREQUAL "Windows" )
+ set( NVML_LIB_PATHS "C:/Program Files/NVIDIA Corporation/GDK/nvml/lib" )
+ if(GPU_DEPLOYMENT_KIT_ROOT_DIR)
+ list(APPEND NVML_LIB_PATHS "${GPU_DEPLOYMENT_KIT_ROOT_DIR}/nvml/lib")
+ endif()
+ set(NVML_NAMES nvml)
+
+ set( NVML_INC_PATHS "C:/Program Files/NVIDIA Corporation/GDK/nvml/include" )
+ if(GPU_DEPLOYMENT_KIT_ROOT_DIR)
+ list(APPEND NVML_INC_PATHS "${GPU_DEPLOYMENT_KIT_ROOT_DIR}/nvml/include")
+ endif()
+else()
+ set( NVML_LIB_PATHS /usr/lib64 )
+ if(GPU_DEPLOYMENT_KIT_ROOT_DIR)
+ list(APPEND NVML_LIB_PATHS "${GPU_DEPLOYMENT_KIT_ROOT_DIR}/src/gdk/nvml/lib")
+ endif()
+ set(NVML_NAMES nvidia-ml)
+
+ set( NVML_INC_PATHS /usr/include/nvidia/gdk/ /usr/include )
+ if(GPU_DEPLOYMENT_KIT_ROOT_DIR)
+ list(APPEND NVML_INC_PATHS "${GPU_DEPLOYMENT_KIT_ROOT_DIR}/include/nvidia/gdk")
+ endif()
+endif()
+
+find_library(NVML_LIBRARY NAMES ${NVML_NAMES} PATHS ${NVML_LIB_PATHS} )
+
+find_path(NVML_INCLUDE_DIR nvml.h PATHS ${NVML_INC_PATHS})
+
+# handle the QUIETLY and REQUIRED arguments and set NVML_FOUND to TRUE if
+# all listed variables are TRUE
+include(FindPackageHandleStandardArgs)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(NVML DEFAULT_MSG NVML_LIBRARY NVML_INCLUDE_DIR)
+
+mark_as_advanced(NVML_LIBRARY NVML_INCLUDE_DIR)
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014,2015, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+set(CMAKE_C_FLAGS_INIT "-mmic")
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014,2015, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+set(CMAKE_CXX_FLAGS_INIT "-mmic")
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014, by the GROMACS development team, led by
+# Copyright (c) 2014,2015, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
#
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+
+set(CMAKE_SYSTEM_NAME Linux)
+set(CMAKE_SYSTEM_PROCESSOR XeonPhi)
if(NOT GMX_MPI)
set(CMAKE_C_COMPILER "icc")
set(CMAKE_CXX_COMPILER "icpc")
else()
- set(CMAKE_C_COMPILER "mpiicc")
+ set(CMAKE_C_COMPILER "mpiicc") #FindMPI doesn't work (#14991)
set(CMAKE_CXX_COMPILER "mpiicpc")
- set(GMX_PREFER_STATIC_LIBS ON CACHE BOOL "Shared libraries on Xeon Phi with MPI don't work.")
endif()
-set(CMAKE_CXX_FLAGS "-mmic" CACHE STRING "Flags used by the compiler during all build types.")
-set(CMAKE_C_FLAGS "-mmic" CACHE STRING "Flags used by the compiler during all build types.")
-set(GMX_FFT_LIBRARY "mkl" CACHE STRING "FFT library")
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+set(GMX_VERSION "@GMX_VERSION@")
+set(GMX_VERSION_MAJOR "@GMX_VERSION_MAJOR@")
+set(GMX_VERSION_MINOR "@GMX_VERSION_MINOR@")
+set(GMX_VERSION_PATCH "@GMX_VERSION_PATCH@")
+set(GMX_VERSION_STRING "@GMX_VERSION_STRING@")
+
+set(GMX_VERSION_STRING_FULL "@GMX_VERSION_STRING_FULL@")
+set(GMX_VERSION_FULL_HASH "@GMX_VERSION_FULL_HASH@")
+set(GMX_VERSION_CENTRAL_BASE_HASH "@GMX_VERSION_CENTRAL_BASE_HASH@")
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-function (generate_installed_file_list SRCDIR BUILDDIR OUTFILE)
- file(GLOB_RECURSE INSTALL_FILE_LIST "${BUILDDIR}/cmake_install.cmake")
- set(MATCH_REGEX "(${SRCDIR}|${BUILDDIR})/.*\\.h")
- set(HEADER_LIST)
- foreach (INSTALL_FILE ${INSTALL_FILE_LIST})
- file(STRINGS ${INSTALL_FILE} HEADER_LINES REGEX "${MATCH_REGEX}")
- foreach (HEADER_LINE ${HEADER_LINES})
- string (REGEX MATCH "${MATCH_REGEX}" HEADER "${HEADER_LINE}")
- list(APPEND HEADER_LIST "${HEADER}")
- endforeach ()
- endforeach ()
- string(REPLACE ";" "\n" HEADER_LIST "${HEADER_LIST}")
- file(WRITE ${OUTFILE} "${HEADER_LIST}")
-endfunction ()
+# Custom build type "Profile", based on "RelWithAssert".
+set( CMAKE_C_FLAGS_PROFILE "${CMAKE_C_FLAGS_RELEASE_INIT} -pg" CACHE STRING "C flags for profile builds.")
+set( CMAKE_CXX_FLAGS_PROFILE "${CMAKE_CXX_FLAGS_RELEASE_INIT} -pg" CACHE STRING "C++ flags for profile builds.")
+set( CMAKE_LD_FLAGS_PROFILE "${CMAKE_LD_FLAGS_RELEASE_INIT} -pg" CACHE STRING "Linking flags for profile builds.")
+mark_as_advanced( CMAKE_CXX_FLAGS_PROFILE CMAKE_C_FLAGS_PROFILE CMAKE_LD_FLAGS_PROFILE)
-if (NOT DEFINED SRCDIR OR NOT DEFINED BUILDDIR OR NOT DEFINED OUTFILE)
- message(FATAL_ERROR "Required input variable (SRCDIR, BUILDDIR, OUTFILE) not set")
-endif ()
-generate_installed_file_list(${SRCDIR} ${BUILDDIR} ${OUTFILE})
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# be set up elsewhere and passed to this function, but it is
# inconvenient in CMake to pass more than one list, and such a
# list is only used here.
- foreach(build_type RELWITHDEBINFO RELWITHASSERT MINSIZEREL)
+ foreach(build_type RELWITHDEBINFO RELWITHASSERT MINSIZEREL PROFILE)
set(GMXC_${language}FLAGS_${build_type} "${GMXC_${language}FLAGS_RELEASE}")
endforeach()
# Copy the flags that are only used by the real Release build
# Since 4.8 on by default. For previous version disabling is a no-op. Only disabling for Release because with assert
# the warnings are OK.
GMX_TEST_CFLAG(CFLAGS_WARN_REL "-Wno-array-bounds" GMXC_CFLAGS_RELEASE_ONLY)
- # Since gcc 4.8 strict - false postives with old gmx_fatal. TODO: Remove in master
- GMX_TEST_CFLAG(CFLAGS_WARN_UNINIT "-Wno-maybe-uninitialized" GMXC_CFLAGS)
if(CYGWIN)
GMX_TEST_CFLAG(CFLAGS_WARN_SUBSCRIPT "-Wno-char-subscripts" GMXC_CFLAGS)
endif()
# new in gcc 4.5
GMX_TEST_CFLAG(CFLAGS_EXCESS_PREC "-fexcess-precision=fast" GMXC_CFLAGS_RELEASE)
- GMX_TEST_CFLAG(CFLAGS_COPT "-fomit-frame-pointer -funroll-all-loops"
+ GMX_TEST_CFLAG(CFLAGS_COPT "-funroll-all-loops"
GMXC_CFLAGS_RELEASE)
GMX_TEST_CFLAG(CFLAGS_NOINLINE "-fno-inline" GMXC_CFLAGS_DEBUG)
endif()
GMX_TEST_CFLAG(CXXFLAGS_WARN_REL "-Wno-array-bounds" GMXC_CXXFLAGS_RELEASE_ONLY)
# new in gcc 4.5
GMX_TEST_CXXFLAG(CXXFLAGS_EXCESS_PREC "-fexcess-precision=fast" GMXC_CXXFLAGS_RELEASE)
- GMX_TEST_CXXFLAG(CXXFLAGS_COPT "-fomit-frame-pointer -funroll-all-loops"
+ GMX_TEST_CXXFLAG(CXXFLAGS_COPT "-funroll-all-loops"
GMXC_CXXFLAGS_RELEASE)
GMX_TEST_CXXFLAG(CXXFLAGS_NOINLINE "-fno-inline" GMXC_CXXFLAGS_DEBUG)
endif()
GMX_TEST_CFLAG(CFLAGS_PRAGMA "-wd161" GMXC_CFLAGS)
endif()
endif()
-# 111: statement is unreachable
-# 177: function ".." was declared but never referenced
-# 181: argument of type ".." is incompatible with format "..", expecting argument of type ".."
+# 177: function/variable ".." was declared but never referenced
# 193: zero used for undefined preprocessing identifier ".."
# 271: trailing comma is nonstandard
# 304: access control not specified ("public" by default)
#3346: dynamic exception specifications are deprecated
#11074: Inlining inhibited by limit max-size(/max-total-size)
#11076: To get full report use -opt-report=3 -opt-report-phase ipo (shown for previous remark)
- GMX_TEST_CFLAG(CFLAGS_WARN "-w3 -wd111 -wd177 -wd181 -wd193 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd11074 -wd11076" GMXC_CFLAGS)
+ GMX_TEST_CFLAG(CFLAGS_WARN "-w3 -wd177 -wd193 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd11074 -wd11076" GMXC_CFLAGS)
GMX_TEST_CFLAG(CFLAGS_STDGNU "-std=gnu99" GMXC_CFLAGS)
GMX_TEST_CFLAG(CFLAGS_OPT "-ip -funroll-all-loops -alias-const -ansi-alias" GMXC_CFLAGS_RELEASE)
+ GMX_TEST_CFLAG(CFLAGS_DEBUG "-O0" GMXC_CFLAGS_DEBUG) #icc defaults to -O2 even with -g
+ GMX_TEST_CFLAG(CFLAGS_FP_RELASSERT "-fp-model except -fp-model precise" GMXC_CFLAGS_RELWITHASSERT)
else()
if(NOT GMX_OPENMP)
if(CMAKE_C_COMPILER_VERSION VERSION_GREATER 13.99.99)
GMX_TEST_CFLAG(CFLAGS_PRAGMA "/wd161" GMXC_CFLAGS)
endif()
endif()
- GMX_TEST_CFLAG(CFLAGS_WARN "/W3 /wd111 /wd177 /wd181 /wd193 /wd271 /wd304 /wd383 /wd424 /wd444 /wd522 /wd593 /wd869 /wd981 /wd1418 /wd1419 /wd1572 /wd1599 /wd2259 /wd2415 /wd2547 /wd2557 /wd3280 /wd3346" GMXC_CFLAGS)
+ GMX_TEST_CFLAG(CFLAGS_WARN "/W3 /wd177 /wd193 /wd271 /wd304 /wd383 /wd424 /wd444 /wd522 /wd593 /wd869 /wd981 /wd1418 /wd1419 /wd1572 /wd1599 /wd2259 /wd2415 /wd2547 /wd2557 /wd3280 /wd3346" GMXC_CFLAGS)
GMX_TEST_CFLAG(CFLAGS_OPT "/Qip" GMXC_CFLAGS_RELEASE)
endif()
endif()
#All but the following warnings are identical for the C-compiler (see above)
#1782: #pragma once is obsolete
#2282: unrecognized GCC pragma
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-w3 -wd111 -wd177 -wd181 -wd193 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd11074 -wd11076 -wd1782 -wd2282" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-w3 -wd177 -wd193 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd11074 -wd11076 -wd1782 -wd2282" GMXC_CXXFLAGS)
GMX_TEST_CXXFLAG(CXXFLAGS_OPT "-ip -funroll-all-loops -alias-const -ansi-alias" GMXC_CXXFLAGS_RELEASE)
+ GMX_TEST_CXXFLAG(CXXFLAGS_DEBUG "-O0" GMXC_CXXFLAGS_DEBUG)
+ GMX_TEST_CXXFLAG(CXXFLAGS_FP_RELASSERT "-fp-model except -fp-model precise" GMXC_CXXFLAGS_RELWITHASSERT)
else()
if(NOT GMX_OPENMP)
if(CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 13.99.99)
GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "/wd161" GMXC_CXXFLAGS)
endif()
endif()
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/W3 /wd111 /wd177 /wd181 /wd193 /wd271 /wd304 /wd383 /wd424 /wd444 /wd522 /wd593 /wd869 /wd981 /wd1418 /wd1419 /wd1572 /wd1599 /wd2259 /wd2415 /wd2547 /wd2557 /wd3280 /wd3346 /wd1782 /wd2282" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/W3 /wd177 /wd193 /wd271 /wd304 /wd383 /wd424 /wd444 /wd522 /wd593 /wd869 /wd981 /wd1418 /wd1419 /wd1572 /wd1599 /wd2259 /wd2415 /wd2547 /wd2557 /wd3280 /wd3346 /wd1782 /wd2282" GMXC_CXXFLAGS)
GMX_TEST_CXXFLAG(CXXFLAGS_OPT "/Qip" GMXC_CXXFLAGS_RELEASE)
endif()
endif()
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+# Helper functions to encapsulate and modularize usage of CPack
+#
+# This file is intended to be the only place that directly sets CPack variables
+# (in gmx_cpack_write_config()), and other parts of the build system should
+# only call the functions declared here to set up the packaging.
+
+# Initialize the machinery that collects CPack information during other
+# build system generation
+#
+# This function should be called before other functions from this file.
+function (gmx_cpack_init)
+ # Add the source tree to the source package.
+ # If we would not set CPACK_SOURCE_INSTALLED_DIRECTORIES, this is what
+ # CPack would set as default.
+ set_property(GLOBAL PROPERTY GMX_CPACK_SOURCE_INSTALLED_DIRECTORIES
+ ${PROJECT_SOURCE_DIR} /)
+endfunction()
+
+# Add a generated directory to be included in the source package.
+#
+# Usage:
+# gmx_cpack_add_generated_source_directory(<dir> [DESTINATION <dest>])
+#
+# <dir> Name of directory to include.
+# Relative paths are interpreted relative to current build dir.
+# <dest> Path in the source package where files from <dir> will be put.
+# If not set, the files are put in the corresponding location in
+# the source tree.
+#
+# By default, CPack source archives includes all files from the source tree.
+# This function adds a directory from the build tree to be packaged into the
+# source archive. These are used for content GROMACS generates as part of the
+# configuration or build.
+# The values end up in CPACK_SOURCE_INSTALLED_DIRECTORIES, which is a list of
+# pairs of names of source and destination directories.
+function (gmx_cpack_add_generated_source_directory DIR)
+ include(CMakeParseArguments)
+ set(_one_value_args DESTINATION)
+ cmake_parse_arguments(ARG "" "${_one_value_args}" "" ${ARGN})
+ if (ARG_UNPARSED_ARGUMENTS)
+ message(FATAL_ERROR "Unknown arguments: ${ARG_UNPARSED_ARGUMENTS}")
+ endif()
+ set(_dir ${DIR})
+ if (NOT IS_ABSOLUTE ${_dir})
+ set(_dir ${CMAKE_CURRENT_BINARY_DIR}/${_dir})
+ endif()
+ if (ARG_DESTINATION)
+ set(_dest ${ARG_DESTINATION})
+ else()
+ file(RELATIVE_PATH _dest ${PROJECT_BINARY_DIR} ${_dir})
+ endif()
+ set_property(GLOBAL APPEND PROPERTY GMX_CPACK_SOURCE_INSTALLED_DIRECTORIES
+ ${_dir} ${_dest})
+endfunction()
+
+# Write CPack configuration files
+#
+# This function should be called at the end of the main CMakeLists.txt, after
+# all other calls to functions in this file.
+# CPack also automatically populates the list of components based on components
+# used in installation rules, so it should come after all install() commands.
+function (gmx_cpack_write_config)
+ # Set basic package information.
+ set(CPACK_PACKAGE_NAME "gromacs")
+ set(CPACK_PACKAGE_VENDOR "gromacs.org")
+ set(CPACK_PACKAGE_CONTACT "gmx-users@gromacs.org")
+ set(CPACK_PACKAGE_DESCRIPTION_SUMMARY
+ "Gromacs - a toolkit for high-performance molecular simulation")
+ # Set version info.
+ set(CPACK_PACKAGE_VERSION_MAJOR ${GMX_VERSION_MAJOR})
+ set(CPACK_PACKAGE_VERSION_MINOR ${GMX_VERSION_MINOR})
+ set(CPACK_PACKAGE_VERSION_PATCH ${GMX_VERSION_PATCH})
+ set(CPACK_PACKAGE_VERSION ${GMX_VERSION_STRING})
+ # Add various text resources for some installers.
+ set(CPACK_RESOURCE_FILE_WELCOME "${PROJECT_SOURCE_DIR}/admin/InstallWelcome.txt")
+ # Its GPL/LGPL, so they do not have to agree to a license for mere usage,
+ # but some installers require this...
+ set(CPACK_RESOURCE_FILE_LICENSE "${PROJECT_SOURCE_DIR}/COPYING")
+ set(CPACK_RESOURCE_FILE_README "${PROJECT_SOURCE_DIR}/admin/InstallInfo.txt")
+
+ # Our custom config file that is run by CPack for each generator, used to
+ # check for prerequisites of the packaging.
+ set(CPACK_PROJECT_CONFIG_FILE "${PROJECT_SOURCE_DIR}/CPackInit.cmake")
+
+ # Settings specific to source packages.
+ set(CPACK_SOURCE_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}")
+ set(CPACK_SOURCE_IGNORE_FILES
+ "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$;\\\\.gitattributes;")
+ # Get the list of directories added with gmx_cpack_add_generated_source_directory()
+ get_property(CPACK_SOURCE_INSTALLED_DIRECTORIES
+ GLOBAL PROPERTY GMX_CPACK_SOURCE_INSTALLED_DIRECTORIES)
+
+ # Propagate additional values for CPackInit.cmake to use.
+ # CPack includes all variables starting with CPACK_ into the generated
+ # config files that are included by CPack.
+ set(CPACK_GMX_BUILD_HELP "${GMX_BUILD_HELP}")
+
+ # Generate the CPack configuration files.
+ include(CPack)
+endfunction()
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+include(${VERSION_VARIABLES})
+configure_file(${VERSION_CMAKEIN} ${VERSION_OUT} @ONLY)
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+# Helper functions for creating custom commands
+#
+# CMake semantics of add_custom_command() and add_custom_target() are not
+# always very convenient or intuitive for creating commands that do not always
+# run. This file provides a gmx_add_custom_output_target() to simplify the
+# task. The function also provides some convenience features to remove code
+# duplication in some parts of the GROMACS build system.
+#
+# Additionally, gmx_get_stamp_filename() and gmx_get_files_with_gitattribute()
+# are provided independently to help in creating custom commands.
+
+# Helper function to create a stamp file name for a target.
+#
+# Usage:
+# gmx_get_stamp_filename(<variable> <targetname>)
+#
+# <variable> - name of variable to receive the stamp name
+# <targetname> - name of target for which to generate the stamp name
+#
+# This is used internally by gmx_add_custom_target(... OUTPUT STAMP ...), but
+# can also be called directly to create uniform stamp file names throughout the
+# build system.
+# <targetname> can be any string that is a part of a valid file name; it does
+# not need to name an existing or to-be-created target.
+function (gmx_get_stamp_filename variable targetname)
+ set(_filename "${targetname}")
+ if (NOT "${targetname}" MATCHES "stamp$")
+ set(_filename "${targetname}-timestamp")
+ endif()
+ set(${variable} "${CMAKE_CURRENT_BINARY_DIR}/${_filename}.txt"
+ PARENT_SCOPE)
+endfunction()
+
+# Helper function to tell gmx_add_custom_output_target() the name of an output
+# file for a custom target.
+#
+# Usage:
+# gmx_set_custom_target_output(<targetname> <output>)
+#
+# <targetname> - name of an existing custom target
+# <output> - path to the output file produced by the custom target
+#
+# This is used internally by gmx_add_custom_output_target(), but can also be
+# called for targets created with add_custom_target() to make them work with
+# the dependency resolution mechanism in gmx_add_custom_output_target() if
+# those targets for some reason cannot be created with that command.
+function (gmx_set_custom_target_output targetname output)
+ # Store the output file name in a custom property to be used in dependency
+ # resolution later.
+ if (NOT IS_ABSOLUTE ${output})
+ set(output ${CMAKE_CURRENT_BINARY_DIR}/${output})
+ endif()
+ set_property(TARGET ${targetname}
+ PROPERTY GMX_CUSTOM_TARGET_OUTPUT_FILE ${output})
+endfunction()
+
+# More flexible alternative to add_custom_command() and add_custom_target()
+# for dependent custom commands. It adds a few convenience features:
+# - Support for custom commands that always run (like add_custom_target()),
+# but still have the ability to act as dependencies of other custom
+# commands (such that the dependent commands run only if the output
+# has been updated) also for Ninja.
+# - Adds file-level dependencies between custom targets added with this
+# command such that if there is a target-level dependency, it also implies
+# that the custom command should always be run if the output file of the
+# dependency has been updated.
+# - Support for creating custom targets that produce stamp files whenever
+# they run successfully, so that other targets can depend on those stamp
+# files.
+#
+# Usage:
+# gmx_add_custom_output_target(<target> [RUN_ALWAYS] [ADD_FAST_TARGET]
+# OUTPUT <STAMP | <output> >
+# [COMMAND <command1> [<args1...>]]
+# [COMMAND <command2> [<args2...>]]
+# [WORKING_DIRECTORY <dir>]
+# [DEPENDS <deps...>]
+# [DEPENDS_FILE_LIST <list>]
+# [COMMENT <comment>])
+#
+# <target>
+# - Name of the custom target to create.
+# RUN_ALWAYS
+# - Create the command such that it always runs.
+# This takes care of differences between the Ninja generator and others,
+# which require different rules to make this happen such that
+# dependencies on the output of the target work correctly, also in the
+# case the command does not always update the timestamp of the output.
+# The dependencies listed with DEPENDS are ignored in this case.
+# ADD_FAST_TARGET
+# - In addition to creating <target>, create a secondary target
+# <target>-fast that always runs the same commands, but does not have
+# any dependencies. Desired dependencies can be added separately using
+# add_dependencies(). This supports cases where some of the dependencies
+# are time-consuming to build, and it is possible to build the target
+# even without up-to-date dependencies for testing only that part of the
+# build.
+# OUTPUT
+# - Sets the name of the output file from this custom target.
+# Can be set to STAMP, in which case a stamp file name is automatically
+# generated and commands to touch that stamp whenever the target is made
+# are added.
+# COMMAND
+# - Passed to add_custom_command()/add_custom_target().
+# If OUTPUT STAMP is used, then a command to touch the stamp is
+# automatically added. In this case, it is allowed to not specify any
+# commands explicitly.
+# WORKING_DIRECTORY
+# - Passed to add_custom_command()/add_custom_target()
+# COMMENT
+# - Passed to add_custom_command()/add_custom_target()
+# DEPENDS
+# - Dependencies passed to add_custom_command(). Any targets in this list
+# that have been created with gmx_add_custom_output_target() are
+# automatically expanded such that the custom command always runs if the
+# output of the dependent target changes. It is not necessary to list
+# those output files here explicitly.
+# DEPENDS_FILE_LIST
+# - Names of variables from which dependencies are added verbatim.
+# The target expansion described above is not performed for these
+# dependencies, and the value passed to the function is the name of a
+# list variable, not the list itself. This provides much better
+# performance if the dependency list is a long list of source files.
+#
+# This function does not need a VERBATIM argument; that is always used when
+# creating the underlying custom commands/targets.
+function (gmx_add_custom_output_target targetname)
+ # Parse the arguments
+ # CMakeParseArguments is not suitable, since it does not support the use of
+ # multiple COMMAND parameters that add_custom_target/command() supports.
+ set(_option "")
+ set(_command_args "")
+ set(_deps "")
+ set(_output "")
+ set(_stamp OFF)
+ set(_always OFF)
+ set(_add_fast OFF)
+ foreach (_arg ${ARGN})
+ if ("x${_arg}" STREQUAL "xRUN_ALWAYS")
+ set(_always ON)
+ elseif ("x${_arg}" STREQUAL "xADD_FAST_TARGET")
+ set(_add_fast ON)
+ elseif ("x${_arg}" MATCHES "^x(OUTPUT|DEPENDS|DEPENDS_FILE_LIST)$")
+ set(_option ${_arg})
+ elseif ("x${_arg}" MATCHES "^x(COMMAND|COMMENT|WORKING_DIRECTORY)$")
+ set(_option "PASS")
+ list(APPEND _command_args "${_arg}")
+ elseif ("x${_option}" STREQUAL "xDEPENDS")
+ list(APPEND _deps "${_arg}")
+ # If the dependency is a target created with this command, also add
+ # the output file as a dependency.
+ if (TARGET "${_arg}")
+ get_property(_target_output
+ TARGET "${_arg}" PROPERTY GMX_CUSTOM_TARGET_OUTPUT_FILE)
+ if (_target_output)
+ list(APPEND _deps ${_target_output})
+ endif()
+ endif()
+ elseif ("x${_option}" STREQUAL "xPASS")
+ list(APPEND _command_args "${_arg}")
+ elseif ("x${_option}" STREQUAL "xDEPENDS_FILE_LIST")
+ list(APPEND _deps ${${_arg}})
+ elseif ("x${_option}" STREQUAL "xOUTPUT")
+ if (_output)
+ message(FATAL_ERROR "Multiple OUTPUTs not supported")
+ endif()
+ if ("x${_arg}" STREQUAL "xSTAMP")
+ gmx_get_stamp_filename(_output ${targetname})
+ set(_stamp ON)
+ else()
+ set(_output ${_arg})
+ endif()
+ else()
+ message(FATAL_ERROR "Unknown option ${_arg}")
+ endif()
+ endforeach()
+ # Add automatically a command to update the stamp if requested
+ if (_stamp)
+ list(APPEND _command_args COMMAND ${CMAKE_COMMAND} -E touch ${_output})
+ endif()
+ # Create the actual command as requested.
+ if (NOT _always)
+ # If the command does not need to run always, the standard CMake
+ # mechanism is sufficient.
+ add_custom_command(OUTPUT ${_output}
+ ${_command_args} DEPENDS ${_deps} VERBATIM)
+ add_custom_target(${targetname} DEPENDS ${_output})
+ elseif (CMAKE_GENERATOR STREQUAL "Ninja")
+ # Ninja requires all generated files mentioned in dependencies of custom
+ # commands to be actually mentioned in the build system, and luckily
+ # add_custom_command() makes that possible.
+ # But it seems impossible to create a robust custom command that would be
+ # always run, so other generators that do not have this constraint simply
+ # use an add_custom_target().
+ #
+ # The second, phony file is never created, so the rule is always
+ # triggered again. TODO: Figure out why this works, even though ninja
+ # very eagerly complains about missing files.
+ # This unfortunately does not work with the make generator, as
+ # the non-existent second file causes some part of the generated system
+ # erase the first file at the beginning of every build, causing a full
+ # rebuild of the dependencies.
+ add_custom_command(OUTPUT ${_output} ${targetname}-phony
+ ${_command_args} VERBATIM)
+ # The generated Ninja build system would probably work fine even
+ # without this target, but CMake requires all custom commands to belong
+ # to a target in the same CMakeLists.txt to generate anything for them.
+ add_custom_target(${targetname} DEPENDS ${_output})
+ else()
+ # For other generators, a target-level dependency on the custom target
+ # ensures that the output is created before the dependent targets'
+ # dependencies are even evaluated.
+ add_custom_target(${targetname} ${_command_args} VERBATIM)
+ endif()
+ # Store the output file name in a custom property to be used in dependency
+ # resolution later.
+ gmx_set_custom_target_output(${targetname} ${_output})
+ # Create the fast target if requested.
+ if (_add_fast)
+ add_custom_target(${targetname}-fast ${_command_args} VERBATIM)
+ endif()
+endfunction()
+
+# Gets list of files in the source tree with the given git attribute set
+#
+# Usage:
+# gmx_get_files_with_gitattribute(<variable> <attribute>)
+#
+# <variable> - name of variable to receive the file list
+# <attribute> - name of git attribute to use
+#
+# This is useful to generate a list of dependencies for custom commands when
+# there is a long list of files that cannot be easily just globbed.
+# Using git attributes allows keeping complicated logic out of the build
+# system, as expressing such logic in a CMake script that would be reasonably
+# fast to evaluate for a long file list is convenient or easy.
+function (gmx_get_files_with_gitattribute variable attribute)
+ execute_process(
+ COMMAND ${GIT_EXECUTABLE} ls-files
+ COMMAND ${GIT_EXECUTABLE} check-attr ${attribute} --stdin
+ WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+ OUTPUT_VARIABLE _files)
+ string(REGEX MATCHALL "[^\n]*: ${attribute}: set\n"
+ _files_with_attr "${_files}")
+ string(REGEX REPLACE "([^;]*): ${attribute}: set\n" "${PROJECT_SOURCE_DIR}/\\1"
+ _files "${_files_with_attr}")
+ set(${variable} ${_files} PARENT_SCOPE)
+endfunction()
message(STATUS "Detecting best SIMD instructions for this CPU")
# Get CPU SIMD properties information
- set(_compile_definitions "${GCC_INLINE_ASM_DEFINE} -I${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders -DGMX_CPUID_STANDALONE")
+ set(_compile_definitions "${GCC_INLINE_ASM_DEFINE} -I${CMAKE_SOURCE_DIR}/src -DGMX_CPUID_STANDALONE")
if(GMX_TARGET_X86)
set(_compile_definitions "${_compile_definitions} -DGMX_TARGET_X86")
endif()
# HPC-ACE is always present. In the future we
# should add detection for HPC-ACE2 here.
set(${_suggested_simd} "Sparc64_HPC_ACE")
+ elseif(GMX_TARGET_MIC)
+ set(${_suggested_simd} "MIC")
elseif(GMX_TARGET_X86)
gmx_suggest_x86_simd(${_suggested_simd})
else()
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-# Due to a bug, gcc 4.4.x crashes when compiling bondfree.c with -O3 and
+# Due to a bug, gcc 4.4.x crashes when compiling listed-forces/bonded.cpp with -O3 and
# -fopenmp, but strangely it does not crash with -O2 + all additional options.
# -O3 uses. Therefore, for the affected files, when compiling in release mode,
# we override -O3 with -O2 and add the additional option.
# PROJECT_SOURCE_DIR - top level source directory (which has to be in git)
# VERSION_CMAKEIN - path to an input template file
# VERSION_OUT - path to the output file
-# VERSION_NO_REMOTE_HASH - if set, GMX_GIT_REMOTE_HASH is not generated
#
# Output:
-# i) Script mode: VERSION_OUT is configured from the input VERSION_CMAKEIN
+# VERSION_OUT is configured from the input VERSION_CMAKEIN
# using the variables listed below.
-# ii) Cache variable mode: the variables below are set in cache.
#
-# GMX_PROJECT_VERSION_STR - version string
-# GMX_GIT_HEAD_HASH - git hash of current local HEAD
-# GMX_GIT_REMOTE_HASH - git hash of the first ancestor commit from the
-# main Gromacs repository
+# GMX_VERSION_STRING_FULL - version string
+# GMX_VERSION_FULL_HASH - git hash of current local HEAD
+# GMX_VERSION_CENTRAL_BASE_HASH - git hash of the first ancestor commit from the
+# main Gromacs repository
#
# Szilard Pall (pszilard@cbr.su.se)
# Teemu Murtola (teemu.murtola@gmail.com)
+# Check input variables.
if("${PROJECT_VERSION}" STREQUAL "")
message(FATAL_ERROR "PROJECT_VERSION undefined!")
endif()
-
-# if we're generating variables for cache unset the variables
-if(GEN_VERSION_INFO_INTERNAL)
- set(GMX_PROJECT_VERSION_STR)
- set(GMX_GIT_HEAD_HASH)
- set(GMX_GIT_REMOTE_HASH)
+if (NOT EXISTS "${GIT_EXECUTABLE}")
+ message(FATAL_ERROR "Git executable is not set correctly")
endif()
-
-# bail if the source tree is not in a git repository
-if(NOT EXISTS "${PROJECT_SOURCE_DIR}/.git")
+if (NOT EXISTS "${PROJECT_SOURCE_DIR}/.git")
message(FATAL_ERROR "Project source directory ${PROJECT_SOURCE_DIR} not in git")
endif()
+if ("${VERSION_CMAKEIN}" STREQUAL "")
+ message(FATAL_ERROR "Missing input parameter VERSION_CMAKEIN!")
+endif()
+if ("${VERSION_OUT}" STREQUAL "")
+ message(FATAL_ERROR "Missing input parameter VERSION_OUT!")
+endif()
-# If git executable exists, build the development version string.
-if(EXISTS "${GIT_EXECUTABLE}")
- # refresh git index
- execute_process(COMMAND ${GIT_EXECUTABLE} update-index -q --refresh
- WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
- TIMEOUT 5
- OUTPUT_QUIET
- ERROR_VARIABLE EXEC_ERR
- OUTPUT_STRIP_TRAILING_WHITESPACE
- )
+# refresh git index
+execute_process(COMMAND ${GIT_EXECUTABLE} update-index -q --refresh
+ WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+ TIMEOUT 5
+ OUTPUT_QUIET
+ ERROR_VARIABLE EXEC_ERR
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+)
- # get the full hash of the current HEAD
- execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse HEAD
- WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
- OUTPUT_VARIABLE HEAD_HASH
- ERROR_VARIABLE EXEC_ERR
- OUTPUT_STRIP_TRAILING_WHITESPACE
- )
- set(GMX_GIT_HEAD_HASH ${HEAD_HASH})
- # extract the shortened hash (7 char)
- execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse --short HEAD
- WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
- OUTPUT_VARIABLE HEAD_HASH_SHORT
- ERROR_VARIABLE EXEC_ERR
- OUTPUT_STRIP_TRAILING_WHITESPACE
- )
+# get the full hash of the current HEAD
+execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse HEAD
+ WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+ OUTPUT_VARIABLE HEAD_HASH
+ ERROR_VARIABLE EXEC_ERR
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+set(GMX_VERSION_FULL_HASH ${HEAD_HASH})
- # if there are local uncommitted changes, the build gets labeled "dirty"
- execute_process(COMMAND ${GIT_EXECUTABLE} diff-index --name-only HEAD
- WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
- OUTPUT_VARIABLE SRC_LOCAL_CHANGES
- ERROR_VARIABLE EXEC_ERR
- OUTPUT_STRIP_TRAILING_WHITESPACE
- )
- if(NOT "${SRC_LOCAL_CHANGES}" STREQUAL "")
- set(DIRTY_STR "-dirty")
- set(GMX_GIT_HEAD_HASH "${GMX_GIT_HEAD_HASH} (dirty)")
- endif()
+# extract the shortened hash (7 char)
+execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse --short HEAD
+ WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+ OUTPUT_VARIABLE HEAD_HASH_SHORT
+ ERROR_VARIABLE EXEC_ERR
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+)
- # get the date of the HEAD commit
- execute_process(COMMAND ${GIT_EXECUTABLE} rev-list -n1 "--pretty=format:%ci" HEAD
- WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
- OUTPUT_VARIABLE HEAD_DATE
- ERROR_VARIABLE EXEC_ERR
- OUTPUT_STRIP_TRAILING_WHITESPACE
- )
- string(REGEX REPLACE "\n| " ";" HEAD_DATE "${HEAD_DATE}")
- list(GET HEAD_DATE 2 HEAD_DATE)
- string(REGEX REPLACE "-" "" HEAD_DATE "${HEAD_DATE}")
+# if there are local uncommitted changes, the build gets labeled "dirty"
+execute_process(COMMAND ${GIT_EXECUTABLE} diff-index --name-only HEAD
+ WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+ OUTPUT_VARIABLE SRC_LOCAL_CHANGES
+ ERROR_VARIABLE EXEC_ERR
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+if(NOT "${SRC_LOCAL_CHANGES}" STREQUAL "")
+ set(DIRTY_STR "-dirty")
+ set(GMX_VERSION_FULL_HASH "${GMX_VERSION_FULL_HASH} (dirty)")
+endif()
- # compile the version string suffix
- set(VERSION_STR_SUFFIX "${HEAD_DATE}-${HEAD_HASH_SHORT}${DIRTY_STR}")
+# get the date of the HEAD commit
+execute_process(COMMAND ${GIT_EXECUTABLE} rev-list -n1 "--pretty=format:%ci" HEAD
+ WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+ OUTPUT_VARIABLE HEAD_DATE
+ ERROR_VARIABLE EXEC_ERR
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+string(REGEX REPLACE "\n| " ";" HEAD_DATE "${HEAD_DATE}")
+list(GET HEAD_DATE 2 HEAD_DATE)
+string(REGEX REPLACE "-" "" HEAD_DATE "${HEAD_DATE}")
- if (DEFINED VERSION_NO_REMOTE_HASH)
- set(GMX_REMOTES "")
- else()
- # find the names of remotes that are located on the official gromacs
- # git/gerrit servers
- execute_process(COMMAND ${GIT_EXECUTABLE} config --get-regexp
- "remote\\..*\\.url" "\\.gromacs\\.org[:/].*gromacs(\\.git)?$"
- WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
- OUTPUT_VARIABLE GMX_REMOTES
- ERROR_VARIABLE EXEC_ERR
- OUTPUT_STRIP_TRAILING_WHITESPACE
- )
- endif()
+# compile the version string suffix
+set(VERSION_STR_SUFFIX "${HEAD_DATE}-${HEAD_HASH_SHORT}${DIRTY_STR}")
- # if there are remotes from the gromacs git servers, try to find ancestor
- # commits of the current HEAD from this remote;
- # otherwise, label the build "unknown"
- if("${GMX_REMOTES}" STREQUAL "")
- if (NOT DEFINED VERSION_NO_REMOTE_HASH)
- set(VERSION_STR_SUFFIX "${VERSION_STR_SUFFIX}-unknown")
- endif()
- set(GMX_GIT_REMOTE_HASH "unknown")
- else()
- string(REPLACE "\n" ";" GMX_REMOTES ${GMX_REMOTES})
- # construct a command pipeline that produces a reverse-time-ordered
- # list of commits and their annotated names in GMX_REMOTES
- # the max-count limit is there to put an upper bound on the execution time
- set(BASEREVCOMMAND "COMMAND ${GIT_EXECUTABLE} rev-list --max-count=1000 HEAD")
- foreach(REMOTE ${GMX_REMOTES})
- string(REGEX REPLACE "remote\\.(.*)\\.url.*" "\\1" REMOTE ${REMOTE})
- set(BASEREVCOMMAND "${BASEREVCOMMAND} COMMAND ${GIT_EXECUTABLE} name-rev --stdin --refs=refs/remotes/${REMOTE}/*")
- endforeach(REMOTE)
- # this is necessary for CMake to properly split the variable into
- # parameters for execute_process().
- string(REPLACE " " ";" BASEREVCOMMAND ${BASEREVCOMMAND})
- # find the first ancestor in the list provided by rev-list (not
- # necessarily the last though) which is in GMX_REMOTE, extract the
- # hash and the number of commits HEAD is ahead with
- execute_process(${BASEREVCOMMAND}
- WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
- OUTPUT_VARIABLE ANCESTOR_LIST
- )
- string(REGEX REPLACE "\n" ";" ANCESTOR_LIST "${ANCESTOR_LIST}")
+# find the names of remotes that are located on the official gromacs
+# git/gerrit servers
+execute_process(COMMAND ${GIT_EXECUTABLE} config --get-regexp
+ "remote\\..*\\.url" "\\.gromacs\\.org[:/].*gromacs(\\.git)?$"
+ WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+ OUTPUT_VARIABLE GMX_REMOTES
+ ERROR_VARIABLE EXEC_ERR
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+)
- set(AHEAD 0)
- set(GMX_GIT_REMOTE_HASH "")
- foreach(ANCESTOR ${ANCESTOR_LIST})
- string(REPLACE "\n" "" HASH_AND_REVNAMES "${ANCESTOR}")
- string(REPLACE " " ";" HASH_AND_REVNAMES "${HASH_AND_REVNAMES}")
- list(LENGTH HASH_AND_REVNAMES COUNT)
- # stop and set the hash if we have a hit, otherwise loop and count
- # how far ahead is the local repo
- if(COUNT GREATER 1)
- LIST(GET HASH_AND_REVNAMES 0 GMX_GIT_REMOTE_HASH)
- break()
- endif()
- math(EXPR AHEAD ${AHEAD}+1)
- endforeach(ANCESTOR)
- # mark the build "local" if didn't find any commits that are from
- # remotes/${GMX_REMOTE}/*
- if("${GMX_GIT_REMOTE_HASH}" STREQUAL "")
- set(GMX_GIT_REMOTE_HASH "unknown")
- set(VERSION_STR_SUFFIX "${VERSION_STR_SUFFIX}-local")
- # don't print the remote hash if there are no local commits
- elseif("${GMX_GIT_REMOTE_HASH}" STREQUAL "${HEAD_HASH}")
- set(GMX_GIT_REMOTE_HASH "")
- else()
- set(GMX_GIT_REMOTE_HASH "${GMX_GIT_REMOTE_HASH} (${AHEAD} newer local commits)")
- endif()
+# if there are remotes from the gromacs git servers, try to find ancestor
+# commits of the current HEAD from this remote;
+# otherwise, label the build "unknown"
+if("${GMX_REMOTES}" STREQUAL "")
+ if (NOT DEFINED VERSION_NO_REMOTE_HASH)
+ set(VERSION_STR_SUFFIX "${VERSION_STR_SUFFIX}-unknown")
endif()
-
- # compile final version string
- set(GMX_PROJECT_VERSION_STR "${PROJECT_VERSION}-${VERSION_STR_SUFFIX}")
+ set(GMX_VERSION_CENTRAL_BASE_HASH "unknown")
else()
- # the version has to be defined
- # set the GIT related information to "unknown"
- message(WARNING "Source tree seems to be a repository, but no compatible git is available, using hard-coded version string")
- set(GMX_PROJECT_VERSION_STR "${PROJECT_VERSION}")
- set(GMX_GIT_HEAD_HASH "unknown")
- set(GMX_GIT_REMOTE_HASH "unknown")
-endif()
+ string(REPLACE "\n" ";" GMX_REMOTES ${GMX_REMOTES})
+ # construct a command pipeline that produces a reverse-time-ordered
+ # list of commits and their annotated names in GMX_REMOTES
+ # the max-count limit is there to put an upper bound on the execution time
+ set(BASEREVCOMMAND "COMMAND ${GIT_EXECUTABLE} rev-list --max-count=1000 HEAD")
+ foreach(REMOTE ${GMX_REMOTES})
+ string(REGEX REPLACE "remote\\.(.*)\\.url.*" "\\1" REMOTE ${REMOTE})
+ set(BASEREVCOMMAND "${BASEREVCOMMAND} COMMAND ${GIT_EXECUTABLE} name-rev --stdin --refs=refs/remotes/${REMOTE}/*")
+ endforeach(REMOTE)
+ # this is necessary for CMake to properly split the variable into
+ # parameters for execute_process().
+ string(REPLACE " " ";" BASEREVCOMMAND ${BASEREVCOMMAND})
+ # find the first ancestor in the list provided by rev-list (not
+ # necessarily the last though) which is in GMX_REMOTE, extract the
+ # hash and the number of commits HEAD is ahead with
+ execute_process(${BASEREVCOMMAND}
+ WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+ OUTPUT_VARIABLE ANCESTOR_LIST
+ )
+ string(REGEX REPLACE "\n" ";" ANCESTOR_LIST "${ANCESTOR_LIST}")
-# if we're generating cache variables set these
-# otherwise it's assumed that it's called in script mode to generate a file
-if(GEN_VERSION_INFO_INTERNAL)
- set(GMX_PROJECT_VERSION_STR ${GMX_PROJECT_VERSION_STR}
- CACHE STRING "Gromacs version string" FORCE)
- set(GMX_GIT_HEAD_HASH ${GMX_GIT_HEAD_HASH}${DIRTY_STR}
- CACHE STRING "Current git HEAD commit object" FORCE)
- set(GMX_GIT_REMOTE_HASH ${GMX_GIT_REMOTE_HASH}
- CACHE STRING "Commmit object of the nearest ancestor present in the Gromacs git repository" FORCE)
- mark_as_advanced(GMX_GIT_HEAD_HASH GMX_GIT_REMOTE_HASH)
-else()
- if("${VERSION_CMAKEIN}" STREQUAL "")
- message(FATAL_ERROR "Missing input parameter VERSION_CMAKEIN!")
- endif()
- if("${VERSION_OUT}" STREQUAL "")
- message(FATAL_ERROR "Missing input parameter VERSION_OUT!")
+ set(AHEAD 0)
+ set(GMX_VERSION_CENTRAL_BASE_HASH "")
+ foreach(ANCESTOR ${ANCESTOR_LIST})
+ string(REPLACE "\n" "" HASH_AND_REVNAMES "${ANCESTOR}")
+ string(REPLACE " " ";" HASH_AND_REVNAMES "${HASH_AND_REVNAMES}")
+ list(LENGTH HASH_AND_REVNAMES COUNT)
+ # stop and set the hash if we have a hit, otherwise loop and count
+ # how far ahead is the local repo
+ if(COUNT GREATER 1)
+ LIST(GET HASH_AND_REVNAMES 0 GMX_VERSION_CENTRAL_BASE_HASH)
+ break()
+ endif()
+ math(EXPR AHEAD ${AHEAD}+1)
+ endforeach(ANCESTOR)
+ # mark the build "local" if didn't find any commits that are from
+ # remotes/${GMX_REMOTE}/*
+ if("${GMX_VERSION_CENTRAL_BASE_HASH}" STREQUAL "")
+ set(GMX_VERSION_CENTRAL_BASE_HASH "unknown")
+ set(VERSION_STR_SUFFIX "${VERSION_STR_SUFFIX}-local")
+ # don't print the remote hash if there are no local commits
+ elseif("${GMX_VERSION_CENTRAL_BASE_HASH}" STREQUAL "${HEAD_HASH}")
+ set(GMX_VERSION_CENTRAL_BASE_HASH "")
+ else()
+ set(GMX_VERSION_CENTRAL_BASE_HASH "${GMX_VERSION_CENTRAL_BASE_HASH} (${AHEAD} newer local commits)")
endif()
- # Generate the output file.
- configure_file(${VERSION_CMAKEIN} ${VERSION_OUT})
endif()
+
+# Compile final version string.
+set(GMX_VERSION_STRING_FULL "${PROJECT_VERSION}-${VERSION_STR_SUFFIX}")
+
+# Generate the output file.
+configure_file(${VERSION_CMAKEIN} ${VERSION_OUT})
endif()
endif() # NOT CUDA_FOUND
endif()
+
+# Try to find NVML if a GPU accelerated binary should be build.
+if (GMX_GPU)
+ find_package(NVML)
+ if(NVML_FOUND)
+ include_directories(${NVML_INCLUDE_DIR})
+ set(HAVE_NVML 1)
+ list(APPEND GMX_EXTRA_LIBRARIES ${NVML_LIBRARY})
+ endif(NVML_FOUND)
+endif()
+
# Annoyingly enough, FindCUDA leaves a few variables behind as non-advanced.
# We need to mark these advanced outside the conditional, otherwise, if the
# user turns GMX_GPU=OFF after a failed cmake pass, these variables will be
"or set the variables reported missing for MPI_C above.")
endif()
- include(gmxTestCatamount)
- gmx_test_catamount(GMX_CRAY_CATAMOUNT)
- if(GMX_CRAY_CATAMOUNT)
- set(GMX_NO_SYSTEM 1)
- set(GMX_NO_NICE 1)
- set(HAVE_PWD_H 0)
- endif()
-
set(GMX_LIB_MPI 1)
- set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_LIB_MPI")
endif()
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
setting CUDA_HOST_COMPILER to the full path of a compatible compiler.
")
else()
- # do not use MPI compiler wrappers, as these are prone to brake nvcc
- if (GMX_MPI AND
- NOT "${${MPI_PREFIX}_FOUND}" AND # FindMPI-based detection
- NOT GMX_THREAD_MPI)
+ # do not use MPI compiler wrappers, as these are prone to break nvcc
+ if (GMX_MPI AND NOT "${${MPI_PREFIX}_FOUND}") # FindMPI-based detection
message(WARNING "
Will not set the nvcc host compiler because the current C compiler is an MPI
compiler wrapper: ${CMAKE_C_COMPILER}
set(CUDA_HOST_COMPILER_OPTIONS "${CUDA_HOST_COMPILER_OPTIONS}-D__STRICT_ANSI__;")
endif()
- # on Linux we need to add -fPIC when building shared gmx libs
- # Note: will add -fPIC for any compiler that supports it as it shouldn't hurt
- if(BUILD_SHARED_LIBS)
- GMX_TEST_CXXFLAG(CXXFLAG_FPIC "-fPIC" _FPIC_NVCC_FLAG)
- if(_FPIC_NVCC_FLAG)
- set(CUDA_HOST_COMPILER_OPTIONS "${CUDA_HOST_COMPILER_OPTIONS}-Xcompiler;${_FPIC_NVCC_FLAG}")
- endif()
- endif()
-
# the legacy CUDA kernels have been dropped, warn with CUDA 4.0
if (CUDA_VERSION VERSION_EQUAL "4.0")
message(WARNING "The legacy GPU kernels optimized for older CUDA compilers, including the detected version 4.0, have been removed. To avoid performance loss, we strongly recommend upgrading to a newer CUDA toolkit.
# Set the CUDA GPU architectures to compile for:
# - with CUDA >v4.2 compute capability 2.0, 2.1 is, but 3.0 is not supported:
- # => compile sm_20, sm_21 cubin, and compute_20 PTX
- # - with CUDA >=4.2 compute capability <=3.0 is supported:
- # => compile sm_20, sm_21, sm_30 cubin, and compute_30 PTX
- # - with CUDA 5.0 and later compute capability 3.5 is supported
- # => compile sm_20, sm_21, sm_30, sm_35 cubin, and compute_35 PTX
+ # => compile sm_20 cubin, and compute_20 PTX
+ # - with CUDA >=4.2 CC <=3.0 is supported:
+ # => compile sm_20, sm_30 cubin, and compute_30 PTX
+ # - with CUDA 5.0 and later CC <=3.5 is supported
+ # => compile sm_20, sm_30, sm_35 cubin, and compute_35 PTX
+ # - with CUDA 6.5 and later compute capability <=3.5 and 5.0 are supported
+ # => compile sm_20, sm_30, sm_35, sm_5.0, cubin, and compute_50 PTX
+ # Note that CUDA 6.5.19 second patch release supports cc 5.2 too, but
+ # CUDA_VERSION does not contain patch version and having PTX 5.0 JIT-ed is
+ # equally fast anyway.
if(CUDA_VERSION VERSION_LESS "4.2")
- set(_CUDA_ARCH_STR "-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=sm_21;-gencode;arch=compute_20,code=compute_20")
+ set(_CUDA_ARCH_STR "-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=compute_20")
elseif(CUDA_VERSION VERSION_LESS "5.0")
- set(_CUDA_ARCH_STR "-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=sm_21;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_30,code=compute_30")
+ set(_CUDA_ARCH_STR "-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_30,code=compute_30")
+ elseif(CUDA_VERSION VERSION_LESS "6.5")
+ set(_CUDA_ARCH_STR "-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_35,code=compute_35")
else()
- set(_CUDA_ARCH_STR "-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=sm_21;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_35,code=compute_35")
+ set(_CUDA_ARCH_STR "-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_50,code=compute_50;")
endif()
# finally set the damn flags
if(OPENMP_FOUND)
# CMake on Windows doesn't support linker flags passed to target_link_libraries
# (i.e. it treats /openmp as \openmp library file). Also, no OpenMP linker flags are needed.
- if(NOT (WIN32 AND NOT CYGWIN AND NOT MINGW))
+ if(NOT (WIN32 AND NOT MINGW))
if(CMAKE_COMPILER_IS_GNUCC AND GMX_PREFER_STATIC_OPENMP AND NOT APPLE)
set(OpenMP_LINKER_FLAGS "-Wl,-static -lgomp -lrt -Wl,-Bdynamic -lpthread")
set(OpenMP_SHARED_LINKER_FLAGS "")
endif()
endif()
endif()
+gmx_dependent_cache_variable(GMX_OPENMP_MAX_THREADS
+ "Maximum number of OpenMP Threads supported. Has to be 32 or a multiple of 64."
+ STRING 32 GMX_OPENMP)
+mark_as_advanced(GMX_OPENMP_MAX_THREADS)
+math(EXPR MAX_THREAD_MOD "${GMX_OPENMP_MAX_THREADS} % 64")
+if (NOT GMX_OPENMP_MAX_THREADS EQUAL 32 AND NOT ${MAX_THREAD_MOD} EQUAL 0)
+ message(FATAL_ERROR "Only 32 or multiples of 64 supported for GMX_OPENMP_MAX_THREADS.")
+endif()
set(SHARED_LIBS_DEFAULT OFF)
endif()
set(GMX_PREFER_STATIC_LIBS_DEFAULT OFF)
-if (WIN32 AND NOT CYGWIN AND NOT BUILD_SHARED_LIBS)
+if (WIN32 AND NOT BUILD_SHARED_LIBS)
set(GMX_PREFER_STATIC_LIBS_DEFAULT ON)
endif()
if (UNIX)
set(GMX_PREFER_STATIC_LIBS_DESCRIPTION
"When finding libraries prefer static archives (it will only work if static versions of external dependencies are available and found)")
-elseif (WIN32 AND NOT CYGWIN)
+elseif (WIN32)
set(GMX_PREFER_STATIC_LIBS_DESCRIPTION
"When finding libraries prefer static system libraries (MT instead of MD)")
endif()
endforeach()
endfunction()
-IF( WIN32 AND NOT CYGWIN)
+IF( WIN32)
if (NOT BUILD_SHARED_LIBS)
if(NOT GMX_PREFER_STATIC_LIBS)
message(WARNING "Shared system libraries requested, and static Gromacs libraries requested.")
#this combination segfaults (illegal passing of file handles)
message(FATAL_ERROR "Static system libraries requested, and shared Gromacs libraries requested.")
endif()
- add_definitions(-DUSE_VISIBILITY -DTMPI_USE_VISIBILITY)
- set(PKG_CFLAGS "$PKG_CFLAGS -DUSE_VISIBILITY -DTMPI_USE_VISIBILITY")
+ # Visibility not yet implemented
+ # add_definitions(-DUSE_VISIBILITY -DTMPI_USE_VISIBILITY)
+ # set(PKG_CFLAGS "$PKG_CFLAGS -DUSE_VISIBILITY -DTMPI_USE_VISIBILITY")
endif()
IF (GMX_PREFER_STATIC_LIBS)
message(STATUS "Using default library suffix: \"${GMX_LIBS_SUFFIX}\"")
endif()
else()
+ if ("${GMX_LIBS_SUFFIX}" MATCHES "^_mdrun")
+ message(FATAL_ERROR "Library suffix (GMX_LIBS_SUFFIX) cannot start with '_mdrun', as that is reserved for internal use")
+ endif()
gmx_check_if_changed(SUFFIXES_CHANGED
GMX_DEFAULT_SUFFIX GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
if (SUFFIXES_CHANGED)
string(REPLACE "[built-in]" "" _allowed "${ARGN}")
# Set the cache properties
- set(${NAME} ${DEFAULT} CACHE STRING ${_description})
+ set(${NAME} ${DEFAULT} CACHE STRING "${_description}")
set_property(CACHE ${NAME} PROPERTY STRINGS ${_allowed})
# Check that the value is one of the allowed
message(FATAL_ERROR "Invalid value for ${NAME}: ${${NAME}}")
endfunction()
+# Declares a cache variable with ON/OFF/AUTO values
+#
+# Usage:
+# gmx_option_trivalue(VAR "Description" DEFAULT)
+#
+# Output:
+# VAR is created in the cache, and the caller can assume that the value is
+# always one of ON/OFF/AUTO. Additionally, VAR_AUTO is set if value is AUTO,
+# and VAR_FORCE is set if value is ON.
+# These make it convenient to check for any combination of states with simple
+# if() statements (simple if(VAR) matches AUTO and ON).
+function(GMX_OPTION_TRIVALUE NAME DESCRIPTION DEFAULT)
+ set(_description "${DESCRIPTION}. ON/OFF/AUTO")
+ set(${NAME} ${DEFAULT} CACHE STRING "${_description}")
+ set_property(CACHE ${NAME} PROPERTY STRINGS ON OFF AUTO)
+
+ set(${NAME}_AUTO OFF)
+ set(${NAME}_FORCE OFF)
+ string(TOUPPER "${${NAME}}" ${NAME})
+ if ("${${NAME}}" STREQUAL "AUTO")
+ set(${NAME}_AUTO ON)
+ elseif (${NAME})
+ set(${NAME}_FORCE ON)
+ set(${NAME} ON)
+ else()
+ set(${NAME} OFF)
+ endif()
+ # Always provide the sanitized value to the caller
+ set(${NAME} "${${NAME}}" PARENT_SCOPE)
+ set(${NAME}_AUTO "${${NAME}_AUTO}" PARENT_SCOPE)
+ set(${NAME}_FORCE "${${NAME}_FORCE}" PARENT_SCOPE)
+endfunction()
+
# Hides or shows a cache value based on conditions
#
# Usage:
if(NOT CMAKE_CROSSCOMPILING)
# Get CPU information, e.g. for deciding what SIMD support exists
- set(_compile_definitions "${GCC_INLINE_ASM_DEFINE} -I${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders -DGMX_CPUID_STANDALONE")
+ set(_compile_definitions "${GCC_INLINE_ASM_DEFINE} -I${CMAKE_SOURCE_DIR}/src -DGMX_CPUID_STANDALONE")
if(GMX_TARGET_X86)
set(_compile_definitions "${_compile_definitions} -DGMX_TARGET_X86")
endif()
include(CheckCXXSourceCompiles)
MACRO(GMX_TEST_CXX11 VARIABLE FLAG)
- if(WIN32)
+ if(WIN32 AND NOT MINGW)
set(CXX11_FLAG "/Qstd=c++0x")
elseif(CYGWIN)
set(CXX11_FLAG "-std=gnu++0x") #required for strdup
typedef VarList<Tail...> VarListTail;
typedef std::pair<Head, typename VarListTail::ListType> ListType;
};
+class a { explicit operator bool() {return true;} };
int main() {
typedef std::unique_ptr<int> intPointer;
intPointer p(new int(10));
message(WARNING "GCC on Windows (GCC older than 4.9 or any version when compiling for 64bit) with AVX (other than AVX_128_FMA) crashes. Choose a different GMX_SIMD or a different compiler.") # GCC bug 49001, 54412.
endif()
- if(CMAKE_C_COMPILER_ID MATCHES "Clang" AND WIN32 AND NOT CYGWIN)
+ if(CMAKE_C_COMPILER_ID MATCHES "Clang" AND WIN32)
if(CMAKE_VERSION VERSION_LESS 3.0.0)
message(WARNING "Clang on Windows requires cmake 3.0.0")
endif()
set(GMX_SIMD_X86_AVX2_256 1)
set(SIMD_STATUS_MESSAGE "Enabling 256-bit AVX2 SIMD instructions")
+elseif(${GMX_SIMD} STREQUAL "MIC")
+
+ # No flags needed. Not testing.
+ set(GMX_SIMD_X86_MIC 1)
+ set(SIMD_STATUS_MESSAGE "Enabling MIC (Xeon Phi) SIMD instructions")
+
+elseif(${GMX_SIMD} STREQUAL "ARM_NEON")
+
+ gmx_find_cflag_for_source(CFLAGS_ARM_NEON "C compiler 32-bit ARM NEON flag"
+ "#include<arm_neon.h>
+ int main(){float32x4_t x=vdupq_n_f32(0.5);x=vmlaq_f32(x,x,x);return vgetq_lane_f32(x,0)>0;}"
+ SIMD_C_FLAGS
+ "-mfpu=neon" "")
+ gmx_find_cxxflag_for_source(CXXFLAGS_ARM_NEON "C++ compiler 32-bit ARM NEON flag"
+ "#include<arm_neon.h>
+ int main(){float32x4_t x=vdupq_n_f32(0.5);x=vmlaq_f32(x,x,x);return vgetq_lane_f32(x,0)>0;}"
+ SIMD_CXX_FLAGS
+ "-mfpu=neon" "-D__STDC_CONSTANT_MACROS" "")
+
+ if(NOT CFLAGS_ARM_NEON OR NOT CXXFLAGS_ARM_NEON)
+ message(FATAL_ERROR "Cannot find ARM 32-bit NEON compiler flag. Use a newer compiler, or disable NEON SIMD.")
+ endif()
+
+ set(GMX_SIMD_ARM_NEON 1)
+ set(SIMD_STATUS_MESSAGE "Enabling 32-bit ARM NEON SIMD instructions")
+
+elseif(${GMX_SIMD} STREQUAL "ARM_NEON_ASIMD")
+ # Gcc-4.8.1 appears to have a bug where the c++ compiler requires
+ # -D__STDC_CONSTANT_MACROS if we include arm_neon.h
+
+ gmx_find_cflag_for_source(CFLAGS_ARM_NEON_ASIMD "C compiler ARM NEON Advanced SIMD flag"
+ "#include<arm_neon.h>
+ int main(){float64x2_t x=vdupq_n_f64(0.5);x=vfmaq_f64(x,x,x);return vgetq_lane_f64(x,0)>0;}"
+ SIMD_C_FLAGS
+ "")
+ gmx_find_cxxflag_for_source(CXXFLAGS_ARM_NEON_ASIMD "C++ compiler ARM NEON Advanced SIMD flag"
+ "#include<arm_neon.h>
+ int main(){float64x2_t x=vdupq_n_f64(0.5);x=vfmaq_f64(x,x,x);return vgetq_lane_f64(x,0)>0;}"
+ SIMD_CXX_FLAGS
+ "-D__STDC_CONSTANT_MACROS" "")
+
+ if(NOT CFLAGS_ARM_NEON_ASIMD OR NOT CXXFLAGS_ARM_NEON_ASIMD)
+ message(FATAL_ERROR "Cannot find ARM (AArch64) NEON Advanced SIMD compiler flag. Use a newer compiler, or disable SIMD.")
+ endif()
+
+ if(CMAKE_C_COMPILER_ID MATCHES "GNU" AND CMAKE_C_COMPILER_VERSION VERSION_LESS "4.9")
+ message(WARNING "At least gcc-4.8.1 has many bugs for ARM (AArch64) NEON Advanced SIMD compilation. You might need gcc version 4.9 or later.")
+ endif()
+
+ if(CMAKE_C_COMPILER_ID MATCHES "Clang" AND CMAKE_C_COMPILER_VERSION VERSION_LESS "3.4")
+ message(FATAL_ERROR "Clang version 3.4 or later is required for ARM (AArch64) NEON Advanced SIMD.")
+ endif()
+
+ set(GMX_SIMD_ARM_NEON_ASIMD 1)
+ set(SIMD_STATUS_MESSAGE "Enabling ARM (AArch64) NEON Advanced SIMD instructions")
+
elseif(${GMX_SIMD} STREQUAL "IBM_QPX")
try_compile(TEST_QPX ${CMAKE_BINARY_DIR}
message(FATAL_ERROR "Cannot compile the requested IBM QPX intrinsics. If you are compiling for BlueGene/Q with the XL compilers, use 'cmake .. -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C' to set up the tool chain.")
endif()
+elseif(${GMX_SIMD} STREQUAL "IBM_VMX")
+
+ gmx_find_cflag_for_source(CFLAGS_IBM_VMX "C compiler IBM VMX SIMD flag"
+ "#include<altivec.h>
+ int main(){vector float x,y=vec_ctf(vec_splat_s32(1),0);x=vec_madd(y,y,y);return vec_all_ge(y,x);}"
+ SIMD_C_FLAGS
+ "-maltivec -mabi=altivec" "-qarch=auto -qaltivec")
+ gmx_find_cxxflag_for_source(CXXFLAGS_IBM_VMX "C++ compiler IBM VMX SIMD flag"
+ "#include<altivec.h>
+ int main(){vector float x,y=vec_ctf(vec_splat_s32(1),0);x=vec_madd(y,y,y);return vec_all_ge(y,x);}"
+ SIMD_CXX_FLAGS
+ "-maltivec -mabi=altivec" "-qarch=auto -qaltivec")
+
+ if(NOT CFLAGS_IBM_VMX OR NOT CXXFLAGS_IBM_VMX)
+ message(FATAL_ERROR "Cannot find IBM VMX SIMD compiler flag. Use a newer compiler, or disable VMX SIMD.")
+ endif()
+
+ set(GMX_SIMD_IBM_VMX 1)
+ set(SIMD_STATUS_MESSAGE "Enabling IBM VMX SIMD instructions")
+
+elseif(${GMX_SIMD} STREQUAL "IBM_VSX")
+
+ gmx_find_cflag_for_source(CFLAGS_IBM_VSX "C compiler IBM VSX SIMD flag"
+ "#include<altivec.h>
+ int main(){vector double x,y=vec_splats(1.0);x=vec_madd(y,y,y);return vec_all_ge(y,x);}"
+ SIMD_C_FLAGS
+ "-mvsx" "-maltivec -mabi=altivec" "-qarch=auto -qaltivec")
+ gmx_find_cxxflag_for_source(CXXFLAGS_IBM_VSX "C++ compiler IBM VSX SIMD flag"
+ "#include<altivec.h>
+ int main(){vector double x,y=vec_splats(1.0);x=vec_madd(y,y,y);return vec_all_ge(y,x);}"
+ SIMD_CXX_FLAGS
+ "-mvsx" "-maltivec -mabi=altivec" "-qarch=auto -qaltivec")
+
+ if(NOT CFLAGS_IBM_VSX OR NOT CXXFLAGS_IBM_VSX)
+ message(FATAL_ERROR "Cannot find IBM VSX SIMD compiler flag. Use a newer compiler, or disable VSX SIMD.")
+ endif()
+
+ set(GMX_SIMD_IBM_VSX 1)
+ set(SIMD_STATUS_MESSAGE "Enabling IBM VSX SIMD instructions")
+
elseif(${GMX_SIMD} STREQUAL "SPARC64_HPC_ACE")
# Note that GMX_RELAXED_DOUBLE_PRECISION is enabled by default in the top-level CMakeLists.txt
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+# Sets version information variables and provides CMake functions for
+# generating files based on them
+#
+# This script provides the following basic version variables that need to be
+# maintained manually:
+# GMX_VERSION_MAJOR Major version number.
+# GMX_VERSION_MINOR Minor version number.
+# GMX_VERSION_PATCH Patch version number.
+# Should always be defined: zero for, e.g., 5.0.
+# GMX_VERSION_SUFFIX String suffix to add to numeric version string.
+# "-dev" is automatically added when not building from a source package,
+# and does not need to be kept here.
+# LIBRARY_SOVERSION so version for the built libraries.
+# Should be increased for each binary incompatible release (in GROMACS,
+# the typical policy is to increase it for each major/minor version
+# change, but not for patch releases, even if the latter may not always
+# be fully binary compatible).
+# LIBRARY_VERSION Full library version.
+# REGRESSIONTEST_BRANCH For builds not from source packages, name of the
+# regressiontests branch at gerrit.gromacs.org whose HEAD can test this
+# code, *if* this code is recent enough (i.e., contains all changes from
+# the corresponding code branch that affects the regression test
+# results).
+# REGRESSIONTEST_MD5SUM
+# The MD5 checksum of the regressiontest tarball. Only used when building
+# from a source package.
+# They are collected into a single section below.
+# The following variables are set based on these:
+# GMX_VERSION String composed from GMX_VERSION_* numeric variables
+# above. Example: 4.6.1, 5.0
+# GMX_VERSION_STRING String with GMX_VERSION suffixed with the given
+# suffix and possibly "-dev" for builds not from a source package.
+# GMX_VERSION_NUMERIC Numeric version number (e.g., 40601 for 4.6.1).
+# GMX_API_VERSION Numeric API version.
+# This is currently set automatically to GMX_VERSION_NUMERIC, but may
+# become manually maintained in the future if there will be releases
+# where the API does not change, but programs/libraries do.
+# In such a case, this should be the first version where the current API
+# appeared.
+# REGRESSIONTEST_VERSION For source packages, version number of the
+# matching regressiontests tarball. Not used for builds not from source
+# packages.
+# The latter two are used to generate gromacs/version.h to allow software
+# written against the GROMACS API to provide some #ifdef'ed code to support
+# multiple GROMACS versions.
+#
+# The following variables are defined without manual intervention:
+# SOURCE_IS_SOURCE_DISTRIBUTION The source tree is from a source tarball.
+# SOURCE_IS_GIT_REPOSITORY The source tree is a git repository.
+# Note that both can be false if the tree has been extracted, e.g., as a
+# tarball directly from git.
+# Additionally, the following variable is defined:
+# BUILD_IS_INSOURCE The build is happening in-source.
+#
+# This script also declares machinery to generate and obtain version
+# information from a git repository. This is enabled by default if the source
+# tree is a git, but can be disabled with
+# GMX_GIT_VERSION_INFO Advanced CMake variable to disable git
+# version info generation.
+# The main interface to this machinery is the gmx_configure_version_file()
+# CMake function. The signature is
+# gmx_configure_version_file(<input> <output>
+# [REMOTE_HASH] [SOURCE_FILE]
+# [TARGET <target>]
+# [COMMENT <comment>])
+# <input> Specify the input and output files as for configure_file().
+# <output> The configuration is done with configure_file(... @ONLY) with
+# the following variables defined (as well as all the
+# GMX_VERSION* variables from above):
+# GMX_VERSION_STRING_FULL
+# GMX_VERSION_FULL_HASH
+# GMX_VERSION_CENTRAL_BASE_HASH
+# The output file is created during build time, so any dependent
+# targets should specify it as a dependency.
+# REMOTE_HASH Currently, this has no effect, but it signifies that the
+# <input> file is using the CENTRAL_BASE_HASH variable.
+# This variable is much more expensive to initialize than the
+# others, so this allows local changes in this file to only
+# compute that value when required if that becomes necessary.
+# SOURCE_FILE Signals that <output> will be used as a source file.
+# The function will set properties for the source file
+# appropriately to signify that it is generated.
+# TARGET By default, this function uses add_custom_command() to
+# generate the output file. If TARGET is specified, then
+# add_custom_target() is used to create a target with the given
+# name <target> that runs this custom command. Use this if
+# the same file will be used for multiple downstream targets,
+# or if the explicit target for the file is otherwise
+# necessary.
+# COMMENT Set a custom comment to be shown when building the rule
+# (see add_custom_command(... COMMENT <comment>)).
+# As an alternative to using this script, also the following variables are
+# provided (can be useful when generating more complex CMake scripts that do
+# build-time tasks):
+# VERSION_INFO_CMAKE_SCRIPT
+# Absolute path to a CMake script that can be included using include()
+# to declare the GMX_VERSION_* variables documented for
+# gmx_configure_version_file().
+# VERSION_INFO_DEPS
+# If a custom command depends on VERSION_INFO_CMAKE_SCRIPT, then it
+# should add ${VERSION_INFO_DEPS} to its DEPENDS list to get the
+# appropriate dependencies.
+# TODO: If someone wants to add a custom target that depends on
+# VERSION_INFO_CMAKE_SCRIPT, a separate variable may be needed for those
+# dependencies.
+#
+# The version string printed by 'gmx -version' (and also printed in the startup
+# header) can provide useful information for, e.g., diagnosing bug reports and
+# identifying what exact version the user was using. The following formats are
+# possible (with examples given for a particular version):
+# 4.6.1 Plain version number without any suffix signifies a build from
+# a released source tarball.
+# 4.6.1-dev '-dev' suffix signifies all other builds. If there is no other
+# information, either the user built the code outside any git
+# repository, or disabled the version info generation.
+# 4.6.1-dev-YYYYMMDD-1234abc
+# The YYYYMMDD part shows the commit date (not author date) of
+# the HEAD commit from which the code was built. The abbreviated
+# hash is the hash of that commit (the full hash is available in
+# 'gmx -version' output).
+# If the HEAD hash is not identified as coming from branches in
+# "authoritative" GROMACS repositories, 'gmx -version' will show
+# the nearest ancestor commit that is identified as such (but see
+# the '-local' and '-unknown' suffixes below).
+# 4.6.1-dev-YYYYMMDD-1234abc-dirty
+# As above, but there were local modifications in the source tree
+# when the code was built.
+# 4.6.1-dev-YYYYMMDD-1234abc-unknown
+# As above, but there were no remotes in the repository that
+# could be identified as "authoritative" GROMACS repositories.
+# This happens if the code is not cloned from git.gromacs.org
+# or gerrit.gromacs.org.
+# 4.6.1-dev-YYYYMMDD-1234abc-local
+# As above, but there were no commits in the recent history of
+# the branch that could be identified as coming from
+# "authoritative" GROMACS repositories. This should be
+# relatively rare.
+#
+# Other variables set here are not intended for use outside this file.
+# The scripts gmxGenerateVersionInfo.cmake and gmxConfigureVersionInfo.cmake
+# are used internally by this machinery, as well as VersionInfo.cmake.cmakein.
+
+#####################################################################
+# Basic nature of the source tree
+
+set(SOURCE_IS_GIT_REPOSITORY OFF)
+set(SOURCE_IS_SOURCE_DISTRIBUTION OFF)
+if (EXISTS "${PROJECT_SOURCE_DIR}/.git")
+ set(SOURCE_IS_GIT_REPOSITORY ON)
+endif()
+# This file is excluded from CPack source packages, but part of the repository,
+# so it should get included everywhere else.
+if (NOT EXISTS "${PROJECT_SOURCE_DIR}/admin/.isreposource")
+ set(SOURCE_IS_SOURCE_DISTRIBUTION ON)
+endif()
+set(BUILD_IS_INSOURCE OFF)
+if ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}")
+ set(BUILD_IS_INSOURCE ON)
+endif()
+
+#####################################################################
+# Manually maintained version info
+
+# The GROMACS convention is that these are the version number of the next
+# release that is going to be made from this branch.
+set(GMX_VERSION_MAJOR 5)
+set(GMX_VERSION_MINOR 1)
+set(GMX_VERSION_PATCH 0)
+# The suffix, on the other hand, is used mainly for betas and release
+# candidates, where it signifies the last such release from this branch;
+# it will be empty before the first such release, as well as after the
+# final release is out.
+set(GMX_VERSION_SUFFIX "")
+
+set(LIBRARY_SOVERSION 1)
+set(LIBRARY_VERSION ${LIBRARY_SOVERSION}.0.0)
+
+set(REGRESSIONTEST_BRANCH "refs/heads/master")
+set(REGRESSIONTEST_MD5SUM "a07524afebca5013540d4f2f72df2dce")
+
+#####################################################################
+# General version management based on manually set numbers
+
+if (GMX_VERSION_PATCH)
+ set(GMX_VERSION "${GMX_VERSION_MAJOR}.${GMX_VERSION_MINOR}.${GMX_VERSION_PATCH}")
+else()
+ set(GMX_VERSION "${GMX_VERSION_MAJOR}.${GMX_VERSION_MINOR}")
+endif()
+set(GMX_VERSION_STRING "${GMX_VERSION}${GMX_VERSION_SUFFIX}")
+if (NOT SOURCE_IS_SOURCE_DISTRIBUTION)
+ set(GMX_VERSION_STRING "${GMX_VERSION_STRING}-dev")
+endif()
+
+set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}")
+
+math(EXPR GMX_VERSION_NUMERIC
+ "${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_MINOR}*100 + ${GMX_VERSION_PATCH}")
+set(GMX_API_VERSION ${NUM_VERSION})
+
+#####################################################################
+# git version info management
+
+# There can be clusters where git and CMake can run on nodes where the other is
+# not available, accessing the same source tree.
+# Should be unlikely, but doesn't hurt to check.
+set(_git_info_default OFF)
+if (SOURCE_IS_GIT_REPOSITORY)
+ find_package(Git)
+ if (GIT_FOUND)
+ set(_git_info_default ON)
+ endif()
+endif()
+option(GMX_GIT_VERSION_INFO "Generate git version information" ${_git_info_default})
+mark_as_advanced(GMX_GIT_VERSION_INFO)
+# Detect preconditions for version info generation if it is requested.
+if (GMX_GIT_VERSION_INFO)
+ if (NOT SOURCE_IS_GIT_REPOSITORY)
+ message(FATAL_ERROR
+ "Cannot generate git version information from source tree not under git. "
+ "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
+ endif()
+ # We need at least git v1.5.3 be able to parse git's date output.
+ if (NOT GIT_FOUND OR GIT_VERSION_STRING VERSION_LESS "1.5.3")
+ message(FATAL_ERROR
+ "No compatible git version found (>= 1.5.3 required). "
+ "Won't be able to generate development version information. "
+ "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
+ endif()
+endif()
+
+include(gmxCustomCommandUtilities)
+
+# The first two are also for use outside this file, encapsulating the details
+# of how to use the generated VersionInfo.cmake.
+set(VERSION_INFO_CMAKE_FILE ${PROJECT_BINARY_DIR}/VersionInfo.cmake)
+set(VERSION_INFO_DEPS ${VERSION_INFO_CMAKE_FILE})
+# Capture the location of the necessary files in internal variables for use in
+# the function below.
+set(VERSION_INFO_CMAKEIN_FILE ${CMAKE_CURRENT_LIST_DIR}/VersionInfo.cmake.cmakein)
+set(VERSION_INFO_CONFIGURE_SCRIPT ${CMAKE_CURRENT_LIST_DIR}/gmxConfigureVersionInfo.cmake)
+
+# Rules to create the VersionInfo.cmake file.
+# For git info, the sequence is:
+# 1. (configure time) VersionInfo.cmake.cmakein -> VersionInfo-partial.cmake.cmakein
+# - Set all variables that are known at configure time.
+# 2. (build time) VersionInfo-partial.cmake.cmakein -> VersionInfo.cmake
+# - Set variables that may change as result of repository state changes
+# (i.e., everything that requires running git).
+# - Runs every time as a git-version-info target, but the output file
+# timestamp only changes if its contents actually change.
+# - Depending on the native build system, this may run once per build
+# or once per each time it is required for step 3.
+# 3. (build time) VersionInfo.cmake -> other files
+# - Set variables in files specified with gmx_configure_version_file()
+# using the values generated in step 2.
+# - Each file runs as a custom command that depends on the previous
+# steps, and runs only if the VersionInfo.cmake file is newer than the
+# output file.
+# Without git info, the sequence is:
+# 1. (configure time) VersionInfo.cmake.cmakein -> VersionInfo.cmake
+# - Everything is known at configure time, so the output is generated
+# immediately with all variables set (git info will be empty).
+# 2. (build time) VersionInfo.cmake -> other files
+# - As with git info, processes files from gmx_configure_version_file().
+# - These are again custom commands that depend on the output from
+# step 1, so they get regenerated only when the static version info
+# changes.
+if (GMX_GIT_VERSION_INFO)
+ # Configure information known at this time into a partially filled
+ # version info file.
+ set(VERSION_INFO_CMAKEIN_FILE_PARTIAL
+ ${PROJECT_BINARY_DIR}/VersionInfo-partial.cmake.cmakein)
+ # Leave these to be substituted by the custom target below.
+ set(GMX_VERSION_STRING_FULL "\@GMX_VERSION_STRING_FULL\@")
+ set(GMX_VERSION_FULL_HASH "\@GMX_VERSION_FULL_HASH\@")
+ set(GMX_VERSION_CENTRAL_BASE_HASH "\@GMX_VERSION_CENTRAL_BASE_HASH\@")
+ configure_file(${VERSION_INFO_CMAKEIN_FILE}
+ ${VERSION_INFO_CMAKEIN_FILE_PARTIAL}
+ @ONLY)
+ # If generating the version info, create a target that runs on every build
+ # and does the actual git calls, storing the results into a CMake script.
+ # This needs to be run at build time to update the version information
+ # properly when the git hash changes, but the build system does not.
+ # All targets added by gmx_configure_version_file() use the information
+ # from this script to get their variables from, removing the need to run
+ # git multiple times and simplifying reuse for other purposes.
+ gmx_add_custom_output_target(git-version-info RUN_ALWAYS
+ OUTPUT ${VERSION_INFO_CMAKE_FILE}
+ COMMAND ${CMAKE_COMMAND}
+ -D GIT_EXECUTABLE=${GIT_EXECUTABLE}
+ -D PROJECT_VERSION=${GMX_VERSION_STRING}
+ -D PROJECT_SOURCE_DIR=${PROJECT_SOURCE_DIR}
+ -D VERSION_CMAKEIN=${VERSION_INFO_CMAKEIN_FILE_PARTIAL}
+ -D VERSION_OUT=${VERSION_INFO_CMAKE_FILE}
+ -P ${CMAKE_CURRENT_LIST_DIR}/gmxGenerateVersionInfo.cmake
+ WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+ COMMENT "Generating git version information")
+ list(APPEND VERSION_INFO_DEPS git-version-info)
+else()
+ # If the version info is static, just generate the CMake script with the
+ # version variables during the CMake run.
+ set(GMX_VERSION_STRING_FULL ${GMX_VERSION_STRING})
+ set(GMX_VERSION_FULL_HASH "")
+ set(GMX_VERSION_CENTRAL_BASE_HASH "")
+ configure_file(${VERSION_INFO_CMAKEIN_FILE} ${VERSION_INFO_CMAKE_FILE})
+endif()
+unset(GMX_VERSION_STRING_FULL)
+unset(GMX_VERSION_FULL_HASH)
+unset(GMX_VERSION_CENTRAL_BASE_HASH)
+
+# The main user-visible interface to the machinery.
+# See documentation at the top of the script.
+function (gmx_configure_version_file INFILE OUTFILE)
+ include(CMakeParseArguments)
+ set(_options REMOTE_HASH SOURCE_FILE)
+ set(_one_value_args COMMENT TARGET)
+ cmake_parse_arguments(ARG "${_options}" "${_one_value_args}" "" ${ARGN})
+ if (ARG_UNPARSED_ARGUMENTS)
+ message(FATAL_ERROR "Unknown arguments: ${ARG_UNPARSED_ARGUMENTS}")
+ endif()
+ # Some callers may pass partial paths that do not really make sense,
+ # so create a default comment that only contains the actual file name.
+ get_filename_component(_basename ${OUTFILE} NAME)
+ set(_comment "Generating ${_basename}")
+ if (ARG_COMMENT)
+ set(_comment ${ARG_COMMENT})
+ endif()
+ # Mimic configure_file()
+ if (NOT IS_ABSOLUTE ${INFILE})
+ set(INFILE ${CMAKE_CURRENT_SOURCE_DIR}/${INFILE})
+ endif()
+ # The touch command is necessary to ensure that after the target is run,
+ # the timestamp is newer than in the input files.
+ add_custom_command(OUTPUT ${OUTFILE}
+ COMMAND ${CMAKE_COMMAND}
+ -D VERSION_VARIABLES=${VERSION_INFO_CMAKE_FILE}
+ -D VERSION_CMAKEIN=${INFILE}
+ -D VERSION_OUT=${OUTFILE}
+ -P ${VERSION_INFO_CONFIGURE_SCRIPT}
+ COMMAND ${CMAKE_COMMAND} -E touch ${OUTFILE}
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ DEPENDS ${INFILE} ${VERSION_INFO_DEPS} ${VERSION_INFO_CONFIGURE_SCRIPT}
+ COMMENT "${_comment}"
+ VERBATIM)
+ if (ARG_TARGET)
+ add_custom_target(${ARG_TARGET} DEPENDS ${OUTFILE} VERBATIM)
+ gmx_set_custom_target_output(${ARG_TARGET} ${OUTFILE})
+ endif()
+ if (ARG_SOURCE_FILE)
+ set_source_files_properties(${OUTFILE} PROPERTIES GENERATED true)
+ endif()
+endfunction()
# Memory leaks in the legacy code are excluded
# Other problems besides memory leaks should NOT be excluded for legacy code
-# Ugly memory leak that depends on global variables being used to pass
-# information between routines.
{
- nsc_dclm_pbc
+ ctime_r
Memcheck:Leak
- fun:calloc
- fun:save_calloc
- fun:ico_dot_dod
- fun:make_unsp
- fun:nsc_dclm_pbc
+ ...
+ fun:ctime_r
}
+
{
libgomp
Memcheck:Leak
...
obj:*/libgomp.so*
}
-{
- ctime_r
- Memcheck:Leak
- ...
- fun:ctime_r
-}
-
{
libz
Memcheck:Cond
fun:gmx_fio_fopen
}
{
- new_symbuf
+ put_symtab
Memcheck:Leak
...
- fun:new_symbuf
+ fun:put_symtab
}
{
bTimeSet/tMPI_Thread_mutex_init_once
...
fun:__kmpc_global_thread_num
}
+
--- /dev/null
+dev-manual/*.md gmx-doxygen
+doxygen/DoxygenLayout.xml gmx-doxygen
+doxygen/**/*.md gmx-doxygen
set(HTML_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}/html")
file(MAKE_DIRECTORY ${HTML_OUTPUT_DIR})
-if(${CMAKE_CURRENT_BINARY_DIR} STREQUAL ${CMAKE_CURRENT_SOURCE_DIR})
+if (BUILD_IS_INSOURCE)
set(MARKDOWN_CONFIGURE_IS_POSSIBLE off)
else()
set(MARKDOWN_CONFIGURE_IS_POSSIBLE on)
# never need to know.
if(GMX_BUILD_WEBPAGE AND
GMX_BUILD_HELP AND
- NOT ${CMAKE_BINARY_DIR} STREQUAL ${CMAKE_SOURCE_DIR} AND
+ NOT BUILD_IS_INSOURCE AND
MARKDOWN_CONFIGURE_IS_POSSIBLE AND
MANUAL_BUILD_IS_POSSIBLE AND
PANDOC_EXECUTABLE AND
set(DOWNLOAD_SECTION
"# Downloads
-* Source code - [gromacs-${PROJECT_VERSION}.tar.gz](gromacs-${PROJECT_VERSION}.tar.gz)
+* Source code - [gromacs-${GMX_VERSION_STRING}.tar.gz](gromacs-${GMX_VERSION_STRING}.tar.gz)
(md5sum ${SOURCE_MD5SUM})
Other source code versions may be found at <ftp://ftp.gromacs.org/pub/gromacs/>
-* Regression tests - [regressiontests-${PROJECT_VERSION}.tar.gz](regressiontests-${PROJECT_VERSION}.tar.gz)
+* Regression tests - [regressiontests-${GMX_VERSION_STRING}.tar.gz](regressiontests-${GMX_VERSION_STRING}.tar.gz)
(md5sum ${REGRESSIONTESTS_MD5SUM})
")
# Copy the source tarball to the webpage output
add_custom_command(
- OUTPUT ${HTML_OUTPUT_DIR}/gromacs-${PROJECT_VERSION}.tar.gz
+ OUTPUT ${HTML_OUTPUT_DIR}/gromacs-${GMX_VERSION_STRING}.tar.gz
COMMAND ${CMAKE_COMMAND}
- -E copy ${SOURCE_TARBALL} ${HTML_OUTPUT_DIR}/gromacs-${PROJECT_VERSION}.tar.gz
+ -E copy ${SOURCE_TARBALL} ${HTML_OUTPUT_DIR}/gromacs-${GMX_VERSION_STRING}.tar.gz
VERBATIM
)
# Copy the regressiontests tarball to the webpage output
add_custom_command(
- OUTPUT ${HTML_OUTPUT_DIR}/regressiontests-${PROJECT_VERSION}.tar.gz
+ OUTPUT ${HTML_OUTPUT_DIR}/regressiontests-${GMX_VERSION_STRING}.tar.gz
COMMAND ${CMAKE_COMMAND}
- -E copy ${REGRESSIONTESTS_TARBALL} ${HTML_OUTPUT_DIR}/regressiontests-${PROJECT_VERSION}.tar.gz
+ -E copy ${REGRESSIONTESTS_TARBALL} ${HTML_OUTPUT_DIR}/regressiontests-${GMX_VERSION_STRING}.tar.gz
VERBATIM
)
else()
# Make the PDF reference guide
# TODO Try to make the PDF arrive directly in ${HTML_OUTPUT_DIR}
add_custom_command(
- OUTPUT ${HTML_OUTPUT_DIR}/manual-${PROJECT_VERSION}.pdf
+ OUTPUT ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf
COMMAND ${CMAKE_COMMAND}
- -E remove -f ${HTML_OUTPUT_DIR}/manual-${PROJECT_VERSION}.pdf
+ -E remove -f ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf
COMMAND ${CMAKE_COMMAND}
- -E copy ${CMAKE_CURRENT_BINARY_DIR}/manual/gromacs.pdf ${HTML_OUTPUT_DIR}/manual-${PROJECT_VERSION}.pdf
+ -E copy ${CMAKE_CURRENT_BINARY_DIR}/manual/gromacs.pdf ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf
# UseLATEX.cmake makes a target called pdf, not ${CMAKE_CURRENT_BINARY_DIR}/manual/gromacs.pdf
DEPENDS pdf
VERBATIM
# tarball
if(BUILD_DOWNLOAD_SECTION)
list(APPEND extra_webpage_dependencies
- ${HTML_OUTPUT_DIR}/gromacs-${PROJECT_VERSION}.tar.gz
- ${HTML_OUTPUT_DIR}/regressiontests-${PROJECT_VERSION}.tar.gz
+ ${HTML_OUTPUT_DIR}/gromacs-${GMX_VERSION_STRING}.tar.gz
+ ${HTML_OUTPUT_DIR}/regressiontests-${GMX_VERSION_STRING}.tar.gz
)
endif()
${HTML_OUTPUT_DIR}/index.html
install-guide
user-guide
- ${HTML_OUTPUT_DIR}/manual-${PROJECT_VERSION}.pdf
+ ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf
${extra_webpage_dependencies}
VERBATIM
)
- add_dependencies(webpage webpage-html doc-all)
+ add_dependencies(webpage webpage-html doxygen-all)
endif()
# Now configure the values for all the variables that might later
# configure any of the markdown files.
-set(PROJECT_VERSION "@PROJECT_VERSION@")
+set(PROJECT_VERSION "@GMX_VERSION_STRING@")
set(GMX_CMAKE_MINIMUM_REQUIRED_VERSION "@GMX_CMAKE_MINIMUM_REQUIRED_VERSION@")
set(REQUIRED_CUDA_VERSION "@REQUIRED_CUDA_VERSION@")
set(REQUIRED_CUDA_COMPUTE_CAPABILITY "@REQUIRED_CUDA_COMPUTE_CAPABILITY@")
--- /dev/null
+Developer manual {#page_devmanual}
+================
+
+This set of pages contains guidelines, instructions, and explanations related
+to \Gromacs development. The actual code is documented in other parts of this
+Doxygen documentation.
+
+The focus is (at least for now) on things that are tightly tied to the code
+itself, such as helper scripts that reside in the source repository, and may
+require the documentation to be updated in sync. Wiki pages at
+<http://www.gromacs.org/Developer_Zone> contain additional information (much of
+it outdated, though), and can be linked from relevant locations in this guide.
+
+ - \subpage page_devtools <br/>
+ Documentation for tools used
+
+ - \subpage page_devstyle <br/>
+ Guidelines to follow when writing new code. For some of the guidelines,
+ scripts exist (see \ref page_devtools) to automatically reformat the code
+ and/or enforce the guidelines for each commit.
--- /dev/null
+Guidelines for code formatting {#page_devstyle_formatting}
+==============================
+
+The following list provides the general formatting/indentation rules for
+\Gromacs code (C/C++):
+ * Basic indentation is four spaces.
+ * Keep lines at a reasonable length. There is no hard limit, but use 80
+ characters as a guideline. If you end up indenting very deeply,
+ consider splitting the code into functions.
+ * Do not use tabs, only spaces. Most editors can be configured to generate
+ spaces even when pressing tab. Tabs (in particular when mixed with spaces)
+ easily break indentation in contexts where settings are not exactly equal
+ (e.g., in `git diff` output).
+ * No trailing whitespace.
+ * Use braces always for delimiting blocks, even when there is only a single
+ statement in an `if` block or similar.
+ * Put braces on their own lines. The only exception is short one-line inline
+ functions in C++ classes, which can be put on a single line.
+ * Use spaces liberally.
+ * `extern "C"` and `namespace` blocks are not indented, but all others
+ (including `class` and `switch` bodies) are.
+
+Additionally:
+ * All source files and other non-trivial scripts should contain a copyright
+ header with a predetermined format and license information (check existing
+ files). Copyright holder should be "the GROMACS development team" for the
+ years where the code has been in the \Gromacs source repository, but earlier
+ years can hold other copyrights.
+ * Whenever you update a file, you should check that the current year is listed
+ as a copyright year.
+
+Most of the above guidelines are enforced using uncrustify, an automatic source
+code formatting tool. The copyright guidelines are enforced by a separate
+Python script. See \ref page_dev_uncrustify for details. Note that due to the
+nature of uncrustify (it only does all-or-nothing formatting), it enforces
+several additional formatting rules in addition to those above.
+
+Enforcing a consistent formatting has a few advantages:
+ * No one needs to manually review code for most of these formatting issues,
+ and people can focus on content.
+ * A separate automatic script (see below) can be applied to re-establish the
+ formatting after refactoring like renaming symbols or changing some
+ parameters, without needing to manually do it all.
--- /dev/null
+Source tree checker scripts {#page_dev_gmxtree}
+===========================
+
+There is a set of Python scripts, currently under `docs/doxygen/`, that check
+various aspects of the source tree for consistency. The script is based on
+producing an abstract representation of the source tree from various sources:
+ * List of files in the source tree (for overall layout of the source tree)
+ * List of installed headers (extracted from the generated build system)
+ * git attributes (to limit the scope of some checks)
+ * Doxygen XML documentation:
+ * For tags about public/private nature of documented headers and other
+ constructs
+ * For actual documented constructs, to check them for consistency
+ * Hard-coded knowledge about the \Gromacs source tree layout
+
+This representation is then used for various purposes:
+ * Checking Doxygen documentation elements for common mistakes: missing brief
+ descriptions, mismatches in file and class visibility, etc.
+ * Checking for consistent usage and documentation of headers: e.g., a header
+ that is documented as internal to a module should not be used outside that
+ module.
+ * Checking for module-level cyclic dependencies
+ * Checking for consistent style and order of \#include directives
+ (see \ref page_devstyle_includes)
+ * Actually sorting and reformatting \#include directives to adhere to the
+ checked style
+ * Generating dependency graphs between modules and for files within modules
+
+The checks are run as part of a single `check-source` target, but are described
+in separate sections below. In addition to printing the issues to `stderr`,
+the script also writes them into `docs/doxygen/check-source.log` for later
+inspection. Jenkins runs the checks as part of the Documentation job, and the
+build is marked unstable if any issues are found.
+
+For correct functionality, the scripts depend on correct usage of Doxygen
+annotations described in \ref page_doxygen, in particular the visibility and
+API definitions in file-level comments.
+
+For some false positives from the script, the suppression mechanism described
+below is the easiest way to silence the script, but otherwise the goal would be
+to minimize the number of suppressions.
+
+The scripts require Python 2.7 (other versions may work, but have not been
+tested).
+
+To understand how the scripts work internally, see comments in the Python
+source files under `docs/doxygen/`.
+
+Checker details
+===============
+
+The `check-source` target currently checks for a few different types of issues.
+These are listed in detail below, mainly related to documentation and include
+dependencies. Note in particular that the include dependency checks are much
+stricter for code in modules/directories that are documented with a
+\c \\defgroup: all undocumented code is assumed to be internal to such modules.
+The rationale is that such code has gotten some more attention, and some effort
+should also have been put into defining what is the external interface of the
+module and documenting it.
+
+* For all Doxygen documentation (currently does not apply for members that do
+ not appear in the documentation):
+ * If a member has documentation, it should have a brief description.
+ * A note is issued for in-body documentation for functions, since this is
+ ignored by our current settings.
+ * If a class has documentation, it should have public documentation only if
+ it appears in an installed header.
+ * If a class and its containing file has documentation, the class
+ documentation should not be visible if the file documentation is not.
+* For all files:
+ * Consistent usage of
+
+ #include "..." // This should be used for Gromacs headers
+
+ and
+
+ #include <...> // This should be used for system and external headers
+
+ * Installed headers must not include non-installed headers.
+ * All source files must include "gmxpre.h" as the first header.
+ * A source/header file should include "config.h" if and only if it uses a
+ macro declared there.
+ * If the file has a git attribute to identify it as a candidate for include
+ sorting, the include sorter described below should not produce any
+ changes (i.e., the file should follow \ref page_devstyle_includes).
+* For documented files:
+ * Installed headers should have public documentation, and other files should
+ not.
+ * The API level specified for a file should not be higher than where its
+ documentation is visible. For example, only publicly documented headers
+ should be specified as part of the public API.
+ * If an \c \\ingroup `module_foo` exists, it should match the subdirectory
+ that the file is actually part of in the file system.
+ * If a \c \\defgroup `module_foo` exists for the subdirectory where the file
+ is, the file should contain \c \\ingroup `module_foo`.
+ * Files should not include other files whose documentation visibility is
+ lower (if the included file is not documented, the check is skipped).
+* For files that are part of documented modules
+ (\c \\defgroup `module_foo` exists for the subdirectory), or are explicitly
+ documented to be internal or in the library API:
+ * Such files should not be included from outside their module if they are
+ undocumented (for documented modules) or are not specified as part of
+ library or public API.
+* For all modules:
+ * There should not be cyclic include dependencies between modules.
+
+As a side effect, the XML extraction makes Doxygen parse all comments in the
+code, even if they do not appear in the documentation. This can reveal latent
+issues in the comments, like invalid Doxygen syntax. The messages from the XML
+parsing are stored in `docs/doxygen/doxygen-xml.log` in the build tree, similar to
+other Doxygen runs.
+
+Suppressing issues
+------------------
+
+The script is not currently perfect (either because of unfinished
+implementation, or because Doxygen bugs or incompleteness of the Doxygen XML
+output), and the current code also contains issues that the script detects, but
+the authors have not fixed. To allow the script to still be used,
+`doxygen/suppressions.txt` contains a list of issues that are filtered out from
+the report. The syntax is simple:
+
+ <file>: <text>
+
+where `<file>` is a path to the file that reports the message, and `<text>` is
+the text reported. Both support `*` as a wildcard. If `<file>` is empty, the
+suppression matches only messages that do not have an associated file.
+`<file>` is matched against the trailing portion of the file name to make it
+work even though the script reports absolute paths.
+Empty lines and lines starting with `#` are ignored.
+
+To add a suppression for an issue, the line that reports the issue can be
+copied into `suppressions.txt`, and the line number (if any) removed. If the
+issue does not have a file name (or a pseudo-file) associated, a leading `:`
+must be added. To cover many similar issues, parts of the line can then be
+replaced with wildcards.
+
+A separate suppression mechanism is in place for cyclic dependencies: to
+suppress a cycle between moduleA and moduleB, add a line with format
+
+ moduleA -> moduleB
+
+into `doxygen/cycle-suppressions.txt`. This suppresses all cycles that contain
+the mentioned edge. Since a cycle contains multiple edges, the suppression
+should be made for the edge that is determined to be an incorrect dependency.
+This also affects the layout of the include dependency graphs (see below): the
+suppressed edge is not considered when determining the dependency order, and is
+shown as invalid in the graph.
+
+Include order sorting {#section_dev_includesorter}
+=====================
+
+The script checks include ordering according to \ref page_devstyle_includes.
+If it is not obvious how the includes should be changed to make the script
+happy, or bulk changes are needed in multiple files, e.g., because of a header
+rename or making a previously public header private, it is possible to run a
+Python script that does the sorting:
+
+ docs/doxygen/includesorter.py -S . -B ../build <files>
+
+The script needs to know the location of the source tree (given with `-S`) and
+the build tree (given with `-B`), and sorts the given files. To sort the whole
+source tree, one can also use:
+
+ admin/reformat_all.sh includesort -B=../build
+
+For the sorter to work correctly, the build tree should contain up-to-date list
+of installed files and Doxygen XML documentation. The former is created
+automatically when `cmake` is run, and the latter can be built using the
+`doxygen-xml` target.
+
+Note that currently, the sorter script does not change between angle brackets
+and quotes in include statements.
+
+Include dependency graphs
+=========================
+
+The same set of Python scripts can also produce include dependency graphs with
+some additional annotations compared to what, e.g., Doxygen produces for a
+directory dependency graph. Currently, a module-level graph is automatically
+built when the Doxygen documentation is built and embedded in the documentation
+(not in the public API documentation). The graph, together with a legend, is
+on a separate page: \ref page_modulegraph.
+
+The Python script produces the graphs in a format suitable for `dot` (from the
+`graphviz` package) to lay them out. The build system also provides a
+`dep-graphs` target that generates PNG files from the intermediate `dot` files.
+In addition to the module-level graph, a file-level graph is produced for
+each module, showing the include dependencies within that module.
+The file-level graphs can only be viewed as the PNG files, with some
+explanation of the notation below. Currently, these are mostly for eye candy,
+but they can also be used for analyzing problematic dependencies to clean up
+the architecture.
+
+Both the intermediate `.dot` files and the final PNG files are put under
+`docs/doxygen/depgraphs/` in the build tree.
+
+File graphs
+-----------
+
+The graphs are written to <em>module_name</em>`-deps.dot.png`.
+
+Node colors:
+<dl>
+<dt>light blue</dt>
+<dd>public API (installed) headers</dd>
+<dt>dark blue</dt>
+<dd>library API headers</dd>
+<dt>gray</dt>
+<dd>source files</dd>
+<dt>light green</dt>
+<dd>test files</dd>
+<dt>white</dt>
+<dd>other files</dd>
+</dl>
+
+Each edge signifies an include dependency; there is no additional information
+currently included.
--- /dev/null
+Guidelines for \#include directives {#page_devstyle_includes}
+===================================
+
+The following include order is used in \Gromacs. An empty line should appear
+between each group, and headers within each group sorted alphabetically.
+
+ 1. Each _source_ file should include `gmxpre.h` first.
+ 2. If a _source_ file has a corresponding header, it should be included next.
+ If the header is in the same directory as the source, then it is included
+ without any path (i.e., relative to the source), otherwise relative to
+ `src/`. The latter case is for headers in `legacyheaders/` and for tests.
+ 3. If the file depends on defines from `config.h`, that comes next.
+ 4. This is followed by standard C/C++ headers, grouped as follows:
+
+ 1. Standard C headers (e.g., `<stdio.h>`)
+ 2. C++ versions of the above (e.g., `<cstdio>`)
+ 3. Standard C++ headers (e.g., `<vector>`)
+
+ Preferably, only one of the first two groups is present, but this is not
+ enforced.
+ 5. This is followed by other system headers: platform-specific headers such as
+ `<unistd.h>`, as well as external libraries such as
+ `<boost/scoped_ptr.hpp>`.
+ 6. \Gromacs-specific libraries from `src/external/`, such as
+ `"thread_mpi/threads.h"`.
+ 7. \Gromacs-specific headers that are not internal to the including module,
+ included with a path relative to `src/`.
+ 8. In _test_ files, headers not internal to the module, but specific to
+ testing code, are in a separate block at this point, paths relative to
+ `src/`.
+ 9. Finally, \Gromacs headers that are internal to the including module are
+ included using a relative path (but never with a path starting with `../`;
+ such headers go into group 7 instead). For test files, this group contains
+ headers that are internal to tests for that module.
+
+All \Gromacs headers are included with quotes (`"gromacs/utility/path.h"`),
+other headers with angle brackets (`<stdio.h>`). Headers under `src/external/`
+are generally included with quotes (whenever the include path is relative to
+`src/`, as well as for thread-MPI and TNG), but larger third-party entities are
+included as if they were provided by the system. The latter group currently
+includes boost and gtest/gmock.
+
+If there are any conditionally included headers (typically, only when some
+\#defines from `config.h` are set), these should be included at the end of
+their respective group. Note that the automatic checker/sorter script does not
+act on such headers, nor on comments that are between \#include statements; it
+is up to the author of the code to put the headers in proper order in such
+cases. Trailing comments on the same line as \#include statements are
+preserved and do not affect the checker/sorter.
+
+The guidelines are enforced by an automatic checker script that can also
+sort/reformat include statements to follow the guidelines.
+See \ref page_dev_gmxtree for details.
+
+Enforcing a consistent order and style has a few advantages:
+ * It makes it easy at a quick glance to find the dependencies of a file,
+ without scanning through a long list of unorganized \#includes.
+ * Including the header corresponding to the source file first makes most
+ headers included first in some source file, revealing potential problems
+ where headers would not compile unless some other header would be included
+ first. With this order, the person working on the header is most likely to
+ see these problems instead of someone else seeing them later when
+ refactoring unrelated code.
+ * Consistent usage of paths in \#include directives makes it easy to use
+ `grep` to find all uses of a header, as well as all include dependencies
+ between two modules.
+ * An automatic script can be used to re-establish clean code after
+ semi-automatic refactoring like renaming an include file with `sed`, without
+ causing other unnecessary changes.
--- /dev/null
+Style guidelines {#page_devstyle}
+================
+
+ - \subpage page_devstyle_formatting <br/>
+ Guidelines for indentation and other code formatting.
+
+ - \subpage page_devstyle_includes <br/>
+ Guidelines for \#include style (ordering, paths to use, etc.).
+
+ - [Doxygen guidelines](\ref section_doxygen_guidelines) <br/>
+ Guidelines for using Doxygen to document the source code are currently in a
+ section on the page on general Doxygen usage.
+
+TODO: Add more guidelines
--- /dev/null
+Development-time tools {#page_devtools}
+======================
+
+TODO: Add details for most of the tools, either in the form of links to wiki,
+or to a separate page that explains more details.
+
+Change management
+=================
+
+<dl>
+
+<dt>git</dt>
+<dd>\Gromacs uses git as the version control system.
+Instructions for setting up git for \Gromacs, as well as tips and tricks for
+its use, can be found on the wiki:
+[Git Tips & Tricks](http://www.gromacs.org/index.php?title=Developer_Zone/Git/Git_Tips_%26_Tricks) <br/>
+Other basic tutorial material for `git` can be found on the web.</dd>
+
+<dt>Gerrit</dt>
+<dd>All code changes go through a code review system at
+<http://gerrit.gromacs.org>.</dd>
+
+<dt>Jenkins</dt>
+<dd>All changes pushed to Gerrit are automatically compiled and otherwise
+checked on various platforms using a continuous integration system at
+<http://jenkins.gromacs.org>.</dd>
+
+<dt>Redmine</dt>
+<dd>Bugs and issues, as well as some random features and discussions,
+are tracked at <http://redmine.gromacs.org>.</dd>
+
+</dl>
+
+Build system
+============
+
+TODO: details, ASAN, others?
+
+<dl>
+
+<dt>CMake</dt>
+<dd></dd>
+
+<dt>packaging for distribution (CPack)</dt>
+<dd></dd>
+
+<dt>unit testing (CTest)</dt>
+<dd>\Gromacs uses a unit testing framework based on Google C++ Testing
+Framework (gtest) and CTest. All unit tests are automatically run on Jenkins
+for each commit.
+Details can be found on a separate page: \subpage page_unittesting.</dd>
+
+<dt>regression tests</dt>
+<dd></dd>
+
+<dt>cppcheck</dt>
+<dd>cppcheck (<http://cppcheck.sourceforge.net>) is used for static code
+analysis, and is run automatically on Jenkins for each commit. Different rules
+are used for C and C++ code (with stricter checking for C++ code, as that is
+newer). The build system provides a `cppcheck` target (produced from
+`tests/CppCheck.cmake`) to run the tool. This target is used also by Jenkins.
+</dd>
+
+<dt>clang static analyzer</dt>
+<dd></dd>
+
+</dl>
+
+Code formatting and style {#section_dev_formattingtools}
+=========================
+
+The tools and scripts listed below are used to automatically check/apply
+formatting that follows \Gromacs style guidelines described on a separate page:
+\ref page_devstyle.
+
+<dl>
+
+<dt>uncrustify</dt>
+<dd>Uncrustify (<http://uncrustify.sourceforge.net>) is used for automatic
+indentation and other formatting of the source code to follow
+\ref page_devstyle_formatting. All code must remain invariant under uncrustify
+with the config at `admin/uncrustify.cfg`. A patched version of uncrustify is
+used. See \ref page_dev_uncrustify for details.</dd>
+
+<dt>`admin/copyright.py`</dt>
+<dd>This Python script adds and formats copyright headers in source files.
+`uncrustify.sh` (see below) uses the script to check/update copyright years on
+changed files automatically.</dd>
+
+<dt>`admin/uncrustify.sh`</dt>
+<dd>This `bash` script runs uncrustify and `copyright.py` for all
+files that have local changes and checks that they conform to the prescribed
+style. Optionally, the script can also apply changes to make the files
+conform.
+This script is automatically run by Jenkins to ensure that all commits adhere
+to \ref page_devstyle_formatting. If the uncrustify job does not succeed, it
+means that this script has something to complain.
+See \ref page_dev_uncrustify for details.</dd>
+
+<dt>`admin/git-pre-commit`</dt>
+<dd>This sample git pre-commit hook can be used if one wants to apply
+`uncrustify.sh` automatically before every commit to check for formatting
+issues. See \ref page_dev_uncrustify for details.</dd>
+
+<dt>`docs/doxygen/includesorter.py`</dt>
+<dd>This Python script sorts and reformats \#include directives according to
+the guidelines at \ref page_devstyle_includes. Details are documented on a
+separate page (with the whole suite of Python scripts used for source code
+checks): \ref section_dev_includesorter.</dd>
+
+<dt>include directive checker</dt>
+<dd>In its present form, the above include sorter script cannot be conveniently
+applied in `uncrustify.sh`. To check for issues, it is instead integrated into
+a `check-source` build target. When this target is built, it also checks for
+include formatting issues. Internally, it uses the sorter script. This check
+is run in Jenkins as part of the Documentation job.
+Details for the checking mechanism are on a separate page (common for several
+checkers): \subpage page_dev_gmxtree.</dd>
+
+<dt>`admin/reformat_all.sh`</dt>
+<dd>This `bash` script runs uncrustify/`copyright.py`/include sorter
+on all relevant files in the source tree (or in a particular directory).
+The script can also produce the list of files where these scripts are applied,
+for use with other scripts. See \ref page_dev_uncrustify for details.</dd>
+
+<dt>git attributes</dt>
+<dd>git attributes (specified in `.gitattributes` files) are used to annotate
+which files are subject to automatic formatting checks (and for automatic
+reformatting by the above scripts). See `man gitattributes` for an overview of
+the mechanism. We use the `filter` attribute to specify the type of automatic
+checking/formatting to apply. Custom attributes are used for specifying some
+build system dependencies for easier processing in CMake.</dd>
+
+<dt>include-what-you-use</dt>
+<dd></dd>
+
+</dl>
+
+Documentation generation
+========================
+
+<dl>
+<dt>Doxygen</dt>
+<dd>Doxygen (<http://www.doxygen.org>) is used to extract documentation from
+source code comments. Also this developer manual and some other overview
+content is laid out by Doxygen from Markdown source files. Currently, version
+1.8.5 is required for a warning-free build. Thorough explanation of the
+Doxygen setup and instructions for documenting the source code can be found on
+a separate page: \subpage page_doxygen.</dd>
+
+<dt>graphviz (dot)</dt>
+<dd>The Doxygen documentation uses `dot` from graphviz
+(<http://www.graphviz.org>) for building some graphs. The tool is not
+mandatory, but the Doxygen build will produce warnings if it is not
+available, and the graphs are omitted from the documentation.</dd>
+
+<dt>mscgen</dt>
+<dd>The Doxygen documentation uses `mscgen`
+(<http://www.mcternan.me.uk/mscgen/>) for building some graphs. As with `dot`,
+the tool is not mandatory, but not having it available will result in warnings
+and missing graphs.</dd>
+
+<dt>Doxygen issue checker</dt>
+<dd>Doxygen produces warnings about some incorrect uses and wrong
+documentation, but there are many common mistakes that it does not detect.
+\Gromacs uses an additional, custom Python script to check for such issues.
+This is most easily invoked through a `check-source` target in the build system.
+The script also checks that documentation for a header matches its use in the
+source code (e.g., that a header documented as internal to a module is not
+actually used from outside the module). These checks are run in Jenkins as
+part of the Documentation job. Details for the custom checker are on a
+separate page (common for several checkers): \subpage page_dev_gmxtree.</dd>
+
+<dt>module dependency graphs</dt>
+<dd>\Gromacs uses a custom Python script to generate an annotated dependency
+graph for the code, showing \#include dependencies between modules.
+The generated graph is embedded into the Doxygen documentation:
+\ref page_modulegraph.
+This script shares most of its implementation with the custom checkers, and is
+documented on the same page: \subpage page_dev_gmxtree.</dd>
+
+<dt>Pandoc</dt>
+<dd>Pandoc (<http://johnmacfarlane.net/pandoc/>) is used for building some
+parts of the documentation from Markdown source files.</dd>
+
+<dt>latex</dt>
+<dd></dd>
+
+<dt>linkchecker</dt>
+<dd></dd>
+
+<dt>documentation exported from source files</dt>
+<dd>For man pages, HTML documentation of command-line options for executables,
+and for shell completions, the `gmx` binary has explicit C++ code to export
+the information required. The build system provides targets that then invoke
+the built `gmx` binary to produce these documentation items. The generated
+items are packaged into source tarballs so that this is not necessary when
+building from a source distribution (since in general, it will not work in
+cross-compilation scenarios). To build and install these from a git
+distribution, explicit action is required.
+See \ref page_wrapperbinary for some additional details.</dd>
+
+</dl>
--- /dev/null
+Automatic source code formatting {#page_dev_uncrustify}
+================================
+
+The source code can be automatically formatted using uncrustify, an automatic
+source code formatting tool, to follow the guidelines in
+\ref page_devstyle_formatting.
+Additionally, Python scripts are used for a few other automatic
+formatting/checking tasks. The overview tools page contains a list of these
+tools: \ref section_dev_formattingtools.
+This page provides more details for uncrustify and copyright scripts.
+
+Jenkins uses these same scripts (in particular, `uncrustify.sh` and the
+`check-source` target) to enforce that the code stays invariant under such
+formatting.
+
+Setting up uncrustify
+=====================
+
+A patched version of uncrustify is used for \Gromacs. To set this up, you need
+to do these (once):
+ 1. Change to a directory under which you want to build uncrustify and run:
+
+ git clone -b gromacs git://github.com/rolandschulz/uncrustify.git
+ cd uncrustify
+ ./configure
+ make
+
+ 2. Copy the binary `src/uncrustify` into a directory of your choice
+ (`/path/to/uncrustify` below).
+
+Alternatively, if you are running Linux, you can try whether the binary from
+<http://redmine.gromacs.org/issues/845> works for you.
+
+In order to use the binary for `uncrustify.sh` and for the pre-commit hook, you
+also need to run this in each of your \Gromacs repositories:
+
+ git config hooks.uncrustifypath /path/to/uncrustify
+
+Alternatively, if you just want to use `uncrustify.sh`, you can set the
+UNCRUSTIFY environment variable to `/path/to/uncrustify`.
+
+Using the pre-commit hook or git filters needs additional setup; see the
+respective sections below.
+
+What is automatically formatted?
+================================
+
+To identify which files are subject to automatic formatting, the scripts use
+git filters, specified in `.gitattributes` files. Only files that have the
+attribute `filter` set to one of the below values are processed:
+ - `filter=uncrustify`: uncrustify is run, copyright headers are checked, and
+ include order is enforced
+ - `filter=uncrustify_only`: only uncrustify is run
+ - `filter=includesort`: include order is enforced and copyright headers are
+ checked
+ - `filter=copyright`: only copyright headers are checked
+Other files are ignored by `uncrustify.sh` and `reformat_all.sh` scripts (see
+below).
+
+
+Scripts
+=======
+
+`copyright.py`
+--------------
+
+This script provides low-level functionality to check and update copyright
+headers in C/C++ source files, as well as in several other types of files like
+CMake and Python scripts.
+
+This file is also used as a loadable Python module for kernel generators, and
+provides the functionality to generate conformant copyright headers for such
+scripts.
+
+The script is similar to uncrustify in that there is rarely need to run it
+directly, but instead the bash scripts below use it internally. You can run
+the script with `--help` option if you want to see what all options it provides
+if you need to do some maintenance on the copyright headers themselves.
+
+`uncrustify.sh`
+---------------
+
+This script runs uncrustify and `copyright.py` on modified files and
+reports/applies the results.
+By default, the current HEAD commit is compared to the work tree,
+and files that
+
+ 1. are different between these two trees and
+ 2. change under uncrustify and/or have outdated copyright header
+
+are reported. This behavior can be changed by
+
+ 1. Specifying an `--rev=REV` argument, which uses `REV` instead of HEAD as
+ the base of the comparison. A typical use case is to specify `--rev=HEAD^`
+ to check the HEAD commit.
+ 2. Specifying an action:
+ - `check-*`: reports the files that uncrustify changes
+ - `diff-*`: prints the actual diff of what would change
+ - `update-*`: applies the changes to the repository
+ - `*-workdir`: operates on the working directory (files on disk)
+ - `*-index`: operates on the index of the repository
+ For convenience, if you omit the workdir/index suffix, workdir is assumed
+ (i.e., `diff` equals `diff-workdir`).
+ 3. Specifying `--uncrustify=off`, which does not run uncrustify.
+ 4. Specifying `--copyright=<mode>`, which alters the level of copyright
+ checking is done:
+ - `off`: does not check copyright headers at all
+ - `year`: only update copyright year in new-format copyright headers
+ - `add`: in addition to 'year', add copyright headers to files that
+ do not have any
+ - `update`: in addition to 'year' and 'add', also update new-format
+ copyright headers if they are broken or outdated.
+ - `replace`: replace any copyright header with a new-format copyright
+ header
+ - `full`: do all of the above
+
+By default, `update-*` refuses to update dirty files (i.e., that differ
+between the disk and the index) to make it easy to revert the changes.
+This can be overridden by adding a `-f`/`--force` option.
+
+git pre-commit hook
+-------------------
+
+If you want to run `uncrustify.sh` automatically for changes you make, you can
+configure a pre-commit hook using `admin/git-pre-commit`:
+ 1. Copy the `git-pre-commit` script to .git/hooks/pre-commit.
+ 2. Specify the path to uncrustify for the hook if you have not already done
+ so:
+ git config hooks.uncrustifypath /path/to/uncrustify
+ 3. Set the operation mode for the hook:
+ git config hooks.uncrustifymode check
+ git config hooks.copyrightmode update
+
+With this configuration, all source files modified in the commit are run
+through uncrustify and checked for correct copyright headers.
+If any file would be changed by `uncrustify.sh`, the names of those files are
+reported and the commit is prevented. The issues can be fixed by running
+`uncrustify.sh` manually.
+
+To disable the hook without removing the `pre-commit` file, you can set
+
+ git config hooks.uncrustifymode off
+ git config hooks.copyrightmode off
+
+To disable it temporarily for a commit, set NO_FORMAT_CHECK environment
+variable. For example,
+
+ NO_FORMAT_CHECK=1 git commit -a
+
+You can also run `git commit --no-verify`, but that also disables other hooks,
+such as the Change-Id commit-msg hook used by Gerrit.
+
+Note that when you run `git commit --amend`, the hook is only run for the
+changes that are getting amended, not for the whole commit. During a rebase,
+the hook is not run.
+
+The actual work is done by the admin/uncrustify.sh script, which gets
+run with the 'check-index' action, and with `--uncrustify` and `--copyright`
+getting set according to the `git config` settings.
+
+`reformat_all.sh`
+-----------------
+
+This script runs uncrustify, `copyright.py`, or the include sorter for all
+applicable files in the source tree. See `reformat_all.sh -h` for the
+invocation.
+
+The script can also produce the list of files for which these commands would be
+run. To do this, specify `list-files` on the command line and use
+`--filter=<type>` to specify which command to get the file list for. This can
+be used together with, e.g., `xargs` to run other scripts on the same set of
+files.
+
+For all the operations, it is also possible to apply patters (of the same style
+that various git commands accept, i.e., `src/*.cpp` matches all `.cpp` files
+recursively under `src/`). The patterns can be specified with
+`--pattern=<pattern>`, and multiple `--pattern` arguments can be given.
+
+As with `uncrustify.sh`, `-f`/`--force` is necessary if the working tree and
+the git index do not match.
+
+
+Using git filters
+=================
+
+An alternative to using a pre-commit hook to automatically apply uncrustify on
+changes is to use a git filter (does not require `uncrustify.sh`, only the
+`.gitattributes` file). You can run
+
+ git config filter.uncrustify.clean \
+ "/path/to/uncrustify -c admin/uncrustify.cfg -q -l cpp"
+
+To configure a filter for all files that specify `filter=uncrustify` attribute.
+
+The pre-commit hook + manually running `uncrustify.sh` gives better/more
+intuitive control (with the filter, it is possible to have a work tree that is
+different from HEAD and still have an empty `git diff`) and provides better
+performance for changes that modify many files. It is the only way that
+currently also checks the copyright headers.
+
+The filter allows one to transparently merge branches that have not been run
+through uncrustify, and is applied more consistently (the pre-commit hook is
+not run for every commit, e.g., during a rebase).
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+include(gmxCustomCommandUtilities)
include(gmxOptionUtilities)
find_package(Doxygen QUIET)
if (DOXYGEN_FOUND)
# This logic closely follows that found in FindDoxygen.cmake for dot,
# except that the PATH variable is not cached.
- FIND_PROGRAM(DOXYGEN_MSCGEN_EXECUTABLE
+ find_program(DOXYGEN_MSCGEN_EXECUTABLE
NAMES mscgen
DOC "Message sequence chart renderer tool (http://www.mcternan.me.uk/mscgen/)")
if (DOXYGEN_MSCGEN_EXECUTABLE)
set(USE_PYTHON_SCRIPTS ON)
endif()
-add_custom_target(find-installed-headers
- COMMAND ${CMAKE_COMMAND}
- -D SRCDIR=${CMAKE_SOURCE_DIR}
- -D BUILDDIR=${CMAKE_BINARY_DIR}
- -D OUTFILE=${CMAKE_CURRENT_BINARY_DIR}/installed-headers.txt
- -P ${CMAKE_CURRENT_SOURCE_DIR}/getInstalledHeaders.cmake
- COMMENT "Generating installed headers list" VERBATIM)
+# Note that if you relocate this file, you also need to change gmxtree.py.
+# TODO: Try to find a solution where this would be hard-coded here, completely
+# separate from the logic that generates it.
+set(INSTALLED_HEADERS_FILE ${PROJECT_BINARY_DIR}/src/gromacs/installed-headers.txt)
########################################################################
# Doxygen configuration
-########################################################################
+#
if (DOXYGEN_FOUND)
- FILE(GLOB NB_KERNEL_DIRS
+ # Generate Doxygen input configuration files
+ file(GLOB NB_KERNEL_DIRS
${CMAKE_SOURCE_DIR}/src/gromacs/gmxlib/nonbonded/nb_kernel_*/)
- LIST(REMOVE_ITEM NB_KERNEL_DIRS
+ list(REMOVE_ITEM NB_KERNEL_DIRS
${CMAKE_SOURCE_DIR}/src/gromacs/gmxlib/nonbonded/nb_kernel_c)
- FOREACH(NB_KERNEL_DIR ${NB_KERNEL_DIRS})
+ foreach (dir ${NB_KERNEL_DIRS})
SET(NB_KERNEL_DIRS_TO_IGNORE_IN_DOXYGEN
- "${NB_KERNEL_DIRS_TO_IGNORE_IN_DOXYGEN} \\\n ${NB_KERNEL_DIR}")
- ENDFOREACH(NB_KERNEL_DIR)
+ "${NB_KERNEL_DIRS_TO_IGNORE_IN_DOXYGEN} \\\n ${dir}")
+ endforeach()
+ set(DEPGRAPH_DIR ${CMAKE_CURRENT_BINARY_DIR}/depgraphs)
set(DOXYGEN_SECTIONS "")
- CONFIGURE_FILE(Doxyfile-common.cmakein Doxyfile-common)
- CONFIGURE_FILE(Doxyfile-full.cmakein Doxyfile-full)
- CONFIGURE_FILE(Doxyfile-lib.cmakein Doxyfile-lib)
- CONFIGURE_FILE(Doxyfile-user.cmakein Doxyfile-user)
- CONFIGURE_FILE(Doxyfile-xml.cmakein Doxyfile-xml)
-
+ set(DOXYGEN_EXTRA_SETTINGS "")
if (GMX_COMPACT_DOXYGEN)
- FILE(APPEND ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile-common
- "@INCLUDE = ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile-compact\n")
+ set(DOXYGEN_EXTRA_SETTINGS "@INCLUDE = ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile-compact")
endif()
+ configure_file(Doxyfile-common.cmakein Doxyfile-common)
+ configure_file(Doxyfile-full.cmakein Doxyfile-full)
+ configure_file(Doxyfile-lib.cmakein Doxyfile-lib)
+ configure_file(Doxyfile-user.cmakein Doxyfile-user)
+ configure_file(Doxyfile-xml.cmakein Doxyfile-xml)
configure_file(RunDoxygen.cmake.cmakein RunDoxygen.cmake @ONLY)
- add_custom_target(doc-full
- ${CMAKE_COMMAND} -DDOCTYPE=full -P RunDoxygen.cmake
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMENT "Generating full documentation with Doxygen" VERBATIM)
- add_custom_target(doc-lib
- ${CMAKE_COMMAND} -DDOCTYPE=lib -P RunDoxygen.cmake
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMENT "Generating library documentation with Doxygen" VERBATIM)
- add_custom_target(doc-user
- ${CMAKE_COMMAND} -DDOCTYPE=user -P RunDoxygen.cmake
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMENT "Generating public API documentation with Doxygen" VERBATIM)
- add_custom_target(doc-xml
- ${CMAKE_COMMAND} -DDOCTYPE=xml -P RunDoxygen.cmake
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMENT "Extracting Doxygen documentation to XML" VERBATIM)
- add_custom_target(doc-all)
- add_dependencies(doc-all doc-full doc-lib doc-user)
+ gmx_configure_version_file(Doxyfile-version.cmakein Doxyfile-version
+ TARGET doxygen-version)
- if (GMX_GIT_VERSION_INFO)
- add_custom_target(doxygen-version
- COMMAND ${CMAKE_COMMAND}
- -D GIT_EXECUTABLE="${GIT_EXECUTABLE}"
- -D PROJECT_VERSION="${PROJECT_VERSION}"
- -D PROJECT_SOURCE_DIR="${PROJECT_SOURCE_DIR}"
- -D VERSION_CMAKEIN="${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile-version.cmakein"
- -D VERSION_OUT="${CMAKE_CURRENT_BINARY_DIR}/Doxyfile-version"
- -D VERSION_NO_REMOTE_HASH=
- -P ${CMAKE_SOURCE_DIR}/cmake/gmxGenerateVersionInfo.cmake
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
- DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile-version.cmakein
- COMMENT "Generating version information for Doxygen")
- add_dependencies(doc-full doxygen-version)
- add_dependencies(doc-lib doxygen-version)
- add_dependencies(doc-user doxygen-version)
- add_dependencies(doc-xml doxygen-version)
+ # Add a stamp that gets updated whenever a source file that contributes to
+ # Doxygen is updated. All Doxygen targets can then depend on this stamp,
+ # instead of each specifying this massive set of dependencies.
+ # TODO: The set of files that affects Doxygen is not exactly the same as
+ # that which affects the dependency graphs, and neither is captured
+ # perfectly with this set, but this can be improved if it becomes a real
+ # issue (the differences are mainly in the generated group kernel files,
+ # but there are some minor other differences as well).
+ if (SOURCE_IS_GIT_REPOSITORY AND GIT_FOUND)
+ gmx_get_files_with_gitattribute(doxygen_sources gmx-doxygen)
+ # Add also common configuration files that influence the generation.
+ set(doxygen_deps
+ ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile-common
+ ${CMAKE_CURRENT_BINARY_DIR}/RunDoxygen.cmake)
+ if (GMX_COMPACT_DOXYGEN)
+ list(APPEND doxygen_deps ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile-compact)
+ endif()
+ gmx_add_custom_output_target(doxygen-source-timestamp
+ OUTPUT STAMP
+ DEPENDS_FILE_LIST doxygen_sources
+ DEPENDS ${doxygen_deps}
+ COMMENT "Updating Doxygen source timestamp")
else()
- set(GMX_PROJECT_VERSION_STR ${PROJECT_VERSION})
- configure_file(Doxyfile-version.cmakein Doxyfile-version)
+ # If there is no git, we just update the stamp every time, and the
+ # builds are triggered every time. This should be rare enough, but
+ # this case still needs to be supported for the Jenkins job that builds
+ # the documentation for a release from the release tarball.
+ gmx_add_custom_output_target(doxygen-source-timestamp
+ RUN_ALWAYS OUTPUT STAMP
+ COMMENT "Updating Doxygen source timestamp")
endif()
+ # Helper function to create a Doxygen build target
+ function (add_doxygen_target TARGET TYPE COMMENT)
+ set(_deps doxygen-source-timestamp doxygen-version
+ ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile-${TYPE})
+ set(_fast_arg "")
+ if ("${ARGN}" STREQUAL "DEPGRAPHS")
+ set(_fast_arg "ADD_FAST_TARGET")
+ if (TARGET dep-graphs-dot)
+ list(APPEND _deps dep-graphs-dot)
+ endif()
+ endif()
+ gmx_add_custom_output_target(${TARGET} OUTPUT STAMP ${_fast_arg}
+ # Ensure the directory exists to avoid spurious warnings
+ COMMAND ${CMAKE_COMMAND} -E make_directory ${DEPGRAPH_DIR}
+ COMMAND ${CMAKE_COMMAND} -DDOCTYPE=${TYPE} -P RunDoxygen.cmake
+ DEPENDS ${_deps}
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMENT "${COMMENT}")
+ if (_fast_arg)
+ add_dependencies(${TARGET}-fast doxygen-version)
+ endif()
+ endfunction()
+
+ # The XML target is necessary for the dependency graphs
+ add_doxygen_target(doxygen-xml xml "Extracting Doxygen documentation to XML")
+
+ # Add targets for generating the dependency graphs; they are necessary for
+ # the full and lib variants of the documentation.
if (USE_PYTHON_SCRIPTS)
- # TODO: Consider whether this is the best name and location for this
- # code, since not all of it is Doxygen-specific (but nearly all of it
- # relies on the Doxygen XML documentation).
- set(doc_check_command
- ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/doxygen-check.py
- -S ${CMAKE_SOURCE_DIR} -B ${CMAKE_BINARY_DIR}
- --installed ${CMAKE_CURRENT_BINARY_DIR}/installed-headers.txt
- -l ${CMAKE_CURRENT_BINARY_DIR}/doxygen-check.log
- --ignore ${CMAKE_CURRENT_SOURCE_DIR}/suppressions.txt)
- add_custom_target(doc-check COMMAND ${doc_check_command}
- COMMENT "Checking Doxygen documentation" VERBATIM)
- add_dependencies(doc-check doc-xml find-installed-headers)
+ # Add target that generates .dot files for the dependency graphs.
+ # The output also depends on the Doxygen source files, but the
+ # dependency on doxygen-xml takes care of that transitively.
+ gmx_add_custom_output_target(dep-graphs-dot ADD_FAST_TARGET
+ OUTPUT STAMP
+ COMMAND ${PYTHON_EXECUTABLE}
+ ${CMAKE_CURRENT_SOURCE_DIR}/graphbuilder.py
+ -S ${CMAKE_SOURCE_DIR} -B ${CMAKE_BINARY_DIR}
+ --ignore-cycles ${CMAKE_CURRENT_SOURCE_DIR}/cycle-suppressions.txt
+ -o ${DEPGRAPH_DIR}
+ DEPENDS doxygen-xml ${INSTALLED_HEADER_FILE}
+ ${CMAKE_CURRENT_SOURCE_DIR}/doxygenxml.py
+ ${CMAKE_CURRENT_SOURCE_DIR}/gmxtree.py
+ ${CMAKE_CURRENT_SOURCE_DIR}/graphbuilder.py
+ ${CMAKE_CURRENT_SOURCE_DIR}/cycle-suppressions.txt
+ COMMENT "Generating include dependency graphs for dot")
- set(graphdir ${CMAKE_CURRENT_BINARY_DIR}/depgraphs)
- set(dep_graphs_command_python
- ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/graphbuilder.py
- -S ${CMAKE_SOURCE_DIR} -B ${CMAKE_BINARY_DIR}
- --installed ${CMAKE_CURRENT_BINARY_DIR}/installed-headers.txt
- -o ${CMAKE_CURRENT_BINARY_DIR}/depgraphs)
+ # Add separate targets for converting the .dot files to .png.
+ # These are not needed by the Doxygen targets, but are useful for
+ # investigating just the graphs.
set(dep_graphs_command_dot
- ${CMAKE_COMMAND} -DGRAPHDIR=${graphdir}
+ ${CMAKE_COMMAND} -DGRAPHDIR=${DEPGRAPH_DIR}
-DDOT_EXECUTABLE=${DOXYGEN_DOT_EXECUTABLE}
-P ${CMAKE_CURRENT_SOURCE_DIR}/generateGraphs.cmake)
- add_custom_target(dep-graphs
- COMMAND ${dep_graphs_command_python}
- COMMAND ${dep_graphs_command_dot}
- COMMENT "Generating include dependency graphs" VERBATIM)
- add_dependencies(dep-graphs doc-xml find-installed-headers)
+ add_custom_target(dep-graphs COMMAND ${dep_graphs_command_dot}
+ COMMENT "Generating PNG include dependency graphs" VERBATIM)
+ add_custom_target(dep-graphs-fast COMMAND ${dep_graphs_command_dot}
+ COMMENT "Generating PNG include dependency graphs" VERBATIM)
+ add_dependencies(dep-graphs dep-graphs-dot)
+ add_dependencies(dep-graphs-fast dep-graphs-dot-fast)
+ endif()
- # These targets are the same as above, but they don't rerun the
- # dependencies each time, making it faster and more convenient for
- # testing.
- add_custom_target(doc-check-fast COMMAND ${doc_check_command}
+ # Create the actual targets to build the documentation.
+ add_doxygen_target(doxygen-full full "Generating full documentation with Doxygen" DEPGRAPHS)
+ add_doxygen_target(doxygen-lib lib "Generating library documentation with Doxygen" DEPGRAPHS)
+ add_doxygen_target(doxygen-user user "Generating public API documentation with Doxygen")
+ # Convenience targets to build all the documentation flavors.
+ add_custom_target(doxygen-all)
+ add_custom_target(doxygen-all-fast)
+ add_dependencies(doxygen-all doxygen-full doxygen-lib doxygen-user)
+ add_dependencies(doxygen-all-fast doxygen-full-fast doxygen-lib-fast doxygen-user)
+
+ # Finally, create the check-source target.
+ if (USE_PYTHON_SCRIPTS)
+ # TODO: Consider whether this is the best location for this code,
+ # since not all of it is Doxygen-specific (but nearly all of it
+ # relies on the Doxygen XML documentation).
+ # The output .log file currently needs to be here, since Jenkins
+ # expects that.
+ set(check_source_command
+ ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/check-source.py
+ -S ${CMAKE_SOURCE_DIR} -B ${CMAKE_BINARY_DIR}
+ -l ${CMAKE_CURRENT_BINARY_DIR}/check-source.log
+ --exitcode
+ --ignore ${CMAKE_CURRENT_SOURCE_DIR}/suppressions.txt
+ --ignore-cycles ${CMAKE_CURRENT_SOURCE_DIR}/cycle-suppressions.txt)
+ add_custom_target(check-source COMMAND ${check_source_command}
+ COMMENT "Checking Doxygen documentation" VERBATIM)
+ add_custom_target(check-source-fast COMMAND ${check_source_command}
COMMENT "Checking Doxygen documentation" VERBATIM)
- add_custom_target(dep-graphs-fast
- COMMAND ${dep_graphs_command_python}
- COMMAND ${dep_graphs_command_dot}
- COMMENT "Generating include dependency graphs" VERBATIM)
+ add_dependencies(check-source doxygen-xml)
endif()
endif()
@INCLUDE = Doxyfile-version
LAYOUT_FILE = @CMAKE_CURRENT_SOURCE_DIR@/DoxygenLayout.xml
INPUT = @CMAKE_CURRENT_SOURCE_DIR@ \
+ @CMAKE_SOURCE_DIR@/docs/dev-manual \
@CMAKE_SOURCE_DIR@/src \
@CMAKE_SOURCE_DIR@/share/template
FILE_PATTERNS = *.c *.cpp *.h *.md
@CMAKE_SOURCE_DIR@/src/gromacs/selection/parser.h \
@CMAKE_SOURCE_DIR@/src/gromacs/selection/scanner.cpp @NB_KERNEL_DIRS_TO_IGNORE_IN_DOXYGEN@
EXCLUDE_SYMBOLS = YY* yy* _gmx_sel_yy*
+EXCLUDE_SYMBOLS += __STDC*
EXCLUDE_SYMBOLS += TEST TEST_F TEST_P TYPED_TEST_CASE TYPED_TEST INSTANTIATE_TEST_CASE_P
EXCLUDE_SYMBOLS += MOCK_METHOD* MOCK_CONST_METHOD*
FULL_PATH_NAMES = YES
STRIP_FROM_PATH = @CMAKE_SOURCE_DIR@
STRIP_FROM_INC_PATH = @CMAKE_SOURCE_DIR@/src
-INCLUDE_PATH = @CMAKE_SOURCE_DIR@/src \
- @CMAKE_SOURCE_DIR@/src/gromacs/legacyheaders
+INCLUDE_PATH = @CMAKE_SOURCE_DIR@/src
HAVE_DOT = @DOXYGEN_DOT_FOUND@
DOT_PATH = @DOXYGEN_DOT_PATH@
MSCGEN_PATH = @DOXYGEN_MSCGEN_PATH@
+DOTFILE_DIRS = @DEPGRAPH_DIR@
+@DOXYGEN_EXTRA_SETTINGS@
ENABLED_SECTIONS = @DOXYGEN_SECTIONS@
# These pages include documentation that does not belong to the public API
# documentation; exclude them from the generated documentation
-EXCLUDE += @CMAKE_SOURCE_DIR@/docs/doxygen/doxygen.md
-EXCLUDE += @CMAKE_SOURCE_DIR@/docs/doxygen/unittesting.md
-EXCLUDE += @CMAKE_SOURCE_DIR@/docs/doxygen/wrapperbinary.md
-EXCLUDE += @CMAKE_SOURCE_DIR@/docs/doxygen/simd.md
+EXCLUDE += @CMAKE_CURRENT_SOURCE_DIR@/lib
+EXCLUDE += @CMAKE_SOURCE_DIR@/docs/dev-manual
INTERNAL_DOCS = NO
HIDE_UNDOC_CLASSES = YES
-PROJECT_NUMBER = @GMX_PROJECT_VERSION_STR@
+PROJECT_NUMBER = @GMX_VERSION_STRING_FULL@
PREDEFINED += F77_FUNC(name,NAME)=name
-ENABLED_SECTIONS += libapi internal
+ENABLED_SECTIONS += libapi internal xml
INTERNAL_DOCS = YES
EXTRACT_LOCAL_CLASSES = YES
EXTRACT_ANON_NSPACES = YES
# Add a note to the warnings that identify the documentation type that
# produces them. This makes it easier to see in Jenkins if a warning type
# is produced only from some documentation types.
- string(REGEX REPLACE "\n" " (in doc-${DOCTYPE})\n"
+ string(REGEX REPLACE "\n" " (in doxygen-${DOCTYPE})\n"
DOXYGEN_WARNINGS "${DOXYGEN_WARNINGS}")
file(WRITE doxygen-${DOCTYPE}.log "${DOXYGEN_WARNINGS}")
endif ()
--- /dev/null
+#!/usr/bin/python
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014,2015, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+"""Check source code and Doxygen documentation for issues
+
+This script checks for some issues in the Doxygen documentation, as well as
+general issues in the source code, mainly using Doxygen XML output and #include
+dependencies parsed from source files. Part of the checks are generic, like
+checking that all documented entities have brief descriptions. Other are
+specific to GROMACS, like checking that only installed headers contribute to
+the public API documentation.
+
+The checks should be self-evident from the source code of the script
+(they are also described in docs/dev-manual/gmxtree.md).
+All the logic of parsing the Doxygen XML output and creating a GROMACS-specific
+representation of the source tree is separated into separate Python modules
+(doxygenxml.py and gmxtree.py, respectively). Similarly, logic for handling
+the output messages is in reporter.py. This leaves only the actual checks and
+the script command-line interface in this file.
+
+The script can be run using the 'check-source' target generated by CMake.
+This target takes care of generating all the necessary input files and passing
+them to the script.
+"""
+
+import sys
+from optparse import OptionParser
+
+import gmxtree
+from gmxtree import GromacsTree, DocType
+from includesorter import IncludeSorter
+from reporter import Reporter
+
+def check_file(fileobj, reporter):
+ """Check file-level issues."""
+ if not fileobj.is_external() and fileobj.get_relpath().startswith('src/'):
+ includes = fileobj.get_includes()
+ if fileobj.is_source_file():
+ if includes:
+ firstinclude = includes[0].get_file()
+ if not firstinclude or firstinclude.get_name() != "gmxpre.h":
+ reporter.code_issue(includes[0],
+ "does not include \"gmxpre.h\" first")
+ else:
+ reporter.code_issue(fileobj, "does not include \"gmxpre.h\"")
+ includes_config_h = False
+ for include in includes:
+ includedfile = include.get_file()
+ if includedfile:
+ if includedfile.get_name() == 'config.h':
+ includes_config_h = True
+ if includes_config_h:
+ if not fileobj.get_used_config_h_defines():
+ reporter.code_issue(fileobj,
+ "includes \"config.h\" unnecessarily")
+ else:
+ if fileobj.get_used_config_h_defines():
+ reporter.code_issue(fileobj, "should include \"config.h\"")
+
+ if not fileobj.is_documented():
+ # TODO: Add rules for required documentation
+ return
+
+ if fileobj.is_source_file():
+ # TODO: Add rule to exclude examples from this check
+ if fileobj.is_installed():
+ reporter.file_error(fileobj, "source file is installed")
+ if fileobj.get_doc_type() != DocType.internal:
+ reporter.file_error(fileobj,
+ "source file documentation appears outside full documentation")
+ elif fileobj.get_api_type() != DocType.internal:
+ reporter.file_error(fileobj, "source file marked as non-internal")
+ elif fileobj.is_test_file() and fileobj.is_installed():
+ reporter.file_error(fileobj, "test file is installed")
+ elif fileobj.is_installed():
+ if fileobj.get_doc_type() != DocType.public:
+ reporter.file_error(fileobj,
+ "public header has non-public documentation")
+ elif fileobj.get_doc_type() == DocType.public:
+ reporter.file_error(fileobj,
+ "non-installed header has public documentation")
+ elif fileobj.get_api_type() == DocType.public:
+ reporter.file_error(fileobj,
+ "non-installed header specified as part of public API")
+ elif fileobj.get_doc_type() < fileobj.get_api_type():
+ reporter.file_error(fileobj,
+ "API type ({0}) conflicts with documentation visibility ({1})"
+ .format(fileobj.get_api_type(), fileobj.get_doc_type()))
+
+ if not fileobj.has_brief_description():
+ reporter.file_error(fileobj,
+ "is documented, but does not have brief description")
+
+ expectedmod = fileobj.get_expected_module()
+ if expectedmod:
+ docmodules = fileobj.get_doc_modules()
+ if docmodules:
+ for module in docmodules:
+ if module != expectedmod:
+ reporter.file_error(fileobj,
+ "is documented in incorrect module: {0}"
+ .format(module.get_name()))
+ elif expectedmod.is_documented():
+ reporter.file_error(fileobj,
+ "is not documented in any module, but {0} exists"
+ .format(expectedmod.get_name()))
+
+def check_include(fileobj, includedfile, reporter):
+ """Check an #include directive."""
+ otherfile = includedfile.get_file()
+ if includedfile.is_system():
+ if not otherfile:
+ return
+ reporter.code_issue(includedfile,
+ "includes local file as {0}".format(includedfile))
+ if not otherfile:
+ reporter.code_issue(includedfile,
+ "includes non-local file as {0}".format(includedfile))
+ # TODO: Reinstantiate a check once there is clarity on what we want
+ # to enforce.
+ #elif fileobj.is_installed() and not includedfile.is_relative():
+ # reporter.code_issue(includedfile,
+ # "installed header includes {0} using non-relative path"
+ # .format(includedfile))
+ if not otherfile:
+ return
+ if fileobj.is_installed() and not otherfile.is_installed():
+ reporter.code_issue(includedfile,
+ "installed header includes non-installed {0}"
+ .format(includedfile))
+ filemodule = fileobj.get_module()
+ othermodule = otherfile.get_module()
+ if fileobj.is_documented() and otherfile.is_documented():
+ filetype = fileobj.get_doc_type()
+ othertype = otherfile.get_doc_type()
+ if filetype > othertype:
+ reporter.code_issue(includedfile,
+ "{0} file includes {1} file {2}"
+ .format(filetype, othertype, includedfile))
+ check_api = (otherfile.api_type_is_reliable() and filemodule != othermodule)
+ if check_api and otherfile.get_api_type() < DocType.library:
+ reporter.code_issue(includedfile,
+ "included file {0} is not documented as exposed outside its module"
+ .format(includedfile))
+
+def check_entity(entity, reporter):
+ """Check documentation for a code construct."""
+ if entity.is_documented():
+ if not entity.has_brief_description():
+ reporter.doc_error(entity,
+ "is documented, but does not have brief description")
+
+def check_class(classobj, reporter):
+ """Check documentation for a class/struct/union."""
+ check_entity(classobj, reporter)
+ if classobj.is_documented():
+ classtype = classobj.get_doc_type()
+ filetype = classobj.get_file_doc_type()
+ if classtype == DocType.public and not classobj.is_in_installed_file():
+ reporter.doc_error(classobj,
+ "has public documentation, but is not in installed header")
+ elif filetype is not DocType.none and classtype > filetype:
+ reporter.doc_error(classobj,
+ "is in {0} file(s), but appears in {1} documentation"
+ .format(filetype, classtype))
+
+def check_member(member, reporter, check_ignored):
+ """Check documentation for a generic member."""
+ check_entity(member, reporter)
+ if member.is_documented():
+ if check_ignored and not member.is_visible():
+ reporter.doc_note(member,
+ "is documented, but is ignored by Doxygen, because its scope is not documented")
+ if member.has_inbody_description():
+ reporter.doc_note(member, "has in-body comments, which are ignored")
+
+def check_cycles(graph, reporter):
+ """Check cyclic dependencies in a dependency graph.
+
+ The graph parameter provides the graph to check. It should be an object
+ that has three methods:
+ iternodes():
+ Return the list of nodes in the graph.
+ iteredges(node):
+ Return the list of edges from a given node.
+ The list should contain (node, edge) pairs, where node is an object
+ returned by iternodes() and edge is any object.
+ report_cycle(cycle, reporter):
+ Process a found cycle. cycle contains a list of (node, edge) pairs
+ that describe the cycle. edge is the edge object that leads _to_
+ the node in the cycle.
+
+ This is implemented using an extended DFS-based strongly connected
+ component (SCC) search, written using a stack instead of recursion.
+ The base algorithm is Tarjan's SCC search:
+ http://en.wikipedia.org/wiki/Tarjan's_strongly_connected_components_algorithm
+
+ Each back edge that is encountered during the search is reported as a
+ cycle. Additionally, if a cross edge is encountered that is within the
+ current SCC, the target node and all its children in the current SCC will
+ be visited again to find all cycles. All steps except cycle detection are
+ omitted for such re-traversal.
+
+ To avoid duplicates from cycles that do not include all nodes in an SCC,
+ a cycle is only reported if the target of the back edge is still active
+ in the search, i.e., all edges from it have not yet been traversed.
+ """
+ # The DFS stack; next node is always popped from the end.
+ # Stores (node, edge) pairs.
+ # edge is None for start nodes and for post-order processing.
+ dfsstack = []
+ for node in graph.iternodes():
+ dfsstack.append((node, None))
+ # Stack of visited nodes that have not yet been assigned to a strongly
+ # connected component.
+ visitstack = []
+ # List of nodes in the DFS recursion stack.
+ currlist = []
+ # Set of nodes in currlist for more efficient searching.
+ currset = set()
+ # Counter for initializing preorder.
+ visit_count = 0
+ # DFS pre-order for nodes: initialized when a node is first encountered
+ # in the search.
+ preorder = dict()
+ # Lowest pre-order index reachable from this node.
+ # Initialized to pre-order, and updated during post-order processing.
+ linkorder = dict()
+ # Set to True for a node when first encountered, and set to False when
+ # a strongly connected component has been processed.
+ in_progress = dict()
+ # The DFS search
+ while dfsstack:
+ currnode, curredge = dfsstack.pop()
+ # curredge is None if this is a start node or post-order traversal.
+ # currlist is empty if this is a start node.
+ if curredge is None and currlist:
+ # All children visited: post-order processing.
+ done = currlist.pop()[0]
+ assert done == currnode
+ currset.remove(currnode)
+ # If this is the first time this node is encountered, fill
+ # linkorder and check for strongly connected components.
+ if linkorder[currnode] == preorder[currnode]:
+ children = [x for x, dummy in graph.iteredges(currnode) if in_progress[x]]
+ if children:
+ linkorder[currnode] = min([linkorder[x] for x in children])
+ if preorder[currnode] <= linkorder[currnode]:
+ # This is a root of a strongly connected component.
+ while visitstack:
+ node = visitstack.pop()
+ in_progress[node] = False
+ if node == currnode:
+ break
+ else:
+ assert False
+ continue
+ if currnode not in preorder:
+ # First encounter of this node: pre-order processing.
+ preorder[currnode] = visit_count
+ linkorder[currnode] = visit_count
+ visitstack.append(currnode)
+ visit_count += 1
+ in_progress[currnode] = True
+ elif not in_progress[currnode]:
+ # Do not enter processed components again.
+ continue
+ currlist.append((currnode, curredge))
+ currset.add(currnode)
+ # add entry for post-order traversal
+ dfsstack.append((currnode, None))
+ for nextnode, edge in graph.iteredges(currnode):
+ if nextnode not in preorder:
+ # Not seen previously: push
+ dfsstack.append((nextnode, edge))
+ else:
+ # If an already visited node is in the same component, it is
+ # either part of a cycle, or we need to traverse it again to
+ # find all cycles.
+ if in_progress[nextnode]:
+ if nextnode not in currset:
+ dfsstack.append((nextnode, edge))
+ # Only report cycles to nodes that haven't been processed
+ # yet to avoid duplicates.
+ elif linkorder[nextnode] == preorder[nextnode]:
+ for index in xrange(len(currlist)):
+ if currlist[index][0] == nextnode:
+ cycle = [(nextnode, edge)]
+ cycle.extend(currlist[index+1:])
+ graph.report_cycle(cycle, reporter)
+ break
+ else:
+ assert False
+
+class ModuleDependencyGraph(object):
+
+ """Module dependency graph representation for check_cycles().
+
+ In the reported graph, the nodes are gmxtree.Module objects and the edges
+ are gmxtree.ModuleDependency objects.
+ """
+
+ def __init__(self, tree):
+ self._tree = tree
+
+ def iternodes(self):
+ return self._tree.get_modules()
+
+ def iteredges(self, module):
+ for dependency in module.get_dependencies():
+ if not dependency.is_test_only_dependency():
+ yield (dependency.get_other_module(), dependency)
+
+ def report_cycle(self, cycle, reporter):
+ if any([x[1].is_cycle_suppressed() for x in cycle]):
+ # TODO: Report unused suppressions.
+ return
+ modulelist = ' -> '.join([x[0].get_name()[7:] for x in cycle])
+ summary = 'module-level cyclic dependency: ' + modulelist
+ reporter.cyclic_issue(summary)
+
+def check_all(tree, reporter, check_ignored):
+ """Do all checks for the GROMACS tree."""
+ includesorter = IncludeSorter()
+ for fileobj in tree.get_files():
+ if isinstance(fileobj, gmxtree.GeneratorSourceFile):
+ continue
+ check_file(fileobj, reporter)
+ for includedfile in fileobj.get_includes():
+ check_include(fileobj, includedfile, reporter)
+ if fileobj.should_includes_be_sorted() \
+ and not includesorter.check_sorted(fileobj):
+ reporter.code_issue(fileobj, "include style/order is not consistent")
+
+ for classobj in tree.get_classes():
+ check_class(classobj, reporter)
+
+ for memberobj in tree.get_members():
+ check_member(memberobj, reporter, check_ignored)
+
+ check_cycles(ModuleDependencyGraph(tree), reporter)
+
+def main():
+ """Run the checking script."""
+ parser = OptionParser()
+ parser.add_option('-S', '--source-root',
+ help='Source tree root directory')
+ parser.add_option('-B', '--build-root',
+ help='Build tree root directory')
+ parser.add_option('-l', '--log',
+ help='Write issues into a given log file in addition to stderr')
+ parser.add_option('--ignore',
+ help='Set file with patterns for messages to ignore')
+ parser.add_option('--ignore-cycles',
+ help='Set file with module dependencies to ignore in cycles')
+ parser.add_option('--check-ignored', action='store_true',
+ help='Issue notes for comments ignored by Doxygen')
+ parser.add_option('-q', '--quiet', action='store_true',
+ help='Do not write status messages')
+ parser.add_option('--exitcode', action='store_true',
+ help='Return non-zero exit code if there are warnings')
+ options, args = parser.parse_args()
+
+ reporter = Reporter(options.log)
+ if options.ignore:
+ reporter.load_filters(options.ignore)
+
+ if not options.quiet:
+ sys.stderr.write('Scanning source tree...\n')
+ tree = GromacsTree(options.source_root, options.build_root, reporter)
+ tree.load_git_attributes()
+ tree.load_installed_file_list()
+ if not options.quiet:
+ sys.stderr.write('Reading source files...\n')
+ # TODO: The checking should be possible without storing everything in memory
+ tree.scan_files(keep_contents=True)
+ if not options.quiet:
+ sys.stderr.write('Finding config.h uses...\n')
+ tree.find_config_h_uses()
+ if options.ignore_cycles:
+ tree.load_cycle_suppression_list(options.ignore_cycles)
+ if not options.quiet:
+ sys.stderr.write('Reading Doxygen XML files...\n')
+ tree.load_xml()
+
+ reporter.write_pending()
+
+ if not options.quiet:
+ sys.stderr.write('Checking...\n')
+
+ check_all(tree, reporter, options.check_ignored)
+
+ reporter.write_pending()
+ reporter.report_unused_filters()
+ reporter.close_log()
+
+ if options.exitcode and reporter.had_warnings():
+ sys.exit(1)
+
+main()
--- /dev/null
+# Order (or more generally, edge selection) is significant (see gmxtree.md);
+# "moduleA -> moduleB" means that moduleA should not depend on moduleB, and is
+# a problem to be addressed at some point.
+fileio -> domdec
+domdec -> imd
+domdec -> ewald
+domdec -> mdlib
+domdec -> pulling
+domdec -> swap
+mdlib -> essentialdynamics
+mdlib -> imd
+mdlib -> ewald
+mdlib -> pulling
+legacyheaders -> swap
+legacyheaders -> fileio
+timing -> legacyheaders
+math -> legacyheaders
+topology -> fileio
+topology -> legacyheaders
+pbcutil -> fileio
+pbcutil -> legacyheaders
+listed-forces -> mdlib
\author Teemu Murtola <teemu.murtola@gmail.com>
*/
-/*!
-\libinternal
-\dir doxygen
+/*! \libinternal
+\dir docs
+\brief Build system and source code for various documentation items.
+ */
+/*! \libinternal
+\dir docs/doxygen
\brief Doxygen build system and general documentation content.
*/
\ingroup module_commandline
*/
-/*!
+/*! \libinternal
\dir src/gromacs/onlinehelp
\brief \ref module_onlinehelp
\ingroup module_testutils
*/
-
/*!
\libinternal
\dir src/testutils/tests
\dir share/template
\brief Template code for writing analysis programs.
*/
-
-/*!
-\file share/template/template.cpp
-\brief Template code for writing analysis programs.
-
-See \ref page_analysistemplate for more information.
- */
-
-/*!
-\example template.cpp
-\brief Template code for writing analysis programs.
-
-See \ref page_analysistemplate for more information.
- */
+++ /dev/null
-#!/usr/bin/python
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2014, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public License
-# as published by the Free Software Foundation; either version 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-"""Check Doxygen documentation for issues that Doxygen does not warn about.
-
-This script for some issues in the Doxygen documentation, using Doxygen XML
-output. Part of the checks are generic, like checking that all documented
-entities have brief descriptions. Other are specific to GROMACS, like checking
-that only installed headers contribute to the public API documentation.
-
-The checks should be self-evident from the source code of the script.
-All the logic of parsing the Doxygen XML output and creating a GROMACS-specific
-representation of the source tree is separated into separate Python modules
-(doxygenxml.py and gmxtree.py, respectively). Similarly, logic for handling
-the output messages is in reporter.py. This leaves only the actual checks and
-the script command-line interface in this file.
-
-The script can be run using the 'doc-check' target generated by CMake.
-This target takes care of generating all the necessary input files and passing
-them to the script.
-"""
-
-import sys
-from optparse import OptionParser
-
-from gmxtree import GromacsTree, DocType
-from reporter import Reporter
-
-def check_file(fileobj, reporter):
- """Check file-level documentation."""
- if not fileobj.is_documented():
- # TODO: Add rules for required documentation
- return
-
- if fileobj.is_source_file():
- # TODO: Add rule to exclude examples from this check
- if fileobj.is_installed():
- reporter.file_error(fileobj, "source file is installed")
- if fileobj.get_documentation_type() != DocType.internal:
- reporter.file_error(fileobj,
- "source file documentation appears outside full documentation")
- elif fileobj.get_api_type() != DocType.internal:
- reporter.file_error(fileobj, "source file marked as non-internal")
- elif fileobj.is_test_file() and fileobj.is_installed():
- reporter.file_error(fileobj, "test file is installed")
- elif fileobj.is_installed():
- if fileobj.get_documentation_type() != DocType.public:
- reporter.file_error(fileobj,
- "public header has non-public documentation")
- elif fileobj.get_documentation_type() == DocType.public:
- reporter.file_error(fileobj,
- "non-installed header has public documentation")
- elif fileobj.get_api_type() == DocType.public:
- reporter.file_error(fileobj,
- "non-installed header specified as part of public API")
- elif fileobj.get_documentation_type() < fileobj.get_api_type():
- reporter.file_error(fileobj,
- "API type ({0}) conflicts with documentation visibility ({1})"
- .format(fileobj.get_api_type(), fileobj.get_documentation_type()))
-
- if not fileobj.has_brief_description():
- reporter.file_error(fileobj,
- "is documented, but does not have brief description")
-
- expectedmod = fileobj.get_expected_module()
- if expectedmod:
- docmodules = fileobj.get_doc_modules()
- if docmodules:
- for module in docmodules:
- if module != expectedmod:
- reporter.file_error(fileobj,
- "is documented in incorrect module: {0}"
- .format(module.get_name()))
- elif expectedmod.is_documented():
- reporter.file_error(fileobj,
- "is not documented in any module, but {0} exists"
- .format(expectedmod.get_name()))
-
-def check_include(fileobj, includedfile, reporter):
- """Check an #include directive."""
- if includedfile.is_system():
- if includedfile.get_file():
- reporter.code_issue(includedfile,
- "includes local file as {0}".format(includedfile))
- else:
- otherfile = includedfile.get_file()
- if not otherfile:
- reporter.code_issue(includedfile,
- "includes non-local file as {0}".format(includedfile))
- elif fileobj.is_installed() and not includedfile.is_relative():
- reporter.code_issue(includedfile,
- "installed header includes {0} using non-relative path"
- .format(includedfile))
- if not otherfile:
- return
- if fileobj.is_installed() and not otherfile.is_installed():
- reporter.code_issue(includedfile,
- "installed header includes non-installed {0}"
- .format(includedfile))
- filemodule = fileobj.get_module()
- othermodule = otherfile.get_module()
- if fileobj.is_documented() and otherfile.is_documented():
- filetype = fileobj.get_documentation_type()
- othertype = otherfile.get_documentation_type()
- if filetype > othertype:
- reporter.code_issue(includedfile,
- "{0} file includes {1} file {2}"
- .format(filetype, othertype, includedfile))
- check_api = (othermodule and othermodule.is_documented() and
- filemodule != othermodule)
- if check_api and otherfile.get_api_type() < DocType.library:
- reporter.code_issue(includedfile,
- "included file {0} is not documented as exposed outside its module"
- .format(includedfile))
-
-def check_entity(entity, reporter):
- """Check documentation for a code construct."""
- if entity.is_documented():
- if not entity.has_brief_description():
- reporter.doc_error(entity,
- "is documented, but does not have brief description")
-
-def check_class(classobj, reporter):
- """Check documentation for a class/struct/union."""
- check_entity(classobj, reporter)
- if classobj.is_documented():
- classtype = classobj.get_documentation_type()
- filetype = classobj.get_file_documentation_type()
- if classtype == DocType.public and not classobj.is_in_installed_file():
- reporter.doc_error(classobj,
- "has public documentation, but is not in installed header")
- elif filetype is not DocType.none and classtype > filetype:
- reporter.doc_error(classobj,
- "is in {0} file(s), but appears in {1} documentation"
- .format(filetype, classtype))
-
-def check_member(member, reporter):
- """Check documentation for a generic member."""
- check_entity(member, reporter)
- if member.is_documented():
- if not member.is_visible():
- # TODO: This is triggered by members in anonymous namespaces.
- reporter.doc_note(member,
- "is documented, but is ignored by Doxygen, because its scope is not documented")
- if member.has_inbody_description():
- reporter.doc_note(member, "has in-body comments, which are ignored")
-
-def main():
- """Run the checking script."""
- parser = OptionParser()
- parser.add_option('-S', '--source-root',
- help='Source tree root directory')
- parser.add_option('-B', '--build-root',
- help='Build tree root directory')
- parser.add_option('--installed',
- help='Read list of installed files from given file')
- parser.add_option('-l', '--log',
- help='Write issues into a given log file in addition to stderr')
- parser.add_option('--ignore',
- help='Set file with patterns for messages to ignore')
- parser.add_option('--check-ignored', action='store_true',
- help='Check documentation ignored by Doxygen')
- parser.add_option('-q', '--quiet', action='store_true',
- help='Do not write status messages')
- options, args = parser.parse_args()
-
- installedlist = []
- if options.installed:
- with open(options.installed, 'r') as outfile:
- for line in outfile:
- installedlist.append(line.strip())
-
- reporter = Reporter(options.log)
- if options.ignore:
- reporter.load_filters(options.ignore)
-
- if not options.quiet:
- sys.stderr.write('Scanning source tree...\n')
- tree = GromacsTree(options.source_root, options.build_root, reporter)
- tree.set_installed_file_list(installedlist)
- if not options.quiet:
- sys.stderr.write('Reading source files...\n')
- tree.scan_files()
- if not options.quiet:
- sys.stderr.write('Reading Doxygen XML files...\n')
- tree.load_xml()
-
- reporter.write_pending()
-
- if not options.quiet:
- sys.stderr.write('Checking...\n')
-
- for fileobj in tree.get_files():
- check_file(fileobj, reporter)
- for includedfile in fileobj.get_includes():
- check_include(fileobj, includedfile, reporter)
-
- for classobj in tree.get_classes():
- check_class(classobj, reporter)
-
- for memberobj in tree.get_members():
- if memberobj.is_visible() or options.check_ignored:
- check_member(memberobj, reporter)
-
- reporter.write_pending()
- reporter.report_unused_filters()
- reporter.close_log()
-
-main()
def __init__(self, name, refid):
Entity.__init__(self, name, refid)
self._parents = set()
+ self._class = None
+ self._namespace = None
+ self._files = set()
+ self._group = None
self._location = None
self._alternates = set()
self._loaded = False
def add_parent_compound(self, compound):
"""Add a compound that contains this member."""
self._parents.add(compound)
+ if isinstance(compound, Class):
+ assert self._class is None
+ self._class = compound
+ elif isinstance(compound, Namespace):
+ assert self._namespace is None
+ self._namespace = compound
+ elif isinstance(compound, File):
+ self._files.add(compound)
+ elif isinstance(compound, Group):
+ assert self._group is None
+ self._group = compound
+ else:
+ assert False
- def _get_raw_location(self):
- """Returns the BodyLocation object associated with this member.
+ def merge_definition(self, definition):
+ """Merge another member into this.
- This is necessary so that EnumValue can override it report a non-empty
- location: Doxygen doesn't provide any location for <enumvalue>.
+ See DocumentationSet.merge_duplicates().
"""
- return self._location
-
- def get_parent_compounds(self):
- return self._parents
-
- def get_inherited_visibility(self):
- return max([parent.get_visibility() for parent in self._parents])
-
- def is_visible(self):
- return self.get_inherited_visibility() != DocType.none
-
- def has_same_body_location(self):
- return self._get_raw_location().has_same_body_location()
-
- def get_reporter_location(self):
- return self._get_raw_location().get_reporter_location()
-
- def get_location(self):
- return self._get_raw_location().get_location()
-
- def get_body_location(self):
- return self._get_raw_location().get_body_location()
-
- def merge_definition(self, definition):
+ assert self._class is None
+ assert definition._class is None
+ assert self._group == definition._group
+ assert self._namespace == definition._namespace
self._parents.update(definition._parents)
+ self._files.update(definition._files)
self._alternates.add(definition)
def load_details_from_element(self, rootelem, xmlpath):
"""
return False
+ def _get_raw_location(self):
+ """Returns the BodyLocation object associated with this member.
+
+ This is necessary so that EnumValue can override it report a non-empty
+ location: Doxygen doesn't provide any location for <enumvalue>.
+ """
+ return self._location
+
+ def get_reporter_location(self):
+ return self._get_raw_location().get_reporter_location()
+
+ def get_location(self):
+ """Return main location for the member.
+
+ This typically corresponds to the declaration.
+ """
+ return self._get_raw_location().get_location()
+
+ def get_body_location(self):
+ """Return location of the body for the member.
+
+ Some types of members do not have a body location, in which case this
+ returns None.
+ """
+ return self._get_raw_location().get_body_location()
+
+ def has_same_body_location(self):
+ """Check whether the main location is the same as body location."""
+ return self._get_raw_location().has_same_body_location()
+
+ def get_namespace(self):
+ return self._namespace
+
+ def get_parent_compounds(self):
+ return self._parents
+
+ def get_inherited_visibility(self):
+ return max([parent.get_visibility() for parent in self._parents])
+
def show(self):
self.show_base()
+ if self._alternates:
+ idlist = [x.get_id() for x in self._alternates]
+ print 'Alt. IDs: {0}'.format(', '.join(idlist))
print 'Parent vis: {0}'.format(self.get_inherited_visibility())
print 'Location: {0}'.format(self.get_location().get_full_string())
print 'Body loc: {0}'.format(self.get_body_location().get_full_string())
contains references to contained compounds, and details of all members
within the compound.
"""
+
def __init__(self, name, refid):
Entity.__init__(self, name, refid)
self._members = dict()
def get_reporter_location(self):
return self._doclocation.get_reporter_location()
+ def is_anonymous(self):
+ return 'anonymous_namespace{' in self.get_name()
+
def show(self):
self.show_base()
print 'Doc. loc.: {0}'.format(self._doclocation.get_full_string())
member.add_parent_compound(compound)
compound.add_member(member)
- def load_file_details(self):
- """Load detailed XML files for all files and possible parents of files."""
+ def load_file_details(self, filelist=None):
+ """Load detailed XML files for all files and possible parents of files.
+
+ If filelist is set, it should be a list of file paths, and details will
+ be loaded only for files in those paths. The path format should match
+ what Doxygen writes into the files (with Gromacs setup, it seems to be
+ absolute paths)."""
for compound in self._compounds.itervalues():
- if isinstance(compound, (File, Directory, Group)):
+ if isinstance(compound, (Directory, Group)):
+ compound.load_details()
+ elif not filelist and isinstance(compound, File):
compound.load_details()
+ self._files[compound.get_path()] = compound
+ if filelist:
+ # We can't access the full path from the File object before the
+ # details are loaded, because Doxygen does not write that into
+ # index.xml. But we can use the Directory objects (which were
+ # loaded above) to get the path.
+ for compound in self._compounds.itervalues():
if isinstance(compound, File):
- self._files[compound.get_path()] = compound
+ dirobj = compound.get_directory()
+ if not dirobj:
+ continue
+ abspath = compound.get_directory().get_path()
+ abspath = os.path.join(abspath, compound.get_name())
+ if abspath in filelist:
+ compound.load_details()
+ self._files[compound.get_path()] = compound
def load_details(self):
"""Load detailed XML files for each compound."""
def merge_duplicates(self):
"""Merge duplicate member definitions based on body location.
- At least for functions that are declared in a header, but have their
- body in a source file, Doxygen seems to create two different IDs, but
- the contents of the members are the same, except for the location
+ At least for some functions that are declared in a header, but have
+ their body in a source file, Doxygen seems to create two different IDs,
+ but the contents of the members are the same, except for the location
attribute. This method merges members that have identical name and
body location into a single member that keeps the information from both
instances (they should only differ in the location attribute and in
def get_groups(self, name):
return self.get_compounds(Group, lambda x: x.get_name() in name)
- def get_namespaces(self, name):
- return self.get_compounds(Namespace, lambda x: x.get_name() in name)
+ def get_namespaces(self, name=None):
+ if name:
+ return self.get_compounds(Namespace, lambda x: x.get_name() in name)
+ else:
+ return self.get_compounds(Namespace)
def get_classes(self, name=None):
if name:
# the research papers on the package. Check out http://www.gromacs.org.
if (DOT_EXECUTABLE)
- message("Running dot...")
file(GLOB DOT_INPUT_FILES ${GRAPHDIR}/*.dot)
execute_process(COMMAND ${DOT_EXECUTABLE} -Tpng -O ${DOT_INPUT_FILES})
endif()
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014, by the GROMACS development team, led by
+# Copyright (c) 2014,2015, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
customizations will be added.
"""
+import collections
import os
import os.path
import re
+import subprocess
import doxygenxml as xml
import reporter
"""Information about an #include directive in a file."""
- def __init__(self, abspath, lineno, included_file, included_path, is_relative, is_system):
- self._abspath = abspath
+ def __init__(self, including_file, lineno, included_file, included_path, is_relative, is_system, line):
+ self._including_file = including_file
self._line_number = lineno
self._included_file = included_file
self._included_path = included_path
#self._used_include_path = used_include_path
self._is_relative = is_relative
self._is_system = is_system
+ self._line = line
def __str__(self):
if self._is_system:
def is_relative(self):
return self._is_relative
+ def get_included_path(self):
+ return self._included_path
+
+ def get_including_file(self):
+ return self._including_file
+
def get_file(self):
return self._included_file
+ def get_line_number(self):
+ return self._line_number
+
+ def get_full_line(self):
+ """Return the full source line on which this include appears.
+
+ Trailing newline is included."""
+ return self._line
+
def get_reporter_location(self):
- return reporter.Location(self._abspath, self._line_number)
+ return reporter.Location(self._including_file.get_abspath(), self._line_number)
+
+class IncludeBlock(object):
+
+ """Block of consequent #include directives in a file."""
+
+ def __init__(self, first_included_file):
+ self._first_line = first_included_file.get_line_number()
+ self._last_line = self._first_line
+ self._files = []
+ self.add_file(first_included_file)
+
+ def add_file(self, included_file):
+ self._files.append(included_file)
+ self._last_line = included_file.get_line_number()
+
+ def get_includes(self):
+ return self._files
+
+ def get_first_line(self):
+ return self._first_line
+
+ def get_last_line(self):
+ return self._last_line
class File(object):
self._apitype = DocType.none
self._modules = set()
self._includes = []
+ self._include_blocks = []
+ self._main_header = None
+ self._lines = None
+ self._filter = None
+ self._used_config_h_defines = set()
directory.add_file(self)
def set_doc_xml(self, rawdoc, sourcetree):
"""Mark the file installed."""
self._installed = True
- def _process_include(self, lineno, is_system, includedpath, sourcetree):
+ def set_git_filter_attribute(self, filtername):
+ """Set the git filter attribute associated with the file."""
+ self._filter = filtername
+
+ def set_main_header(self, included_file):
+ """Set the main header file for a source file."""
+ assert self.is_source_file()
+ self._main_header = included_file
+
+ def _process_include(self, lineno, is_system, includedpath, line, sourcetree):
"""Process #include directive during scan()."""
is_relative = False
if is_system:
fileobj = sourcetree.get_file(fullpath)
else:
fileobj = sourcetree.find_include_file(includedpath)
- self._includes.append(IncludedFile(self.get_abspath(), lineno, fileobj, includedpath,
- is_relative, is_system))
+ included_file = IncludedFile(self, lineno, fileobj, includedpath,
+ is_relative, is_system, line)
+ self._includes.append(included_file)
+ return included_file
- def scan_contents(self, sourcetree):
+ def scan_contents(self, sourcetree, keep_contents):
"""Scan the file contents and initialize information based on it."""
# TODO: Consider a more robust regex.
- include_re = r'^#\s*include\s+(?P<quote>["<])(?P<path>[^">]*)[">]'
+ include_re = r'^\s*#\s*include\s+(?P<quote>["<])(?P<path>[^">]*)[">]'
+ current_block = None
with open(self._abspath, 'r') as scanfile:
- for lineno, line in enumerate(scanfile, 1):
- match = re.match(include_re, line)
- if match:
- is_system = (match.group('quote') == '<')
- includedpath = match.group('path')
- self._process_include(lineno, is_system, includedpath,
- sourcetree)
+ contents = scanfile.read()
+ lines = contents.splitlines(True)
+ for lineno, line in enumerate(lines, 1):
+ match = re.match(include_re, line)
+ if match:
+ is_system = (match.group('quote') == '<')
+ includedpath = match.group('path')
+ included_file = self._process_include(lineno, is_system,
+ includedpath, line, sourcetree)
+ if current_block is None:
+ current_block = IncludeBlock(included_file)
+ self._include_blocks.append(current_block)
+ else:
+ current_block.add_file(included_file)
+ elif line and not line.isspace():
+ current_block = None
+ if keep_contents:
+ self._lines = lines
+
+ def add_used_config_h_defines(self, defines):
+ """Set config.h defines used in this file.
+
+ Used internally by find_config_h_uses()."""
+ self._used_config_h_defines.update(defines)
def get_reporter_location(self):
return reporter.Location(self._abspath, None)
def is_test_file(self):
return self._dir.is_test_directory()
+ def should_includes_be_sorted(self):
+ """Return whether the include directives in the file should be sorted."""
+ return self._filter in ('includesort', 'uncrustify')
+
def is_documented(self):
return self._rawdoc and self._rawdoc.is_documented()
def get_name(self):
return os.path.basename(self._abspath)
- def get_documentation_type(self):
+ def get_directory(self):
+ return self._dir
+
+ def get_doc_type(self):
if not self._rawdoc:
return DocType.none
return self._rawdoc.get_visibility()
def get_api_type(self):
return self._apitype
+ def api_type_is_reliable(self):
+ if self._apitype in (DocType.internal, DocType.library):
+ return True
+ module = self.get_module()
+ return module and module.is_documented()
+
+ def is_public(self):
+ if self.api_type_is_reliable():
+ return self.get_api_type() == DocType.public
+ return self.get_api_type() == DocType.public or self.is_installed()
+
+ def is_module_internal(self):
+ if self.is_source_file():
+ return True
+ return not self.is_installed() and self.get_api_type() <= DocType.internal
+
def get_expected_module(self):
return self._dir.get_module()
def get_includes(self):
return self._includes
+ def get_include_blocks(self):
+ return self._include_blocks
+
+ def get_main_header(self):
+ return self._main_header
+
+ def get_contents(self):
+ return self._lines
+
+ def get_used_config_h_defines(self):
+ """Return set of defines from config.h that are used in this file.
+
+ The return value is empty if find_config_h_uses() has not been called,
+ as well as for headers that declare these defines."""
+ return self._used_config_h_defines
+
class GeneratedFile(File):
- pass
+ def __init__(self, abspath, relpath, directory):
+ File.__init__(self, abspath, relpath, directory)
+ self._generator_source_file = None
+
+ def scan_contents(self, sourcetree, keep_contents):
+ if os.path.exists(self.get_abspath()):
+ File.scan_contents(self, sourcetree, keep_contents)
+
+ def set_generator_source(self, sourcefile):
+ self._generator_source_file = sourcefile
+
+ def get_reporter_location(self):
+ if self._generator_source_file:
+ return self._generator_source_file.get_reporter_location()
+ return File.get_reporter_location(self)
+
+class GeneratorSourceFile(File):
+ def __init__(self, abspath, relpath, directory):
+ File.__init__(self, abspath, relpath, directory)
+ self._defines = None
+
+ def scan_contents(self, sourcetree, keep_contents):
+ detect_defines = (self.get_name() == 'config.h.cmakein')
+ File.scan_contents(self, sourcetree, keep_contents or detect_defines)
+ if detect_defines:
+ self._defines = []
+ define_re = r'^#.*define\s+(\w*)'
+ for line in self.get_contents():
+ match = re.match(define_re, line)
+ if match:
+ self._defines.append(match.group(1))
+
+ def get_defines(self):
+ """Return set of possible defines from config.h.cmakein.
+
+ The information is only populated for config.h.cmakein."""
+ return self._defines
class Directory(object):
for fileobj in self._files:
yield fileobj
+ def contains(self, fileobj):
+ """Check whether file is within the directory or its subdirectories."""
+ dirobj = fileobj.get_directory()
+ while dirobj:
+ if dirobj == self:
+ return True
+ dirobj = dirobj._parent
+ return False
+
+class ModuleDependency(object):
+
+ """Dependency between modules."""
+
+ def __init__(self, othermodule):
+ """Initialize empty dependency object with given module as dependency."""
+ self._othermodule = othermodule
+ self._includedfiles = []
+ self._cyclesuppression = None
+ self._is_test_only_dependency = True
+
+ def add_included_file(self, includedfile):
+ """Add IncludedFile that is part of this dependency."""
+ assert includedfile.get_file().get_module() == self._othermodule
+ if not includedfile.get_including_file().is_test_file():
+ self._is_test_only_dependency = False
+ self._includedfiles.append(includedfile)
+
+ def set_cycle_suppression(self):
+ """Set suppression on cycles containing this dependency."""
+ self._cyclesuppression = True
+
+ def is_cycle_suppressed(self):
+ """Return whether cycles containing this dependency are suppressed."""
+ return self._cyclesuppression is not None
+
+ def is_test_only_dependency(self):
+ """Return whether this dependency is only from test code."""
+ return self._is_test_only_dependency
+
+ def get_other_module(self):
+ """Get module that this dependency is to."""
+ return self._othermodule
+
+ def get_included_files(self):
+ """Get IncludedFile objects for the individual include dependencies."""
+ return self._includedfiles
+
class Module(object):
"""Code module in the GROMACS source tree.
self._rawdoc = None
self._rootdir = rootdir
self._group = None
+ self._dependencies = dict()
def set_doc_xml(self, rawdoc, sourcetree):
"""Assiociate Doxygen documentation entity with the module."""
if groupname.startswith('group_'):
self._group = groupname[6:]
+ def add_dependency(self, othermodule, includedfile):
+ """Add #include dependency from a file in this module."""
+ assert includedfile.get_file().get_module() == othermodule
+ if othermodule not in self._dependencies:
+ self._dependencies[othermodule] = ModuleDependency(othermodule)
+ self._dependencies[othermodule].add_included_file(includedfile)
+
def is_documented(self):
return self._rawdoc is not None
def get_group(self):
return self._group
+ def get_dependencies(self):
+ return self._dependencies.itervalues()
+
+class Namespace(object):
+
+ """Namespace in the GROMACS source code."""
+
+ def __init__(self, rawdoc):
+ self._rawdoc = rawdoc
+
+ def is_anonymous(self):
+ return self._rawdoc.is_anonymous()
class Class(object):
def has_brief_description(self):
return self._rawdoc.has_brief_description()
- def get_documentation_type(self):
+ def get_doc_type(self):
+ """Return documentation type (visibility) for the class.
+
+ In addition to the actual code, this encodes GROMACS-specific logic
+ of setting EXTRACT_LOCAL_CLASSES=YES only for the full documentation.
+ Local classes never appear outside the full documentation, no matter
+ what is their visibility.
+ """
if not self.is_documented():
return DocType.none
if self._rawdoc.is_local():
return DocType.internal
return self._rawdoc.get_visibility()
- def get_file_documentation_type(self):
- return max([fileobj.get_documentation_type() for fileobj in self._files])
+ def get_file_doc_type(self):
+ return max([fileobj.get_doc_type() for fileobj in self._files])
def is_in_installed_file(self):
return any([fileobj.is_installed() for fileobj in self._files])
+class Member(object):
+
+ """Member (in Doxygen terminology) in the GROMACS source tree.
+
+ Currently, modeling is limited to the minimal set of properties that the
+ checker uses.
+ """
+
+ def __init__(self, rawdoc, namespace):
+ self._rawdoc = rawdoc
+ self._namespace = namespace
+
+ def get_name(self):
+ return self._rawdoc.get_name()
+
+ def get_reporter_location(self):
+ return self._rawdoc.get_reporter_location()
+
+ def is_documented(self):
+ return self._rawdoc.is_documented()
+
+ def has_brief_description(self):
+ return self._rawdoc.has_brief_description()
+
+ def has_inbody_description(self):
+ return self._rawdoc.has_inbody_description()
+
+ def is_visible(self):
+ """Return whether the member is visible in Doxygen documentation.
+
+ Doxygen ignores members whose parent compounds are not documented.
+ However, when EXTRACT_ANON_NPACES=ON (which is set for our full
+ documentation), members of anonymous namespaces are extracted even if
+ the namespace is the only parent and is not documented.
+ """
+ if self._namespace and self._namespace.is_anonymous():
+ return True
+ return self._rawdoc.get_inherited_visibility() != DocType.none
+
+
class GromacsTree(object):
"""Root object for navigating the GROMACS source tree.
subdirectories. At this point, only information that is accessible from
file names and paths only is available.
- set_installed_file_list() can be called to set the list of installed
- files.
+ load_git_attributes() can be called to load attribute information from
+ .gitattributes for all the files.
+
+ load_installed_file_list() can be called to load the list of installed
+ files from the build tree (generated by CMake).
scan_files() can be called to read all the files and initialize #include
dependencies between the files based on the information. This is done like
(Doxygen only sees those #includes that the preprocessor sees, which
depends on what #defines it has seen).
+ find_config_h_uses() can be called to find all uses of defines declared in
+ config.h. In the current implementation, scan_files() must have been
+ called earlier.
+
load_xml() can be called to load information from Doxygen XML data in
the build tree (the Doxygen XML data must have been built separately).
"""
self._files = dict()
self._modules = dict()
self._classes = set()
+ self._namespaces = set()
+ self._members = set()
self._walk_dir(os.path.join(self._source_root, 'src'))
+ for fileobj in self.get_files():
+ if fileobj and fileobj.is_source_file() and not fileobj.is_external():
+ (basedir, name) = os.path.split(fileobj.get_abspath())
+ (basename, ext) = os.path.splitext(name)
+ header = self.get_file(os.path.join(basedir, basename + '.h'))
+ if not header and ext == '.cu':
+ header = self.get_file(os.path.join(basedir, basename + '.cuh'))
+ if not header and fileobj.is_test_file():
+ basedir = os.path.dirname(basedir)
+ header = self.get_file(os.path.join(basedir, basename + '.h'))
+ if not header:
+ # Somewhat of a hack; currently, the tests for
+ # analysisdata/modules/ and trajectoryanalysis/modules/
+ # is at the top-level tests directory.
+ # TODO: It could be clearer to split the tests so that
+ # there would be a separate modules/tests/.
+ header = self.get_file(os.path.join(basedir, 'modules', basename + '.h'))
+ if not header and basename.endswith('_tests'):
+ header = self.get_file(os.path.join(basedir, basename[:-6] + '.h'))
+ if not header and fileobj.get_relpath().startswith('src/gromacs'):
+ header = self._files.get(os.path.join('src/gromacs/legacyheaders', basename + '.h'))
+ if header:
+ fileobj.set_main_header(header)
rootdir = self._get_dir(os.path.join('src', 'gromacs'))
for subdir in rootdir.get_subdirectories():
self._create_module(subdir)
elif extension == '.cmakein':
extension = os.path.splitext(basename)[1]
if extension in extensions:
+ fullpath = os.path.join(dirpath, filename)
+ relpath = self._get_rel_path(fullpath)
+ sourcefile = GeneratorSourceFile(fullpath, relpath, currentdir)
+ self._files[relpath] = sourcefile
fullpath = os.path.join(dirpath, basename)
relpath = self._get_rel_path(fullpath)
- fullpath = os.path.join(dirpath, filename)
- self._files[relpath] = GeneratedFile(fullpath, relpath, currentdir)
+ fullpath = os.path.join(self._build_root, relpath)
+ generatedfile = GeneratedFile(fullpath, relpath, currentdir)
+ self._files[relpath] = generatedfile
+ generatedfile.set_generator_source(sourcefile)
+ elif extension in ('.l', '.y', '.pre'):
+ fullpath = os.path.join(dirpath, filename)
+ relpath = self._get_rel_path(fullpath)
+ self._files[relpath] = GeneratorSourceFile(fullpath, relpath, currentdir)
def _create_module(self, rootdir):
"""Create module for a subdirectory."""
rootdir.set_module(moduleobj)
self._modules[name] = moduleobj
- def scan_files(self):
+ def scan_files(self, only_files=None, keep_contents=False):
"""Read source files to initialize #include dependencies."""
- for fileobj in self._files.itervalues():
+ if only_files:
+ filelist = only_files
+ else:
+ filelist = self._files.itervalues()
+ for fileobj in filelist:
if not fileobj.is_external():
- fileobj.scan_contents(self)
-
- def load_xml(self, only_files=False):
+ fileobj.scan_contents(self, keep_contents)
+ module = fileobj.get_module()
+ if module:
+ for includedfile in fileobj.get_includes():
+ otherfile = includedfile.get_file()
+ if otherfile:
+ othermodule = otherfile.get_module()
+ if othermodule and othermodule != module:
+ module.add_dependency(othermodule, includedfile)
+
+ def load_xml(self, only_files=None):
"""Load Doxygen XML information.
If only_files is True, XML data is not loaded for code constructs, but
xmldir = os.path.join(self._build_root, 'docs', 'html', 'doxygen', 'xml')
self._docset = xml.DocumentationSet(xmldir, self._reporter)
if only_files:
- self._docset.load_file_details()
+ if isinstance(only_files, collections.Iterable):
+ filelist = [x.get_abspath() for x in only_files]
+ self._docset.load_file_details(filelist)
+ else:
+ self._docset.load_file_details()
else:
self._docset.load_details()
self._docset.merge_duplicates()
self._load_modules()
self._load_files()
if not only_files:
+ self._load_namespaces()
self._load_classes()
+ self._load_members()
def _load_dirs(self):
"""Load Doxygen XML directory information."""
"""Load Doxygen XML file information."""
for filedoc in self._docset.get_files():
path = filedoc.get_path()
+ if not path:
+ # In case of only partially loaded file information,
+ # the path information is not set for unloaded files.
+ continue
if not os.path.isabs(path):
self._reporter.xml_assert(filedoc.get_xml_path(),
"expected absolute path in Doxygen-produced XML file")
continue
- extension = os.path.splitext(filedoc.get_path())[1]
+ extension = os.path.splitext(path)[1]
# We don't care about Markdown files that only produce pages
# (and fail the directory check below).
if extension == '.md':
fileobj.set_doc_xml(filedoc, self)
self._docmap[filedoc] = fileobj
+ def _load_namespaces(self):
+ """Load Doxygen XML namespace information."""
+ nsdocs = self._docset.get_namespaces()
+ for nsdoc in nsdocs:
+ nsobj = Namespace(nsdoc)
+ self._docmap[nsdoc] = nsobj
+ self._namespaces.add(nsobj)
+
def _load_classes(self):
"""Load Doxygen XML class information."""
classdocs = self._docset.get_classes()
self._docmap[classdoc] = classobj
self._classes.add(classobj)
+ def _load_members(self):
+ """Load Doxygen XML member information."""
+ memberdocs = self._docset.get_members()
+ for memberdoc in memberdocs:
+ nsdoc = memberdoc.get_namespace()
+ nsobj = self.get_object(nsdoc)
+ memberobj = Member(memberdoc, nsobj)
+ self._docmap[memberdoc] = memberobj
+ self._members.add(memberobj)
+
def _get_dir(self, relpath):
"""Get directory object for a path relative to source tree root."""
return self._dirs.get(relpath)
def find_include_file(self, includedpath):
"""Find a file object corresponding to an include path."""
- for testdir in ('src', 'src/gromacs/legacyheaders', 'src/external/thread_mpi/include'):
+ for testdir in ('src', 'src/external/thread_mpi/include',
+ 'src/external/tng_io/include'):
testpath = os.path.join(testdir, includedpath)
if testpath in self._files:
return self._files[testpath]
- def set_installed_file_list(self, installedfiles):
- """Set list of installed files."""
- for path in installedfiles:
- if not os.path.isabs(path):
- self._reporter.input_error(
- "installed file not specified with absolute path: {0}"
- .format(path))
- continue
- relpath = self._get_rel_path(path)
- if relpath not in self._files:
- self._reporter.input_error(
- "installed file not in source tree: {0}".format(path))
- continue
- self._files[relpath].set_installed()
+ def load_git_attributes(self):
+ """Load git attribute information for files."""
+ args = ['git', 'check-attr', '--stdin', 'filter']
+ git_check_attr = subprocess.Popen(args, stdin=subprocess.PIPE,
+ stdout=subprocess.PIPE, cwd=self._source_root)
+ filelist = '\n'.join(map(File.get_relpath, self._files.itervalues()))
+ filters = git_check_attr.communicate(filelist)[0]
+ for fileinfo in filters.splitlines():
+ path, dummy, value = fileinfo.split(': ')
+ fileobj = self._files.get(path)
+ assert fileobj is not None
+ fileobj.set_git_filter_attribute(value)
+
+ def find_config_h_uses(self):
+ """Find files that use defines from config.h."""
+ # Executing git grep is substantially faster than using the define_re
+ # directly on the contents of the file in Python.
+ args = ['git', 'grep', '-zwIF']
+ configfile = self._files['src/config.h.cmakein']
+ for define in configfile.get_defines():
+ args.extend(['-e', define])
+ args.extend(['--', '*.cpp', '*.c', '*.cu', '*.h', '*.cuh'])
+ define_re = r'\b(?:' + '|'.join(configfile.get_defines())+ r')\b'
+ output = subprocess.check_output(args, cwd=self._source_root)
+ for line in output.splitlines():
+ (filename, text) = line.split('\0')
+ fileobj = self._files.get(filename)
+ if fileobj is not None:
+ if fileobj.get_name() not in ('config.h', 'config.h.cmakein',
+ 'gmxpre-config.h', 'gmxpre-config.h.cmakein'):
+ defines = re.findall(define_re, text)
+ fileobj.add_used_config_h_defines(defines)
+
+ def load_installed_file_list(self):
+ """Load list of installed files from the build tree."""
+ listpath = os.path.join(self._build_root, 'src', 'gromacs', 'installed-headers.txt')
+ with open(listpath, 'r') as installedfp:
+ for line in installedfp:
+ path = line.strip()
+ if not os.path.isabs(path):
+ self._reporter.input_error(
+ "installed file not specified with absolute path: {0}"
+ .format(path))
+ continue
+ relpath = self._get_rel_path(path)
+ if relpath not in self._files:
+ self._reporter.input_error(
+ "installed file not in source tree: {0}".format(path))
+ continue
+ self._files[relpath].set_installed()
+
+ def load_cycle_suppression_list(self, filename):
+ """Load a list of edges to suppress in cycles.
+
+ These edges between modules, if present, will be marked in the
+ corresponding ModuleDependency objects.
+ """
+ with open(filename, 'r') as fp:
+ for line in fp:
+ line = line.strip()
+ if not line or line.startswith('#'):
+ continue
+ modulenames = ['module_' + x.strip() for x in line.split('->')]
+ if len(modulenames) != 2:
+ self._reporter.input_error(
+ "invalid cycle suppression line: {0}".format(line))
+ continue
+ firstmodule = self._modules.get(modulenames[0])
+ secondmodule = self._modules.get(modulenames[1])
+ if not firstmodule or not secondmodule:
+ self._reporter.input_error(
+ "unknown modules mentioned on cycle suppression line: {0}".format(line))
+ continue
+ for dep in firstmodule.get_dependencies():
+ if dep.get_other_module() == secondmodule:
+ # TODO: Check that each suppression is actually part of
+ # a cycle.
+ dep.set_cycle_suppression()
def get_object(self, docobj):
"""Get tree object for a Doxygen XML object."""
+ if docobj is None:
+ return None
return self._docmap.get(docobj)
def get_files(self):
def get_members(self):
"""Get iterable for all members (in Doxygen terms) in the source tree."""
- # TODO: Add wrappers to solve some issues.
- return self._docset.get_members()
+ return self._members
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# Intramodule dependency
EdgeType.intramodule = EdgeType(5)
EdgeType.legacy = EdgeType(6)
+EdgeType.cyclic = EdgeType(7)
# Invalid dependency
-EdgeType.undocumented = EdgeType(7)
+EdgeType.undocumented = EdgeType(8)
class Edge(object):
def format(self):
"""Format this edge for 'dot'."""
+ # If you change these styles, update also the legend in modulegraph.md
if self._fromnode.is_file_node() and self._tonode.is_file_node():
properties = ''
elif self._edgetype == EdgeType.intramodule:
properties = ''
elif self._edgetype == EdgeType.test:
- properties = 'color=".33 .8 .8", style=dashed'
+ # TODO: Consider if only some test edges should be made non-constraints
+ properties = 'color=".33 .8 .8", style=dashed, constraint=no'
elif self._edgetype == EdgeType.libimpl:
properties = 'color=".66 .8 .8", style=dashed'
elif self._edgetype == EdgeType.pubimpl:
properties = 'color=black'
elif self._edgetype == EdgeType.legacy:
properties = 'color=grey75'
+ elif self._edgetype == EdgeType.cyclic:
+ properties = 'color=red, constraint=no'
else: # undocumented
properties = 'color=red'
return '{0} -> {1} [{2}]'.format(self._fromnode.get_nodename(),
filenodes[fileobj] = node
return node
- def _create_file_edge(self, fromfile, tofile, filenodes):
- """Create edge between two file objects.
+ def _get_file_edge_type(self, fromfile, tofile):
+ """Get EdgeType for an edge between two file objects.
Determines the type for the edge from the information provided by
gmxtree.
"""
intramodule = (fromfile.get_module() == tofile.get_module())
- is_legacy = not tofile.get_module().is_documented()
+ is_legacy = not tofile.api_type_is_reliable()
if fromfile.get_module() == tofile.get_module():
- edgetype = EdgeType.intramodule
- elif tofile.get_api_type() == DocType.internal:
+ return EdgeType.intramodule
+ elif tofile.get_api_type() == DocType.internal and not tofile.is_public():
if is_legacy:
- edgetype = EdgeType.legacy
+ return EdgeType.legacy
else:
- edgetype = EdgeType.undocumented
+ return EdgeType.undocumented
elif fromfile.is_test_file():
- edgetype = EdgeType.test
+ return EdgeType.test
elif tofile.is_test_file():
- edgetype = EdgeType.undocumented
- elif fromfile.is_source_file() or \
- (fromfile.get_api_type() <= DocType.internal and \
- not fromfile.is_installed()):
- if tofile.get_api_type() == DocType.public:
- edgetype = EdgeType.pubimpl
+ return EdgeType.undocumented
+ elif fromfile.is_module_internal():
+ if tofile.is_public():
+ return EdgeType.pubimpl
elif tofile.get_api_type() == DocType.library:
- edgetype = EdgeType.libimpl
- elif is_legacy or not tofile.is_documented():
- edgetype = EdgeType.legacy
+ return EdgeType.libimpl
+ elif is_legacy:
+ return EdgeType.legacy
+ elif not tofile.is_documented():
+ return EdgeType.undocumented
else:
raise ValueError('Unknown edge type between {0} and {1}'
- .format(fromfile.path, tofile.path))
+ .format(fromfile.get_relpath(), tofile.get_relpath()))
elif fromfile.get_api_type() == DocType.library:
- edgetype = EdgeType.library
- elif fromfile.get_api_type() == DocType.public or fromfile.is_installed():
- if tofile.get_api_type() == DocType.public or \
- tofile.get_documentation_type() == DocType.public or \
- (tofile.is_installed() and not tofile.is_documented()):
- edgetype = EdgeType.public
+ return EdgeType.library
+ elif fromfile.is_public() or fromfile.is_installed():
+ if tofile.is_public() or tofile.is_installed():
+ return EdgeType.public
else:
- edgetype = EdgeType.undocumented
+ return EdgeType.undocumented
+ elif is_legacy:
+ return EdgeType.legacy
else:
raise ValueError('Unknown edge type between {0} and {1}'
- .format(fromfile.path, tofile.path))
+ .format(fromfile.get_relpath(), tofile.get_relpath()))
+
+ def _create_file_edge(self, fromfile, tofile, filenodes):
+ """Create edge between two file objects.
+
+ Determines the type for the edge from the information provided by
+ gmxtree.
+ """
+ edgetype = self._get_file_edge_type(fromfile, tofile)
return Edge(filenodes[fromfile], filenodes[tofile], edgetype)
def _create_file_edges(self, filenodes):
edges.append(edge)
return edges
- def _create_module_node(self, module, filenodes):
- """Create node for a module.
-
- The created node will have all files in the module as its child nodes.
- All created file nodes are added to the filenodes dict.
- """
+ def _get_module_color(self, modulegroup):
+ # If you change these styles, update also the legend in modulegraph.md
+ if modulegroup == 'legacy':
+ return 'fillcolor=grey75'
+ elif modulegroup == 'analysismodules':
+ return 'fillcolor="0 .2 1"'
+ elif modulegroup == 'utilitymodules':
+ return 'fillcolor=".08 .2 1"'
+ elif modulegroup == 'mdrun':
+ return 'fillcolor=".75 .2 1"'
+ return None
+
+ def _create_module_node(self, module):
+ """Create node for a module."""
style = []
properties = []
properties.append('shape=ellipse')
- properties.append('URL="\\ref module_{0}"'.format(module.get_name()))
+ if module.is_documented():
+ properties.append('URL="\\ref {0}"'.format(module.get_name()))
if not module.is_documented():
+ fillcolor = self._get_module_color('legacy')
+ else:
+ fillcolor = self._get_module_color(module.get_group())
+ if fillcolor:
style.append('filled')
- properties.append('fillcolor=grey75')
- elif module.get_group() == 'analysismodules':
- style.append('filled')
- properties.append('fillcolor="0 .2 1"')
- elif module.get_group() == 'utilitymodules':
- style.append('filled')
- properties.append('fillcolor=".08 .2 1"')
- elif module.get_group() == 'mdrun':
- style.append('filled')
- properties.append('fillcolor=".75 .2 1"')
+ properties.append(fillcolor)
rootdir = module.get_root_dir()
if rootdir.has_installed_files():
properties.append('color=".66 .5 1"')
nodename = 'module_' + re.subn(r'[-./]', '_', rootdir.get_relpath())[0]
label = module.get_name()[7:]
node = Node(nodename, label, style, properties)
- for childfile in module.get_files():
- node.add_child(self._create_file_node(childfile, filenodes))
return node
+ def _create_module_edges(self, modulenodes):
+ """Create edges between all module nodes.
+
+ Create edges between module nodes specified in modulenodes from all
+ include dependencies. An edge is created only if both ends of the
+ dependency are in the list of nodes.
+ """
+ edges = []
+ for moduleobj in modulenodes.iterkeys():
+ for dep in moduleobj.get_dependencies():
+ othermodule = dep.get_other_module()
+ if othermodule and othermodule in modulenodes:
+ if dep.is_cycle_suppressed():
+ edgetype = EdgeType.cyclic
+ else:
+ edgetype = max([
+ self._get_file_edge_type(x.get_including_file(), x.get_file())
+ for x in dep.get_included_files()])
+ edge = Edge(modulenodes[moduleobj], modulenodes[othermodule], edgetype)
+ edges.append(edge)
+ return edges
+
def create_modules_graph(self):
"""Create module dependency graph."""
- filenodes = dict()
nodes = []
- modulenodes = []
+ modulenodes = dict()
libgromacsnode = Node('libgromacs', 'libgromacs')
nodes.append(libgromacsnode)
for moduleobj in self._tree.get_modules():
- node = self._create_module_node(moduleobj, filenodes)
+ node = self._create_module_node(moduleobj)
if moduleobj.get_root_dir().get_relpath().startswith('src/gromacs'):
libgromacsnode.add_child(node)
else:
nodes.append(node)
- modulenodes.append(node)
- edges = self._create_file_edges(filenodes)
+ modulenodes[moduleobj] = node
+ edges = self._create_module_edges(modulenodes)
graph = Graph(nodes, edges)
- for node in modulenodes:
- graph.collapse_node(node)
graph.set_options(concentrate=False)
return graph
help='Source tree root directory')
parser.add_option('-B', '--build-root',
help='Build tree root directory')
- parser.add_option('--installed',
- help='Read list of installed files from given file')
+ parser.add_option('--ignore-cycles',
+ help='Set file with module dependencies to ignore in cycles')
parser.add_option('-o', '--outdir', default='.',
help='Specify output directory for graphs')
parser.add_option('-q', '--quiet', action='store_true',
help='Do not write status messages')
options, args = parser.parse_args()
- installedlist = []
- if options.installed:
- with open(options.installed, 'r') as outfile:
- for line in outfile:
- installedlist.append(line.strip())
-
reporter = Reporter(quiet=True)
if not options.quiet:
sys.stderr.write('Scanning source tree...\n')
tree = GromacsTree(options.source_root, options.build_root, reporter)
- tree.set_installed_file_list(installedlist)
+ tree.load_installed_file_list()
if not options.quiet:
sys.stderr.write('Reading source files...\n')
tree.scan_files()
+ if options.ignore_cycles:
+ tree.load_cycle_suppression_list(options.ignore_cycles)
if not options.quiet:
sys.stderr.write('Reading Doxygen XML files...\n')
tree.load_xml(only_files=True)
--- /dev/null
+#!/usr/bin/python
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+"""Include directive sorter for GROMACS.
+
+This module implements an #include directive sorter for GROMACS C/C++ files.
+It allows (in most cases) automatically sorting includes and formatting
+the paths to use either relative paths or paths relative to src/.
+It groups includes in groups of related headers, sorts the headers
+alphabetically within each block, and inserts empty lines in between.
+It can be run as a standalone script, in which case it requires an up-to-date
+list of installed headers and Doxygen XML documentation to be present in the
+build tree. It can also be imported as a module to be embedded in other
+scripts. In the latter case, the IncludeSorter provides the main interface.
+
+The sorting assumes some conventions (e.g., that system headers are included
+with angle brackets instead of quotes). Generally, these conventions are
+checked by the check-source.py script.
+"""
+
+import os.path
+import re
+import sys
+
+class IncludeGroup(object):
+
+ """Enumeration type for grouping includes."""
+
+ def __init__(self, value):
+ """Initialize a IncludeGroup instance.
+
+ IncludeGroup.{main,system_c,...} should be used outside the
+ class instead of calling the constructor.
+ """
+ self._value = value
+
+ def __cmp__(self, other):
+ """Order include groups in the desired order."""
+ return cmp(self._value, other._value)
+
+# gmxpre.h is always first
+IncludeGroup.pre = IncludeGroup(0)
+# "main" include file for the source file is next
+IncludeGroup.main = IncludeGroup(1)
+# config.h is next, if present, to keep its location consistent
+IncludeGroup.config = IncludeGroup(2)
+# Followed by system headers, with C first and C++ following
+IncludeGroup.system_c = IncludeGroup(3)
+IncludeGroup.system_c_cpp = IncludeGroup(4)
+IncludeGroup.system_cpp = IncludeGroup(5)
+# System headers not in standard C/C++ are in a separate block
+IncludeGroup.system_other = IncludeGroup(6)
+# src/external/ contents that are included with quotes go here
+IncludeGroup.nonsystem_other = IncludeGroup(7)
+# Other GROMACS headers
+IncludeGroup.gmx_general = IncludeGroup(8)
+# This group is for shared (unit) testing utilities
+IncludeGroup.gmx_test = IncludeGroup(9)
+# This group is for headers local to the including file/module
+IncludeGroup.gmx_local = IncludeGroup(10)
+
+class GroupedSorter(object):
+
+ """Grouping and formatting logic for #include directives.
+
+ This class implements the actual logic that decides how includes are
+ grouped and sorted, and how they are formatted."""
+
+ # These variables contain the list of system headers for various blocks
+ _std_c_headers = ['assert.h', 'ctype.h', 'errno.h', 'float.h',
+ 'inttypes.h', 'limits.h', 'math.h', 'signal.h', 'stdarg.h',
+ 'stddef.h', 'stdint.h', 'stdio.h', 'stdlib.h', 'string.h',
+ 'time.h']
+ _std_c_cpp_headers = ['c' + x[:-2] for x in _std_c_headers]
+ _std_cpp_headers = ['algorithm', 'deque', 'exception', 'fstream',
+ 'iomanip', 'ios', 'iosfwd', 'iostream', 'istream', 'iterator',
+ 'limits', 'list', 'map', 'memory', 'new', 'numeric', 'ostream',
+ 'regex', 'set', 'sstream', 'stdexcept', 'streambuf', 'string', 'strstream',
+ 'typeinfo', 'vector', 'utility']
+
+ def __init__(self, style='pub-priv', absolute=False):
+ """Initialize a sorted with the given style."""
+ if style == 'single-group':
+ self._local_group = 'none'
+ elif style == 'pub-priv':
+ self._local_group = 'private'
+ else:
+ self._local_group = 'local'
+ if absolute:
+ self._abspath_main = True
+ self._abspath_local = True
+ else:
+ self._abspath_main = False
+ self._abspath_local = False
+
+ def _get_path(self, included_file, group, including_file):
+ """Compute include path to use for an #include.
+
+ The path is made either absolute (i.e., relative to src/), or
+ relative to the location of the including file, depending on the group
+ the file is in.
+ """
+ use_abspath = including_file is None or group is None
+ if not use_abspath:
+ if group in (IncludeGroup.gmx_general, IncludeGroup.gmx_test):
+ use_abspath = True
+ elif group == IncludeGroup.main and self._abspath_main:
+ use_abspath = True
+ elif group == IncludeGroup.gmx_local and self._abspath_local:
+ use_abspath = True
+ if not use_abspath:
+ fromdir = os.path.dirname(including_file.get_abspath())
+ relpath = os.path.relpath(included_file.get_abspath(), fromdir)
+ if not relpath.startswith('..'):
+ return relpath
+ path = included_file.get_relpath()
+ assert path.startswith('src/')
+ return path[4:]
+
+ def _get_gmx_group(self, including_file, included_file):
+ """Determine group for GROMACS headers.
+
+ Helper function to determine the group for an #include directive
+ when the #include is in one of the gmx_* groups (or in the main group).
+ """
+ main_header = including_file.get_main_header()
+ if main_header and main_header == included_file:
+ return IncludeGroup.main
+ if included_file.get_directory().get_name() == 'testutils':
+ return IncludeGroup.gmx_test
+ if including_file.get_directory().contains(included_file):
+ if self._local_group == 'local':
+ return IncludeGroup.gmx_local
+ if self._local_group == 'private':
+ if included_file.api_type_is_reliable() \
+ and included_file.is_module_internal():
+ return IncludeGroup.gmx_local
+ if not included_file.api_type_is_reliable() \
+ and including_file.get_relpath().startswith('src/programs'):
+ return IncludeGroup.gmx_local
+ if included_file.is_test_file():
+ return IncludeGroup.gmx_test
+ return IncludeGroup.gmx_general
+
+ def get_sortable_object(self, include):
+ """Produce a sortable, opaque object for an include.
+
+ Includes are sorted by calling this function for each #include object,
+ and sorting the list made up of these objects (using the default
+ comparison operators). Each element from the sorted list is then
+ passed to format_include(), which extracts information from the opaque
+ object and formats the #include directive for output.
+ """
+ included_file = include.get_file()
+ if not included_file:
+ path = include.get_included_path()
+ if path in self._std_c_headers:
+ group = IncludeGroup.system_c
+ elif path in self._std_c_cpp_headers:
+ group = IncludeGroup.system_c_cpp
+ elif path in self._std_cpp_headers:
+ group = IncludeGroup.system_cpp
+ else:
+ group = IncludeGroup.system_other
+ elif included_file.is_external():
+ group = IncludeGroup.nonsystem_other
+ if 'external/' in include.get_included_path():
+ path = self._get_path(included_file, group, None)
+ else:
+ path = include.get_included_path()
+ elif included_file.get_name() == 'gmxpre.h':
+ group = IncludeGroup.pre
+ path = self._get_path(included_file, group, None)
+ elif included_file.get_name() == 'config.h':
+ group = IncludeGroup.config
+ path = self._get_path(included_file, group, None)
+ else:
+ including_file = include.get_including_file()
+ group = self._get_gmx_group(including_file, included_file)
+ path = self._get_path(included_file, group, including_file)
+ return (group, os.path.split(path), include)
+
+ def format_include(self, obj, prev):
+ """Format an #include directive after sorting."""
+ result = []
+ if prev:
+ if prev[0] != obj[0]:
+ # Print empty line between groups
+ result.append('\n')
+ elif prev[1] == obj[1]:
+ # Skip duplicates
+ return result
+ include = obj[2]
+ line = include.get_full_line()
+ include_re = r'^(?P<head>\s*#\s*include\s+)["<][^">]*[">](?P<tail>.*)$'
+ match = re.match(include_re, line)
+ assert match
+ if include.is_system():
+ path = '<{0}>'.format(os.path.join(obj[1][0], obj[1][1]))
+ else:
+ path = '"{0}"'.format(os.path.join(obj[1][0], obj[1][1]))
+ result.append('{0}{1}{2}\n'.format(match.group('head'), path, match.group('tail')))
+ return result
+
+class IncludeSorter(object):
+
+ """High-level logic for sorting includes.
+
+ This class contains the high-level logic for sorting include statements.
+ The actual ordering and formatting the includes is delegated to a sort method
+ (see GroupedSorter) to keep things separated.
+ """
+
+ def __init__(self, sortmethod=None, quiet=True):
+ """Initialize the include sorter with the given sorter and options."""
+ if not sortmethod:
+ sortmethod = GroupedSorter()
+ self._sortmethod = sortmethod
+ self._quiet = quiet
+ self._changed = False
+
+ def _sort_include_block(self, block, lines):
+ """Sort a single include block.
+
+ Returns a new list of lines for the block.
+ If anything is changed, self._changed is set to True, and the caller
+ can check that."""
+ includes = map(self._sortmethod.get_sortable_object, block.get_includes())
+ includes.sort()
+ result = []
+ prev = None
+ current_line_number = block.get_first_line()-1
+ for include in includes:
+ newlines = self._sortmethod.format_include(include, prev)
+ result.extend(newlines)
+ if not self._changed:
+ for offset, newline in enumerate(newlines):
+ if lines[current_line_number + offset] != newline:
+ self._changed = True
+ break
+ current_line_number += len(newlines)
+ prev = include
+ return result
+
+ def sort_includes(self, fileobj):
+ """Sort all includes in a file."""
+ lines = fileobj.get_contents()
+ # Format into a list first:
+ # - avoid bugs or issues in the script truncating the file
+ # - can check whether anything was changed before touching the file
+ newlines = []
+ prev = 0
+ self._changed = False
+ for block in fileobj.get_include_blocks():
+ newlines.extend(lines[prev:block.get_first_line()-1])
+ newlines.extend(self._sort_include_block(block, lines))
+ # The returned values are 1-based, but indexing here is 0-based,
+ # so an explicit +1 is not needed.
+ prev = block.get_last_line()
+ if self._changed:
+ if not self._quiet:
+ sys.stderr.write('{0}: includes reformatted\n'.format(fileobj.get_relpath()))
+ newlines.extend(lines[prev:])
+ with open(fileobj.get_abspath(), 'w') as fp:
+ fp.write(''.join(newlines))
+
+ def check_sorted(self, fileobj):
+ """Check that includes within a file are sorted."""
+ # TODO: Make the checking work without full contents of the file
+ lines = fileobj.get_contents()
+ self._changed = False
+ for block in fileobj.get_include_blocks():
+ self._sort_include_block(block, lines)
+ return not self._changed
+
+def main():
+ """Run the include sorter script."""
+ import os
+ import sys
+
+ from optparse import OptionParser
+
+ from gmxtree import GromacsTree
+ from reporter import Reporter
+
+ parser = OptionParser()
+ parser.add_option('-S', '--source-root',
+ help='Source tree root directory')
+ parser.add_option('-B', '--build-root',
+ help='Build tree root directory')
+ parser.add_option('-F', '--files',
+ help='Specify files to sort')
+ parser.add_option('-q', '--quiet', action='store_true',
+ help='Do not write status messages')
+ # This is for evaluating different options; can be removed from the final
+ # version.
+ parser.add_option('-s', '--style', type='choice', default='pub-priv',
+ choices=('single-group', 'pub-priv', 'pub-local'),
+ help='Style for Gromacs includes')
+ parser.add_option('--absolute', action='store_true',
+ help='Write all include paths relative to src/')
+ options, args = parser.parse_args()
+
+ filelist = args
+ if options.files:
+ if options.files == '-':
+ lines = sys.stdin.readlines()
+ else:
+ with open(options.files, 'r') as fp:
+ lines = fp.readlines()
+ filelist.extend([x.strip() for x in lines])
+
+ reporter = Reporter(quiet=True)
+
+ if not options.quiet:
+ sys.stderr.write('Scanning source tree...\n')
+ tree = GromacsTree(options.source_root, options.build_root, reporter)
+ tree.load_installed_file_list()
+ files = []
+ for filename in filelist:
+ fileobj = tree.get_file(os.path.abspath(filename))
+ if not fileobj:
+ sys.stderr.write('warning: ignoring unknown file {0}\n'.format(filename))
+ continue
+ files.append(fileobj)
+ if not options.quiet:
+ sys.stderr.write('Reading source files...\n')
+ tree.scan_files(only_files=files, keep_contents=True)
+ extfiles = set(files)
+ for fileobj in files:
+ for included_file in fileobj.get_includes():
+ other_file = included_file.get_file()
+ if other_file:
+ extfiles.add(other_file)
+ if not options.quiet:
+ sys.stderr.write('Reading Doxygen XML files...\n')
+ tree.load_xml(only_files=extfiles)
+
+ if not options.quiet:
+ sys.stderr.write('Sorting includes...\n')
+
+ sorter = IncludeSorter(GroupedSorter(options.style, options.absolute), options.quiet)
+
+ for fileobj in files:
+ sorter.sort_includes(fileobj)
+
+if __name__ == '__main__':
+ main()
Documentation flavors
=====================
+
The \Gromacs source tree is set up to produce three different levels of Doxygen
documentation:
You can run Doxygen directly with one of the generated files (all output will
be produced under the current working directory), or build one of the
-`doc-user`, `doc-lib`, and `doc-full` targets. The targets run Doxygen in a
-quieter mode and only show the warnings if there were any, and put the output
-under `docs/html/doxygen/` in the build tree, so that the Doxygen build
-cooperates with the broader `webpage` target. The `doc-all` target builds all three
-targets with less typing.
+`doxygen-user`, `doxygen-lib`, and `doxygen-full` targets. The targets run
+Doxygen in a quieter mode and only show the warnings if there were any, and put
+the output under `docs/html/doxygen/` in the build tree, so that the Doxygen
+build cooperates with the broader `webpage` target.
+The `doxygen-all` target builds all three targets with less typing.
The generated documentation is put under `html-user/`, `html-lib/`, and/or
`html-full/`. Open `index.xhtml` file from one of
figures will be missing from the documentation.
-General guidelines for Doxygen markup
+General guidelines for Doxygen markup {#section_doxygen_guidelines}
=====================================
Doxygen provides quite a few different alternative styles for documenting the
documentation, as well as how \Gromacs uses Doxygen groups to organize the
documentation.
+Some consistency checks are done automatically using custom scripts.
+See \ref page_dev_gmxtree for details.
+
Controlling documentation visibility
------------------------------------
separate page in the generated documentation can only belong to one group;
in such a case, the module group is preferred over the API group.
-Automatic dependency checking
------------------------------
-
-The build system provides a `doc-check` target that automatically checks some
-aspects of the documentation, as well as checking that header files are
-actually used according to their API specifications (i.e., an internal headers
-are not included from other modules). The checks depend on correct usage of
-the commands listed above, in particular the visibility and API definitions in
-file-level comments. These checks also provide some level of enforcement for
-rules about dependencies between the modules, but currently the checks are not
-run automatically.
-
-The checker currently checks for a few different types of issues:
-* For all Doxygen documentation (currently does not apply for members within
- anonymous namespaces or members that do not appear in the documentation):
- * If a member has documentation, it should have a brief description.
- * A note is issued for in-body documentation for functions, since this is
- ignored by our current settings.
- * If a class has documentation, it should have public documentation only if
- it appears in an installed header.
- * If a class and its containing file has documentation, the class
- documentation should not be visible if the file documentation is not.
-* For all files:
- * Consistent usage of
-
- #include "..." // This should be used for Gromacs headers
-
- and
-
- #include <...> // This should be used for system and external headers
-
- * Installed headers must not include non-installed headers, and must include
- all other \Gromacs headers using relative paths so that they resolve
- correctly also when installed.
-* For documented files:
- * Installed headers should have public documentation, and other files should
- not.
- * The API level specified for a file should not be higher than where its
- documentation is visible. For example, only publicly documented headers
- should be specified as part of the public API.
- * If an \c \\ingroup module_foo exists, it should match the subdirectory
- that the file is actually part of in the file system.
- * If a \c \\defgroup module_foo exists for the subdirectory where the file is,
- the file should contain \c \\ingroup module_foo.
- * Files should not include other files whose documentation visibility is
- lower (if the included file is not documented, the check is skipped).
-* For files that are part of documented modules
- (\c \\defgroup module_foo exists for the subdirectory):
- * Such files should not be included from outside their module if they are
- undocumented or are not specified as part of library or public API.
-
-The checker is based on extracting the Doxygen documentation in XML format.
-This information is then read using a Python script, and combined with
-information extracted from the file system and knowledge about the \Gromacs
-source tree layout. The Python scripts are in the `doxygen/` folder.
-In addition to printing the issues, they are also written into
-`doxygen/doxygen-check.log` for later inspection.
-
-The script is not currently perfect (either because of unfinished
-implementation, or because Doxygen bugs or incompleteness of the Doxygen XML
-output), and the current code also contains issues that the script detects, but
-the authors have not fixed. To allow the script to still be used,
-`doxygen/suppressions.txt` contains a list of issues that are filtered out from
-the report. The syntax is simple:
-
- <file>: <text>
-
-where `<file>` is a path to the file that reports the message, and `<text>` is
-the text reported. Both support `*` as a wildcard. If `<file>` is empty, the
-suppression matches only messages that do not have an associated file.
-`<file>` is matched against the trailing portion of the file name to make it
-work even though the script reports absolute paths.
-Empty lines and lines starting with `#` are ignored.
-
-To add suppression for an issue, the line that reports the issue can be copied
-into `suppressions.txt`, and the line number (if any) removed. If the
-issue does not have a file name (or a pseudo-file) associated, a leading `:`
-must be added. To cover many similar issues, parts of the line can then be
-replaced with wildcards.
-
-For some false positives from the script, the suppression mechanism is the
-easiest way to silence the script, but otherwise the goal would be to minimize
-the number of suppressions.
-
-As a side effect, the XML extraction makes Doxygen parse all comments in the
-code, even if they do not appear in the documentation. This can reveal latent
-issues in the comments, like invalid Doxygen syntax. The messages from the XML
-parsing are stored in `docs/doxygen/doxygen-xml.log` in the build tree, similar to
-other Doxygen runs.
-
-The `doc-check` target requires Python 2.7 (other versions may work, but have
-not been tested).
-
-Include dependency graphs
--------------------------
-
-The build system also provides an `dep-graphs` target that generates include
-dependency graphs with some additional annotations.
-One graph is produced that shows all the modules under `src/gromacs/`, and
-their include dependencies. Additionally, a file-level graph is produced for
-each module, showing the include dependencies within that module. Currently,
-these are mostly for eye candy, but they can also be used for analyzing
-problematic dependencies to clean up the architecture.
-The output is put in `doxygen/depgraphs/` in the build tree.
-
-As with `doc-check`, Python 2.7 is required (other versions may work, but have
-not been tested). To get `.png` versions of the graphs, `graphviz` is
-additionally required.
-
-### Module graph ###
-
-The graph is written into `module-deps.dot.png`.
-
-Node colors:
-<dl>
-<dt>gray background</dt>
-<dd>undocumented module</dd>
-<dt>orange background</dt>
-<dd>documented utility modules</dd>
-<dt>red background</dt>
-<dd>documented analysis modules</dd>
-<dt>violet background</dt>
-<dd>documented MD execution modules</dd>
-<dt>light blue border</dt>
-<dd>module contains public API (installed) headers</dd>
-</dl>
-
-Edge colors (an edge with a certain color indicates that types above it in the
-list are not present):
-<dl>
-<dt>red</dt>
-<dd>invalid dependency</dd>
-<dt>gray</dt>
-<dd>legacy dependency
-(dependency on undocumented file, or to undocumented directories)</dd>
-<dt>solid black</dt>
-<dd>public header depends on the other module</dd>
-<dt>solid blue</dt>
-<dd>library header depends on the other module</dd>
-<dt>dashed blue</dt>
-<dd>source file depends on library header in the other module</dd>
-<dt>dashed black</dt>
-<dd>source file depends on public header in the other module</dd>
-<dt>dashed green</dt>
-<dd>test file depends on the other module</dd>
-</dl>
-
-### File graph ###
-
-The graphs are written to <em>module_name</em>`-deps.dot.png`.
-
-Node colors:
-<dl>
-<dt>light blue</dt>
-<dd>public API (installed) headers</dd>
-<dt>dark blue</dt>
-<dd>library API headers</dd>
-<dt>gray</dt>
-<dd>source files</dd>
-<dt>light green</dt>
-<dd>test files</dd>
-<dt>white</dt>
-<dd>other files</dd>
-</dl>
-
-Each edge signifies an include dependency; there is no additional information
-currently included.
Documenting specific code constructs
====================================
should be referenced once using \c \\subpage. `mainpage.md` is the root of the
hierarchy.
-If you need to exclude a page from the public API docs, you need to add it to
-an exclude list in `Doxyfile-user.cmakein`, and ensure that there are no
-references to the page from public API documentation. \c \\if `libapi` can be
-used to add references in content that is otherwise public.
+There are two subdirectories, `user/` and `lib/`, determining the highest
+documentation level where the page appears. If you add pages to `lib/`, ensure
+that there are no references to the page from public API documentation.
+\c \\if `libapi` can be used to add references in content that is otherwise
+public.
Generally, the pages should be on a high enough level and provide overview
content that is useful enough such that it is not necessary to exclude them
from the library API documentation.
--- /dev/null
+Module dependency graph {#page_modulegraph}
+=======================
+
+The graph below shows the dependencies between the source code modules,
+computed from include statements in the code.
+For documented modules (those that do not have a gray background), clicking on
+the module takes you to the module documentation.
+Legend for the graph can be found below the graph.
+
+\ifnot xml
+\dotfile module-deps.dot
+\endif
+
+Legend
+======
+
+The graph below annotates the colors and line styles used in the module
+dependency graph above. More detailed textual annotation is below the graph.
+
+\dot
+digraph legend {
+ node [fontname="FreeSans",fontsize=10,height=.2,shape=box]
+ edge [fontname="FreeSans",fontsize=10]
+ rankdir = "LR"
+ subgraph cluster_nodes {
+ label = "Nodes"
+ legacy [label="undocumented", fillcolor=grey75, style="filled"]
+ analysis [label="analysis", fillcolor="0 .2 1", style="filled"]
+ utility [label="utility", fillcolor=".08 .2 1", style="filled"]
+ mdrun [label="mdrun", fillcolor=".75 .2 1", style="filled"]
+ installed [label="installed", color=".66 .5 1", penwidth=3]
+ }
+ subgraph cluster_edges {
+ label = "Edges"
+ node [label="<any>"]
+ invalid1 -> invalid2 [label="invalid", color=red]
+ legacy1 -> legacy2 [label="legacy", color=grey75]
+ legacy2 [label="undoc"]
+ public1 -> public2 [label="public", color=black]
+ public1 [label="public"]
+ public2 [label="public"]
+ library1 -> library2 [label="library", color=".66 .8 .8"]
+ library1 [label="library"]
+ pubimpl1 -> pubimpl2 [color=black, style=dashed]
+ pubimpl1 [label="internal"]
+ pubimpl2 [label="public"]
+ libimpl1 -> libimpl2 [color=".66 .8 .8", style=dashed]
+ libimpl1 [label="internal"]
+ libimpl2 [label="library"]
+ test1 -> test2 [label="test", color=".33 .8 .8", style=dashed]
+ test1 [label="test"]
+ }
+ legacy -> invalid1 [style="invis"]
+}
+\enddot
+
+Node colors:
+<dl>
+<dt>gray background</dt>
+<dd>undocumented module</dd>
+<dt>orange background</dt>
+<dd>documented utility modules</dd>
+<dt>red background</dt>
+<dd>documented analysis modules</dd>
+<dt>violet background</dt>
+<dd>documented MD execution modules</dd>
+<dt>light blue border</dt>
+<dd>module contains public API (installed) headers</dd>
+</dl>
+
+Edge colors (an edge with a certain color indicates that types above it in the
+list are not present):
+<dl>
+<dt>red</dt>
+<dd>invalid dependency</dd>
+<dt>gray</dt>
+<dd>legacy dependency
+(dependency on undocumented file, or to undocumented directories)</dd>
+<dt>solid black</dt>
+<dd>public header depends on the other module</dd>
+<dt>solid blue</dt>
+<dd>library header depends on the other module</dd>
+<dt>dashed blue</dt>
+<dd>source file depends on library header in the other module</dd>
+<dt>dashed black</dt>
+<dd>source file depends on public header in the other module</dd>
+<dt>dashed green</dt>
+<dd>test file depends on the other module</dd>
+</dl>
The %main() method also catches all exceptions, and if one is caught, prints an
error message and terminates the program cleanly.
-Command line manager
+Command line modules
+====================
+
+All modules within the wrapper binary are implemented as classes that implement
+the gmx::CommandLineModuleInterface interface. There is generally some helper
+class in between:
+ * General C++ modules typically use gmx::Options for their command-line
+ handling. Instead of each module implementing parsing and help separately
+ with identical code, they implement gmx::CommandLineOptionsModuleInterface
+ instead. The framework then provides a bridge class that contains the
+ common code and wraps gmx::CommandLineOptionsModuleInterface into a
+ gmx::CommandLineModuleInterface.
+ * For C++ trajectory analysis modules, there is a general implementation for
+ running the gmx::TrajectoryAnalysisModule subclasses in cmdlinerunner.cpp.
+ * For old C-style %main() functions, see \ref section_wrapperbinary_cmain.
+
+Command line manager {#section_wrapperbinary_manager}
====================
The core of the wrapper binary is the gmx::CommandLineModuleManager::run()
method. This method:
- 1. Checks whether the binary is invoked through a symlink. If it is, it
- searches the registered modules for names matching the name of the symlink
- (with certain prefixes in the symlink name ignored). If a match is found,
- it continues as if the command was invoked as `gmx` _module_ `...`, where
- _module_ is the name of the found module and `...` are the rest of the
- arguments.
- 2. Parses the command line arguments before the module name as arguments to
+ 1. Parses the command line arguments before the module name as arguments to
the wrapper binary. Some arguments such as `-h` and `-version` cause rest
of the command (the module name and all that follows) to be ignored.
- 3. If a module is specified, also checks the command line arguments after the
+ 2. If a module is specified, also checks the command line arguments after the
module name for the options understood by the wrapper binary, such as `-h`
and `-version` (see below for details of how `-h` works). Any such options
are handled by the manager and removed from the command line for further
processing.
- 4. Print the startup header (contents of which can be controlled by the
+ 3. Print the startup header (contents of which can be controlled by the
command line options).
- 5. If a command line option requests termination after the startup header
+ 4. If a command line option requests termination after the startup header
(such as `-version`), return.
- 6. Passes control to the selected module. If there is no module specified,
+ 5. Passes control to the selected module. If there is no module specified,
the help module is invoked (see below).
- 7. Print a quote at the end, and return the exit code from the module.
+ 6. Print a quote at the end, and return the exit code from the module.
Command line help
-----------------
these partial HTML files.
The final HTML help is produced in `share/html/final/`.
-Handling C %main() functions
+Handling C %main() functions {#section_wrapperbinary_cmain}
----------------------------
Many pre-5.0 modules are still implemented as a function with a C %main()
\ref page_analysisframework
*/
-/*!
+/*! \libinternal
\defgroup group_mdrun Modules for simulation functionality
\brief
Modules used in running simulations with mdrun
classes. These are not meant for direct user access, but typically reside
in public headers because of implementation reasons.
*/
+
+/*!
+\file share/template/template.cpp
+\brief Template code for writing analysis programs.
+
+See \ref page_analysistemplate for more information.
+ */
+
+/*!
+\example template.cpp
+\brief Template code for writing analysis programs.
+
+See \ref page_analysistemplate for more information.
+ */
self._messages = []
self._filters = []
self._quiet = quiet
+ self._had_warnings = False
def _write(self, message):
"""Implement actual message writing."""
sys.stderr.write(wholemsg)
if self._logfp:
self._logfp.write(wholemsg)
+ self._had_warnings = True
def _report(self, message):
"""Handle a single reporter message."""
text = 'warning: unused filter: ' + filterobj.get_text()
self._write(Message(text))
+ def had_warnings(self):
+ """Return true if any warnings have been reported."""
+ return self._had_warnings
+
def close_log(self):
"""Close the log file if one exists."""
assert not self._messages
self._report(Message('warning: ' + message, details,
location=entity.get_reporter_location()))
+ def cyclic_issue(self, message, details=None):
+ """Report a cyclic dependency issue."""
+ self._report(Message('warning: ' + message, details))
+
def doc_error(self, entity, message):
"""Report an issue in documentation."""
self._report(Message('error: ' + entity.get_name() + ': ' + message,
-# These look like bugs in Doxygen 1.8.5
-src/gromacs/gmxlib/gmx_cpuid.c: warning: duplicate declarations for a member 'gmx_cpuid_vendor'
-src/gromacs/gmxlib/gmx_cpuid.c: warning: duplicate declarations for a member 'gmx_cpuid_x86_smt'
-src/gromacs/gmxlib/gmx_cpuid.c: warning: duplicate declarations for a member 'gmx_cpuid_simd_suggest'
-
# The script is currently a bit too eager
share/template/template.cpp: error: source file documentation appears outside full documentation
+# The parser in the script is not clever enough
+src/gromacs/version.h: warning: includes local file as <gromacs/version.h>
+
+# These are OK
+src/gromacs/math/vec.h: warning: installed header includes non-installed "config.h"
+src/gromacs/linearalgebra/eigensolver.c: warning: should include "config.h"
+src/gromacs/linearalgebra/gmx_arpack.c: warning: should include "config.h"
+src/gromacs/linearalgebra/gmx_blas/*: warning: does not include "gmxpre.h" first
+src/gromacs/linearalgebra/gmx_blas/*: warning: should include "config.h"
+src/gromacs/linearalgebra/gmx_lapack/*: warning: does not include "gmxpre.h" first
+src/gromacs/linearalgebra/gmx_lapack/*: warning: should include "config.h"
+src/gromacs/utility/baseversion-gen.c: warning: does not include "gmxpre.h" first
# This module name doesn't really fall into any currently used pattern; needs some thought
: error: no matching directory for module: module_mdrun_integration_tests
# These would be nice to fix, but can wait for later
-*: warning: includes local file as <config.h>
src/gromacs/gmxlib/nonbonded/nb_kernel_*/*: warning: included file "gromacs/simd/math_x86_*.h" is not documented as exposed outside its module
+src/gromacs/gmxlib/nonbonded/nb_kernel_*/*: warning: includes "config.h" unnecessarily
+src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.c: warning: includes "config.h" unnecessarily
+src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c: warning: includes "config.h" unnecessarily
+src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c: warning: includes "config.h" unnecessarily
+src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h: warning: should include "config.h"
+src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c: warning: includes "config.h" unnecessarily
# These are specific to Folding@Home, and easiest to suppress here
*: warning: includes non-local file as "corewrap.h"
-src/config.h.cmakein: warning: includes non-local file as "swindirect.h"
-
-# These are limitations in the current script
-src/gromacs/utility/gmx_header_config.h: warning: includes non-local file as "gmx_header_config_gen.h"
+src/gmxpre.h: warning: includes non-local file as "swindirect.h"
</dd>
\endif
</dl>
+\if libapi
+\subpage page_modulegraph
+\endif
Organization under `src/gromacs/`
---------------------------------
\endif
When compiling, the include search path is set to `src/`. This means that
-source files include headers as
+files include headers as
#include "gromacs/<module>/<file>.h"
#include "<file>.h"
-Header files include other headers using
-
- #include "../<othermodule>/<file>.h"
-
-because relative paths work best for installed headers. For non-installed
-headers, the path relative to `src/` is sometimes also used.
-
For historical reasons, there are directories `src/gromacs/gmxana/`,
`src/gromacs/gmxlib/`, `src/gromacs/mdlib/`, and `src/gromacs/gmxpreprocess/`
that do not follow the above rules. The installed headers for these are in
`src/gromacs/legacyheaders/`. The aim is to gradually get rid of these
directories and move code into proper modules.
-For similar historical reasons, the include path also includes
-`src/gromacs/legacyheaders/`. It is preferred that new code does not depend on
-this.
-
Documentation organization
==========================
Provides general guidance for writing software that uses the \Gromacs
library.
\if libapi
- - \subpage page_doxygen <br/>
- Provides an overview and some instructions for using Doxygen to document the
- source code.
- - \subpage page_unittesting <br/>
- Provides an overview of unit testing in \Gromacs.
- \subpage page_wrapperbinary <br/>
Provides an overview of how the `gmx` wrapper binary is implemented.
- \subpage page_simd <br/>
\endif
This list will hopefully expand over time.
+
+\if libapi
+Additionally, a separate section contains a \subpage page_devmanual, which provides
+resources for developers, such as and documentation for development-time tools
+and guidelines.
+\endif
--- /dev/null
+Using \Gromacs as a library {#page_usinglibrary}
+===========================
+
+Getting started
+===============
+
+The \Gromacs library (`libgromacs`) provides a few different alternatives for
+using it. These are listed here from the highest level of abstraction to the
+low-level functions.
+ - If you are writing a trajectory analysis tool, please see
+ \ref page_analysisframework. \ref page_analysistemplate should contain
+ all the ingredients to get started.
+ If you have an existing tool written using the analysis template from 4.5 or
+ 4.6 (using the selection engine added in 4.5), you need to do some
+ conversion work to get this work with the new template. This is mostly
+ straightforward, but requires some studying to understand the new framework.
+ - If you are writing a command line tool for some other purpose, you can use
+ the facilities provided by \ref module_commandline. There are a few
+ different alternatives, depending on how much control you want to give
+ \Gromacs:
+ - For C++ code, you can implement gmx::CommandLineOptionsModuleInterface and
+ use gmx::runCommandLineModule() to execute it. This interface assumes
+ the use of the gmx::Options mechanism for declaring command-line options
+ (see \ref module_options).
+ For a lower-level interface, gmx::CommandLineModuleInterface can be used,
+ but this requires you to implement `-h` output and command-line parsing
+ yourself (possibly using classes that \Gromacs provides).
+ - For C code, you can use gmx_run_cmain() to wrap an existing C main
+ method. The only constraint on the provided main method is that it
+ should use parse_common_args() for argument processing.
+ This approach should allow you to convert existing C tools written
+ against pre-5.0 \Gromacs (e.g., using the analysis template from 4.0 or
+ earlier) to the new version.
+ - If you want more control (for example, you do not want the default
+ command line options added by \Gromacs), you can directly initialize
+ \Gromacs using gmx::initForCommandLine() before calling other \Gromacs
+ routines. This allows you to write your own handling for command line
+ options from scratch. This is also discussed in \ref module_commandline.
+ - For most control, you can use gmx::init() to do basic initialization, create
+ your own implementation for gmx::ProgramContextInterface, and set that using
+ gmx::setProgramContext(). This allows you to customize how the \Gromacs
+ library shows the name of the program in messages, as well as how it locates
+ its own data files.
+
+If these do not fit your needs, you may need to modify the \Gromacs source code
+yourself. In particular, it is currently relatively difficult to extend the
+functionality of `mdrun` without modifying the source code directly.
+If you think that some particular API would be necessary for your work, and
+think that it would be easy to expose, please drop a line on the
+`gmx-developers` mailing list, or contribute the necessary changes on
+http://gerrit.gromacs.org/.
+
+Linking against `libgromacs`
+============================
+
+\Gromacs is a bit picky on how the headers need to be used: depending on
+compilation options used for \Gromacs, some preprocessor defines may need to be
+set, the required include path may also depend on compilation options, and some
+extra libraries may need to be linked. You will also likely need to use the
+same compiler (or sufficiently similar one that uses the same standard library)
+that was used to compile \Gromacs.
+
+To manage this more easily, \Gromacs provides two mechanisms for getting the
+correct flags for compilation and linking against the \Gromacs library:
+ - `pkg-config`: \Gromacs installs `libgromacs.pc` file (suffixed with the
+ library suffix) for use with `pkg-config` if that is present on the system.
+ Sourcing `GMXRC` adjusts the `pkg-config` search path such that these files
+ are found automatically.
+ See `Makefile.pkg` installed with the analysis template for one example of
+ how to use it (to use it with a differently suffixed \Gromacs, just replace
+ `libgromacs` with `libgromacs`<em>_suffix</em> in the `pkg-config` calls).
+ - CMake package configuration files and a find module that allow
+ `find_package(GROMACS)` to work. See below for details about how to use
+ this in CMake. Sourcing `GMXRC` sets an environment variable that allows
+ CMake to find the configuration file automatically.
+ See `CMakeLists.txt` installed with the analysis template for one example of
+ how to use it.
+
+These mechanisms are currently provided on a best-effort basis, but are not
+routinely tested on a wide range of configurations. Please report any issues
+with details of how \Gromacs was built so that the mechanism can be improved.
+Known issues:
+ - `pkg-config` files are not relocatable, i.e., they hard-code the
+ installation prefix as an absolute path.
+ - Installing both static and shared libraries with the same suffix to the same
+ installation prefix is guaranteed to work only if both are built with
+ exactly the same configuration options (except for `BUILD_SHARED_LIBS`) from
+ exactly the same version. There are several files that are shared between
+ the installations in such a case, and the latter installation will overwrite
+ those from the former.
+ - Further, if both static and shared libraries have been installed in the past
+ to a prefix, then future installations to the same prefix should also
+ install both static and shared libraries. Otherwise, some obsolete CMake
+ package configuration files will be left behind which can lead to finding
+ the old library. Alternatively, you can delete `share/cmake/` from the
+ installation directory before doing the install.
+ - If a mechanism other than the CMake-generated `install` target is used to
+ install \Gromacs over an existing installation, and the build type (e.g.,
+ Release vs.\ Debug) does not match what was previously installed, some
+ obsolete CMake import target definition files are left behind in
+ `share/cmake/`, and may cause failures whey trying to use the package
+ configuration files.
+ - If \Gromacs is built with `GMX_BUILD_OWN_FFTW=ON`, the CMake-generated
+ import definitions for `libgromacs` reference a `gmxfftw` target that was
+ used in the build to reference the `fftw` library. As this library only
+ exists in the \Gromacs build tree, and the CMake machinery does not write
+ any import definitions for it anywhere, linking will fail with errors about
+ not being able to find a `gmxfftw` library. So the CMake package
+ configuration files can only be used with `GMX_BUILD_OWN_FFTW=OFF`.
+
+CMake `find_package(GROMACS)` details
+-------------------------------------
+
+The CMake machinery to support `find_package(GROMACS)` has two parts: a
+`FindGROMACS.cmake` find module (found in `share/gromacs/template/cmake/` in
+the installation and `share/template/cmake/` in the source tree), and actual
+package configuration files (`gromacs-config.cmake` and supporting files
+installed to `share/cmake/` from input files in `src/gromacs/`).
+
+`FindGROMACS.cmake` is a simple wrapper over the package configuration files,
+providing a somewhat more convenient interface to the machinery that supports
+multiple suffixed \Gromacs installations in the same installation prefix (see
+`GROMACS_SUFFIX` variable below). This file is intended to be version-agnostic
+and remain both forward- and backward-compatible even between major \Gromacs
+releases. All version-specific information and the actual details about the
+compilation and linking settings is in the package configuration files.
+Build systems willing to utilize `FindGROMACS.cmake` can create a local copy of
+it and use it like it is used in the installed
+`share/gromacs/template/CMakeLists.txt`.
+The package configuration files can also be used directly if desired, bypassing
+`FindGROMACS.cmake`.
+
+Input options for influencing what to find:
+
+<dl>
+<dt>`GROMACS_SUFFIX` (only for `FindGROMACS.cmake`)</dt>
+<dd>This CMake variable can be set before calling `find_package(GROMACS)` to
+specify the \Gromacs suffix to search for. If not set, an unsuffixed version
+is searched for. If using the package configuration files directly, the suffix
+must be set using `find_package(GROMACS NAMES gromacs<suffix>)`.</dd>
+<dt>`GROMACS_PREFER_STATIC`</dt>
+<dd>This CMake variable can be set before calling `find_package(GROMACS)` to
+specify whether static or shared libraries are preferred if both are available.
+It does not affect which \Gromacs installation is chosen, but if that
+installation has both static and shared libraries available (installed from two
+different builds with the same suffix), then this chooses the library to be
+returned in `GROMACS_LIBRARIES`.</dd>
+<dt>`GROMACS_DIR`</dt>
+<dd>This CMake (cache) variable is a standard mechanism provided by
+`find_package`, and can be used to specify a hint where to search for \Gromacs.
+Also `CMAKE_PREFIX_PATH` can be used for this purpose; see CMake documentation
+for `find_package` for more details.
+`GROMACS_DIR` can also be set as an environment variable, and this is done by
+`GMXRC`.</dd>
+</dl>
+
+Output variables that specify how the found `libgromacs` and header should be
+used:
+
+<dl>
+<dt>`GROMACS_INCLUDE_DIRS`</dt>
+<dd>List of include directories necessary to compile against the \Gromacs
+headers. Currently, this includes the path to \Gromacs headers, as well as the
+path to Boost headers that were used to compile \Gromacs.</dd>
+<dt>`GROMACS_LIBRARIES`</dt>
+<dd>List of libraries to link with to link against \Gromacs.
+Under the hood, this uses imported CMake targets to represent `libgromacs`.</dd>
+<dt>`GROMACS_DEFINITIONS`</dt>
+<dd>List of compile definitions (with `-D` in front) that are required to
+compile the \Gromacs headers.</dd>
+<dt>`GROMACS_IS_DOUBLE`</dt>
+<dd>Whether the found \Gromacs was compiled in double precision.</dd>
+</dl>
+
+Declared macros/functions that can be used for checking for correctness of some
+settings:
+
+<dl>
+<dt>`gromacs_check_double(GMX_DOUBLE)`</dt>
+<dd>Checks that the found \Gromacs is in the expected precision.
+The parameter `GMX_DOUBLE` should be the name of a cache variable that
+specified whether double-precision was requested.</dd>
+<dt>`gromacs_check_compiler(LANG)`<dt>
+<dd>Checks that the found \Gromacs was compiled with the same compiler
+that is used by the current CMake system.
+Currently only `LANG=CXX` is supported.</dd>
+</dl>
+
+Notes on \Gromacs API
+=====================
+
+The headers for the public \Gromacs API are installed in `include/gromacs/`
+under the installation directory. The layout reflects the source code layout
+under the `src/gromacs/` directory (see \ref page_codelayout). The headers
+directly under `include/gromacs/` do not contain any declarations, but instead
+include a collection of headers from subdirectories.
+You should prefer to include these convenience headers instead of individual
+headers from the subdirectories, since they are much more stable. The
+individual headers in the subdirectories can be renamed or moved, but the goal
+is to only rarely change the name of these top-level headers.
+
+Pre-5.0 versions of \Gromacs installed (nearly) all headers directly under
+`include/gromacs/`. Most of these headers still exist, but now under
+`include/gromacs/legacyheaders/`. The long-term goal is to move these to
+proper module hierarchy or get rid of them, but unfortunately this can take a
+long time. Thus, you should not expect much stability from the API in these
+headers. Some have already been moved, so if you do not find your favorite
+header there, try searching for a declaration from the other subdirectories.
+
+For headers under other subdirectories, some effort has been put to design the
+API for stability. However, with limited development resources, and the focus
+of \Gromacs being in high performance simulations, all the APIs are subject to
+change without notice. With each new release (with possible exception of patch
+releases), you should expect incompatible API changes. This is in particular
+true until the planned reorganization of the `legacyheaders/` subdirectory is
+complete.
+
+The header version.h (installed as `gromacs/version.h`) provides defines that
+calling code can use to check the exact (released) version of \Gromacs that
+installed the headers.
+
+This Doxygen documentation only covers part of the API. In particular, nearly
+all of `include/gromacs/legacyheaders/` is undocumented, as well as code
+recently moved from there.
+++ /dev/null
-Using \Gromacs as a library {#page_usinglibrary}
-===========================
-
-Getting started
-===============
-
-\todo
-Describe how to link against \Gromacs (pkg-config, FindGromacs.cmake, etc.)
-
-The \Gromacs library (`libgromacs`) provides a few different alternatives for
-using it. These are listed here from the highest level of abstraction to the
-low-level functions.
- - If you are writing a trajectory analysis tool, please see
- \ref page_analysisframework. \ref page_analysistemplate should contain
- all the ingredients to get started.
- If you have an existing tool written using the analysis template from 4.5 or
- 4.6 (using the selection engine added in 4.5), you need to do some
- conversion work to get this work with the new template. This is mostly
- straightforward, but requires some studying to understand the new framework.
- - If you are writing a command line tool for some other purpose, you can use
- the facilities provided by \ref module_commandline. There are a few
- different alternatives, depending on how much control you want to give
- \Gromacs:
- - For C++ code, you can implement gmx::CommandLineModuleInterface, and
- use gmx::runCommandLineModule() to execute it. This requires using some
- additional \Gromacs classes (in particular, for implementing
- gmx::CommandLineModuleInterface::writeHelp(), if you want to support the
- `-h` option).
- - For C code, you can use gmx_run_cmain() to wrap an existing C main
- method. The only constraint on the provided main method is that it
- should use parse_common_args() for argument processing.
- This approach should allow you to convert existing C tools written
- against pre-5.0 \Gromacs (e.g., using the analysis template from 4.0 or
- earlier) to the new version.
- - If you want more control (for example, you do not want the default
- command line options added by \Gromacs), you can directly initialize
- \Gromacs using gmx::initForCommandLine() before calling other \Gromacs
- routines. This allows you to write your own handling for command line
- options from scratch. This is also discussed in \ref module_commandline.
- - For most control, you can use gmx::init() to do basic initialization, create
- your own implementation for gmx::ProgramContextInterface, and set that using
- gmx::setProgramContext(). This allows you to customize how the \Gromacs
- library shows the name of the program in messages, as well as how it locates
- its own data files.
-
-If these do not fit your needs, you may need to modify the \Gromacs source code
-yourself. In particular, it is currently relatively difficult to extend the
-functionality of `mdrun` without modifying the source code directly.
-If you think that some particular API would be necessary for your work, and
-think that it would be easy to expose, please drop a line on the
-`gmx-developers` mailing list, or contribute the necessary changes on
-http://gerrit.gromacs.org/.
-
-Notes on \Gromacs API
-=====================
-
-The headers for the public \Gromacs API are installed in `include/gromacs/`
-under the installation directory. The layout reflects the source code layout
-under the `src/gromacs/` directory (see \ref page_codelayout). The headers
-directly under `include/gromacs/` do not contain any declarations, but instead
-include a collection of headers from subdirectories.
-You should prefer to include these convenience headers instead of individual
-headers from the subdirectories, since they are much more stable. The
-individual headers in the subdirectories can be renamed or moved, but the goal
-is to only rarely change the name of these top-level headers.
-
-Pre-5.0 versions of \Gromacs installed (nearly) all headers directly under
-`include/gromacs/`. Most of these headers still exist, but now under
-`include/gromacs/legacyheaders/`. The long-term goal is to move these to
-proper module hierarchy or get rid of them, but unfortunately this can take a
-long time. Thus, you should not expect much stability from the API in these
-headers. Some have already been moved, so if you do not find your favorite
-header there, try searching for a declaration from the other subdirectories.
-
-For headers under other subdirectories, some effort has been put to design the
-API for stability. However, with limited development resources, and the focus
-of \Gromacs being in high performance simulations, all the APIs are subject to
-change without notice. With each new release (with possible exception of patch
-releases), you should expect incompatible API changes. This is in particular
-true until the planned reorganization of the `legacyheaders/` subdirectory is
-complete.
-
-The header version.h (installed as `gromacs/version.h`) provides defines that
-calling code can use to check the exact (released) version of \Gromacs that
-installed the headers.
-
-This Doxygen documentation only covers part of the API. In particular, nearly
-all of `include/gromacs/legacyheaders/` is undocumented, as well as code
-recently moved from there.
As [PDF](install-guide.pdf)
* [User Guide](user-guide.html)
+ Includes getting started, .mdp options, advice using mdrun and more.
As [PDF](user-guide.pdf)
* [Online Reference](online.html)
* [Reference manual](manual-@PROJECT_VERSION@.pdf) (PDF format)
+* [Doxygen public API documentation](doxygen/html-user/index.xhtml)
+
* Answers to [Frequently Asked Questions](http://www.gromacs.org/Documentation/FAQs)
* Coping with [GROMACS errors](http://www.gromacs.org/Documentation/Errors)
# Documentation for developers
-* [Doxygen code documentation](doxygen/html-lib/index.xhtml)
-
-* Developer Guide - coming soon (in master branch)!
+* [Doxygen code documentation](doxygen/html-lib/index.xhtml)
+ This contains the public API documentation as a subset, but also has more
+ details on the internal implementation of GROMACS.
-[/b/]: # (TODO in master branch: consolidate much of the wiki material into a proper developer guide, and link to it here)
+* [Developer Guide](doxygen/html-lib/page_devmanual.xhtml)--
+ Resources for developers, e.g., related to guidelines and tools used during
+ development.
${HTML_OUTPUT_DIR}/${name}.pdf
VERBATIM
)
+ gmx_cpack_add_generated_source_directory(final DESTINATION /)
endif()
Technically, GROMACS can be compiled on any platform with an ANSI C99
and C++98 compiler, and their respective standard C/C++ libraries.
+We use only a few C99 features, but note that the C++ compiler also needs to
+support these C99 features (notably, int64_t and related things), which are not
+part of the C++98 standard.
Getting good performance on an OS and architecture requires choosing a
good compiler. In practice, many compilers struggle to do a good job
optimizing the GROMACS architecture-optimized SIMD kernels.
CMakeLists.txt.
`bin/`
- : The standard location for executables, some scripts, and some symlinks.
+ : The standard location for executables and some scripts.
Some of the scripts hardcode the absolute installation prefix, which needs
to be changed if the scripts are relocated.
`include/gromacs/`
is determined by CMake.
The name of the directory can be changed using `GMX_LIB_INSTALL_DIR` CMake
variable.
+`lib/pkgconfig/`
+ : Information about the installed `libgromacs` library for `pkg-config` is
+ installed here. The `lib/` part adapts to the installation location of the
+ libraries. The installed files contain the installation prefix as absolute
+ paths.
+`share/cmake/`
+ : CMake package configuration files are installed here.
`share/gromacs/`
: Various data files and some documentation go here.
The `gromacs` part can be changed using `GMX_DATA_INSTALL_DIR`. Using this
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+if (NOT DEFINED GMX_EXECUTABLE OR NOT DEFINED SOURCE_DIR)
+ message(FATAL_ERROR "Required input parameter not set")
+endif()
+
+file(MAKE_DIRECTORY man1)
+file(MAKE_DIRECTORY man7)
+file(COPY ${SOURCE_DIR}/man7/gromacs.7.in DESTINATION man7/)
+execute_process(
+ COMMAND ${GMX_EXECUTABLE} -quiet help -export man
+ RESULT_VARIABLE exitcode)
+if (exitcode)
+ # Ensure that no partial output is left behind.
+ file(REMOVE_RECURSE man1)
+ file(REMOVE man7/gromacs.7)
+ if (ERRORS_ARE_FATAL)
+ message(FATAL_ERROR
+ "Failed to generate man pages. "
+ "Set GMX_BUILD_HELP=OFF if you want to skip them.\n"
+ "Error/exit code: ${exitcode}")
+ else()
+ message(
+ "Failed to generate man pages, will build GROMACS without. "
+ "Set GMX_BUILD_HELP=OFF if you want to skip this notification and "
+ "warnings during installation.")
+ endif()
+endif()
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-if(SOURCE_IS_SOURCE_DISTRIBUTION)
- # Make sure source package contains all man pages.
- if(NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/man1/gmx-view.1")
- message(FATAL_ERROR "Man pages are missing from source package.")
- endif()
-endif()
-
-add_custom_target(man
- ${CMAKE_COMMAND} -E make_directory man1
- COMMAND ${CMAKE_COMMAND} -E make_directory man7
- COMMAND ${CMAKE_COMMAND} -E copy "${CMAKE_CURRENT_SOURCE_DIR}/man7/gromacs.7.in" man7/
- COMMAND gmx -quiet help -export man
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMENT "Generating man pages"
- VERBATIM)
+include(gmxCustomCommandUtilities)
set(MAN_PAGE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
if (GMX_BUILD_HELP)
+ gmx_add_custom_output_target(man OUTPUT STAMP
+ COMMAND ${CMAKE_COMMAND}
+ -D GMX_EXECUTABLE=$<TARGET_FILE:gmx>
+ -D SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR}
+ -D ERRORS_ARE_FATAL=${GMX_BUILD_HELP_FORCE}
+ -P ${CMAKE_CURRENT_SOURCE_DIR}/BuildManPages.cmake
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ DEPENDS gmx
+ ${CMAKE_CURRENT_SOURCE_DIR}/man7/gromacs.7.in
+ ${CMAKE_CURRENT_SOURCE_DIR}/BuildManPages.cmake
+ COMMENT "Generating man pages")
set_target_properties(man PROPERTIES EXCLUDE_FROM_ALL OFF)
set_directory_properties(PROPERTIES
ADDITIONAL_MAKE_CLEAN_FILES "man1;man7/gromacs.7")
if (SOURCE_IS_SOURCE_DISTRIBUTION OR GMX_BUILD_HELP)
install(FILES ${MAN_PAGE_DIR}/man7/gromacs.7
DESTINATION ${MAN_INSTALL_DIR}/man7
- COMPONENT man)
+ COMPONENT man OPTIONAL)
install(DIRECTORY ${MAN_PAGE_DIR}/man1
DESTINATION ${MAN_INSTALL_DIR}
- COMPONENT man)
+ COMPONENT man OPTIONAL)
endif()
+gmx_cpack_add_generated_source_directory(man1)
+gmx_cpack_add_generated_source_directory(man7)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-if(${CMAKE_BINARY_DIR} STREQUAL ${CMAKE_SOURCE_DIR})
+if (BUILD_IS_INSOURCE)
# UseLATEX.cmake does not work with an in-source build
message(STATUS "Cannot build the manual when building in the source directory")
set(MANUAL_BUILD_IS_POSSIBLE OFF)
#
# Only files that can be built should be listed in DEPENDS. Makefile
# rules are generated for those files.
- #
- # The .mdp options section is now intended to be built directly
- # from a GROMACS source directory. This facilitates drafting
- # updates in that HTML file without copying files by hand.
-
- ADD_CUSTOM_COMMAND(OUTPUT ${output_dir}/mdp_opt.tex
- COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/mkmdp ARGS ${CMAKE_CURRENT_SOURCE_DIR}/../old-html
- DEPENDS mkmdp ${CMAKE_CURRENT_SOURCE_DIR}/../old-html/online/mdp_opt.html
- )
# Finally, the command to build the manual.
ADD_LATEX_DOCUMENT(gromacs.tex
# Normal LaTeX \included files
INPUTS algorithms.tex defunits.tex implement.tex macros.tex special.tex
- analyse.tex files.tex install.tex topology.tex
+ analyse.tex files.tex topology.tex
averages.tex forcefield.tex gromacs.tex intro.tex programs.tex
# CMake does variable replacement in these files
CONFIGURE macros.tex
- # These files we're responsible for creating in the
- # add_custom_targets() above. They should not be in the git
- # repository, or its directory, or the dependencies will not work
- # properly.
- DEPENDS mdp_opt.tex
-
BIBFILES monster.bib unpubl.bib
IMAGE_DIRS plots
DEFAULT_PDF
So, you want to build the manual? This is now easy.
1. Configure the main GROMACS repo with GMX_BUILD_MANUAL=on
-2. cmake will run some detection about whetehr this is possible
+2. cmake will run some detection about whether this is possible
3. Later, use "make manual," which will build GROMACS in the
usual way, and use the generated binaries to build the manual.
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013,2014, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
be excluded\index{exclusions}
\ifthenelse{\equal{\gmxlite}{1}}
{.}
-{(see \secref{mdpopt}).}
+{(see details in the User Guide).}
Pairs of particles from excluded pairs of energy-monitor groups
are not put into the pair list.
This can result in a significant speedup
\secref{mod_nb_int}). One then has a buffer with the size equal to the
neighbor list cut-off less the longest interaction cut-off.
-With the
-group cut-off scheme, one can also choose to let {\tt mdrun} only
-update the neighbor list when required. That is when one or more
-particles have moved more than half the buffer size from the center of
-geometry of the \swapindex{charge}{group} to which they belong (see
-\secref{chargegroup}), as determined at the previous neighbor search.
-This option guarantees that there are no cut-off artifacts. {\bf
- Note} that for larger systems this comes at a high computational
-cost, since the neighbor list update frequency will be determined by
-just one or two particles moving slightly beyond the half buffer
-length (which not even necessarily implies that the neighbor list is
-invalid), while 99.99\% of the particles are fine.
-
} % Brace matches ifthenelse test for gmxlite
\subsubsection{Simple search\swapindexquiet{simple}{search}}
the velocity Verlet variants, the Martyna-Tuckerman-Tobias-Klein
(MTTK) implementation of pressure
control~\cite{Martyna1996}. Parrinello-Rahman and Berendsen can be
-combined with any of the temperature coupling methods above; MTTK can
-only be used with Nos{\'e}-Hoover temperature control.
+combined with any of the temperature coupling methods above. MTTK can
+only be used with Nos{\'e}-Hoover temperature control. From 5.1 afterwards,
+it can only used when the system does not have constraints.
\subsubsection{Berendsen pressure coupling\pawsindexquiet{Berendsen}{pressure coupling}\index{weak coupling}}
\label{sec:berendsen_pressure_coupling}
&&\exp\left(iL_{\mathrm{NHC}}\dt/2\right) \exp\left(iL_{\epsilon,1}\dt\right) \exp\left(iL_1 \dt\right) \exp\left(iL_{\mathrm{NHC}}\dt/2\right) \nonumber \\
&&\exp\left(iL_2 \dt/2\right) \exp\left(iL_{\epsilon,2}\dt/2\right) \exp\left(iL_{\mathrm{NHC-baro}}\dt/2\right) + \mathcal{O}(\dt^3)
\eea
-With constraints, the equations become significantly more
-complicated, in that each of these equations need to be solved
-iteratively for the constraint forces. The discussion of the details of the iteration
-is beyond the scope of this manual; readers are encouraged to see the
-implementation described in~\cite{Yu2010}.
+With constraints, the equations become significantly more complicated,
+in that each of these equations need to be solved iteratively for the
+constraint forces. Previous to Gromacs 5.1, these iterative
+constraints were solved as described in~\cite{Yu2010}. From Gromacs
+5.1 onward, MTTK with constraints has been removed because of
+numerical stability issues with the iterations.
\subsubsection{Infrequent evaluation of temperature and pressure coupling}
{\gromacs} can also write reduced-precision coordinates for a subset of
the simulation system to a special compressed trajectory file
format. All the other tools can read and write this format. See
-\secref{mdpopt} for details on how to set up your {\tt .mdp} file
+the User Guide for details on how to set up your {\tt .mdp} file
to have {\tt mdrun} use this feature.
% \ifthenelse{\equal{\gmxlite}{1}}{}{
% LocalWords: GROningen MAchine BIOSON Groningen GROMACS Berendsen der Spoel
% LocalWords: Drunen Comp Phys Comm ROck NS FFT pbc EM ifthenelse gmxlite ff
% LocalWords: octahedra triclinic Ewald PME PPPM trjconv xy solvated
-% LocalWords: boxtypes boxshapes editconf Lennard mdpopt COM XTC TNG kT defunits
+% LocalWords: boxtypes boxshapes editconf Lennard COM XTC TNG kT defunits
% LocalWords: Boltzmann's Mueller nb int mdrun chargegroup simplerc prefactor
% LocalWords: pme waterloops CH NH CO df com virial integrator Verlet vverlet
% LocalWords: integrators ref timepoint timestep timesteps mdp md vv avek NVE
\section{Radius of gyration and distances}
\label{sec:rg}
-{\tt gmx gyrate, gmx distance, gmx mindist, gmx mdmat, gmx xpm2ps}\\
+{\tt gmx gyrate, gmx distance, gmx mindist, gmx mdmat, gmx pairdist, gmx xpm2ps}\\
To have a rough measure for the compactness of a structure, you can calculate
the {\em radius of gyration} with the program {\tt \normindex{gmx gyrate}} as follows:
\beq
calculated with the program
%\ifthenelse{\equal{\gmxlite}{1}}{
{{\tt \normindex{gmx distance}}, as explained in \secref{bad}.}
-\item[$\bullet$]
+\item[$\bullet$]
The {\em minimum distance} between two groups of atoms during time
can be calculated with the program {\tt \normindex{gmx mindist}}. It also calculates the
{\em number of contacts} between these groups
within a certain radius $r_{max}$.
-\item[$\bullet$]
+\item[$\bullet$]
+{\tt \normindex{gmx pairdist}} is a selection-enabled version of
+{\tt gmx mindist}.
+\item[$\bullet$]
To monitor the {\em minimum distances between amino acid residues}
within a (protein) molecule, you can use
the program {\tt \normindex{gmx mdmat}}. This minimum distance between two residues
% LocalWords: dssp rama xrama rg Ramachandran phipsi amphipathic HPr xvgr pvd
% LocalWords: Scripps RDF online usinggroups mdrun groupconcept HOH
% LocalWords: residuetypes determinding OpenGL traj ov rcl ij ps nm
-% LocalWords: autocorrelation interfacial
+% LocalWords: autocorrelation interfacial pairdist
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013,2014, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
\end{table}
+\section{Mixed or Double precision}
+{\gromacs} can be compiled in either mixed\index{mixed
+precision|see{precision, mixed}}\index{precision, mixed} or
+\pawsindex{double}{precision}. Documentation of previous {\gromacs}
+versions referred to ``single precision'', but the implementation
+has made selective use of double precision for many years.
+Using single precision
+for all variables would lead to a significant reduction in accuracy.
+Although in ``mixed precision'' all state vectors, i.e. particle coordinates,
+velocities and forces, are stored in single precision, critical variables
+are double precision. A typical example of the latter is the virial,
+which is a sum over all forces in the system, which have varying signs.
+In addition, in many parts of the code we managed to avoid double precision
+for arithmetic, by paying attention to summation order or reorganization
+of mathematical expressions. The default configuration uses mixed precision,
+but it is easy to turn on double precision by adding the option
+{\tt -DGMX_DOUBLE=on} to {\tt cmake}. Double precision
+will be 20 to 100\% slower than mixed precision depending on the
+architecture you are running on. Double precision will use somewhat
+more memory and run input, energy and full-precision trajectory files
+will be almost twice as large.
+
+The energies in mixed precision are accurate up to the last decimal,
+the last one or two decimals of the forces are non-significant.
+The virial is less accurate than the forces, since the virial is only one
+order of magnitude larger than the size of each element in the sum over
+all atoms (\secref{virial}).
+In most cases this is not really a problem, since the fluctuations in the
+virial can be two orders of magnitude larger than the average.
+Using cut-offs for the Coulomb interactions cause large errors
+in the energies, forces, and virial.
+Even when using a reaction-field or lattice sum method, the errors
+are larger than, or comparable to, the errors due to the partial use of
+single precision.
+Since MD is chaotic, trajectories with very similar starting conditions will
+diverge rapidly, the divergence is faster in mixed precision than in double
+precision.
+
+For most simulations, mixed precision is accurate enough.
+In some cases double precision is required to get reasonable results:
+\begin{itemize}
+\item normal mode analysis,
+for the conjugate gradient or l-bfgs minimization and the calculation and
+diagonalization of the Hessian
+\item long-term energy conservation, especially for large systems
+\end{itemize}
+
+
% LocalWords: ij basicunits derivedunits kJ mol mV kcal consts LJ BT
% LocalWords: nm ps
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013,2014, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
\tt conf & \tt esp & Asc & \tt -c & Coordinate file in ESPResSo format \\[-0.1ex]
\tt conf & \tt g96 & Asc & \tt -c & Coordinate file in Gromos-96 format \\[-0.1ex]
\tt conf & \tt gro & Asc & \tt -c & Coordinate file in Gromos-87 format \\[-0.1ex]
-\tt conf & \tt gro & & \tt -c & Structure: \tt gro g96 pdb esp tpr tpb tpa \\[-0.1ex]
+\tt conf & \tt gro & & \tt -c & Structure: \tt gro g96 pdb esp tpr \\[-0.1ex]
\tt out & \tt gro & & \tt -o & Structure: \tt gro g96 pdb esp \\[-0.1ex]
\tt polar & \tt hdb & Asc & \tt & Hydrogen data base \\[-0.1ex]
\tt topinc & \tt itp & Asc & \tt & Include file for topology \\[-0.1ex]
\tt residue & \tt rtp & Asc & \tt & Residue Type file used by {\tt pdb2gmx} \\[-0.1ex]
\tt doc & \tt tex & Asc & \tt -o & LaTeX file \\[-0.1ex]
\tt topol & \tt top & Asc & \tt -p & Topology file \\[-0.1ex]
-\tt topol & \tt tpb & Bin & \tt -s & Binary run input file \\[-0.1ex]
-\tt topol & \tt tpr & & \tt -s & Generic run input: \tt tpr tpb tpa \\[-0.1ex]
-\tt topol & \tt tpr & & \tt -s & Structure+mass(db): \tt tpr tpb tpa gro g96 pdb \\[-0.1ex]
+\tt topol & \tt tpr & & \tt -s & Generic run input: \tt tpr \\[-0.1ex]
+\tt topol & \tt tpr & & \tt -s & Structure+mass(db): \tt tpr gro g96 pdb \\[-0.1ex]
\tt topol & \tt tpr & xdr & \tt -s & Portable xdr run input file \\[-0.1ex]
-\tt traj & \tt trj & Bin & \tt & Trajectory file (architecture specific) \\[-0.1ex]
-\tt traj & \tt trr & & \tt & Full precision trajectory: \tt trr trj cpt \\[-0.1ex]
+\tt traj & \tt trr & & \tt & Full precision trajectory: \tt trr cpt \\[-0.1ex]
\tt traj & \tt trr & xdr & \tt & Trajectory in portable xdr format \\[-0.1ex]
\tt root & \tt xpm & Asc & \tt & X PixMap compatible matrix file \\[-0.1ex]
-\tt traj & \tt xtc & & \tt -f & Trajec., input: \tt xtc trr trj cpt gro g96 pdb \\[-0.1ex]
-\tt traj & \tt xtc & & \tt -f & Trajectory, output: \tt xtc trr trj gro g96 pdb \\[-0.1ex]
+\tt traj & \tt xtc & & \tt -f & Trajec., input: \tt xtc trr tng cpt gro g96 pdb \\[-0.1ex]
+\tt traj & \tt xtc & & \tt -f & Trajectory, output: \tt xtc trr tng gro g96 pdb \\[-0.1ex]
\tt traj & \tt xtc & xdr & \tt & Compressed trajectory (portable xdr format) \\[-0.1ex]
\tt graph & \tt xvg & Asc & \tt -o & xvgr/xmgr file \\[-0.1ex]
\dline
% LocalWords: lccX atomtp atp Asc Atomtype pdb gmx eiwit brk Brookhaven cpt tm
% LocalWords: xdr nnnice dat dlg ngmx sam edi edo ener edr ene ent eps conf ss
-% LocalWords: PostScript ESPResSo gtraj Gromos gro tpr tpb tpa hdb topinc itp
-% LocalWords: grompp mdp mtx ndx rtp tex LaTeX topol traj trj trr xpm PixMap
+% LocalWords: PostScript ESPResSo gtraj Gromos gro tpr hdb topinc itp
+% LocalWords: grompp mdp mtx ndx rtp tex LaTeX topol traj trr xpm PixMap
% LocalWords: xtc Trajec xvg xvgr xmgr ps
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013,2014, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
\beq
d_g(\ve{r}_i;\ve{R}_i) = |\ve{r}_i-\ve{R}_i|
\eeq
-{\bfseries Cylinder} ($g=2$): The particle is kept in a cylinder of given radius
-parallel to the $z$-axis. The force from the flat-bottomed potential acts
-towards the axis of the cylinder. The $z$-component of the force is zero.
+{\bfseries Cylinder} ($g=6,7,8$): The particle is kept in a cylinder of given radius
+parallel to the $x$ ($g=6$), $y$ ($g=7$), or $z$-axis ($g=8$). For backwards compatibility, setting
+$g=2$ is mapped to $g=8$ in the code so that old {\tt .tpr} files and topologies work.
+The force from the flat-bottomed potential acts towards the axis of the cylinder.
+The component of the force parallel to the cylinder axis is zero.
+For a cylinder aligned along the $z$-axis:
\beq
d_g(\ve{r}_i;\ve{R}_i) = \sqrt{ (x_i-X_i)^2 + (y_i - Y_i)^2 }
\eeq
\subsubsection{Constraints}
\label{subsubsec:constraints}
-\newcommand{\clam}{C_{\lambda}}
The constraints are formally part of the Hamiltonian, and therefore
they give a contribution to the free energy. In {\gromacs} this can be
calculated using the \normindex{LINCS} or the \normindex{SHAKE} algorithm.
-If we have a number of constraint equations $g_k$:
+If we have $k = 1 \ldots K$ constraint equations $g_k$ for LINCS, then
\beq
-g_k = \ve{r}_{k} - d_{k}
+g_k = |\ve{r}_{k}| - d_{k}
\eeq
-where $\ve{r}_k$ is the distance vector between two particles and
-$d_k$ is the constraint distance between the two particles, we can write
-this using a $\LAM$-dependent distance as
+where $\ve{r}_k$ is the displacement vector between two particles and
+$d_k$ is the constraint distance between the two particles. We can express
+the fact that the constraint distance has a $\LAM$ dependency by
\beq
-g_k = \ve{r}_{k} - \left(\LL d_{k}^A + \LAM d_k^B\right)
+d_k = \LL d_{k}^A + \LAM d_k^B
\eeq
-the contribution $\clam$
-to the Hamiltonian using Lagrange multipliers $\lambda$:
+
+Thus the $\LAM$-dependent constraint equation is
+\beq
+g_k = |\ve{r}_{k}| - \left(\LL d_{k}^A + \LAM d_k^B\right).
+\eeq
+
+The (zero) contribution $G$ to the Hamiltonian from the constraints
+(using Lagrange multipliers $\lambda_k$, which are logically distinct
+from the free-energy $\LAM$) is
\bea
-\clam &=& \sum_k \lambda_k g_k \\
-\dvdl{\clam} &=& \sum_k \lambda_k \left(d_k^B-d_k^A\right)
+G &=& \sum^K_k \lambda_k g_k \\
+\dvdl{G} &=& \frac{\partial G}{\partial d_k} \dvdl{d_k} \\
+ &=& - \sum^K_k \lambda_k \left(d_k^B-d_k^A\right)
\eea
+For SHAKE, the constraint equations are
+\beq
+g_k = \ve{r}_{k}^2 - d_{k}^2
+\eeq
+with $d_k$ as before, so
+\bea
+\dvdl{G} &=& -2 \sum^K_k \lambda_k \left(d_k^B-d_k^A\right)
+\eea
\subsection{Soft-core interactions\index{soft-core interactions}}
\begin{figure}
For both Coulomb and van der Waals interactions there are interaction
type selectors (termed {\tt vdwtype} and {\tt coulombtype}) and two
parameters, for a total of six non-bonded interaction parameters. See
-\secref{mdpopt} for a complete description of these parameters.
+the User Guide for a complete description of these parameters.
The neighbor searching (NS) can be performed using a single-range, or a twin-range
approach. Since the former is merely a special case of the latter, we will
% LocalWords: fc ravdisre nstdisreout dipolar lll ccc orientational MSD const
% LocalWords: orire fitgrp nstorireout Drude intra Noskov et al fecalc coulrf
% LocalWords: polarizabilities parameterized sigeps Ek sc softcore GROMOS NBF
-% LocalWords: hydrogens alkane vdwtype coulombtype mdpopt rlist rcoulomb rvdw
+% LocalWords: hydrogens alkane vdwtype coulombtype rlist rcoulomb rvdw
% LocalWords: nstlist virial funcparm VdW jk jl fvsite fd vsites lcr vsitetop
% LocalWords: vsite lclllll lcl parameterize parameterization enercorr avcsix
% LocalWords: pcorr ecorr totalcoulomb dir fourierspacing ewald rtol Darden gz
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013,2014, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
\ifthenelse{\equal{\gmxlite}{1}}
{
-\fcolorbox{blue}{blue}{\textcolor{white}{\fontsize{56}{64} \selectfont User Manual {\em ~Lite~}}}
+\fcolorbox{blue}{blue}{\textcolor{white}{\fontsize{56}{64} \selectfont Reference Manual {\em ~Lite~}}}
}
{
-\fcolorbox{blue}{blue}{\textcolor{white}{\fontsize{56}{64} \selectfont ~USER MANUAL~}}
+\fcolorbox{blue}{blue}{\textcolor{white}{\fontsize{56}{64} \selectfont ~Reference Manual~}}
} % Brace matches ifthenelse test for gmxlite
\vspace{4mm}
\vspace{1cm}
{\fontsize{40}{50} \selectfont
GROMACS\\
-USER MANUAL\\[1cm]
+Reference Manual\\[1cm]
}
{\LARGE\bf Version \gmxver}\\[1cm]
% A P P E N D I C E S
%
\appendix
-\include{install}
+\include{technical}
\include{implement}
\include{averages}
} % Brace matches ifthenelse test for gmxlite
+++ /dev/null
-%
-% This file is part of the GROMACS molecular simulation package.
-%
-% Copyright (c) 2013,2014, by the GROMACS development team, led by
-% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-% and including many others, as listed in the AUTHORS file in the
-% top-level source directory and at http://www.gromacs.org.
-%
-% GROMACS is free software; you can redistribute it and/or
-% modify it under the terms of the GNU Lesser General Public License
-% as published by the Free Software Foundation; either version 2.1
-% of the License, or (at your option) any later version.
-%
-% GROMACS is distributed in the hope that it will be useful,
-% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-% Lesser General Public License for more details.
-%
-% You should have received a copy of the GNU Lesser General Public
-% License along with GROMACS; if not, see
-% http://www.gnu.org/licenses, or write to the Free Software Foundation,
-% Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-%
-% If you want to redistribute modifications to GROMACS, please
-% consider that scientific software is very special. Version
-% control is crucial - bugs must be traceable. We will be happy to
-% consider code for inclusion in the official distribution, but
-% derived work must not be called official GROMACS. Details are found
-% in the README & COPYING files - if they are missing, get the
-% official version at http://www.gromacs.org.
-%
-% To help us fund GROMACS development, we humbly ask that you cite
-% the research papers on the package. Check out http://www.gromacs.org.
-
-\chapter{Technical Details}
-
-\section{Mixed or Double precision}
-{\gromacs} can be compiled in either mixed\index{mixed
-precision|see{precision, mixed}}\index{precision, mixed} or
-\pawsindex{double}{precision}. Documentation of previous {\gromacs}
-versions referred to ``single precision'', but the implementation
-has made selective use of double precision for many years.
-Using single precision
-for all variables would lead to a significant reduction in accuracy.
-Although in ``mixed precision'' all state vectors, i.e. particle coordinates,
-velocities and forces, are stored in single precision, critical variables
-are double precision. A typical example of the latter is the virial,
-which is a sum over all forces in the system, which have varying signs.
-In addition, in many parts of the code we managed to avoid double precision
-for arithmetic, by paying attention to summation order or reorganization
-of mathematical expressions. The default configuration uses mixed precision,
-but it is easy to turn on double precision by adding the option
-{\tt -DGMX_DOUBLE=on} to {\tt cmake}. Double precision
-will be 20 to 100\% slower than mixed precision depending on the
-architecture you are running on. Double precision will use somewhat
-more memory and run input, energy and full-precision trajectory files
-will be almost twice as large.
-
-The energies in mixed precision are accurate up to the last decimal,
-the last one or two decimals of the forces are non-significant.
-The virial is less accurate than the forces, since the virial is only one
-order of magnitude larger than the size of each element in the sum over
-all atoms (\secref{virial}).
-In most cases this is not really a problem, since the fluctuations in the
-virial can be two orders of magnitude larger than the average.
-Using cut-offs for the Coulomb interactions cause large errors
-in the energies, forces, and virial.
-Even when using a reaction-field or lattice sum method, the errors
-are larger than, or comparable to, the errors due to the partial use of
-single precision.
-Since MD is chaotic, trajectories with very similar starting conditions will
-diverge rapidly, the divergence is faster in mixed precision than in double
-precision.
-
-For most simulations, mixed precision is accurate enough.
-In some cases double precision is required to get reasonable results:
-\begin{itemize}
-\item normal mode analysis,
-for the conjugate gradient or l-bfgs minimization and the calculation and
-diagonalization of the Hessian
-\item long-term energy conservation, especially for large systems
-\end{itemize}
-
-\section{Environment Variables}
-{\gromacs} programs may be influenced by the use of
-\normindex{environment variables}. First of all, the variables set in
-the {\tt \normindex{GMXRC}} file are essential for running and
-compiling {\gromacs}. Some other useful environment variables are
-listed in the following sections. Most environment variables function
-by being set in your shell to any non-NULL value. Specific
-requirements are described below if other values need to be set. You
-should consult the documentation for your shell for instructions on
-how to set environment variables in the current shell, or in config
-files for future shells. Note that requirements for exporting
-environment variables to jobs run under batch control systems vary and
-you should consult your local documentation for details.
-
-{\bf Output Control}
-
-\begin{enumerate}
-
-\item {\tt GMX_CONSTRAINTVIR}: print constraint virial and force virial energy terms.
-\item {\tt GMX_MAXBACKUP}: {\gromacs} automatically backs up old
- copies of files when trying to write a new file of the same
- name, and this variable controls the maximum number of
- backups that will be made, default 99. If set to 0 it fails to
- run if any output file already exists. And if set to -1 it
- overwrites any output file without making a backup.
-\item {\tt GMX_NO_QUOTES}: if this is explicitly set, no cool quotes
- will be printed at the end of a program.
-\item {\tt GMX_SUPPRESS_DUMP}: prevent dumping of step files during
- (for example) blowing up during failure of constraint
- algorithms.
-\item {\tt GMX_TPI_DUMP}: dump all configurations to a {\tt .pdb}
- file that have an interaction energy less than the value set
- in this environment variable.
-\item {\tt GMX_VIEW_XPM}: {\tt GMX_VIEW_XVG}, {\tt
- GMX_VIEW_EPS} and {\tt GMX_VIEW_PDB}, commands used to
- automatically view \@ {\tt .xvg}, {\tt .xpm}, {\tt .eps}
- and {\tt .pdb} file types, respectively; they default to {\tt xv}, {\tt xmgrace},
- {\tt ghostview} and {\tt rasmol}. Set to empty to disable
- automatic viewing of a particular file type. The command will
- be forked off and run in the background at the same priority
- as the {\gromacs} tool (which might not be what you want).
- Be careful not to use a command which blocks the terminal
- ({\eg} {\tt vi}), since multiple instances might be run.
-\item {\tt GMX_VIRIAL_TEMPERATURE}: print virial temperature energy term
-\item {\tt GMX_LOG_BUFFER}: the size of the buffer for file I/O. When set
- to 0, all file I/O will be unbuffered and therefore very slow.
- This can be handy for debugging purposes, because it ensures
- that all files are always totally up-to-date.
-\item {\tt GMX_LOGO_COLOR}: set display color for logo in {\tt \normindex{ngmx}}.
-\item {\tt GMX_PRINT_LONGFORMAT}: use long float format when printing
- decimal values.
-\item {\tt GMX_COMPELDUMP}: Applies for computational electrophysiology setups
- only (see section \ref{sec:compel}). The initial structure gets dumped to
- {\tt .pdb} file, which allows to check whether multimeric channels have
- the correct PBC representation.
-\end{enumerate}
-
-
-{\bf Debugging}
-
-\begin{enumerate}
-
-\item {\tt GMX_PRINT_DEBUG_LINES}: when set, print debugging info on line numbers.
-\item {\tt GMX_DD_NST_DUMP}: number of steps that elapse between dumping
- the current DD to a PDB file (default 0). This only takes effect
- during domain decomposition, so it should typically be
- 0 (never), 1 (every DD phase) or a multiple of {\tt nstlist}.
-\item {\tt GMX_DD_NST_DUMP_GRID}: number of steps that elapse between dumping
- the current DD grid to a PDB file (default 0). This only takes effect
- during domain decomposition, so it should typically be
- 0 (never), 1 (every DD phase) or a multiple of {\tt nstlist}.
-\item {\tt GMX_DD_DEBUG}: general debugging trigger for every domain
- decomposition (default 0, meaning off). Currently only checks
- global-local atom index mapping for consistency.
-\item {\tt GMX_DD_NPULSE}: over-ride the number of DD pulses used
- (default 0, meaning no over-ride). Normally 1 or 2.
-
-%\item There are a number of extra environment variables like these
-% that are used in debugging - check the code!
-
-\end{enumerate}
-
-{\bf Performance and Run Control}
-
-\begin{enumerate}
-
-\item {\tt GMX_DO_GALACTIC_DYNAMICS}: planetary simulations are made possible (just for fun) by setting
- this environment variable, which allows setting {\tt epsilon_r = -1} in the {\tt .mdp}
- file. Normally, {\tt epsilon_r} must be greater than zero to prevent a fatal error.
- See {\wwwpage} for example input files for a planetary simulation.
-\item {\tt GMX_ALLOW_CPT_MISMATCH}: when set, runs will not exit if the
- ensemble set in the {\tt .tpr} file does not match that of the
- {\tt .cpt} file.
-\item {\tt GMX_CUDA_NB_EWALD_TWINCUT}: force the use of twin-range cutoff kernel even if {\tt rvdw} =
- {\tt rcoulomb} after PP-PME load balancing. The switch to twin-range kernels is automated,
- so this variable should be used only for benchmarking.
-\item {\tt GMX_CUDA_NB_ANA_EWALD}: force the use of analytical Ewald kernels. Should be used only for benchmarking.
-\item {\tt GMX_CUDA_NB_TAB_EWALD}: force the use of tabulated Ewald kernels. Should be used only for benchmarking.
-\item {\tt GMX_CUDA_STREAMSYNC}: force the use of cudaStreamSynchronize on ECC-enabled GPUs, which leads
- to performance loss due to a known CUDA driver bug present in API v5.0 NVIDIA drivers (pre-30x.xx).
- Cannot be set simultaneously with {\tt GMX_NO_CUDA_STREAMSYNC}.
-\item {\tt GMX_CYCLE_ALL}: times all code during runs. Incompatible with threads.
-\item {\tt GMX_CYCLE_BARRIER}: calls MPI_Barrier before each cycle start/stop call.
-\item {\tt GMX_DD_ORDER_ZYX}: build domain decomposition cells in the order
- (z, y, x) rather than the default (x, y, z).
-\item {\tt GMX_DD_USE_SENDRECV2}: during constraint and vsite communication, use a pair
- of {\tt MPI_SendRecv} calls instead of two simultaneous non-blocking calls
- (default 0, meaning off). Might be faster on some MPI implementations.
-\item {\tt GMX_DLB_BASED_ON_FLOPS}: do domain-decomposition dynamic load balancing based on flop count rather than
- measured time elapsed (default 0, meaning off).
- This makes the load balancing reproducible, which can be useful for debugging purposes.
- A value of 1 uses the flops; a value $>1$ adds $(\mbox{value} - 1)\times5\%$ of noise to the flops to increase the imbalance and the scaling.
-\item {\tt GMX_DLB_MAX_BOX_SCALING}: maximum percentage box scaling permitted per domain-decomposition
- load-balancing step (default 10)
-\item {\tt GMX_DD_RECORD_LOAD}: record DD load statistics for reporting at end of the run (default 1, meaning on)
-\item {\tt GMX_DD_NST_SORT_CHARGE_GROUPS}: number of steps that elapse between re-sorting of the charge
- groups (default 1). This only takes effect during domain decomposition, so should typically
- be 0 (never), 1 (to mean at every domain decomposition), or a multiple of {\tt nstlist}.
-\item {\tt GMX_DETAILED_PERF_STATS}: when set, print slightly more detailed performance information
- to the {\tt .log} file. The resulting output is the way performance summary is reported in versions
- 4.5.x and thus may be useful for anyone using scripts to parse {\tt .log} files or standard output.
-\item {\tt GMX_DISABLE_SIMD_KERNELS}: disables architecture-specific SIMD-optimized (SSE2, SSE4.1, AVX, etc.)
- non-bonded kernels thus forcing the use of plain C kernels.
-\item {\tt GMX_DISABLE_CUDA_TIMING}: timing of asynchronously executed GPU operations can have a
- non-negligible overhead with short step times. Disabling timing can improve performance in these cases.
-\item {\tt GMX_DISABLE_GPU_DETECTION}: when set, disables GPU detection even if {\tt \normindex{mdrun}} was compiled
- with GPU support.
-\item {\tt GMX_DISABLE_PINHT}: disable pinning of consecutive threads to physical cores when using
- Intel hyperthreading. Controlled with {\tt \normindex{mdrun} -nopinht} and thus this environment
- variable will likely be removed.
-\item {\tt GMX_DISRE_ENSEMBLE_SIZE}: the number of systems for distance restraint ensemble
- averaging. Takes an integer value.
-\item {\tt GMX_EMULATE_GPU}: emulate GPU runs by using algorithmically equivalent CPU reference code instead of
- GPU-accelerated functions. As the CPU code is slow, it is intended to be used only for debugging purposes.
- The behavior is automatically triggered if non-bonded calculations are turned off using {\tt GMX_NO_NONBONDED}
- case in which the non-bonded calculations will not be called, but the CPU-GPU transfer will also be skipped.
-\item {\tt GMX_ENX_NO_FATAL}: disable exiting upon encountering a corrupted frame in an {\tt .edr}
- file, allowing the use of all frames up until the corruption.
-\item {\tt GMX_FORCE_UPDATE}: update forces when invoking {\tt \normindex{mdrun} -rerun}.
-\item {\tt GMX_GPU_ID}: set in the same way as the {\tt \normindex{mdrun}} option {\tt -gpu_id}, {\tt GMX_GPU_ID}
- allows the user to specify different GPU id-s, which can be useful for selecting different
- devices on different compute nodes in a cluster. Cannot be used in conjunction with {\tt -gpu_id}.
-\item {\tt GMX_IGNORE_FSYNC_FAILURE_ENV}: allow {\tt \normindex{mdrun}} to continue even if
- a file is missing.
-\item {\tt GMX_LJCOMB_TOL}: when set to a floating-point value, overrides the default tolerance of
- 1e-5 for force-field floating-point parameters.
-\item {\tt GMX_MAX_MPI_THREADS}: sets the maximum number of MPI-threads that {\tt \normindex{mdrun}}
- can use.
-\item {\tt GMX_MAXCONSTRWARN}: if set to -1, {\tt \normindex{mdrun}} will
- not exit if it produces too many LINCS warnings.
-\item {\tt GMX_NB_GENERIC}: use the generic C kernel. Should be set if using
- the group-based cutoff scheme and also sets {\tt GMX_NO_SOLV_OPT} to be true,
- thus disabling solvent optimizations as well.
-\item {\tt GMX_NB_MIN_CI}: neighbor list balancing parameter used when running on GPU. Sets the
- target minimum number pair-lists in order to improve multi-processor load-balance for better
- performance with small simulation systems. Must be set to a positive integer, the default value
- is optimized for NVIDIA Fermi and Kepler GPUs, therefore changing it is not necessary for
- normal usage, but it can be useful on future architectures.
-\item {\tt GMX_NBLISTCG}: use neighbor list and kernels based on charge groups.
-\item {\tt GMX_NBNXN_CYCLE}: when set, print detailed neighbor search cycle counting.
-\item {\tt GMX_NBNXN_EWALD_ANALYTICAL}: force the use of analytical Ewald non-bonded kernels,
- mutually exclusive of {\tt GMX_NBNXN_EWALD_TABLE}.
-\item {\tt GMX_NBNXN_EWALD_TABLE}: force the use of tabulated Ewald non-bonded kernels,
- mutually exclusive of {\tt GMX_NBNXN_EWALD_ANALYTICAL}.
-\item {\tt GMX_NBNXN_SIMD_2XNN}: force the use of 2x(N+N) SIMD CPU non-bonded kernels,
- mutually exclusive of {\tt GMX_NBNXN_SIMD_4XN}.
-\item {\tt GMX_NBNXN_SIMD_4XN}: force the use of 4xN SIMD CPU non-bonded kernels,
- mutually exclusive of {\tt GMX_NBNXN_SIMD_2XNN}.
-\item {\tt GMX_NO_ALLVSALL}: disables optimized all-vs-all kernels.
-\item {\tt GMX_NO_CART_REORDER}: used in initializing domain decomposition communicators. Rank reordering
- is default, but can be switched off with this environment variable.
-\item {\tt GMX_NO_CUDA_STREAMSYNC}: the opposite of {\tt GMX_CUDA_STREAMSYNC}. Disables the use of the
- standard cudaStreamSynchronize-based GPU waiting to improve performance when using CUDA driver API
- ealier than v5.0 with ECC-enabled GPUs.
-\item {\tt GMX_NO_INT}, {\tt GMX_NO_TERM}, {\tt GMX_NO_USR1}: disable signal handlers for SIGINT,
- SIGTERM, and SIGUSR1, respectively.
-\item {\tt GMX_NO_NODECOMM}: do not use separate inter- and intra-node communicators.
-\item {\tt GMX_NO_NONBONDED}: skip non-bonded calculations; can be used to estimate the possible
- performance gain from adding a GPU accelerator to the current hardware setup -- assuming that this is
- fast enough to complete the non-bonded calculations while the CPU does bonded force and PME computation.
-\item {\tt GMX_NO_PULLVIR}: when set, do not add virial contribution to COM pull forces.
-\item {\tt GMX_NOCHARGEGROUPS}: disables multi-atom charge groups, {\ie} each atom
- in all non-solvent molecules is assigned its own charge group.
-\item {\tt GMX_NOPREDICT}: shell positions are not predicted.
-\item {\tt GMX_NO_SOLV_OPT}: turns off solvent optimizations; automatic if {\tt GMX_NB_GENERIC}
- is enabled.
-\item {\tt GMX_NSCELL_NCG}: the ideal number of charge groups per neighbor searching grid cell is hard-coded
- to a value of 10. Setting this environment variable to any other integer value overrides this hard-coded
- value.
-\item {\tt GMX_PME_NTHREADS}: set the number of OpenMP or PME threads (overrides the number guessed by
- {\tt \normindex{mdrun}}.
-\item {\tt GMX_PME_P3M}: use P3M-optimized influence function instead of smooth PME B-spline interpolation.
-\item {\tt GMX_PME_THREAD_DIVISION}: PME thread division in the format ``x y z'' for all three dimensions. The
- sum of the threads in each dimension must equal the total number of PME threads (set in
- {\tt GMX_PME_NTHREADS}).
-\item {\tt GMX_PMEONEDD}: if the number of domain decomposition cells is set to 1 for both x and y,
- decompose PME in one dimension.
-\item {\tt GMX_REQUIRE_SHELL_INIT}: require that shell positions are initiated.
-\item {\tt GMX_REQUIRE_TABLES}: require the use of tabulated Coulombic
- and van der Waals interactions.
-\item {\tt GMX_SCSIGMA_MIN}: the minimum value for soft-core $\sigma$. {\bf Note} that this value is set
- using the {\tt sc-sigma} keyword in the {\tt .mdp} file, but this environment variable can be used
- to reproduce pre-4.5 behavior with respect to this parameter.
-\item {\tt GMX_TPIC_MASSES}: should contain multiple masses used for test particle insertion into a cavity.
- The center of mass of the last atoms is used for insertion into the cavity.
-\item {\tt GMX_USE_GRAPH}: use graph for bonded interactions.
-\item {\tt GMX_VERLET_BUFFER_RES}: resolution of buffer size in Verlet cutoff scheme. The default value is
- 0.001, but can be overridden with this environment variable.
-\item {\tt GMX_VERLET_SCHEME}: convert from group-based to Verlet cutoff scheme, even if the {\tt cutoff_scheme} is
- not set to use Verlet in the {\tt .mdp} file. It is unnecessary since the {\tt -testverlet} option of
- {\tt \normindex{mdrun}} has the same functionality, but it is maintained for backwards compatibility.
-\item {\tt MPIRUN}: the {\tt mpirun} command used by {\tt \normindex{g_tune_pme}}.
-\item {\tt MDRUN}: the {\tt \normindex{mdrun}} command used by {\tt \normindex{g_tune_pme}}.
-\item {\tt GMX_NSTLIST}: sets the default value for {\tt nstlist}, preventing it from being tuned during
- {\tt \normindex{mdrun}} startup when using the Verlet cutoff scheme.
-\item {\tt GMX_USE_TREEREDUCE}: use tree reduction for nbnxn force reduction. Potentially faster for large number of
- OpenMP threads (if memory locality is important).
-
-\end{enumerate}
-
-{\bf Analysis and Core Functions}
-
-\begin{enumerate}
-
-\item {\tt GMX_QM_ACCURACY}: accuracy in Gaussian L510 (MC-SCF) component program.
-\item {\tt GMX_QM_ORCA_BASENAME}: prefix of {\tt .tpr} files, used in Orca calculations
- for input and output file names.
-\item {\tt GMX_QM_CPMCSCF}: when set to a nonzero value, Gaussian QM calculations will
- iteratively solve the CP-MCSCF equations.
-\item {\tt GMX_QM_MODIFIED_LINKS_DIR}: location of modified links in Gaussian.
-\item {\tt DSSP}: used by {\tt \normindex{do_dssp}} to point to the {\tt dssp}
- executable (not just its path).
-\item {\tt GMX_QM_GAUSS_DIR}: directory where Gaussian is installed.
-\item {\tt GMX_QM_GAUSS_EXE}: name of the Gaussian executable.
-\item {\tt GMX_DIPOLE_SPACING}: spacing used by {\tt \normindex{g_dipoles}}.
-\item {\tt GMX_MAXRESRENUM}: sets the maximum number of residues to be renumbered by
- {\tt \normindex{grompp}}. A value of -1 indicates all residues should be renumbered.
-\item {\tt GMX_FFRTP_TER_RENAME}: Some force fields (like AMBER) use specific names for N- and C-
- terminal residues (NXXX and CXXX) as {\tt .rtp} entries that are normally renamed. Setting
- this environment variable disables this renaming.
-\item {\tt GMX_PATH_GZIP}: {\tt gunzip} executable, used by {\tt \normindex{g_wham}}.
-\item {\tt GMX_FONT}: name of X11 font used by {\tt \normindex{ngmx}}.
-\item {\tt GMXTIMEUNIT}: the time unit used in output files, can be
- anything in fs, ps, ns, us, ms, s, m or h.
-\item {\tt GMX_QM_GAUSSIAN_MEMORY}: memory used for Gaussian QM calculation.
-\item {\tt MULTIPROT}: name of the {\tt multiprot} executable, used by the
- contributed program {\tt \normindex{do_multiprot}}.
-\item {\tt NCPUS}: number of CPUs to be used for Gaussian QM calculation
-\item {\tt GMX_ORCA_PATH}: directory where Orca is installed.
-\item {\tt GMX_QM_SA_STEP}: simulated annealing step size for Gaussian QM calculation.
-\item {\tt GMX_QM_GROUND_STATE}: defines state for Gaussian surface hopping calculation.
-\item {\tt GMX_TOTAL}: name of the {\tt total} executable used by the contributed
- {\tt \normindex{do_shift}} program.
-\item {\tt GMX_ENER_VERBOSE}: make {\tt \normindex{g_energy}} and {\tt \normindex{eneconv}}
- loud and noisy.
-\item {\tt VMD_PLUGIN_PATH}: where to find VMD plug-ins. Needed to be
- able to read file formats recognized only by a VMD plug-in.
-\item {\tt VMDDIR}: base path of VMD installation.
-\item {\tt GMX_USE_XMGR}: sets viewer to {\tt xmgr} (deprecated) instead of {\tt xmgrace}.
-
-\end{enumerate}
-
-\section{Running {\gromacs} in parallel}
-By default {\gromacs} will be compiled with the built-in thread-MPI library.
-This library handles communication between threads on a single
-node more efficiently than using an external MPI library.
-To run {\gromacs} in parallel over multiple nodes, e.g. on a cluster,
-you need to configure and compile {\gromacs} with an external
-MPI library. All supercomputers are shipped with MPI libraries optimized for
-that particular platform, and there are several good free MPI
-implementations; OpenMPI is usually a good choice.
-Note that MPI and thread-MPI support are mutually incompatible.
-
-In addition to MPI parallelization, {\gromacs} supports also
-thread-parallelization through \normindex{OpenMP}. MPI and OpenMP parallelization
-can be combined, which results in, so called, hybrid parallelization. It can offer
-better performance and scaling in some cases.
-
-See {\wwwpage} for details on the use and performance of the different
-parallelization schemes.
-
-\section{Running {\gromacs} on \normindex{GPUs}}
-As of version 4.6, {\gromacs} has native GPU support through CUDA.
-Note that {\gromacs} only off-loads the most compute intensive parts
-to the GPU, currently the non-bonded interactions, and does all other
-parts of the MD calculation on the CPU. The requirements for the CUDA code
-are an Nvidia GPU with compute capability $\geq 2.0$, i.e. at
-least Fermi class.
-In many cases {\tt cmake} can auto-detect GPUs and the support will be
-configured automatically. To be sure GPU support is configured, pass
-the {\tt -DGMX_GPU=on} option to {\tt cmake}. The actual use of GPUs
-is decided at run time by {\tt mdrun}, depending on the availability
-of (suitable) GPUs and on the run input settings. A binary compiled
-with GPU support can also run CPU only simulations. Use {\tt mdrun -nb cpu}
-to force a simulation to run on CPUs only. Only simulations with the Verlet
-cut-off scheme will run on a GPU. To test performance of old tpr files
-with GPUs, you can use the {\tt -testverlet} option of {\tt mdrun},
-but as this doesn't do the full parameter consistency check of {\tt grommp},
-you should not use this option for production simulations.
-Getting good performance with {\gromacs} on GPUs is easy,
-but getting best performance can be difficult.
-Please check {\wwwpage} for up to date information on GPU usage.
-
-% LocalWords: Opteron Itanium PowerPC Altivec Athlon Fortran virial bfgs Nasm
-% LocalWords: diagonalization Cygwin MPI Multi GMXHOME extern gmx tx pid buf
-% LocalWords: bufsize txs rx rxs init nprocs fp msg GMXRC DUMPNL BUFS GMXNPRI
-% LocalWords: unbuffered SGI npri mdrun covar nmeig setenv XPM XVG EPS
-% LocalWords: PDB xvg xpm eps pdb xmgrace ghostview rasmol GMXTIMEUNIT fs dssp
-% LocalWords: mpi distclean ing mpirun goofus doofus fred topol np
-% LocalWords: internet gromacs DGMX cmake SIMD intrinsics AVX PME XN
-% LocalWords: Verlet pre config CONSTRAINTVIR MAXBACKUP TPI ngmx mdp
-% LocalWords: LONGFORMAT DISTGCT CPT tpr cpt CUDA EWALD TWINCUT rvdw
-% LocalWords: rcoulomb STREAMSYNC cudaStreamSynchronized ECC GPUs sc
-% LocalWords: ZYX PERF GPU PINHT hyperthreading DISRE NONBONDED ENX
-% LocalWords: edr ENER gpu FSYNC ENV LJCOMB TOL MAXCONSTRWARN LINCS
-% LocalWords: SOLV NBLISTCG NBNXN XNN ALLVSALL cudaStreamSynchronize
-% LocalWords: USR SIGINT SIGTERM SIGUSR NODECOMM intra PULLVIR multi
-% LocalWords: NOCHARGEGROUPS NOPREDICT NSCELL NCG NTHREADS OpenMP CP
-% LocalWords: PMEONEDD Coulombic der Waals SCSIGMA TPIC GMXNPRIALL
-% LocalWords: GOMP KMP pme NSTLIST ENVVAR nstlist startup OMP NUM ps
-% LocalWords: ACC SCF BASENAME Orca CPMCSCF MCSCF DEVEL EXE GKRWIDTH
-% LocalWords: MAXRESRENUM grompp FFRTP TER NXXX CXXX rtp GZIP gunzip
-% LocalWords: GMXFONT ns MEM MULTIPROT multiprot NCPUS CPUs OPENMM
-% LocalWords: PLUGIN OpenMM plugins SASTEP TESTMC eneconv VMD VMDDIR
-% LocalWords: GMX_USE_XMGR xmgr parallelization nt online Nvidia nb cpu
-% LocalWords: testverlet grommp
\newcommand{\ttw}{4.33cm} % 1/3 of the textwidth
\newcommand{\htw}{7.5cm} % 1/2 of the textwidth
\newcommand{\ntw}{13cm} % 0.9 of the textwidth
-\newcommand{\gmxver}{@PROJECT_VERSION@}
+\newcommand{\gmxver}{@GMX_VERSION_STRING@}
\newcommand{\gmxyear}{\the\year}
\newcommand{\figref}[1]{Fig.~\ref{fig:#1}}
\newcommand{\figsref}[2]{Figs.~\ref{fig:#1} and ~\ref{fig:#2}}
+++ /dev/null
-#!/bin/bash
-
-if [[ ! -d $1 ]]; then
- echo "Error: provide the GROMACS html directory as first argument."
- exit
-fi
-
-GMXHTMLDIR=$1
-
-dir=${PWD}
-
-TEXDIR=.
-MANDIR=online
-HTML=$GMXHTMLDIR
-HTMLOL=$HTML/$MANDIR
-HTMLMDPOPT=$HTMLOL/mdp_opt.html
-TEXMDPOPT=$TEXDIR/mdp_opt.tex
-
-echo "Will convert $HTMLMDPOPT (html format)"
-echo "to $TEXMDPOPT (latex format)"
-
-echo -n "parsing."
-sed \
--e 's/<[aA] [^>]*>//g' \
--e 's/<\/[aA]>//g' \
--e 's/<[iI][mM][gG] [^>]*>//g' \
--e 's/<[pP]>//g' \
--e 's/<\/[pP]>//g' \
--e 's/&[nN][bB][sS][pP];/~/g' \
--e 's/<[hH][rR]>//g' \
-$HTMLMDPOPT > temp1
-
-echo -n "."
-awk '{
- if (NF) {
- if ( ($1 == "<P>") || ($1 == "<p>") || ($1 == "<BR>") || ($1 == "<br>") )
- print ""
- else
- print $0
- }
- }' temp1 > temp2
-echo -n "."
-sed \
--e 's/>=/$\\geq$/g;s/≥/$\\geq$/g' \
--e 's/>/$\>$/g' \
--e 's/<=/$\\leq$/g;s/≤/$\\leq$/g' \
--e 's/</$\<$/g' \
--e 's/_/_/g' \
--e 's/%/\\%/g' \
--e 's/&/\\&/g' \
--e 's/<sup>\([^<]*\)<\/sup>/$^{\1}$/g' \
--e 's/<sub>\([^<]*\)<\/sub>/$_{\1}$/g' \
--e 's/<[tT][tT]>\([^<]*\)<\/[tT][tT]>/{\\tt \1}/g' \
--e 's/<[pP][rR][eE]>\([^<]*\)<\/[pP][rR][eE]>/\\\\{\\tt\1}\\\\/g' \
--e 's/<\!--Idx-->\([^>]*\)<\!--EIdx-->/\\normindex{\1}/g' \
--e 's/<\!--QuietIdx-->\([^>]*\)<\!--EQuietIdx-->/\\index{\1}/g' \
--e 's/<[hH]1>\([^<]*\)<\/[hH]1>/\\section{\1}/g' \
--e 's/<[hH]3>\([^<]*\)<\/[hH]3>/\\subsection{\1}/g' \
-temp2 > temp3
-
-echo -n "."
-sed \
--e 's/<[uU][lL]>/\\begin{itemize}/g' \
--e 's/<\/[uU][lL]>/\\end{itemize}/g' \
--e 's/<[lL][iI]>/\\item /g' \
--e 's/<[dD][lL] [cC][oO][^>]*>/\\vspace{-2ex}\\begin{description}[font=\\ttfamily]/g' \
--e 's/<[dD][lL][^>]*>/\\begin{description}[font=\\ttfamily]/g' \
--e 's/<\/[dD][lL]>/\\end{description}/g' \
--e 's/<[dD][tT]><[bB]>\(.*\)<\/[bB]>\(.*\)<\/[dD][tT]>/\\item[\1] \2\\hfill\\\\/g' \
--e 's/<[dD][tT]>\([^<]*\)<\/[dD][tT]>/\\item[\1]\\hfill\\\\/g' \
--e 's/<[bB]>\([^<]*\)<\/[bB]>/{\\tt \1}/g' \
--e 's/<[iI]>\([^<]*\)<\/[iI]>/{\\em \1}/g' \
--e 's/<[dD][dD]>//g' \
--e 's/<\/[dD][dD]>//g' \
--e 's/<\/[dD][tT]>//g' \
--e 's/ \(\[[^]]*\]\)\]/ {\1}\]/g' \
--e 's/\$lt\$/$<$/g' \
--e 's/\$gt\$/$>$/g' \
--e 's/e\.g\./{\\eg}/g' \
--e 's/i\.e\./{\\ie}/g' \
-temp3 > temp4
-
-echo -n "."
-awk 'BEGIN { printf("\\label{sec:mdpopt}\n"); }\
-{\
- if ( index($0,"subsection") ) {\
- if ( index($0,"General") ) {\
- output=1;\
- } else if ( index($0,"Index") )\
- output=0;\
- }\
- if (output) print;\
-}' temp4 > $TEXMDPOPT
-
-echo "."
-
-rm temp1 temp2 temp3 temp4
-
-#last line
-exit
@Article{PSmith93c,
author = {P. E. Smith and W. F. van Gunsteren},
title = {{The Viscosity of SPC and SPC/E Water}},
- journal = BTcpc,
+ journal = BTcpl,
year = 1993,
volume = 215,
pages = {315--318}
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013,2014, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
\input{files}
\section{Run Parameters\swapindexquiet{run}{parameter}}
-\input{mdp_opt}
+% TODO Check this is up to date when things stabilize
+The descriptions of {\tt .mdp} parameters can be found at
+\url{http://manual.gromacs.org/current/mdp-options.html}
+or in your installation at {\tt share/gromacs/html/mdp-options.html}
% LocalWords: online html GMXRC MANPATH grompp xdr NFS
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013,2014, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
groups of atoms, this can be set through energy groups.
Different tables can be used for non-bonded interactions between
different energy groups pairs through the {\tt .mdp} option {\tt energygrp-table}
-(see \secref{mdpopt}).
+(see details in the User Guide).
Atoms that should interact with a different potential should
be put into different energy groups.
Between group pairs which are not listed in {\tt energygrp-table},
% LocalWords: vsitehydro planarity chirality pdb gmx virtualize virtualized xz
% LocalWords: vis massless tryptophan histidine phenyl parameterizing ij PPPM
% LocalWords: parameterization Berendsen rlist coulombtype rcoulomb vdwtype LJ
-% LocalWords: rvdw energygrp mdrun pre GMXLIB mdpopt MOPAC GAMESS CPMD ONIOM
+% LocalWords: rvdw energygrp mdrun pre GMXLIB MOPAC GAMESS CPMD ONIOM
% LocalWords: Morokuma iJ AQ AJ initio atomtype QMatom MMatom QMMM grps et al
% LocalWords: QMmethod QMbasis QMMMscheme RHF DFT LYP CASSCF MMVB CASelectrons
% LocalWords: CASorbitals planewavecutoff STO QMcharge QMmult diabatic edr
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-if (NOT DEFINED OUTPUT_DIR OR NOT DEFINED SOURCE_HTML_DIR)
+if (NOT DEFINED GMX_EXECUTABLE OR NOT DEFINED OUTPUT_DIR OR NOT DEFINED SOURCE_HTML_DIR)
message(FATAL_ERROR "Required input parameter not set")
endif()
-function(PRE_EXPORT_ACTIONS)
- file(MAKE_DIRECTORY ${OUTPUT_DIR})
- file(MAKE_DIRECTORY ${OUTPUT_DIR}/programs)
- file(COPY ${SOURCE_HTML_DIR}/header.html.in DESTINATION .)
- file(COPY ${SOURCE_HTML_DIR}/footer.html DESTINATION .)
- file(COPY ${SOURCE_HTML_DIR}/links.dat DESTINATION .)
-endfunction()
+file(MAKE_DIRECTORY ${OUTPUT_DIR})
+file(MAKE_DIRECTORY ${OUTPUT_DIR}/programs)
+file(COPY ${SOURCE_HTML_DIR}/header.html.in DESTINATION .)
+file(COPY ${SOURCE_HTML_DIR}/footer.html DESTINATION .)
+file(COPY ${SOURCE_HTML_DIR}/links.dat DESTINATION .)
+
+# This is generated by gmx help -export html
+set(HEADER_FILE header.html)
-function(POST_EXPORT_ACTIONS)
- # This is generated by gmx help -export html
- set(HEADER_FILE header.html)
- set(FOOTER_FILE ${SOURCE_HTML_DIR}/footer.html)
- file(READ ${HEADER_FILE} HEADER_TEXT)
- file(READ ${FOOTER_FILE} FOOTER_TEXT)
- set(_title_re "[Tt][Ii][Tt][Ll][Ee]")
+execute_process(
+ COMMAND ${GMX_EXECUTABLE} -quiet help -export html
+ RESULT_VARIABLE exitcode)
+if (exitcode)
+ # Ensure that no partial output is left behind.
+ file(REMOVE_RECURSE ${OUTPUT_DIR})
+ file(REMOVE ${HEADER_FILE})
+ message(FATAL_ERROR
+ "Failed to generate HTML help. "
+ "Set GMX_BUILD_HELP=OFF or GMX_BUILD_HELP=AUTO if you want to skip them.\n"
+ "Error/exit code: ${exitcode}")
+endif()
- function(CREATE_HTML_FILE SOURCE_FILE ROOTPATH)
- file(RELATIVE_PATH _rel_path ${SOURCE_HTML_DIR} ${SOURCE_FILE})
- file(READ ${SOURCE_FILE} _content)
- string(REGEX REPLACE "^ *<${_title_re}>(.*)</${_title_re}>\n" "" _content "${_content}")
- set(TITLE "${CMAKE_MATCH_1}")
- string(CONFIGURE "${HEADER_TEXT}" _header @ONLY)
- set(_content "${_header}${_content}${FOOTER_TEXT}")
- file(WRITE ${OUTPUT_DIR}/${_rel_path} "${_content}")
- endfunction()
+set(FOOTER_FILE ${SOURCE_HTML_DIR}/footer.html)
+file(READ ${HEADER_FILE} HEADER_TEXT)
+file(READ ${FOOTER_FILE} FOOTER_TEXT)
+set(_title_re "[Tt][Ii][Tt][Ll][Ee]")
- create_html_file(${SOURCE_HTML_DIR}/online.html "")
- file(COPY ${SOURCE_HTML_DIR}/images DESTINATION ${OUTPUT_DIR})
- file(MAKE_DIRECTORY ${OUTPUT_DIR}/online)
- file(COPY ${SOURCE_HTML_DIR}/online/style.css DESTINATION ${OUTPUT_DIR}/online)
- file(GLOB _source_files ${SOURCE_HTML_DIR}/online/*.html)
- foreach(_file ${_source_files})
- create_html_file(${_file} "../")
- endforeach()
+function(CREATE_HTML_FILE SOURCE_FILE ROOTPATH)
+ file(RELATIVE_PATH _rel_path ${SOURCE_HTML_DIR} ${SOURCE_FILE})
+ file(READ ${SOURCE_FILE} _content)
+ string(REGEX REPLACE "^ *<${_title_re}>(.*)</${_title_re}>\n" "" _content "${_content}")
+ set(TITLE "${CMAKE_MATCH_1}")
+ string(CONFIGURE "${HEADER_TEXT}" _header @ONLY)
+ set(_content "${_header}${_content}${FOOTER_TEXT}")
+ file(WRITE ${OUTPUT_DIR}/${_rel_path} "${_content}")
endfunction()
-if (STEP STREQUAL "PRE")
- pre_export_actions()
-elseif (STEP STREQUAL "POST")
- post_export_actions()
-else()
- message(FATAL_ERROR "Unknown parameter STEP=${STEP}")
-endif()
+create_html_file(${SOURCE_HTML_DIR}/online.html "")
+file(COPY ${SOURCE_HTML_DIR}/images DESTINATION ${OUTPUT_DIR})
+file(MAKE_DIRECTORY ${OUTPUT_DIR}/online)
+file(COPY ${SOURCE_HTML_DIR}/online/style.css DESTINATION ${OUTPUT_DIR}/online)
+file(GLOB _source_files ${SOURCE_HTML_DIR}/online/*.html)
+foreach(_file ${_source_files})
+ create_html_file(${_file} "../")
+endforeach()
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+include(gmxCustomCommandUtilities)
+
set(OUTPUT_DIR final)
-set(HTML_PAGE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/${OUTPUT_DIR})
-if(SOURCE_IS_SOURCE_DISTRIBUTION)
- # Make sure source package contains HTML pages.
- if(NOT EXISTS "${HTML_PAGE_DIR}/online.html")
- message(FATAL_ERROR "Online HTML pages are missing from source package.")
- endif()
-endif()
+set(HTML_PAGE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/${OUTPUT_DIR})
+if (GMX_BUILD_HELP)
+ # Unlike the man and completion targets, this target is not built
+ # automatically with GMX_BUILD_HELP=AUTO, since most people will not
+ # notice it missing.
+ file(GLOB_RECURSE deps
+ ${CMAKE_CURRENT_SOURCE_DIR}/images/*
+ ${CMAKE_CURRENT_SOURCE_DIR}/*.html
+ ${CMAKE_CURRENT_SOURCE_DIR}/*.css
+ )
+ list(APPEND deps
+ ${CMAKE_CURRENT_SOURCE_DIR}/BuildHtmlHelp.cmake
+ ${CMAKE_CURRENT_SOURCE_DIR}/header.html.in
+ ${CMAKE_CURRENT_SOURCE_DIR}/links.dat
+ )
-add_custom_target(html
- ${CMAKE_COMMAND}
- -D SOURCE_HTML_DIR=${CMAKE_CURRENT_SOURCE_DIR}
- -D OUTPUT_DIR=${OUTPUT_DIR}
- -D STEP=PRE
- -P ${CMAKE_CURRENT_SOURCE_DIR}/BuildHtmlHelp.cmake
- COMMAND gmx -quiet help -export html
- COMMAND ${CMAKE_COMMAND}
- -D SOURCE_HTML_DIR=${CMAKE_CURRENT_SOURCE_DIR}
- -D OUTPUT_DIR=${OUTPUT_DIR}
- -D STEP=POST
- -P ${CMAKE_CURRENT_SOURCE_DIR}/BuildHtmlHelp.cmake
- COMMENT "Generating HTML help"
- VERBATIM)
+ gmx_add_custom_output_target(html OUTPUT STAMP
+ COMMAND ${CMAKE_COMMAND}
+ -D GMX_EXECUTABLE=$<TARGET_FILE:gmx>
+ -D SOURCE_HTML_DIR=${CMAKE_CURRENT_SOURCE_DIR}
+ -D OUTPUT_DIR=${OUTPUT_DIR}
+ -P ${CMAKE_CURRENT_SOURCE_DIR}/BuildHtmlHelp.cmake
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ DEPENDS gmx ${deps}
+ COMMENT "Generating HTML help")
-if (GMX_BUILD_HELP)
- set_target_properties(html PROPERTIES EXCLUDE_FROM_ALL OFF)
+ if (GMX_BUILD_HELP_FORCE)
+ set_target_properties(html PROPERTIES EXCLUDE_FROM_ALL OFF)
+ endif()
set_directory_properties(PROPERTIES
ADDITIONAL_MAKE_CLEAN_FILES "${OUTPUT_DIR};header.html")
set(HTML_PAGE_DIR ${CMAKE_CURRENT_BINARY_DIR}/${OUTPUT_DIR})
endif()
-if (SOURCE_IS_SOURCE_DISTRIBUTION OR GMX_BUILD_HELP)
+if (SOURCE_IS_SOURCE_DISTRIBUTION OR GMX_BUILD_HELP_FORCE)
install(DIRECTORY ${HTML_PAGE_DIR}/
DESTINATION ${DATA_INSTALL_DIR}/html
COMPONENT html)
endif()
+gmx_cpack_add_generated_source_directory(${OUTPUT_DIR})
tex
top
tng
-tpa
-tpb
tpr
-trj
trr
xpm
xtc
+<!-- TODO migrate remaining content to new user guide (in future commits) -->
<TITLE>GROMACS Online Reference</TITLE>
<TABLE BORDER=0 CELLSPACING=0 CELLPADDING=10>
<TR>
<TD VALIGN=top WIDTH="25%">
<h3>General</h3>
-<A HREF="online/getting_started.html">Getting Started</a>
-<br><br>
<A HREF="online/flow.html">Flow Chart</a>
<br><br>
<A HREF="online/files.html">File Formats</a>
<br><br>
-<A HREF="online/mdp_opt.html">mdp options</a>
-<br><br>
-<A HREF="http://www.gromacs.org/Documentation/FAQs">FAQ</a>
-<br>
-</TD>
-<TD VALIGN=top WIDTH=75%>
-<h3>Programs</h3>
-<A HREF="online/options.html">Options</a>
-<br><br>
-<a href="programs/byname.html">All Programs Alphabetically</a>
-<br><br>
-<a href="programs/bytopic.html">Programs by Topic</a>
</TD>
</TR>
</TABLE>
<h3>Description</h3>
The dlg file format is used as input for the
<a href="../programs/gmx-view.html">gmx view</a>
-trajectory viewer. These files are not meant to be altered bu the end user.
+trajectory viewer. These files are not meant to be altered by the end user.
<h3>Sample</h3>
<pre>
grid 39 18 {
<dt><b>Generic structure formats:</b>
<a href="gro.html">gro</a>,
<a href="g96.html">g96</a>,
-<a href="pdb.html">pdb</a>,
-<a href="tpr.html">tpr</a>,
-<a href="tpb.html">tpb</a> or
-<a href="tpa.html">tpa</a>
+<a href="pdb.html">pdb</a>, or
+<a href="tpr.html">tpr</a>
<dt><b>Structure+mass(db):</b>
<a href="tpr.html">tpr</a>,
-<a href="tpb.html">tpb</a>,
-<a href="tpa.html">tpa</a>,
<a href="gro.html">gro</a>,
<a href="g96.html">g96</a> or
<a href="pdb.html">pdb</a>.
<dd><dl compact>
<dt><a href="tpr.html">tpr</a> <dd>system topology, parameters, coordinates
and velocities (binary, portable)
-<dt><a href="tpa.html">tpa</a> <dd>system topology, parameters, coordinates
-and velocities (ascii)
-<dt><a href="tpb.html">tpb</a> <dd>system topology, parameters, coordinates
-and velocities (binary)
<dt><b>Generic run input file formats:</b>
-<a href="tpr.html">tpr</a>,
-<a href="tpb.html">tpb</a> or
-<a href="tpa.html">tpa</a>
+<a href="tpr.html">tpr</a>
</dl>
<br><dt><h3>Trajectory files</h3>
<dd><dl compact>
<dt><a href="tng.html">tng</a> <dd>Any kind of data (compressed, portable, any precision)
-<dt><a href="trj.html">trj</a> <dd>x, v and f (binary, full precision)
<dt><a href="trr.html">trr</a> <dd>x, v and f (binary, full precision, portable)
<dt><a href="xtc.html">xtc</a> <dd>x only (compressed, portable, any precision)
<dt><a href="gro.html">gro</a> <dd>x and v (ascii, any precision)
<dt><a href="g96.html">g96</a> <dd>x only (ascii, fixed high precision)
<dt><a href="pdb.html">pdb</a> <dd>x only (ascii, reduced precision)
<dt><b>Formats for full-precision data:</b>
-<a href="tng.html">tng</a>,
-<a href="trr.html">trr</a> or
-<a href="trj.html">trj</a>
+<a href="tng.html">tng</a> or
+<a href="trr.html">trr</a>
<dt><b>Generic trajectory formats:</b>
<a href="tng.html">tng</a>,
<a href="xtc.html">xtc</a>,
<a href="trr.html">trr</a>,
-<a href="trj.html">trj</a>,
<a href="gro.html">gro</a>,
<a href="g96.html">g96</a>,
<a href="pdb.html">pdb</a> or
<p>This is a flow chart of a typical GROMACS MD run of a protein
in a box of water.
A more detailed example is available in the
-<A HREF="getting_started.html">Getting Started</A>
+<A HREF="../user-guide.html#getting-started-with-gromacs">Getting Started</A>
section. Several steps of energy minimization may be necessary,
these consist of cycles: grompp -> mdrun.
<p>
+++ /dev/null
-<TITLE>Getting started</TITLE>
-<H3>Contents</H3>
-
-<ul>
-<li><a href="#start">Introduction</a>
-<ul>
- <li><a href="#setup">Setting up your environment</a>
-</ul>
-<li><a href="#files">GROMACS files</a>
-<ul>
- <li><a href="#top">Molecular topology file</a>
- <li><a href="#gro">Molecular structure file</a>
- <li><a href="#mdp">Molecular dynamics parameter file</a>
- <li><a href="#ndx">Index file</a>
- <li><a href="#tpr">Run input file</a>
- <li><a href="#trx">Trajectory file</a>
-</ul>
-<li><a href="#ref">References</a>
-</ul>
-
-<P>
-More info can be found in the
-<A HREF="flow.html">flowchart</A>
-(for a quick overview) and the
-<A HREF="http://www.gromacs.org/Documentation/FAQs">GROMACS FAQs</A>.
-</P>
-
-<br><hr><br>
-
-<a name="start"><H2>Introduction</A></H2>
-<p>
-In this chapter we assume the reader is familiar with Molecular
-Dynamics and familiar with Unix, including the use of a text editor
-such as <tt>jot</tt>, <tt>emacs</tt> or <tt>vi</tt>. We furthermore assume the
-GROMACS software is installed properly on your system. When you see a line
-like</p>
-
-<table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
-<tr NOSAVE>
-<td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
-<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
-
-<tt> ls -l
-</tt>
-<td></td>
-</tr>
-</table>
-<br>
-you are supposed to type the contents of that line on your computer.
-
-<H3><A NAME="setup">Setting up your environment</A></H3>
-<p>
-In order to check whether you have access to the GROMACS software, please
-start by entering the command:
-</p>
-<table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
-<tr NOSAVE>
-<td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
-<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
-
-<tt> mdrun -version
-</tt>
-<td></td>
-</tr>
-</table>
-<br>
-This command should print out information about the version of Gromacs
-installed.
-
-If this, in contrast, returns the phrase
-<pre>
-mdrun: command not found.
-</pre>
-
-then you have to verify where your version of GROMACS is installed.
-
-In the default case, the binaries are located in
-'/usr/local/gromacs/bin', however, you can ask your local system
-administrator for more information. If we assume that GROMACS is
-installed in directory <tt>XXX</tt> you would find the executables (programs) in
-<tt>XXX/bin</tt>. To be able to access the programs without
-problems, you will have to edit the login file for your shell. If you
-use the C shell, this file is called <TT>.cshrc</TT> or
-<TT>.tcshrc</TT>, and it is located in your home directory. Add a line
-like:
-
-<br><br>
-<table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
-<tr NOSAVE>
-<td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
-<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
-<tt>
-source XXX/bin/GMXRC
-</tt>
-<td></td>
-</tr>
-</table>
-<br>
-
-Issue this command at the prompt too, or log off and on again to
-automatically get the environment.
-You should have an environment variable set now that is called
-GMXDATA that we will use further on. Let us check whether this was
-successful using:<br><br>
-
-<table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
-<tr NOSAVE>
-<td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
-<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
-
-<tt> echo $GMXDATA
-</tt>
-<td></td>
-</tr>
-</table>
-<br>
-If it prints a directory name you are ready to rock, otherwise go back two steps.
-
-<br><hr><br>
-<H2><A NAME="files">GROMACS files</A></h2>
-Here is an overview of the most important GROMACS file types that you will
-encounter during the tutorial.
-<DL>
-<DT>
-<h3><A NAME="top">Molecular Topology file (<TT><a href="top.html">.top</a></TT>)</A></h3>
-<DD>
-The molecular topology file is generated by the program <TT>
-<a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a></TT>.
-<a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a> translates a
-<a href="pdb.html">pdb</a> structure file of any peptide or protein
-to a molecular topology file. This topology file contains a complete
-description of all the interactions in your peptide or protein.
-<P></P>
-
-<DT>
-<h3><A NAME="gro">Molecular Structure file (<TT><a href="gro.html">.gro</a></TT>, <TT><a href="pdb.html">.pdb</a></TT>)</A></h3>
-<DD>
-When the <a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a> program is executed
-to generate a molecular
-topology, it also translates the structure file (<TT><a href="pdb.html">.pdb</a></TT> file)
-to a gromos
-structure file (<TT><a href="gro.html">.gro</a></TT> file). The main difference between a
-<a href="pdb.html">pdb</a> file and a gromos file is their format and that
-a <TT><a href="gro.html">.gro</a></TT> file can also hold velocities. However, if you do not need the
-velocities, you can also use a <a href="pdb.html">pdb</a> file in all programs.
-To generate a box of solvent molecules
-around the peptide, the program
-<a href="../programs/gmx-solvate.html">gmx solvate</a> is used. First the program
-<a href="../programs/gmx-editconf.html">gmx editconf</a> should be used to
-define a box of appropriate size around the molecule.
-<a href="../programs/gmx-solvate.html">gmx solvate</a>
-solvates a solute molecule (the peptide) into any solvent (in this
-case water). The output of <TT><a href="../programs/gmx-solvate.html">gmx solvate</a></TT>
-is a gromos structure file of the peptide solvated in water. The
-<a href="../programs/gmx-solvate.html">gmx solvate</a> program also changes the
-molecular topology file (generated by <a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>)
-to add solvent to the topology.
-<P></P>
-
-<DT>
-<h3><A NAME="mdp">Molecular Dynamics parameter file (<TT><a href="mdp_opt.html">.mdp</a></TT>)</A></h3>
-<DD>
-The Molecular Dynamics Parameter (<TT><a href="mdp_opt.html">.mdp</a></TT>) file contains all
-information about the Molecular Dynamics simulation itself
-e.g. time-step, number of steps, temperature, pressure etc. The
-easiest way of handling such a file is by adapting a sample <TT><a href="mdp_opt.html">.mdp</a></TT>
-file. A <TT><a href="mdp.html">sample mdp file</a></TT>
-can be found online.
-<P></P>
-
-<DT>
-<h3><A NAME="ndx">Index file (<TT><a href="ndx.html">.ndx</a></TT>)</A></h3>
-<DD>
-Sometimes you may need an index file to specify actions on groups of atoms
-(e.g. Temperature coupling, accelerations, freezing). Usually the default index
-groups will be sufficient, so for this demo we will
-not consider the use of index files.
-<P></P>
-
-<DT>
-<h3><A NAME="tpr">Run input file (<TT><a href="tpr.html">.tpr</a></TT>)</A></h3>
-<DD>
-The next step is to combine the molecular structure (<TT><a href="gro.html">.gro</a></TT> file),
-topology (<TT><a href="top.html">.top</a></TT> file) MD-parameters (<TT><a href="mdp_opt.html">.mdp</a></TT> file) and
-(optionally) the
-index file (<TT><a href="ndx.html">ndx</a></TT>) to generate a run input file (<TT><a href="tpr.html">.tpr</a></tt> extension or
-<TT><a href="tpb.html">.tpb</a></tt> if you don't have XDR).
-This file contains all information needed to start a simulation with GROMACS.
-The
-<a href="../programs/gmx-grompp.html">gmx grompp</a> program processes all
-input files and generates the run input
-<tt><a href="tpr.html">.tpr</a></tt> file.
-<P></P>
-
-<DT>
-<h3><A NAME="trx">Trajectory file (<TT><a href="trr.html">.trr</a></TT></A>)</h3>
-<DD>
-Once the run input file is available, we can start the
-simulation. The program which starts the simulation is called
-<a href="../programs/gmx-mdrun.html">gmx mdrun</a>. The only input file
-of <TT><a href="../programs/gmx-mdrun.html">gmx mdrun</a></TT> you usually need
-to start a run
-is the run input file (<TT><a href="tpr.html">.tpr</a></TT> file).
-The output files of
-<TT><a href="../programs/gmx-mdrun.html">gmx mdrun</a></TT> are the
-trajectory file (<TT><a href="trr.html">.trr</a></TT> file
-or <TT><a href="trj.html">.trj</a></TT> if you don't have XDR) and a logfile (
-<TT><a href="log.html">.log</A></TT> file).
-<P></P>
-
-</DL>
-
-<br><hr><br>
-
-<P><H2><A NAME="ref">References</A></h2>
-
-<blockquote>
-<dl>
-
-<dt><A NAME="berendsen81">Berendsen, H.J.C., Postma, J.P.M., van
-Gunsteren, W.F., Hermans, J. (1981) <dd><it>Intermolecular
-Forces</it>, chapter Interaction models for water in relation to
-protein hydration, pp 331-342. Dordrecht: D. Reidel Publishing Company
-Dordrecht</dd><p>
-
-<dt><A NAME="kabsch83">Kabsch, W., Sander, C. (1983). <dd>Dictionary
-of protein secondary structure: Pattern recognition of hydrogen-bonded
-and geometrical features. <it>Biopolymers</it> <b>22</b>,
-2577--2637.</dd><p>
-
-<dt><A NAME="mierke91">Mierke, D.F., Kessler, H. (1991). <dd>Molecular
-dynamics with dimethyl sulfoxide as a solvent. Conformation of a
-cyclic hexapeptide. <it>J. Am. Chem. Soc.</it> <b>113</b>, 9446.</dd><p>
-
-<dt><A NAME="stryer88">Stryer, L. (1988). <dd><it>Biochemistry</it>
-vol. 1, p. 211. New York: Freeman, 3 edition.</dd><p>
-
-</dl>
-</blockquote>
<title>mdp file format</title>
-<P> Follow <a href="mdp_opt.html">this link</a> for a detailed description of the options</a>. </P>
+<P> See the <a href="../user-guide.html#molecular-dynamics-parameters-.mdp-options">user guide</a>
+for a detailed description of the options</a>. </P>
<P> Below is a sample mdp file.
The ordering of the items is not important, but if you enter the same
+++ /dev/null
-<TITLE>mdp options</TITLE>
-<!--
-
-PLEASE BE VERY CAREFUL WHEN EDITING THIS FILE: IT MUST BE
-AUTOMATICALLY PARSED BY A SIMPLE SCRIPT (mkmdp in the GROMACS manual repository) TO PRODUCE A
-CORRESPONDING LATEX FILE.
-
-IF YOU'RE NOT SURE ABOUT WHAT YOU'RE DOING, DON'T DO IT!
-
--->
-
-<H3>Table of Contents</H3>
-
-<ul>
-<li><A HREF="#general"><b>General remarks</b></A>
-<p> </p>
-<li><A HREF="#pp"><b>preprocessing</b></A> (include, define)
-<li><A HREF="#run"><b>run control</b></A> (integrator, tinit, dt, nsteps, init-step, comm-mode, nstcomm, comm-grps)
-<li><A HREF="#ld"><b>langevin dynamics</b></A> (bd-fric, ld-seed)
-<li><A HREF="#em"><b>energy minimization</b></A> (emtol, emstep, nstcgsteep)
-<li><a HREF="#shellmd"><b>shell molecular dynamics</b></a>(emtol,niter,fcstep)
-<li><a HREF="#tpi"><b>test particle insertion</b></a>(rtpi)
-<li><A HREF="#out"><b>output control</b></A> (nstxout, nstvout, nstfout, nstlog, nstcalcenergy, nstenergy, nstxout-compressed, compressed-x-precision, compressed-x-grps, energygrps)
-<li><A HREF="#nl"><b>neighbor searching</b></A> (cutoff-scheme, nstlist, nstcalclr, ns-type, pbc, periodic-molecules, verlet-buffer-tolerance, rlist, rlistlong)
-<li><A HREF="#el"><b>electrostatics</b></A> (coulombtype, coulomb-modifier, rcoulomb-switch, rcoulomb, epsilon-r, epsilon-rf)
-<li><A HREF="#vdw"><b>VdW</b></A> (vdwtype, vdw-modifier, rvdw-switch, rvdw, DispCorr)
-<li><A HREF="#table"><b>tables</b></A> (table-extension, energygrp-table)
-<li><A HREF="#ewald"><b>Ewald</b></A> (fourierspacing, fourier-nx, fourier-ny, fourier-nz, pme-order, ewald-rtol, ewald-geometry, epsilon-surface)
-<li><A HREF="#tc"><b>Temperature coupling</b></A> (tcoupl, nsttcouple, tc-grps, tau-t, ref-t)
-<li><A HREF="#pc"><b>Pressure coupling</b></A> (pcoupl, pcoupltype,
- nstpcouple, tau-p, compressibility, ref-p, refcoord-scaling)
-<li><A HREF="#sa"><b>simulated annealing</b></A> (annealing, annealing-npoints, annealing-time, annealing-temp)
-<li><A HREF="#vel"><b>velocity generation</b></A> (gen-vel, gen-temp, gen-seed)
-<li><A HREF="#bond"><b>bonds</b></A> (constraints, constraint-algorithm, continuation, shake-tol, lincs-order, lincs-iter, lincs-warnangle, morse)
-<li><A HREF="#egexcl"><b>Energy group exclusions</b></A> (energygrp-excl)
-<li><A HREF="#walls"><b>Walls</b></A> (nwall, wall-type, wall-r-linpot, wall-atomtype,
-wall-density, wall-ewald-zfac)
-<li><A HREF="#pull"><b>COM pulling</b></A> (pull, ...)
-<li><A HREF="#nmr"><b>NMR refinement</b></A> (disre, disre-weighting, disre-mixed, disre-fc, disre-tau, nstdisreout, orire, orire-fc, orire-tau, orire-fitgrp, nstorireout)
-<li><A HREF="#free"><b>Free energy calculations</b></A> (free-energy, nstdhdl, dhdl-print-energy, init-lambda, delta-lambda, fep-lambdas, coul-lambdas, vdw-lambdas, bonded-lambdas, restraint-lambdas, mass-lambdas, temperature-lambdas, sc-alpha, sc-coul, sc-power, sc-r-power, sc-sigma, couple-moltype, couple-lambda0, couple-lambda1, couple-intramol)
-<li><A HREF="#expanded"><b>Expanded ensemble simulation</b></A> (lmc-stats, lmc-mc-move, lmc-seed, lmc-gibbsdelta, mc-temperature, nst-transition-matrix, init-lambda-weights, initial-wl-delta, wl-scale, wl-ratio, symmetrized-transition-matrix, lmc-forced-nstart, mininum-var-min, lmc-weights-equil, weight-equil-wl-delta, weight-equil-number-all-lambda, weight-equil-number-steps, weight-equil-number-samples, weight-equil-count-ratio, simulated-tempering, simulated-tempering-scaling, sim-temp-low, sim-temp-high)
-<li><A HREF="#neq"><b>Non-equilibrium MD</b></A> (acc-grps, accelerate, freezegrps, freezedim, cos-acceleration, deform)
-<li><A HREF="#ef"><b>Electric fields</b></A> (E-x, E-xt, E-y, E-yt, E-z, E-zt )
-<li><A HREF="#qmmm"><b>Mixed quantum/classical dynamics</b></A> (QMMM, QMMM-grps, QMMMscheme, QMmethod, QMbasis, QMcharge, Qmmult, CASorbitals, CASelectrons, SH)
-<li><A HREF="#gbsa"><b>Implicit solvent</b></A> (implicit-solvent, gb-algorithm, nstgbradii, rgbradii, gb-epsilon-solvent, gb-saltconc, gb-obc-alpha, gb-obc-beta, gb-obc-gamma, gb-dielectric-offset, sa-algorithm, sa-surface-tension)
-<li><A HREF="#adress"><b>AdResS settings</b></A> (adress, adress_type, adress_const_wf, adress_ex_width, adress_hy_width, adress_ex_forcecap, adress_interface_correction, adress_site, adress_reference_coords, adress_tf_grp_names, adress_cg_grp_names)
-<li><A HREF="#user"><b>User defined thingies</b></A> (user1-grps, user2-grps, userint1, userint2, userint3, userint4, userreal1, userreal2, userreal3, userreal4)
-<li><A HREF="#idx"><b>Index</b></A>
-</ul>
-</P>
-
-<HR>
-
-<A NAME="general"><br>
-<h3>General</h3>
-
-<P>
-Default values are given in parentheses. The first option in
-the list is always the default option. Units are given in
-square brackets The difference between a dash and an underscore
-is ignored. </P>
-
-<P>
-A <a href="mdp.html">sample <TT>.mdp</TT> file</a> is
-available. This should be appropriate to start a normal
-simulation. Edit it to suit your specific needs and desires. </P>
-
-<A NAME="pp"><br>
-<hr>
-<h3>Preprocessing</h3>
-
-<dl>
-<dt><b>include:</b></dt>
-<dd>directories to include in your topology. Format:
-<PRE>-I/home/john/mylib -I../otherlib</PRE></dd>
-<dt><b>define:</b></dt>
-<dd>defines to pass to the preprocessor, default is no defines. You can use
-any defines to control options in your customized topology files. Options
-that are already available by default are:
-<dd><dl compact>
-<dt>-DFLEXIBLE</dt>
-<dd>Will tell <tt>grompp</tt> to include flexible water in stead of rigid water into your
-topology, this can be useful for normal mode analysis.</dd>
-<dt>-DPOSRES</dt>
-<dd>Will tell <tt>grompp</tt> to include posre.itp into your topology, used for
-<!--Idx-->position restraint<!--EIdx-->s.</dd>
-</dl>
-</dl>
-
-<A NAME="run"><br>
-<hr>
-<h3>Run control</h3>
-
-<dl>
-<dt><b>integrator:</b> (Despite the name, this list includes algorithms that are not actually integrators. <tt>steep</tt> and all entries following it are in this category)</dt>
-<dd><dl compact>
-<dt><b>md</b></dt>
-<dd>A leap-frog algorithm<!--QuietIdx-->leap-frog integrator<!--EQuietIdx-->
-for integrating Newton's equations of motion.</dd>
-<dt><b>md-vv</b></dt>
-<dd>A velocity Verlet algorithm for integrating Newton's equations of motion.
-For constant NVE simulations started from corresponding points in the same trajectory, the trajectories
-are analytically, but not binary, identical to the <b>md</b> leap-frog integrator. The the kinetic
-energy, which is determined from the whole step velocities and is therefore
-slightly too high. The advantage of this integrator is more accurate,
-reversible Nose-Hoover and Parrinello-Rahman coupling integration
-based on Trotter expansion, as well as (slightly too small) full step velocity
-output. This all comes at the cost off extra computation, especially with
-constraints and extra communication in parallel. Note that for nearly all
-production simulations the <b>md</b> integrator is accurate enough.
-</dd>
-<dt><b>md-vv-avek</b></dt>
-<dd>A velocity Verlet algorithm identical to <b>md-vv</b>, except that
-the kinetic energy is determined as the average of
-the two half step kinetic energies as in the <b>md</b> integrator, and this thus more accurate.
-With Nose-Hoover and/or Parrinello-Rahman coupling this comes with
-a slight increase in computational cost.
-</dd>
-<dt><b>sd</b></dt>
-<dd> An accurate and efficient leap-frog stochastic dynamics integrator.
-With constraints, coordinates needs to be constrained twice per integration step.
-Depending on the computational cost of the force calculation,
-this can take a significant part of the simulation time.
-The temperature for one or more groups of atoms
-(<b><A HREF="#tc">tc-grps</A></b>)
-is set with <b><A HREF="#tc">ref-t</A></b> [K],
-the inverse friction constant for each group is set with
-<b><A HREF="#tc">tau-t</A></b> [ps].
-The parameter <b><A HREF="#tc">tcoupl</A></b> is ignored.
-The random generator is initialized with <b><A HREF="#ld">ld-seed</A></b>.
-When used as a thermostat, an appropriate value for <b>tau-t</b> is 2 ps,
-since this results in a friction that is lower than the internal friction
-of water, while it is high enough to remove excess heat
-NOTE: temperature deviations decay twice as fast as with
-a Berendsen thermostat with the same <b>tau-t</b>.</dd>
-<dt><b>sd2</b></dt>
-<dd> This used to be the default sd integrator, but is now deprecated.
-Four Gaussian random numbers are required per coordinate per step.
-With constraints, the temperature will be slightly too high.</dd>
-<dt><b>bd</b></dt>
-<dd>An Euler integrator for Brownian or position Langevin dynamics, the
-velocity is the force divided by a friction coefficient
-(<b><A HREF="#ld">bd-fric</A></b> [amu ps<sup>-1</sup>])
-plus random thermal noise (<b><A HREF="#tc">ref-t</A></b>).
-When <b><A HREF="#ld">bd-fric</A></b><tt>=0</tt>, the friction coefficient for each
-particle is calculated as mass/<b><A HREF="#tc">tau-t</A></b>, as for the
-integrator <tt>sd</tt>.
-The random generator is initialized with <b><A HREF="#ld">ld-seed</A></b>.</dd>
-
-<dt><b>steep</b></dt>
-<dd>A <!--Idx-->steepest descent<!--EIdx--> algorithm for energy
-minimization. The maximum step size is <b><A HREF="#em">emstep</A></b>
-[nm], the tolerance is <b><A HREF="#em">emtol</A></b> [kJ
-mol<sup>-1</sup> nm<sup>-1</sup>].</dd>
-<dt><b>cg</b></dt>
-<dd>A <!--Idx-->conjugate gradient<!--EIdx--> algorithm for energy
-minimization, the tolerance is <b>emtol</b> [kJ mol<sup>-1</sup>
-nm<sup>-1</sup>]. CG is more efficient when a steepest descent step
-is done every once in a while, this is determined by
-<b><A HREF="#em">nstcgsteep</A></b>.
-For a minimization prior to a normal mode analysis, which requires
-a very high accuracy, GROMACS should be compiled in double precision.</dd>
-<dt><b>l-bfgs</b></dt>
-<dd>A <!--Idx-->quasi-Newtonian<!--EIdx--> algorithm for energy minimization
-according to the low-memory Broyden-Fletcher-Goldfarb-Shanno approach.
-In practice this seems to converge faster than Conjugate Gradients, but due
-to the correction steps necessary it is not (yet) parallelized.
-</dd>
-<dt><b>nm</b></dt>
-<dd>Normal mode analysis<!--QuietIdx-->normal-mode analysis<!--EQuietIdx--> is performed
-on the structure in the <tt>tpr</tt> file. GROMACS should be
-compiled in double precision.</dd>
-<dt><b>tpi</b></dt>
-<dd> Test particle insertion. The last molecule in the topology
-is the test particle. A trajectory should be provided with
-the <tt>-rerun</tt> option of <tt>mdrun</tt>. This trajectory
-should not contain the molecule to be inserted. Insertions
-are performed <b>nsteps</b> times in each frame at random locations
-and with random orientiations of the molecule. When <b>nstlist</b>
-is larger than one, <b>nstlist</b> insertions are performed
-in a sphere with radius <b><A HREF="#tpi">rtpi</A></b>
-around a the same random location using the same neighborlist
-(and the same long-range energy when <b>rvdw</b> or <b>rcoulomb</b>><b>rlist</b>,
-which is only allowed for single-atom molecules).
-Since neighborlist construction is expensive, one can perform several
-extra insertions with the same list almost for free.
-The random seed is set with <b><A HREF="#ld">ld-seed</A></b>.
-The temperature for the Boltzmann weighting is set with
-<b><A HREF="#tc">ref-t</A></b>, this should match the temperature
-of the simulation of the original trajectory.
-Dispersion correction is implemented correctly for tpi.
-All relevant quantities are written to the file specified with
-the <tt>-tpi</tt> option of <tt>mdrun</tt>.
-The distribution of insertion energies is written to the file specified with
-the <tt>-tpid</tt> option of <tt>mdrun</tt>.
-No trajectory or energy file is written.
-Parallel tpi gives identical results to single node tpi.
-For charged molecules, using PME with a fine grid is most accurate
-and also efficient, since the potential in the system only needs
-to be calculated once per frame.
-</dd>
-<dt><b>tpic</b></dt>
-<dd> Test particle insertion into a predefined cavity location.
-The procedure is the same as for <b>tpi</b>, except that one coordinate
-extra is read from the trajectory, which is used as the insertion location.
-The molecule to be inserted should be centered at 0,0,0. Gromacs does
-not do this for you, since for different situations a different
-way of centering might be optimal.
-Also <b><A HREF="#tpi">rtpi</A></b> sets the radius for the sphere
-around this location. Neighbor searching is done only once per frame,
-<b>nstlist</b> is not used.
-Parallel tpic gives identical results to single node tpic.
-</dl>
-
-<dt><b>tinit: (0) [ps]</b></dt>
-<dd>starting time for your run (only makes sense for integrators <tt>md</tt>,
-<tt>sd</tt> and <tt>bd</tt>)</dd>
-<dt><b>dt: (0.001) [ps]</b></dt></dd>
-<dd>time step for integration (only makes sense for integrators <tt>md</tt>,
-<tt>sd</tt> and <tt>bd</tt>)</dd>
-<dt><b>nsteps: (0)</b></dt>
-<dd>maximum number of steps to integrate or minimize, -1 is no maximum</dd>
-<dt><b>init-step: (0)</b></dt>
-<dd>The starting step.
-The time at an step i in a run is calculated as: t = <tt>tinit</tt> + <tt>dt</tt>*(<tt>init-step</tt> + i).
-The free-energy lambda is calculated as: lambda = <tt>init-lambda</tt> + <tt>delta-lambda</tt>*(<tt>init-step</tt> + i).
-Also non-equilibrium MD parameters can depend on the step number.
-Thus for exact restarts or redoing part of a run it might be necessary to
-set <tt>init-step</tt> to the step number of the restart frame.
-<tt>gmx convert-tpr</tt> does this automatically.
-</dd>
-<dt><b>comm-mode:</b></dt>
-<dd><dl compact>
-<dt><b>Linear</b></dt>
-<dd>Remove center of mass translation</dd>
-<dt><b>Angular</b></dt>
-<dd>Remove center of mass translation and rotation around the center of mass
-</dd>
-<dt><b>None</b></dt>
-<dd>No restriction on the center of mass motion
-</dl></dd>
-<dt><b>nstcomm: (100) [steps]</b></dt>
-<dd>frequency for center of mass motion removal</dd>
-<dt><b>comm-grps:</b></dt>
-<dd>group(s) for center of mass motion removal, default is the whole system</dd>
-</dl>
-
-<A NAME="ld"><br>
-<hr>
-<h3><!--Idx-->Langevin dynamics<!--EIdx--></h3>
-
-<dl>
-<dt><b>bd-fric: (0) [amu ps<sup>-1</sup>]</b></dt>
-<dd>Brownian dynamics friction coefficient.
-When <b>bd-fric</b><tt>=0</tt>, the friction coefficient for each
-particle is calculated as mass/<b><A HREF="#tc">tau-t</A></b>.</dd>
-<dt><b>ld-seed: (-1) [integer]</b></dt>
-<dd>used to initialize random generator for thermal noise
-for stochastic and Brownian dynamics.
-When <b>ld-seed</b> is set to -1, a pseudo random seed is used.
-When running BD or SD on multiple processors, each processor uses a seed equal
-to <b>ld-seed</b> plus the processor number.</dd>
-</dl>
-
-<A NAME="em"><br>
-<hr>
-<h3>Energy minimization<!--QuietIdx-->energy minimization<!--EQuietIdx--></h3>
-<dl>
-<dt><b>emtol: (10.0) [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
-<dd>the minimization is converged when the maximum force is smaller than
-this value</dd>
-<dt><b>emstep: (0.01) [nm]</b></dt>
-<dd>initial step-size</dd>
-<dt><b>nstcgsteep: (1000) [steps]</b></dt>
-<dd>frequency of performing 1 steepest descent step while doing
-conjugate gradient energy minimization.</dd>
-<dt><b>nbfgscorr: (10)</b></dt>
-<dd>Number of correction steps to use for L-BFGS minimization. A higher
-number is (at least theoretically) more accurate, but slower.</dd>
-</dl>
-
-<A NAME="shellmd"><br>
-<hr>
-<h3>Shell Molecular Dynamics<!--QuietIdx-->shell molecular dynamics<!--EQuietIdx--></h3>
-When shells or
-flexible constraints are present in the system the positions of the shells
-and the lengths of the flexible constraints are optimized at
-every time step until either the RMS force on the shells and constraints
-is less than emtol, or a maximum number of iterations (niter) has been reached
-<dl>
-<dt><b>emtol: (10.0) [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
-<dd>the minimization is converged when the maximum force is smaller than
-this value. For shell MD this value should be 1.0 at most, but since the
-variable is used for energy minimization as well the default is 10.0.</dd>
-<dt><b>niter: (20)</b></dt>
-<dd>maximum number of iterations for optimizing the shell positions
-and the flexible constraints.</dd>
-<dt><b>fcstep: (0) [ps<sup>2</sup>]</b></dt>
-<dd>the step size for optimizing the flexible constraints.
-Should be chosen as mu/(d<sup>2</sup>V/dq<sup>2</sup>)
-where mu is the reduced mass of two particles in a flexible constraint
-and d<sup>2</sup>V/dq<sup>2</sup> is the second derivative of the potential
-in the constraint direction. Hopefully this number does not differ too
-much between the flexible constraints, as the number of iterations
-and thus the runtime is very sensitive to <tt>fcstep</tt>.
-Try several values!</dd>
-</dl>
-
-<A NAME="tpi"><br>
-<hr>
-<h3>Test particle insertion</h3>
-<dl>
-<dt><b>rtpi: (0.05) [nm]</b></dt>
-<dd>the test particle insertion radius see integrators
-<b><a href="#run">tpi</a></b> and <b><a href="#run">tpic</a></b></dd>
-</dl>
-
-<A NAME="out"><br>
-<hr>
-<h3>Output control</h3>
-<dl>
-<dt><b>nstxout: (0) [steps]</b></dt>
-<dd>number of steps that elapse between writing coordinates to output
-<!--Idx-->trajectory file<!--EIdx-->, the last coordinates are always written</dd>
-<dt><b>nstvout: (0) [steps]</b></dt>
-<dd>number of steps that elapse between writing velocities to output trajectory,
-the last velocities are always written</dd>
-<dt><b>nstfout: (0) [steps]</b></dt>
-<dd>number of steps that elapse between writing forces to output trajectory.</dd>
-<dt><b>nstlog: (1000) [steps]</b></dt>
-<dd>number of steps that elapse between writing energies to the <!--Idx-->log file<!--EIdx-->,
-the last energies are always written</dd>
-<dt><b>nstcalcenergy: (100)</b></dt>
-<dd>number of steps that elapse between calculating the energies, 0 is never.
-This option is only relevant with dynamics.
-With a twin-range cut-off setup <b>nstcalcenergy</b> should be equal to
-or a multiple of <b>nstlist</b>.
-This option affects the performance in parallel simulations,
-because calculating energies requires global communication between all
-processes which can become a bottleneck at high parallelization.
-</dd>
-<dt><b>nstenergy: (1000) [steps]</b></dt>
-<dd>number of steps that else between writing energies to energy file,
-the last energies are always written,
-should be a multiple of <b>nstcalcenergy</b>.
-Note that the exact sums and fluctuations over all MD steps
-modulo <b>nstcalcenergy</b> are stored in the energy file,
-so <tt>g_energy</tt> can report exact
-energy averages and fluctuations also when <b>nstenergy</b><tt>>1</tt></dd>
-<dt><b>nstxout-compressed: (0) [steps]</b></dt>
-<dd>number of steps that elapse between writing position coordinates using lossy compression</dd>
-<dt><b>compressed-x-precision: (1000) [real]</b></dt>
-<dd>precision with which to write to the compressed trajectory file</dd>
-<dt><b>compressed-x-grps:</b></dt>
-<dd>group(s) to write to the compressed trajectory file, by default the whole system is written
-(if <b>nstxout-compressed</b> > 0)</dd>
-<dt><b>energygrps:</b></dt>
-<dd>group(s) to write to energy file</dd>
-</dl>
-
-<A NAME="nl"><br>
-<hr>
-<h3>Neighbor searching<!--QuietIdx-->neighbor searching<!--EQuietIdx--></h3>
-<dl>
-<dt><b>cutoff-scheme:</b></dt>
-<dd><dl compact>
-<dt><b>Verlet</b></dt>
-<dd>Generate a pair list with buffering. The buffer size is automatically set
-based on <b>verlet-buffer-tolerance</b>, unless this is set to -1, in which case
-<b>rlist</b> will be used. This option has an explicit, exact cut-off at
-<b>rvdw</b>=<b>rcoulomb</b>. Currently only cut-off, reaction-field,
-PME electrostatics and plain LJ are supported. Some <tt>mdrun</tt> functionality
-is not yet supported with the <b>Verlet</b> scheme, but <tt>grompp</tt> checks for this.
-Native GPU acceleration is only supported with <b>Verlet</b>.
-With GPU-accelerated PME or with separate PME ranks,
-<tt>mdrun</tt> will automatically tune the CPU/GPU load balance by
-scaling <b>rcoulomb</b> and the grid spacing. This can be turned off with
-<tt>-notunepme</tt>.
-
-<b>Verlet</b> is faster than <b>group</b> when there is no water, or if <b>group</b> would use a pair-list buffer to conserve energy.
-</dd>
-<dt><b>group</b></dt>
-<dd>Generate a pair list for groups of atoms. These groups correspond to the
-charge groups in the topology. This was the only cut-off treatment scheme
-before version 4.6.
-There is no explicit buffering of the pair list. This enables efficient force
-calculations for water, but energy is only conserved when a buffer is explicitly added.</dd>
-
-</dl></dd>
-
-<dt><b>nstlist: (10) [steps]</b></dt>
-<dd><dl compact>
-<dt><b>>0</b></dt>
-<dd>Frequency to update the <!--Idx-->neighbor list<!--EIdx--> (and
-the long-range forces, when using twin-range cut-offs). When this is 0,
-the neighbor list is made only once.
-With energy minimization the neighborlist will be updated for every
-energy evaluation when <b>nstlist</b><tt>>0</tt>.
-With <b>cutoff-scheme=Verlet</b> and <b>verlet-buffer-tolerance</b> set,
-<b>nstlist</b> is actually a minimum value and <tt>mdrun</tt> might increase it, unless it is set to 1.
-With parallel simulations and/or non-bonded force calculation on the GPU,
-a value of 20 or 40 often gives the best performance.
-With <b>cutoff-scheme=Group</b> and non-exact cut-off's, <b>nstlist</b> will
-affect the accuracy of your simulation and it can not be chosen freely.
-</dd>
-<dt><b>0</b></dt>
-<dd>The neighbor list is only constructed once and never updated.
-This is mainly useful for vacuum simulations in which all particles
-see each other.</dd>
-<dt><b>-1</b></dt>
-<dd>Automated update frequency, only supported with <b>cutoff-scheme</b>=<b>group</b>.
-This can only be used with switched, shifted or user potentials where
-the cut-off can be smaller than <b>rlist</b>. One then has a buffer
-of size <b>rlist</b> minus the longest cut-off.
-The neighbor list is only updated when one or more particles have moved further
-than half the buffer size from the center of geometry of their charge group
-as determined at the previous neighbor search.
-Coordinate scaling due to pressure coupling or the <b>deform</b> option
-is taken into account.
-This option guarantees that their are no cut-off artifacts,
-but for larger systems this can come at a high computational cost,
-since the neighbor list update frequency will be determined
-by just one or two particles moving slightly beyond the half buffer length
-(which does not necessarily imply that the neighbor list is invalid),
-while 99.99% of the particles are fine.
-</dd>
-</dl></dd>
-
-<dt><b>nstcalclr: (-1) [steps]</b></dt>
-<dd>
-Controls the period between calculations of long-range forces when
-using the group cut-off scheme.
-<dl compact>
-<dt><b>1</b></dt>
-<dd>Calculate the long-range forces every single step. This is useful
-to have separate neighbor lists with buffers for electrostatics and Van
-der Waals interactions, and in particular it makes it possible to have
-the Van der Waals cutoff longer than electrostatics (useful e.g. with
-PME). However, there is no point in having identical long-range
-cutoffs for both interaction forms and update them every step - then
-it will be slightly faster to put everything in the short-range
-list.</dd>
-<dt><b>>1</b></dt>
-<dd>Calculate the long-range forces every <b>nstcalclr</b> steps and
-use a multiple-time-step integrator to combine forces. This can now be
-done more frequently than <b>nstlist</b> since the lists are stored,
-and it might be a good idea e.g. for Van der Waals interactions that
-vary slower than electrostatics.</dd>
-<dt><b>-1</b></dt>
-<dd>Calculate long-range forces on steps where neighbor searching is
-performed. While this is the default value, you might want to consider
-updating the long-range forces more frequently.</dd>
-</dl>
-Note that twin-range force evaluation might be enabled automatically
-by PP-PME load balancing. This is done in order to maintain the chosen
-Van der Waals interaction radius even if the load balancing is
-changing the electrostatics cutoff. If the <tt>.mdp</tt> file already
-specifies twin-range interactions (e.g. to evaluate Lennard-Jones
-interactions with a longer cutoff than the PME electrostatics every
-2-3 steps), the load balancing will have also a small effect on
-Lennard-Jones, since the short-range cutoff (inside which forces are
-evaluated every step) is changed.
-</dd>
-
-
-
-<dt><b>ns-type:</b></dt>
-<dd><dl compact>
-<dt><b>grid</b></dt>
-<dd>Make a grid in the box and only check atoms in neighboring grid
-cells when constructing a new neighbor list every <b>nstlist</b> steps.
-In large systems grid search is much faster than simple search.</dd>
-<dt><b>simple</b></dt>
-<dd>Check every atom in the box when constructing a new neighbor list
-every <b>nstlist</b> steps (only with <b>cutoff-scheme=group</b>).</dd>
-</dl></dd>
-
-<dt><b>pbc:</b></dt>
-<dd><dl compact>
-<dt><b>xyz</b></dt>
-<dd>Use periodic boundary conditions in all directions.</dd>
-<dt><b>no</b></dt>
-<dd>Use no periodic boundary conditions, ignore the box.
-To simulate without cut-offs, set all cut-offs to 0 and <b>nstlist</b><tt>=0</tt>.
-For best performance without cut-offs on a single MPI rank,
-use <b>nstlist</b><tt>=0</tt>, <b>ns-type</b><tt>=simple</tt></dd>
-<dt><b>xy</b></dt>
-<dd>Use periodic boundary conditions in x and y directions only.
-This works only with <b>ns-type</b><tt>=grid</tt> and can be used
-in combination with <b><a href="#walls">walls</a></b>.
-Without walls or with only one wall the system size is infinite
-in the z direction. Therefore pressure coupling or Ewald summation
-methods can not be used.
-These disadvantages do not apply when two walls are used.</dd>
-</dl></dd>
-
-<dt><b>periodic-molecules:</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>molecules are finite, fast molecular PBC can be used</dd>
-<dt><b>yes</b></dt>
-<dd>for systems with molecules that couple to themselves through
-the periodic boundary conditions, this requires a slower PBC algorithm
-and molecules are not made whole in the output</dd>
-</dl></dd>
-
-<dt><b>verlet-buffer-tolerance: (0.005) [kJ/mol/ps]</b></dt>
-<dd>Useful only with <b>cutoff-scheme</b>=<b>Verlet</b>. This sets the maximum
-allowed error for pair interactions per particle caused by the Verlet buffer,
-which indirectly sets <b>rlist</b>.
-As both <b>nstlist</b> and the Verlet buffer size are fixed
-(for performance reasons), particle pairs not in the pair list can occasionally
-get within the cut-off distance during <b>nstlist</b>-1 nsteps. This
-causes very small jumps in the energy. In a constant-temperature ensemble,
-these very small energy jumps can be
-estimated for a given cut-off and <b>rlist</b>. The estimate assumes a
-homogeneous particle distribution, hence the errors might be slightly
-underestimated for multi-phase systems. For longer pair-list life-time
-(<b>nstlist</b>-1)*dt the buffer is overestimated, because the interactions
-between particles are ignored. Combined with cancellation of errors,
-the actual drift of the total energy is usually one to two orders of magnitude
-smaller.
-Note that the generated buffer size takes into account that
-the GROMACS pair-list setup leads to a reduction in the drift by
-a factor 10, compared to a simple particle-pair based list.
-Without dynamics (energy minimization etc.), the buffer is 5% of the cut-off.
-For NVE simulations the initial temperature is used, unless this is zero,
-in which case a buffer of 10% is used. For NVE simulations the tolerance
-usually needs to be lowered to achieve proper energy conservation on
-the nanosecond time scale. To override the automated buffer setting,
-use <b>verlet-buffer-tolerance</b>=-1 and set <b>rlist</b> manually.</dd>
-
-<dt><b>rlist: (1) [nm]</b></dt>
-<dd>Cut-off distance for the short-range neighbor list.
-With <b>cutoff-scheme</b>=<b>Verlet</b>, this is by default set by the
-<b>verlet-buffer-tolerance</b> option and the value of <b>rlist</b> is ignored.</dd>
-
-<dt><b>rlistlong: (-1) [nm]</b></dt>
-<dd>Cut-off distance for the long-range neighbor list.
-This parameter is only relevant for a twin-range cut-off setup
-with switched potentials. In that case a buffer region is required to account
-for the size of charge groups. In all other cases this parameter
-is automatically set to the longest cut-off distance.</dd>
-</dl>
-
-
-<A NAME="el"><br>
-<hr>
-<h3>Electrostatics<!--QuietIdx-->electrostatics<!--EQuietIdx--></h3>
-<dl>
-<dt><b>coulombtype:</b></dt>
-<dd><dl compact>
-
-<dt><b>Cut-off</b></dt>
-<dd>Twin range cut-offs with neighborlist cut-off <b>rlist</b> and
-Coulomb cut-off <b>rcoulomb</b>,
-where <b>rcoulomb</b>≥<b>rlist</b>.
-
-<dt><b>Ewald</b></dt>
-<dd>Classical <!--Idx-->Ewald sum<!--EIdx--> electrostatics.
-The real-space cut-off <b>rcoulomb</b> should be equal to <b>rlist</b>.
-Use e.g. <b>rlist</b><tt>=0.9</tt>, <b>rcoulomb</b><tt>=0.9</tt>. The highest magnitude of
-wave vectors used in reciprocal space is controlled by <b>fourierspacing</b>.
-The relative accuracy of direct/reciprocal space
-is controlled by <b>ewald-rtol</b>.
-<br>
-NOTE: Ewald scales as O(N<sup>3/2</sup>)
-and is thus extremely slow for large systems. It is included mainly for
-reference - in most cases PME will perform much better.</dd>
-
-<dt><b><!--Idx-->PME<!--EIdx--></b></dt>
-<dd>Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct space is similar
-to the Ewald sum, while the reciprocal part is performed with
-FFTs. Grid dimensions are controlled with <b>fourierspacing</b> and the
-interpolation order with <b>pme-order</b>. With a grid spacing of 0.1
-nm and cubic interpolation the electrostatic forces have an accuracy
-of 2-3*10<sup>-4</sup>. Since the error from the vdw-cutoff is larger than this you
-might try 0.15 nm. When running in parallel the interpolation
-parallelizes better than the FFT, so try decreasing grid dimensions
-while increasing interpolation.</dd>
-
-<dt><b><!--Idx-->P3M-AD<!--EIdx--></b></dt>
-<dd>Particle-Particle Particle-Mesh algorithm with analytical derivative
-for for long range electrostatic interactions. The method and code
-is identical to SPME, except that the influence function is optimized
-for the grid. This gives a slight increase in accuracy.</dd>
-
-<dt><b>Reaction-Field electrostatics<!--QuietIdx-->reaction-field electrostatics<!--EQuietIdx--></b></dt>
-<dd>Reaction field with Coulomb cut-off <b>rcoulomb</b>,
-where <b>rcoulomb</b> ≥ <b>rlist</b>.
-The dielectric constant beyond the cut-off is <b>epsilon-rf</b>.
-The dielectric constant can be set to infinity by setting <b>epsilon-rf</b><tt>=0</tt>.</dd>
-
-<dt><b>Generalized-Reaction-Field</b></dt>
-<dd>Generalized reaction field with Coulomb cut-off <b>rcoulomb</b>,
-where <b>rcoulomb</b> ≥ <b>rlist</b>.
-The dielectric constant beyond the cut-off is <b>epsilon-rf</b>.
-The ionic strength is computed from the number of charged
-(i.e. with non zero charge) <!--Idx-->charge group<!--EIdx-->s.
-The temperature for the GRF potential is set with
-<b><A HREF="#tc">ref-t</A></b> [K].</dd>
-
-<dt><b>Reaction-Field-zero</b></dt>
-<dd>In GROMACS, normal reaction-field electrostatics with
-<b>cutoff-scheme</b><b>=group</b> leads to bad
-energy conservation. <b>Reaction-Field-zero</b> solves this
-by making the potential zero beyond the cut-off. It can only
-be used with an infinite dielectric constant (<b>epsilon-rf=0</b>),
-because only for that value the force vanishes at the cut-off.
-<b>rlist</b> should be 0.1 to 0.3 nm larger than <b>rcoulomb</b>
-to accommodate for the size of charge groups and diffusion
-between neighbor list updates. This, and the fact that table lookups
-are used instead of analytical functions make <b>Reaction-Field-zero</b>
-computationally more expensive than normal reaction-field.</dd>
-
-<dt><b>Reaction-Field-nec</b></dt>
-<dd>The same as <b>Reaction-Field</b>, but implemented as in
-GROMACS versions before 3.3. No reaction-field correction is applied
-to excluded atom pairs and self pairs.
-The 1-4 interactions are calculated using a reaction-field.
-The missing correction due to the excluded pairs that do not have a 1-4
-interaction is up to a few percent of the total electrostatic
-energy and causes a minor difference in the forces and the pressure.</dd>
-
-<dt><b>Shift</b></dt>
-<dd>Analogous to <b>Shift</b> for <b>vdwtype</b>.
-You might want to use <b>Reaction-Field-zero</b> instead,
-which has a similar potential shape, but has a physical interpretation
-and has better energies due to the exclusion correction terms.
-</dd>
-
-<dt><b>Encad-Shift</b></dt>
-<dd>The Coulomb
-potential is decreased over the whole range, using the definition
-from the Encad simulation package.</dd>
-
-<dt><b>Switch</b></dt>
-<dd>Analogous to <b>Switch</b> for <b>vdwtype</b>.
-Switching the Coulomb potential can lead to serious artifacts,
-advice: use <b>Reaction-Field-zero</b> instead.</dd>
-
-<dt><b>User</b></dt>
-<dd><a name="usertab"></a><tt>mdrun</tt> will now expect to find a file
-<tt>table.xvg</tt> with user-defined potential functions for
-repulsion, dispersion and Coulomb. When pair interactions are present,
-<tt>mdrun</tt> also expects to find a file <tt>tablep.xvg</tt> for
-the pair interactions. When the same interactions should be used
-for non-bonded and pair interactions the user can specify the same
-file name for both table files.
-These files should contain 7
-columns: the <tt>x</tt> value,
-<tt>f(x)</tt>, <tt>-f'(x)</tt>,
-<tt>g(x)</tt>, <tt>-g'(x)</tt>,
-<tt>h(x)</tt>, <tt>-h'(x)</tt>,
-where <tt>f(x)</tt> is the Coulomb function, <tt>g(x)</tt> the dispersion function
-and <tt>h(x)</tt> the repulsion function.
-When <b>vdwtype</b> is not set to <b>User</b> the values
-for <tt>g</tt>, <tt>-g'</tt>, <tt>h</tt> and <tt>-h'</tt> are ignored.
-For the non-bonded interactions <tt>x</tt> values should run
-from 0 to the largest cut-off distance + <b>table-extension</b>
-and should be uniformly spaced. For the pair interactions the table
-length in the file will be used.
-The optimal spacing, which is used for non-user tables,
-is <tt>0.002</tt> [nm] when you run in mixed precision
-or <tt>0.0005</tt> [nm] when you run in double precision.
-The function value at <tt>x=0</tt> is not important. More information is
-in the printed manual.</dd>
-
-<dt><b>PME-Switch</b></dt>
-<dd>A combination of PME and a switch function for the direct-space part
-(see above). <b>rcoulomb</b> is allowed to be smaller than <b>rlist</b>.
-This is mainly useful constant energy simulations (note that using
-<b>PME</b> with <b>cutoff-scheme</b>=<b>Verlet</b> will be more efficient).
-</dd>
-
-<dt><b>PME-User</b></dt>
-<dd>A combination of PME and user tables (see above).
-<b>rcoulomb</b> is allowed to be smaller than <b>rlist</b>.
-The PME mesh contribution is subtracted from the user table by <tt>mdrun</tt>.
-Because of this subtraction the user tables should contain
-about 10 decimal places.</dd>
-
-<dt><b>PME-User-Switch</b></dt>
-<dd>A combination of PME-User and a switching function (see above).
-The switching function is applied to final particle-particle interaction,
-i.e. both to the user supplied function and the PME Mesh correction part.</dd>
-
-</dl></dd>
-
-<dt><b>coulomb-modifier:</b></dt>
-<dd><dl compact>
-<dt><b>Potential-shift-Verlet</b></dt>
-<dd>Selects <b>Potential-shift</b> with the Verlet cutoff-scheme,
-as it is (nearly) free; selects <b>None</b> with the group cutoff-scheme.</dd>
-<dt><b>Potential-shift</b></dt>
-<dd>Shift the Coulomb potential by a constant such that it is zero at the cut-off.
-This makes the potential the integral of the force. Note that this does not
-affect the forces or the sampling.</dd>
-<dt><b>None</b></dt>
-<dd>Use an unmodified Coulomb potential. With the group scheme this means no exact cut-off is used, energies and forces are calculated for all pairs in the neighborlist.</dd>
-</dl></dd>
-
-
-<A NAME="el2">
-<dt><b>rcoulomb-switch: (0) [nm]</b></dt>
-<dd>where to start switching the Coulomb potential, only relevant when force or potential switching is used</dd>
-
-<dt><b>rcoulomb: (1) [nm]</b></dt>
-<dd>distance for the Coulomb <!--Idx-->cut-off<!--EIdx--></dd>
-
-<dt><b>epsilon-r: (1)</b></dt>
-<dd>The relative <!--Idx-->dielectric constant<!--EIdx-->.
-A value of 0 means infinity.</dd>
-
-<dt><b>epsilon-rf: (0)</b></dt>
-<dd>The relative dielectric constant of the reaction field.
-This is only used with reaction-field electrostatics.
-A value of 0 means infinity.</dd>
-</dl>
-
-<A NAME="vdw">
-<hr>
-<h3>VdW</h3>
-<dl>
-<dt><b>vdwtype:</b></dt>
-<dd><dl compact>
-<dt><b>Cut-off</b></dt>
-<dd>Twin range cut-offs with neighbor list cut-off <b>rlist</b> and
-VdW cut-off <b>rvdw</b>,
-where <b>rvdw</b> <tt>≥</tt> <b>rlist</b>.</dd>
-
-<dt><b>PME</b></dt>
-<dd>Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
-grid dimensions are controlled with <b>fourierspacing</b> in the same
-way as for electrostatics, and the interpolation order is controlled
-with <b>pme-order</b>. The relative accuracy of direct/reciprocal
-space is controlled by <b>ewald-rtol-lj</b>, and the specific
-combination rules that are to be used by the reciprocal routine are
-set using <b>lj-pme-comb-rule</b>.</dd>
-
-<dt><b>Shift</b></dt>
-<dd>This functionality is deprecated and replaced by <b>vdw-modifier = Force-switch</b>.
-The LJ (not Buckingham) potential is decreased over the whole
-range and the forces decay smoothly to zero between <b>rvdw-switch</b>
-and <b>rvdw</b>. The neighbor search cut-off <b>rlist</b> should be
-0.1 to 0.3 nm larger than <b>rvdw</b> to accommodate for the size of
-charge groups and diffusion between neighbor list
-updates.</dd>
-
-<dt><b>Switch</b></dt>
-<dd>This functionality is deprecated and replaced by <b>vdw-modifier = Potential-switch</b>.
-The LJ (not Buckingham)
-potential is normal out to <b>rvdw-switch</b>, after which it is switched
-off to reach zero at <b>rvdw</b>. Both the potential and force functions
-are continuously smooth, but be aware that all switch functions will give rise
-to a bulge (increase) in the force (since we are switching the potential).
-The neighbor search cut-off <b>rlist</b> should be 0.1 to 0.3 nm larger than
-<b>rvdw</b> to accommodate for the size of charge groups and diffusion
-between neighbor list updates.</dd>
-
-<dt><b>Encad-Shift</b></dt>
-<dd>The LJ (not Buckingham)
-potential is decreased over the whole range, using the definition
-from the Encad simulation package.</dd>
-
-<dt><b>User</b></dt>
-<dd>See <b><a href="#usertab">user</a></b> for <b>coulombtype</b>.
-The function value at <tt>x=0</tt> is not important. When you want to
-use LJ correction, make sure that <b>rvdw</b> corresponds to the
-cut-off in the user-defined function.
-When <b>coulombtype</b> is not set to <b>User</b> the values
-for <tt>f</tt> and <tt>-f'</tt> are ignored.</dd>
-</dl></dd>
-
-<dt><b>vdw-modifier:</b></dt>
-<dd><dl compact>
-<dt><b>Potential-shift-Verlet</b></dt>
-<dd>Selects <b>Potential-shift</b> with the Verlet cutoff-scheme,
-as it is (nearly) free; selects <b>None</b> with the group cutoff-scheme.</dd>
-<dt><b>Potential-shift</b></dt>
-<dd>Shift the Van der Waals potential by a constant such that it is zero at the cut-off.
-This makes the potential the integral of the force. Note that this does not
-affect the forces or the sampling.</dd>
-<dt><b>None</b></dt>
-<dd>Use an unmodified Van der Waals potential. With the group scheme this means no exact cut-off is used, energies and forces are calculated for all pairs in the neighborlist.</dd>
-<dt><b>Force-switch</b></dt>
-<dd>Smoothly switches the forces to zero between <b>rvdw-switch</b> and <b>rvdw</b>. This shifts the potential shift over the whole range and switches it to zero at the cut-off. Note that this is more expensive to calculate than a plain cut-off and it is not required for energy conservation, since <b>Potential-shift</b> conserves energy just as well.</dd>
-<dt><b>Potential-switch</b></dt>
-<dd>Smoothly switches the potential to zero between <b>rvdw-switch</b> and <b>rvdw</b>. Note that this introduces articifically large forces in the switching region and is much more expensive to calculate. This option should only be used if the force field you are using requires this.</dd>
-</dl></dd>
-
-<dt><b>rvdw-switch: (0) [nm]</b></dt>
-<dd>where to start switching the LJ force and possibly the potential, only relevant when force or potential switching is used</dd>
-
-<dt><b>rvdw: (1) [nm]</b></dt>
-<dd>distance for the LJ or Buckingham <!--Idx-->cut-off<!--EIdx--></dd>
-
-<dt><b>DispCorr:</b></dt>
-<dd><dl compact></dd>
-<dt><b>no</b></dt>
-<dd>don't apply any correction</dd>
-<dt><b>EnerPres</b></dt>
-<dd>apply long range <!--Idx-->dispersion correction<!--EIdx-->s for Energy
-and Pressure</dd>
-<dt><b>Ener</b></dt>
-<dd>apply long range dispersion corrections for Energy
-only</dd>
-</dl>
-</dl>
-
-<A NAME="table">
-<hr>
-<h3>Tables</h3>
-<dl>
-<dt><b>table-extension: (1) [nm]</b></dt>
-<dd>Extension of the non-bonded potential lookup tables beyond the largest cut-off distance.
-The value should be large enough to account for charge group sizes
-and the diffusion between neighbor-list updates.
-Without user defined potential the same table length is used
-for the lookup tables for the 1-4 interactions,
-which are always tabulated irrespective of the use of
-tables for the non-bonded interactions. The value of <b>table-extension</b> in no way
-affects the values of <b>rlist</b>, <b>rcoulomb</b>, or <b>rvdw</b>. </dd>
-
-<dt><b>energygrp-table:</b></dt>
-<dd>When user tables are used for electrostatics and/or VdW,
-here one can give pairs of energy groups for which seperate
-user tables should be used.
-The two energy groups will be appended to the table file name,
-in order of their definition in <b>energygrps</b>, seperated by underscores.
-For example, if <tt>energygrps = Na Cl Sol</tt>
-and <tt>energygrp-table = Na Na Na Cl</tt>, <tt>mdrun</tt> will read
-<tt>table_Na_Na.xvg</tt> and <tt>table_Na_Cl.xvg</tt> in addition
-to the normal <tt>table.xvg</tt> which will be used for all other
-energy group pairs.
-</dd>
-</dl>
-
-<A NAME="ewald">
-<hr>
-<h3>Ewald</h3>
-<dl>
-<dt><b>fourierspacing: (0.12) [nm]</b></dt>
-<dd>For ordinary Ewald, the ratio of the box dimensions and the spacing
-determines a lower bound for the number of wave vectors to use in each
-(signed) direction. For PME and P3M, that ratio determines a lower bound
-for the number of Fourier-space grid points that will be used along that
-axis. In all cases, the number for each direction can be overridden by
-entering a non-zero value for <b>fourier_n[xyz]</b>.
-For optimizing the relative load of the particle-particle interactions
-and the mesh part of PME, it is useful to know that
-the accuracy of the electrostatics remains nearly constant
-when the Coulomb cut-off and the PME grid spacing are scaled
-by the same factor.</dd>
-
-<dt><b>fourier-nx (0) ; fourier-ny (0) ; fourier-nz: (0)</b></dt>
-<dd>Highest magnitude of wave vectors in reciprocal space when using Ewald.</dd>
-<dd>Grid size when using PME or P3M. These values override
-<b>fourierspacing</b> per direction. The best choice is powers of
-2, 3, 5 and 7. Avoid large primes.</dd>
-
-<dt><b>pme-order (4)</b></dt>
-<dd>Interpolation order for PME. 4 equals cubic interpolation. You might try
-6/8/10 when running in parallel and simultaneously decrease grid dimension.</dd>
-
-<dt><b>ewald-rtol (1e-5)</b></dt>
-<dd>The relative strength of the Ewald-shifted direct potential at
-<b>rcoulomb</b> is given by <b>ewald-rtol</b>.
-Decreasing this will give a more accurate direct sum,
-but then you need more wave vectors for the reciprocal sum.</dd>
-
-<dt><b>ewald-rtol-lj (1e-3)</b></dt>
-<dd>When doing PME for VdW-interactions, <b>ewald-rtol-lj</b> is used
-to control the relative strength of the dispersion potential at <b>rvdw</b> in
-the same way as <b>ewald-rtol</b> controls the electrostatic potential.</dd>
-
-<dt><b>lj-pme-comb-rule (Geometric)</b></dt>
-<dd>The combination rules used to combine VdW-parameters in the reciprocal part of LJ-PME.
-Geometric rules are much faster than Lorentz-Berthelot and usually the recommended choice, even
-when the rest of the force field uses the Lorentz-Berthelot rules.</dd>
-<dd><dl compact>
-<dt><b>Geometric</b></dt>
-<dd>Apply geometric combination rules</dd>
-<dt><b>Lorentz-Berthelot</b></dt>
-<dd>Apply Lorentz-Berthelot combination rules</dd>
-</dl></dd>
-
-<dt><b>ewald-geometry: (3d)</b></dt>
-<dd><dl compact>
-<dt><b>3d</b></dt>
-<dd>The Ewald sum is performed in all three dimensions.</dd>
-<dt><b>3dc</b></dt>
-<dd>The reciprocal sum is still performed in 3D,
-but a force and potential correction applied in the <tt>z</tt>
-dimension to produce a pseudo-2D summation.
-If your system has a slab geometry in the <tt>x-y</tt> plane you can
-try to increase the <tt>z</tt>-dimension of the box (a box height of 3 times
-the slab height is usually ok)
-and use this option.</dd>
-</dl></dd>
-
-<dt><b>epsilon-surface: (0)</b></dt>
-<dd>This controls the dipole correction to the Ewald summation in 3D. The
-default value of zero means it is turned off. Turn it on by setting it to the value
-of the relative permittivity of the imaginary surface around your infinite system. Be
-careful - you shouldn't use this if you have free mobile charges in your system.
-This value does not affect the slab 3DC variant of the long range corrections.</dd>
-
-</dl>
-
-<A NAME="tc"><br>
-<hr>
-<h3>Temperature coupling<!--QuietIdx-->temperature coupling<!--EQuietIdx--></h3>
-
-<dl>
-<dt><b>tcoupl:</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>No temperature coupling.</dd>
-<dt><b>berendsen</b></dt>
-<dd>Temperature coupling with a Berendsen-thermostat to a bath with
-temperature <b>ref-t</b> [K], with time constant <b>tau-t</b> [ps].
-Several groups can be coupled separately, these are specified in the
-<b>tc-grps</b> field separated by spaces.</dd>
-<dt><b>nose-hoover</b></dt>
-<dd>Temperature coupling using a Nose-Hoover extended
-ensemble. The reference temperature and coupling groups are selected
-as above, but in this case <b>tau-t</b> [ps] controls the period
-of the temperature fluctuations at equilibrium, which is slightly
-different from a relaxation time.
-For NVT simulations the conserved energy quantity is written
-to energy and log file.</dd>
-<dt><b>andersen</b></dt>
-<dd>Temperature coupling by randomizing a fraction of the particles
-at each timestep. Reference temperature and coupling groups are selected
-as above. <b>tau-t</b> is the average time between randomization of each molecule.
-Inhibits particle dynamics somewhat, but little or no ergodicity issues. Currently
-only implemented with velocity Verlet, and not implemented with constraints.</dd>
-<dt><b>andersen-massive</b></dt>
-<dd>Temperature coupling by randomizing all particles at infrequent timesteps.
-Reference temperature and coupling groups are selected
-as above. <b>tau-t</b> is the time between randomization of all molecules.
-Inhibits particle dynamics somewhat, but little or no ergodicity issues. Currently
-only implemented with velocity Verlet.</dd>
-<dt><b>v-rescale</b></dt>
-<dd>Temperature coupling using velocity rescaling with a stochastic term
-(JCP 126, 014101).
-This thermostat is similar to Berendsen coupling, with the same scaling
-using <b>tau-t</b>, but the stochastic term ensures that a proper
-canonical ensemble is generated. The random seed is set with
-<b><A HREF="#ld">ld-seed</A></b>.
-This thermostat works correctly even for <b>tau-t</b><tt>=0</tt>.
-For NVT simulations the conserved energy quantity is written
-to the energy and log file.</dd>
-</dl>
-<dt><b>nsttcouple: (-1)</b></dt>
-<dd>The frequency for coupling the temperature.
-The default value of -1 sets <b>nsttcouple</b> equal to <b>nstlist</b>,
-unless <b>nstlist</b>≤0, then a value of 10 is used.
-For velocity Verlet integrators <b>nsttcouple</b> is set to 1.</dd>
-</dd>
-<dt><b>nh-chain-length (10)</b></dt>
-<dd>the number of chained Nose-Hoover thermostats for velocity Verlet integrators, the leap-frog <b>md</b> integrator only supports 1. Data for the NH chain variables is not printed to the .edr, but can be using the <tt>GMX_NOSEHOOVER_CHAINS</tt> environment variable</dd>
-<dt><b>tc-grps:</b></dt>
-<dd>groups to couple separately to temperature bath</dd>
-<dt><b>tau-t: [ps]</b></dt>
-<dd>time constant for coupling (one for each group in <b>tc-grps</b>),
--1 means no temperature coupling</dd>
-<dt><b>ref-t: [K]</b></dt>
-<dd>reference temperature for coupling (one for each group in <b>tc-grps</b>)</dd>
-</dl>
-
-<A NAME="pc"><br>
-<hr>
-<h3>Pressure coupling<!--QuietIdx-->pressure coupling<!--EQuietIdx--></h3>
-
-<dl>
-<dt><b>pcoupl:</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>No pressure coupling. This means a fixed box size.</dd>
-<dt><b>berendsen</b></dt>
-<dd>Exponential relaxation pressure coupling with time constant
-<b>tau-p</b> [ps]. The box is scaled every timestep. It has been
-argued that this does not yield a correct thermodynamic ensemble,
-but it is the most efficient way to scale a box at the beginning
-of a run.</dd>
-<dt><b>Parrinello-Rahman</b></dt>
-<dd>Extended-ensemble pressure coupling where the box vectors are
-subject to an equation of motion. The equation of motion for the atoms
-is coupled to this. No instantaneous scaling takes place. As for
-Nose-Hoover temperature coupling the time constant <b>tau-p</b> [ps]
-is the period of pressure fluctuations at equilibrium. This is
-probably a better method when you want to apply pressure scaling
-during data collection, but beware that you can get very large
-oscillations if you are starting from a different pressure. For
-simulations where the exact fluctation of the NPT ensemble are
-important, or if the pressure coupling time is very short it may not
-be appropriate, as the previous time step pressure is used in some
-steps of the GROMACS implementation for the current time step pressure.</dd>
-</dl></dd>
-<dt><b>MTTK</b></dt>
-<dd>Martyna-Tuckerman-Tobias-Klein implementation, only useable with <b>md-vv</b>
-or <b>md-vv-avek</b>, very similar to Parrinello-Rahman.
-As for Nose-Hoover temperature coupling the time constant <b>tau-p</b>
-[ps] is the period of pressure fluctuations at equilibrium. This is
-probably a better method when you want to apply pressure scaling
-during data collection, but beware that you can get very large
-oscillations if you are starting from a different pressure. Currently only supports isotropic scaling.</dd>
-</dl></dd>
-
-<dl>
-<dt><b>pcoupltype:</b></dt>
-<dd><dl compact>
-<dt><b>isotropic</b></dt>
-<dd>Isotropic pressure coupling with time constant <b>tau-p</b> [ps].
-The compressibility and reference pressure are set with
-<b>compressibility</b> [bar<sup>-1</sup>] and <b>ref-p</b> [bar], one
-value is needed.</dd>
-<dt><b>semiisotropic</b></dt>
-<dd>Pressure coupling which is isotropic in the <tt>x</tt> and <tt>y</tt> direction,
-but different in the <tt>z</tt> direction.
-This can be useful for membrane simulations.
-2 values are needed for <tt>x/y</tt> and <tt>z</tt> directions respectively.</dd>
-<dt><b>anisotropic</b></dt>
-<dd>Idem, but 6 values are needed for <tt>xx</tt>, <tt>yy</tt>, <tt>zz</tt>, <tt>xy/yx</tt>, <tt>xz/zx</tt> and <tt>yz/zy</tt>
-components, respectively.
-When the off-diagonal compressibilities are set to zero,
-a rectangular box will stay rectangular.
-Beware that anisotropic scaling can lead to extreme deformation
-of the simulation box.</dd>
-<dt><b>surface-tension</b></dt>
-<dd>Surface tension coupling for surfaces parallel to the xy-plane.
-Uses normal pressure coupling for the <tt>z</tt>-direction, while the surface tension
-is coupled to the <tt>x/y</tt> dimensions of the box.
-The first <b>ref-p</b> value is the reference surface tension times
-the number of surfaces [bar nm],
-the second value is the reference <tt>z</tt>-pressure [bar].
-The two <b>compressibility</b> [bar<sup>-1</sup>] values are the compressibility
-in the <tt>x/y</tt> and <tt>z</tt> direction respectively.
-The value for the <tt>z</tt>-compressibility should be reasonably accurate since it
-influences the convergence of the surface-tension, it can also be set to zero
-to have a box with constant height.</dd>
-</dl></dd>
-
-<dt><b>nstpcouple: (-1)</b></dt>
-<dd>The frequency for coupling the pressure.
-The default value of -1 sets <b>nstpcouple</b> equal to <b>nstlist</b>,
-unless <b>nstlist</b> ≤0, then a value of 10 is used.
-For velocity Verlet integrators <b>nstpcouple</b> is set to 1.</dd>
-</dd>
-
-<dt><b>tau-p: (1) [ps]</b></dt>
-<dd>time constant for coupling</dd>
-<dt><b>compressibility: [bar<sup>-1</sup>]</b></dt>
-<dd>compressibility (NOTE: this is now really in bar<sup>-1</sup>)
-For water at 1 atm and 300 K the compressibility is 4.5e-5 [bar<sup>-1</sup>].</dd>
-<dt><b>ref-p: [bar]</b></dt>
-<dd>reference pressure for coupling</dd>
-<dt><b>refcoord-scaling:</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>The reference coordinates for position restraints are not modified.
-Note that with this option the virial and pressure will depend on the absolute
-positions of the reference coordinates.</dd>
-<dt><b>all</b></dt>
-<dd>The reference coordinates are scaled with the scaling matrix of the pressure coupling.</dd>
-<dt><b>com</b></dt>
-<dd>Scale the center of mass of the reference coordinates with the scaling matrix of the pressure coupling. The vectors of each reference coordinate to the center of mass are not scaled. Only one COM is used, even when there are multiple molecules with position restraints. For calculating the COM of the reference coordinates in the starting configuration, periodic boundary conditions are not taken into account.
-</dl></dd>
-</dd>
-</dl>
-
-<A NAME="sa"><br>
-<hr>
-<h3>Simulated annealing<!--QuietIdx-->simulated annealing<!--EQuietIdx--></h3>
-
-Simulated annealing is controlled separately for each temperature group in GROMACS. The reference temperature is a piecewise linear function, but you can use an arbitrary number of points for each group, and choose either a single sequence or a periodic behaviour for each group. The actual annealing is performed by dynamically changing the reference temperature used in the thermostat algorithm selected, so remember that the system will usually not instantaneously reach the reference temperature!
-<dl>
-<dt><b>annealing:</b></dt>
-<dd>Type of annealing for each temperature group</dd>
-<dd><dl compact></dd>
-<dt><b>no</b></dt>
-<dd>No simulated annealing - just couple to reference temperature value.</dd>
-<dt><b>single</b></dt>
-<dd>A single sequence of annealing points. If your simulation is longer than the time of the last point, the temperature will be coupled to this constant value after the annealing sequence has reached the last time point.</dd>
-<dt><b>periodic</b></dt>
-<dd>The annealing will start over at the first reference point once the last reference time is reached. This is repeated until the simulation ends.
-</dd>
-</dl>
-
-<dt><b>annealing-npoints:</b></dt>
-<dd>A list with the number of annealing reference/control points used for
-each temperature group. Use 0 for groups that are not annealed. The number of entries should equal the number of temperature groups.</dd>
-
-<dt><b>annealing-time:</b></dt>
-<dd>List of times at the annealing reference/control points for each group. If you are using periodic annealing, the times will be used modulo the last value, i.e. if the values are 0, 5, 10, and 15, the coupling will restart at the 0ps value after 15ps, 30ps, 45ps, etc. The number of entries should equal the sum of the numbers given in <tt>annealing-npoints</tt>.</dd>
-
-<dt><b>annealing-temp:</b></dt>
-<dd>List of temperatures at the annealing reference/control points for each group. The number of entries should equal the sum of the numbers given in <tt>annealing-npoints</tt>.</dd>
-<br>
-Confused? OK, let's use an example. Assume you have two temperature groups, set the group selections to <tt>annealing = single periodic</tt>, the number of points of each group to <tt>annealing-npoints = 3 4</tt>, the times to <tt>annealing-time = 0 3 6 0 2 4 6</tt> and finally temperatures to <tt>annealing-temp = 298 280 270 298 320 320 298</tt>.
-The first group will be coupled to 298K at 0ps, but the reference temperature will drop linearly to reach 280K at 3ps, and then linearly between 280K and 270K from 3ps to 6ps. After this is stays constant, at 270K. The second group is coupled to 298K at 0ps, it increases linearly to 320K at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it decreases to 298K, and then it starts over with the same pattern again, i.e. rising linearly from 298K to 320K between 6ps and 8ps. Check the summary printed by <tt>grompp</tt> if you are unsure!
-</dl>
-
-<A NAME="vel"><br>
-<hr>
-<h3>Velocity generation</h3>
-
-<dl>
-<dt><b>gen-vel:</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd> Do not generate velocities. The velocities are set to zero
-when there are no velocities in the input structure file.</dd>
-<dt><b>yes</b></dt>
-<dd>Generate velocities in <tt>grompp</tt> according to a Maxwell distribution at
-temperature <b>gen-temp</b> [K], with random seed <b>gen-seed</b>.
-This is only meaningful with integrator <b><A HREF="#run">md</A></b>.</dd>
-</dl></dd>
-<dt><b>gen-temp: (300) [K]</b></dt>
-<dd>temperature for Maxwell distribution</dd>
-<dt><b>gen-seed: (-1) [integer]</b></dt>
-<dd>used to initialize random generator for random velocities,
-when <b>gen-seed</b> is set to -1, a pseudo random seed is used.
-</dl>
-
-<A NAME="bond"><br>
-<hr>
-<h3>Bonds</h3>
-
-<dl>
-<dt><b>constraints<!--QuietIdx-->constraint algorithms<!--EQuietIdx-->:</b></dt>
-<dd><dl compact>
-<dt><b>none</b></dt>
-<dd>No constraints except for those defined explicitly in the topology,
-i.e. bonds are represented by a harmonic (or other) potential
-or a Morse potential (depending on the setting of <b>morse</b>)
-and angles by a harmonic (or other) potential.
-<dt><b>h-bonds</b></dt>
-<dd>Convert the bonds with H-atoms to constraints.</dd>
-<dt><b>all-bonds</b></dt>
-<dd>Convert all bonds to constraints.</dd>
-<dt><b>h-angles</b></dt>
-<dd>Convert all bonds and additionally the angles that involve H-atoms
-to bond-constraints.</dd>
-<dt><b>all-angles</b></dt>
-<dd>Convert all bonds and angles to bond-constraints.</dd>
-</dl>
-
-<dt><b>constraint-algorithm:</b></dt>
-<dd><dl compact>
-<dt><b><!--Idx-->LINCS<!--EIdx--></b></dt>
-<dd>LINear Constraint Solver.
-With domain decomposition the parallel version P-LINCS is used.
-The accuracy in set with
-<b>lincs-order</b>, which sets the number of matrices in the expansion
-for the matrix inversion.
-After the matrix inversion correction the algorithm does
-an iterative correction to compensate for lengthening due to rotation.
-The number of such iterations can be controlled with
-<b>lincs-iter</b>. The root mean square relative constraint deviation
-is printed to the log file every <b>nstlog</b> steps.
-If a bond rotates more than <b>lincs-warnangle</b> [degrees] in one step,
-a warning will be printed both to the log file and to <TT>stderr</TT>.
-LINCS should not be used with coupled angle constraints.
-</dd>
-<dt><b><!--Idx-->SHAKE<!--EIdx--></b></dt>
-<dd>SHAKE is slightly slower and less stable than LINCS, but does work with
-angle constraints.
-The relative tolerance is set with <b>shake-tol</b>, 0.0001 is a good value
-for ``normal'' MD. SHAKE does not support constraints between atoms
-on different nodes, thus it can not be used with domain decompositon
-when inter charge-group constraints are present.
-SHAKE can not be used with energy minimization.
-</dd>
-</dl></dd>
-<dt><b>continuation:</b></dt>
-<dd>This option was formerly known as <tt>unconstrained-start</tt>.</dd>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>apply constraints to the start configuration and reset shells</dd>
-<dt><b>yes</b></dt>
-<dd>do not apply constraints to the start configuration
-and do not reset shells, useful for exact coninuation and reruns</dd>
-</dl></dd>
-
-<A NAME="bond2">
-<dt><b>shake-tol: (0.0001)</b></dt>
-<dd>relative tolerance for SHAKE</dd>
-<dt><b>lincs-order: (4)</b></dt>
-<dd>Highest order in the expansion of the constraint coupling matrix.
-When constraints form triangles, an additional expansion of the same
-order is applied on top of the normal expansion only for the couplings
-within such triangles.
-For ``normal'' MD simulations an order of 4 usually suffices, 6 is
-needed for large time-steps with virtual sites or BD.
-For accurate energy minimization an order of 8 or more might be required.
-With domain decomposition, the cell size is limited by the distance
-spanned by <b>lincs-order</b>+1 constraints. When one wants to scale
-further than this limit, one can decrease <b>lincs-order</b> and increase
-<b>lincs-iter</b>, since the accuracy does not deteriorate
-when (1+<b>lincs-iter</b>)*<b>lincs-order</b> remains constant.</dd>
-<dt><b>lincs-iter: (1)</b></dt>
-<dd>Number of iterations to correct for rotational lengthening in LINCS.
-For normal runs a single step is sufficient, but for NVE
-runs where you want to conserve energy accurately or for accurate
-energy minimization you might want to increase it to 2.
-<dt><b>lincs-warnangle: </b>(30) [degrees]</dt>
-<dd>maximum angle that a bond can rotate before LINCS will complain</dd>
-
-<dt><b>morse:</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>bonds are represented by a harmonic potential</dd>
-<dt><b>yes</b></dt>
-<dd>bonds are represented by a Morse potential</dd>
-</dl></dd>
-</dl>
-
-<A NAME="egexcl"><br>
-<hr>
-<h3>Energy group <!--Idx-->exclusions<!--EIdx--></h3>
-<dl>
-<dt><b>energygrp-excl: </b></dt>
-<dd>Pairs of energy groups for which all non-bonded interactions are
-excluded. An example: if you have two energy groups <tt>Protein</tt>
-and <tt>SOL</tt>, specifying
-<br>
-<tt>energygrp-excl = Protein Protein SOL SOL</tt>
-<br>
-would give only the non-bonded interactions between the protein and the
-solvent. This is especially useful for speeding up energy calculations with
-<tt>mdrun -rerun</tt> and for excluding interactions within frozen groups.</dd>
-</dl>
-
-<A NAME="walls"><br>
-<hr>
-<h3>Walls<!--QuietIdx-->walls<!--EQuietIdx--></h3>
-<dl>
-<dt><b>nwall: 0</b></dt>
-<dd>When set to <b>1</b> there is a wall at <tt>z=0</tt>, when set to <b>2</b>
-there is also a wall at <tt>z=z-box</tt>. Walls can only be used with <b>pbc=xy</b>.
-When set to <b>2</b> pressure coupling and Ewald summation can be used
-(it is usually best to use semiisotropic pressure coupling with
-the <tt>x/y</tt> compressibility set to 0, as otherwise the surface area will change).
-Walls interact wit the rest of the system through an optional <tt>wall-atomtype</tt>.
-Energy groups <tt>wall0</tt> and <tt>wall1</tt> (for <b>nwall=2</b>) are
-added automatically to monitor the interaction of energy groups
-with each wall.
-The <A HREF="#run">center of mass motion removal</A> will be turned
-off in the <tt>z</tt>-direction.</dd>
-<dt><b>wall-atomtype:</b></dt>
-<dd>the atom type name in the force field for each wall.
-By (for example) defining a special wall atom type in the topology with its
-own combination rules, this allows for independent tuning of the interaction
-of each atomtype with the walls.</dd>
-<dt><b>wall-type:</b></dt>
-<dd><dl compact>
-<dt><b>9-3</b></dt>
-<dd>LJ integrated over the volume behind the wall: 9-3 potential</dd>
-<dt><b>10-4</b></dt>
-<dd>LJ integrated over the wall surface: 10-4 potential</dd>
-<dt><b>12-6</b></dt>
-<dd>direct LJ potential with the z distance from the wall</dd>
-<dt><b>table</b></dt><dd>user defined potentials indexed with the z distance from the wall, the tables are read analogously to
-the <b><A HREF="#table">energygrp-table</A></b> option,
-where the first name is for a ``normal'' energy group and the second name
-is <tt>wall0</tt> or <tt>wall1</tt>,
-only the dispersion and repulsion columns are used</dd>
-</dl></dd>
-<dt><b>wall-r-linpot: -1 (nm)</b></dt>
-<dd>Below this distance from the wall the potential is continued
-linearly and thus the force is constant. Setting this option to
-a postive value is especially useful for equilibration when some atoms
-are beyond a wall.
-When the value is ≤0 (<0 for <b>wall-type=table</b>),
-a fatal error is generated when atoms are beyond a wall.
-</dd>
-<dt><b>wall-density: [nm<sup>-3</sup>/nm<sup>-2</sup>]</b></dt>
-<dd>the number density of the atoms for each wall for wall types
-<b>9-3</b> and <b>10-4</b>
-<dt><b>wall-ewald-zfac: 3</b></dt>
-<dd>The scaling factor for the third box vector for Ewald summation only,
-the minimum is 2.
-Ewald summation can only be used with <b>nwall=2</b>, where one
-should use <b><A HREF="#ewald">ewald-geometry</A><tt>=3dc</tt></b>.
-The empty layer in the box serves to decrease the unphysical Coulomb
-interaction between periodic images.</dd>
-</dl>
-
-<A NAME="pull"><br>
-<hr>
-<h3>COM <!--Idx-->pulling<!--EIdx--></h3>
-<dl>
-<dt><b>pull:</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>No center of mass pulling.
-All the following pull options will be ignored
-(and if present in the <tt>.mdp</tt> file, they unfortunately generate warnings)</dd>
-<dt><b>umbrella</b></dt>
-<dd>Center of mass pulling using an umbrella potential
-between the reference group and one or more groups.</dd>
-<dt><b>constraint</b></dt>
-<dd>Center of mass pulling using a constraint
-between the reference group and one or more groups.
-The setup is identical to the option <b>umbrella</b>, except for the fact
-that a rigid constraint is applied instead of a harmonic potential.</dd>
-<dt><b>constant-force</b></dt>
-<dd>Center of mass pulling using a linear potential and therefore
-a constant force. For this option there is no reference position
-and therefore the parameters <b>pull-init</b> and <b>pull-rate</b>
-are not used.</dd>
-</dl></dd>
-<dt><b>pull-geometry:</b></dt>
-<dd><dl compact>
-<dt><b>distance</b></dt>
-<dd>Pull along the vector connecting the two groups.
-Components can be selected with <b>pull-dim</b>.</dd>
-<dt><b>direction</b></dt>
-<dd>Pull in the direction of <b>pull-vec</b>.</dd>
-<dt><b>direction-periodic</b></dt>
-<dd>As <b>direction</b>, but allows the distance to be larger than
-half the box size. With this geometry the box should not be dynamic
-(e.g. no pressure scaling) in the pull dimensions and the pull force
-is not added to virial.</dd>
-<dt><b>cylinder</b></dt>
-<dd>Designed for pulling with respect to a layer where the reference COM
-is given by a local cylindrical part of the reference group.
-The pulling is in the direction of <b>pull-vec</b>.
-From the reference group a cylinder is selected around the axis going
-through the pull group with direction <b>pull-vec</b> using two radii.
-The radius <b>pull-r1</b> gives the radius within which all
-the relative weights are one, between <b>pull-r1</b> and
-<b>pull-r0</b> the weights are switched to zero. Mass weighting is also used.
-Note that the radii should be smaller than half the box size.
-For tilted cylinders they should be even smaller than half the box size
-since the distance of an atom in the reference group
-from the COM of the pull group has both a radial and an axial component.</dd>
-</dl></dd>
-<dt><b>pull-dim: (Y Y Y)</b></dt>
-<dd>the distance components to be used with geometry <b>distance</b>,
-and also sets which components are printed
-to the output files</dd>
-<dt><b>pull-r1: (1) [nm]</b></dt>
-<dd>the inner radius of the cylinder for geometry <b>cylinder</b></dd>
-<dt><b>pull-r0: (1) [nm]</b></dt>
-<dd>the outer radius of the cylinder for geometry <b>cylinder</b></dd>
-<dt><b>pull-constr-tol: (1e-6)</b></dt>
-<dd>the relative constraint tolerance for constraint pulling</dd>
-<dt><b>pull-start:</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>do not modify <b>pull-init</b>
-<dt><b>yes</b></dt>
-<dd>add the COM distance of the starting conformation to <b>pull-init</b></dd>
-</dl>
-<dt><b>pull-print-reference: (10)</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>do not print the COM of the first group in each pull coordinate</dd>
-<dt><b>yes</b></dt>
-<dd>print the COM of the first group in each pull coordinate</dd>
-</dl>
-<dt><b>pull-nstxout: (10)</b></dt>
-<dd>frequency for writing out the COMs of all the pull group</dd>
-<dt><b>pull-nstfout: (1)</b></dt>
-<dd>frequency for writing out the force of all the pulled group</dd>
-<dt><b>pull-ngroups: (1)</b></dt>
-<dd>The number of pull groups, not including the absolute reference group,
-when used. Pull groups can be reused in multiple pull coordinates.
-Below only the pull options for group 1 are given, further groups simply
-increase the group index number.</dd>
-<dt><b>pull-ncoords: (1)</b></dt>
-<dd>The number of pull coordinates. Below only the pull options for
-coordinate 1 are given, further coordinates simply increase the coordinate
-index number.</dd>
-
-<dt><b>pull-group1-name: </b></dt>
-<dd>The name of the pull group, is looked up in the index file
-or in the default groups to obtain the atoms involved.</dd>
-<dt><b>pull-group1-weights: </b></dt>
-<dd>Optional relative weights which are multiplied with the masses of the atoms
-to give the total weight for the COM. The number should be 0, meaning all 1,
-or the number of atoms in the pull group.</dd>
-<dt><b>pull-group1-pbcatom: (0)</b></dt>
-<dd>The reference atom for the treatment of periodic boundary conditions
-inside the group
-(this has no effect on the treatment of the pbc between groups).
-This option is only important when the diameter of the pull group
-is larger than half the shortest box vector.
-For determining the COM, all atoms in the group are put at their periodic image
-which is closest to <b>pull-group1-pbcatom</b>.
-A value of 0 means that the middle atom (number wise) is used.
-This parameter is not used with geometry <b>cylinder</b>.
-A value of -1 turns on cosine weighting, which is useful for a group
-of molecules in a periodic system, e.g. a water slab (see Engin et al.
-J. Chem. Phys. B 2010).</dd>
-
-<dt><b>pull-coord1-groups: </b></dt>
-<dd>The two groups indices should be given on which this pull coordinate
-will operate. The first index can be 0, in which case an absolute reference
-of <b>pull-coord1-origin</b> is used. With an absolute reference the system
-is no longer translation invariant and one should think about what to do with
-the <A HREF="#run">center of mass motion</A>.</dd>
-<dt><b>pull-coord1-origin: (0.0 0.0 0.0)</b></dt>
-<dd>The pull reference position for use with an absolute reference.</dd>
-<dt><b>pull-coord1-vec: (0.0 0.0 0.0)</b></dt>
-<dd>The pull direction. <tt>grompp</tt> normalizes the vector.</dd>
-<dt><b>pull-coord1-init: (0.0) [nm]</b></dt>
-<dd>The reference distance at t=0.</dd>
-<dt><b>pull-coord1-rate: (0) [nm/ps]</b></dt>
-<dd>The rate of change of the reference position.</dd>
-<dt><b>pull-coord1-k: (0) [kJ mol<sup>-1</sup> nm<sup>-2</sup>] / [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
-<dd>The force constant. For umbrella pulling this is the harmonic force
-constant in [kJ mol<sup>-1</sup> nm<sup>-2</sup>]. For constant force pulling
-this is the force constant of the linear potential, and thus minus (!)
-the constant force in [kJ mol<sup>-1</sup> nm<sup>-1</sup>].</dd>
-<dt><b>pull-coord1-kB: (pull-k1) [kJ mol<sup>-1</sup> nm<sup>-2</sup>] / [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
-<dd>As <b>pull-coord1-k</b>, but for state B. This is only used when
-<A HREF="#free"><b>free-energy</b></A> is turned on.
-The force constant is then (1 - lambda)*<b>pull-coord1-k</b> + lambda*<b>pull-coord1-kB</b></dt>.
-
-</dl>
-
-<A NAME="nmr"><br>
-<hr>
-<h3><!--Idx-->NMR refinement<!--EIdx--></h3>
-<dl>
-<dt><b>disre:</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>ignore <!--Idx-->distance restraint<!--EIdx--> information in topology file</dd>
-<dt><b>simple</b></dt>
-<dd>simple (per-molecule) distance restraints.
-<dt><b>ensemble</b></dt>
-<dd>distance restraints over an ensemble of molecules in one
-simulation box. Normally, one would perform ensemble averaging over
-multiple subsystems, each in a separate box, using <tt>mdrun -multi</tt>;s
-upply <tt>topol0.tpr</tt>, <tt>topol1.tpr</tt>, ... with different
-coordinates and/or velocities.
-The environment variable <tt>GMX_DISRE_ENSEMBLE_SIZE</tt> sets the number
-of systems within each ensemble (usually equal to the <tt>mdrun -multi</tt> value).</dd>
-</dd>
-</dl></dd>
-<dt><b>disre-weighting:</b></dt>
-<dd><dl compact>
-<dt><b>equal</b> (default)</dt>
-<dd>divide the restraint force equally over all atom pairs in the restraint</dd>
-<dt><b>conservative</b></dt>
-<dd>the forces are the derivative of the restraint potential,
-this results in an r<sup>-7</sup> weighting of the atom pairs.
-The forces are conservative when <tt>disre-tau</tt> is zero.</dd>
-</dl></dd>
-<dt><b>disre-mixed:</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>the violation used in the calculation of the restraint force is the
-time-averaged violation </dd>
-<dt><b>yes</b></dt>
-<dd>the violation used in the calculation of the restraint force is the
-square root of the product of the time-averaged violation and the instantaneous violation</dd>
-</dl></dd>
-
-<dt><b>disre-fc: (1000) [kJ mol<sup>-1</sup> nm<sup>-2</sup>]</b></dt>
-<dd>force constant for distance restraints, which is multiplied by a
-(possibly) different factor for each restraint given in the <tt>fac</tt>
-column of the interaction in the topology file.</dd>
-
-<dt><b>disre-tau: (0) [ps]</b></dt>
-<dd>time constant for distance restraints running average. A value of zero turns off time averaging.</dd>
-
-<dt><b>nstdisreout: (100) [steps]</b></dt>
-<dd>period between steps when the running time-averaged and instantaneous distances
-of all atom pairs involved in restraints are written to the energy file
-(can make the energy file very large)</dd>
-
-<A NAME="nmr2">
-<dt><b>orire:</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>ignore <!--Idx-->orientation restraint<!--EIdx--> information in topology file</dd>
-<dt><b>yes</b></dt>
-<dd>use orientation restraints, ensemble averaging can be performed
-with <tt>mdrun -multi</tt></dd>
-</dl>
-<dt><b>orire-fc: (0) [kJ mol]</b></dt>
-<dd>force constant for orientation restraints, which is multiplied by a
-(possibly) different weight factor for each restraint, can be set to zero to
-obtain the orientations from a free simulation</dd>
-<dt><b>orire-tau: (0) [ps]</b></dt>
-<dd>time constant for orientation restraints running average. A value of zero turns off time averaging.</dd>
-<dt><b>orire-fitgrp: </b></dt>
-<dd>fit group for orientation restraining. This group of atoms is used
-to determine the rotation <b>R</b> of the system with respect to the
-reference orientation. The reference orientation is the starting
-conformation of the first subsystem. For a protein, backbone is a reasonable
-choice</dd>
-<dt><b>nstorireout: (100) [steps]</b></dt>
-<dd>period between steps when the running time-averaged and instantaneous orientations
-for all restraints, and the molecular order tensor are written to the energy file
-(can make the energy file very large)</dd>
-</dl>
-
-<A NAME="free"><br>
-<hr>
-<h3>Free energy calculations<!--QuietIdx-->free energy calculations<!--EQuietIdx--></h3>
-
-<dl>
-<dt><b>free-energy:</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>Only use topology A.</dd>
-<dt><b>yes</b></dt>
-<dd>Interpolate between topology A (lambda=0) to topology B (lambda=1)
-and write the derivative of the Hamiltonian with respect to lambda (as specified with <b>dhdl-derivatives</b>), or the Hamiltonian differences with respect to other lambda values (as specified with <b>foreign-lambda</b>) to
-the energy file and/or to <tt>dhdl.xvg</tt>, where they can be processed by, for example <tt>g_bar</tt>.
-The potentials, bond-lengths and angles are interpolated linearly as
-described in the manual. When <b>sc-alpha</b> is larger than zero, soft-core
-potentials are used for the LJ and Coulomb interactions.</dd>
-<dt><b>expanded</b></dt>
-<dd> Turns on expanded ensemble simulation, where the alchemical state becomes a dynamic variable, allowing jumping between different Hamiltonians. See the <A HREF="#expanded">expanded ensemble options</A> for controlling how expanded ensemble simulations are performed. The different Hamiltonians used in expanded ensemble simulations are defined by the other free energy options.</dd>
-</dl></dd>
-<dt><b>init-lambda: (-1)</b></dt>
-<dd>starting value for lambda (float). Generally, this should only be used with slow growth (i.e. nonzero <b>delta-lambda</b>). In other cases, <b>init-lambda-state</b> should be specified instead. Must be greater than or equal to 0.</dd>
-<dt><b>delta-lambda: (0)</b></dt>
-<dd>increment per time step for lambda</dd>
-<dt><b>init-lambda-state: (-1)</b></dt>
-<dd>starting value for the lambda state (integer). Specifies which columm of the lambda vector (<b>coul-lambdas</b>, <b>vdw-lambdas</b>, <b>bonded-lambdas</b>, <b>restraint-lambdas</b>, <b>mass-lambdas</b>, <b>temperature-lambdas</b>, <b>fep-lambdas</b>) should be used. This is a zero-based index: <b>init-lambda-state</b> 0 means the first column, and so on.</dd>
-<dt><b>fep-lambdas: ()</b></dt>
-<dd>Zero, one or more lambda values for which Delta H values will
-be determined and written to dhdl.xvg every <b>nstdhdl</b> steps.
-Values must be between 0 and 1.
-Free energy differences between different lambda values can then
-be determined with <tt>g_bar</tt>. <b>fep-lambdas</b> is different from the other -lambdas keywords because
-all components of the lambda vector that are not specified will use <b>fep-lambdas</b> (including restraint-lambdas and therefore the pull code restraints).</dd>
-<dt><b>coul-lambdas: ()</b></dt>
-<dd>Zero, one or more lambda values for which Delta H values will
-be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
-Only the electrostatic interactions are controlled with this component of the lambda vector (and only if the lambda=0 and lambda=1 states have differing electrostatic interactions).</dd>
-<dt><b>vdw-lambdas: ()</b></dt>
-<dd>Zero, one or more lambda values for which Delta H values will
-be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
-Only the van der Waals interactions are controlled with this component of the lambda vector.</dd>
-<dt><b>bonded-lambdas: ()</b></dt>
-<dd>Zero, one or more lambda values for which Delta H values will
-be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
-Only the bonded interactions are controlled with this component of the lambda vector.</dd>
-<dt><b>restraint-lambdas: ()</b></dt>
-<dd>Zero, one or more lambda values for which Delta H values will
-be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
-Only the restraint interactions: dihedral restraints, and the pull code restraints are controlled with this component of the lambda vector. </dd>
-<dt><b>mass-lambdas: ()</b></dt>
-<dd>Zero, one or more lambda values for which Delta H values will
-be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
-Only the particle masses are controlled with this component of the lambda vector.</dd>
-<dt><b>temperature-lambdas: ()</b></dt>
-<dd>Zero, one or more lambda values for which Delta H values will
-be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
-Only the temperatures controlled with this component of the lambda vector.
-Note that these lambdas should not be used for replica exchange, only for simulated tempering.</dd>
-<dt><b>calc-lambda-neighbors (1)</b></dt>
-<dd>Controls the number of lambda values for which Delta H values will be
-calculated and written out, if <b>init-lambda-state</b> has been set. A
-positive value will limit the number of lambda points calculated to only the
-nth neighbors of <b>init-lambda-state</b>: for example, if
-<b>init-lambda-state</b> is 5 and this parameter has a value of 2, energies for
-lambda points 3-7 will be calculated and writen out. A value of -1 means all
-lambda points will be written out. For normal BAR such as with g_bar, a value
-of 1 is sufficient, while for MBAR -1 should be used.</dd>
-<dt><b>sc-alpha: (0)</b></dt>
-<dd>the soft-core alpha parameter, a value of 0 results in linear interpolation of the LJ and Coulomb interactions</dd>
-<dt><b>sc-r-power: (6)</b></dt>
-<dd>the power of the radial term in the soft-core equation. Possible values are 6 and 48. 6 is more standard, and is the default. When 48 is used, then sc-alpha should generally be much lower (between 0.001 and 0.003).</dd>
-<dt><b>sc-coul: (no)</b></dt>
-<dd>Whether to apply the soft core free energy interaction transformation to the Columbic interaction of a molecule. Default is no, as it is generally
-more efficient to turn off the Coulomic interactions linearly before turning off the van der Waals interactions.</dd>
-<dt><b>sc-power: (0)</b></dt>
-<dd>the power for lambda in the soft-core function, only the values 1 and 2 are supported</dd>
-<dt><b>sc-sigma: (0.3) [nm]</b></dt>
-<dd>the soft-core sigma for particles which have a C6 or C12 parameter equal
-to zero or a sigma smaller than <b>sc-sigma</b></dd>
-<dt><b>couple-moltype:</b></dt>
-<dd>Here one can supply a molecule type (as defined in the topology)
-for calculating solvation or coupling free energies.
-There is a special option <b>system</b> that couples all molecule types
-in the system. This can be useful for equilibrating a system
-starting from (nearly) random coordinates.
-<b>free-energy</b> has to be turned on.
-The Van der Waals interactions and/or charges in this molecule type can be
-turned on or off between lambda=0 and lambda=1, depending on the settings
-of <b>couple-lambda0</b> and <b>couple-lambda1</b>. If you want to decouple
-one of several copies of a molecule, you need to copy and rename
-the molecule definition in the topology.</dd>
-<dt><b>couple-lambda0:</b></dt>
-<dd><dl compact>
-<dt><b>vdw-q</b></dt>
-<dd>all interactions are on at lambda=0
-<dt><b>vdw</b></dt>
-<dd>the charges are zero (no Coulomb interactions) at lambda=0
-<dt><b>q</b></dt>
-<dd>the Van der Waals interactions are turned at lambda=0; soft-core interactions will be required to avoid singularities
-<dt><b>none</b></dt>
-<dd>the Van der Waals interactions are turned off and the charges are zero at lambda=0; soft-core interactions will be required to avoid singularities.
-</dl>
-<dt><b>couple-lambda1:</b></dt>
-<dd> analogous to <b>couple-lambda1</b>, but for lambda=1
-<dt><b>couple-intramol:</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>All intra-molecular non-bonded interactions for moleculetype <b>couple-moltype</b> are replaced by exclusions and explicit pair interactions. In this manner the decoupled state of the molecule corresponds to the proper vacuum state without periodicity effects.
-<dt><b>yes</b></dt>
-<dd>The intra-molecular Van der Waals and Coulomb interactions are also turned on/off. This can be useful for partitioning free-energies of relatively large molecules, where the intra-molecular non-bonded interactions might lead to kinetically trapped vacuum conformations. The 1-4 pair interactions are not turned off.
-</dl>
-<dt><b>nstdhdl: (100)</b></dt>
-<dd>the frequency for writing dH/dlambda and possibly Delta H to dhdl.xvg,
-0 means no ouput, should be a multiple of <b>nstcalcenergy</b></dd>.</dd>
-<dt><b>dhdl-derivatives: (yes)</b></dt>
-<dd>If yes (the default), the derivatives of the Hamiltonian with respect to lambda at each <b>nstdhdl</b> step are written out. These values are needed for interpolation of linear energy differences with <tt>g_bar</tt> (although the same can also be achieved with the right <b>foreign lambda</b> setting, that may not be as flexible), or with thermodynamic integration</dd>
-<dt><b>dhdl-print-energy: (no)</b></dt>
-<dd> Include either the total or the potential energy in the dhdl file. Options are 'no', 'potential', or 'total'. This information is needed for later free energy analysis if the states of interest are at different temperatures. If all states are at the same temperature, this information is not needed. 'potential' is useful in case one is using <tt>mdrun -rerun</tt> to generate the <tt>dhdl.xvg</tt> file. When rerunning from an existing trajectory, the kinetic energy will often not be correct, and thus one must compute the residual free energy from the potential alone, with the kinetic energy component computed analytically.
-</dd>
-<dt><b>separate-dhdl-file: (yes)</b></dt>
-<dd><dl compact>
-<dt><b>yes</b></dt>
-<dd>the free energy values that are calculated (as specified with the <b>foreign-lambda</b> and <b>dhdl-derivatives</b> settings) are written out to a separate file, with the default name <tt>dhdl.xvg</tt>. This file can be used directly with <tt>g_bar</tt>.</dd>
-<dt><b>no</b></dt>
-<dd>The free energy values are written out to the energy output file (<tt>ener.edr</tt>, in accumulated blocks at every <b>nstenergy</b> steps), where they can be extracted with <tt>g_energy</tt> or used directly with <tt>g_bar</tt>.</dd>
-</dl>
-<dt><b>dh-hist-size: (0)</b></dt>
-<dd>If nonzero, specifies the size of the histogram into which the Delta H values (specified with <b>foreign-lambda</b>) and the derivative dH/dl values are binned, and written to ener.edr. This can be used to save disk space while calculating free energy differences. One histogram gets written for each <b>foreign lambda</b> and two for the dH/dl, at every <b>nstenergy</b> step. Be aware that incorrect histogram settings (too small size or too wide bins) can introduce errors. Do not use histograms unless you're certain you need it.</dd>
-<dt><b>dh-hist-spacing (0.1)</b></dt>
-<dd>Specifies the bin width of the histograms, in energy units. Used in conjunction with <b>dh-hist-size</b>. This size limits the accuracy with which free energies can be calculated. Do not use histograms unless you're certain you need it.</dd>
-</dl>
-<A NAME="expanded"><br>
-<hr>
-<h3><!--Idx-->Expanded Ensemble calculations<!--EIdx--></h3>
-
-<dl>
-<dt><b>nstexpanded</b></dt> <dd>The number of integration steps beween attempted moves changing the system Hamiltonian in expanded ensemble simulations. Must be a multiple of <b>nstcalcenergy</b>, but can be greater or less than <b>nstdhdl</b>.</dd>
-<dt><b>lmc-stats:</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>No Monte Carlo in state space is performed.</dd>
-<dt><b>metropolis-transition</b></dt>
-<dd> Uses the Metropolis weights to update the expanded ensemble weight of each state.
-Min{1,exp(-(beta_new u_new - beta_old u_old)}</dd>
-<dt><b>barker-transition</b></dt>
-<dd> Uses the Barker transition critera to update the expanded ensemble weight of each state i, defined by
-exp(-beta_new u_new)/[exp(-beta_new u_new)+exp(-beta_old u_old)</dd>
-<dt><b>wang-landau</b></dt>
-<dd>Uses the Wang-Landau algorithm (in state space, not energy space) to update the expanded ensemble weights.</dd>
-<dt><b>min-variance</b></dt>
-<dd>Uses the minimum variance updating method of Escobedo et al. to update the expanded ensemble weights. Weights
-will not be the free energies, but will rather emphasize states that need more sampling to give even uncertainty.</dd>
-</dl>
-<dt><b>lmc-mc-move:</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>No Monte Carlo in state space is performed.</dd>
-<dt><b>metropolis-transition</b></dt>
-<dd> Randomly chooses a new state up or down, then uses the Metropolis critera to decide whether to accept or reject:
-Min{1,exp(-(beta_new u_new - beta_old u_old)}</dd>
-<dt><b>barker-transition</b></dt>
-<dd> Randomly chooses a new state up or down, then uses the Barker transition critera to decide whether to accept or reject: exp(-beta_new u_new)/[exp(-beta_new u_new)+exp(-beta_old u_old)]</dd>
-<dt><b>gibbs</b></dt>
-<dd> Uses the conditional weights of the state given the coordinate (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to
-decide which state to move to.</dd>
-<dt><b>metropolized-gibbs</b></dt>
-<dd>
-<dd> Uses the conditional weights of the state given the coordinate (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to
-decide which state to move to, EXCLUDING the current state, then uses a rejection step to ensure detailed
-balance. Always more efficient that Gibbs, though only marginally so in many situations, such as when only the nearest neighbors have decent phase space overlap.</dd>
-</dl>
-<dt><b>lmc-seed: (-1)</b></dt>
-<dd> random seed to use for Monte Carlo moves in state space. When <b>lmc-seed</b> is set to -1, a pseudo random seed is us</dd>
-<dt><b>mc-temperature:</b></dt>
-<dd> Temperature used for acceptance/rejection for Monte Carlo moves. If not specified, the temperature of the
-simulation specified in the first group of <b>ref_t</b> is used.</dd>
-<dt><b>wl-ratio: (0.8)</b></dt>
-<dd>The cutoff for the histogram of state occupancies to be reset, and the free energy incrementor to be reset as delta -> delta*wl-scale. If we define the Nratio = (number of samples at each histogram) / (average number of samples at each histogram). <b>wl-ratio</b> of 0.8 means that means that the histogram is only considered flat if all Nratio > 0.8 AND simultaneously all 1/Nratio > 0.8.</dd>
-<dt><b>wl-scale: (0.8)</b></dt>
-<dd> Each time the histogram is considered flat, then the current value of the Wang-Landau incrementor for the free energies is multiplied by <b>wl-scale</b>. Value must be between 0 and 1.</dd>
-<dt><b>init-wl-delta: (1.0)</b></dt>
-<dd>The initial value of the Wang-Landau incrementor in kT. Some value near 1 kT is usually most efficient, though sometimes a value of 2-3 in units of kT works better if the free energy differences are large.</dd>
-<dt><b>wl-oneovert: (no)</b></dt>
-<dd>Set Wang-Landau incrementor to scale with 1/(simulation time) in the large sample limit. There is significant evidence that the standard Wang-Landau algorithms in state space presented here result in free energies getting 'burned in' to incorrect values that depend on the initial state. when <b>wl-oneovert</b> is true, then when the incrementor becomes less than 1/N, where N is the mumber of samples collected (and thus proportional to the data collection time, hence '1 over t'), then the Wang-Lambda incrementor is set to 1/N, decreasing every step. Once this occurs, <b>wl-ratio</b> is ignored, but the weights will still stop updating when the equilibration criteria set in <b>lmc-weights-equil</b> is achieved.</dd>
-<dt><b>lmc-repeats: (1)</b></dt>
-<dd>Controls the number of times that each Monte Carlo swap type is performed each iteration. In the limit of large numbers of Monte Carlo repeats, then all methods converge to Gibbs sampling. The value will generally not need to be different from 1.</dd>
-<dt><b>lmc-gibbsdelta: (-1)</b></dt>
-<dd> Limit Gibbs sampling to selected numbers of neighboring states. For Gibbs sampling, it is sometimes inefficient to perform Gibbs sampling over all of the states that are defined. A positive value of <b>lmc-gibbsdelta</b> means that only states plus or minus <b>lmc-gibbsdelta</b> are considered in exchanges up and down. A value of -1 means that all states are considered. For less than 100 states, it is probably not that expensive to include all states.</dd>
-<dt><b>lmc-forced-nstart: (0)</b></dt>
-<dd> Force initial state space sampling to generate weights. In order to come up with reasonable initial weights, this setting allows the simulation to drive from the initial to the final lambda state, with <b>lmc-forced-nstart</b> steps at each state before moving on to the next lambda state. If <b>lmc-forced-nstart</b> is sufficiently long (thousands of steps, perhaps), then the weights will be close to correct. However, in most cases, it is probably better to simply run the standard weight equilibration algorithms.
-<dt><b>nst-transition-matrix: (-1)</b></dt>
-<dd>Frequency of outputting the expanded ensemble transition matrix. A negative number means it will only be printed at the end of the simulation.<dd>
-<dt><b>symmetrized-transition-matrix: (no) </b></dt>
-<dd>Whether to symmetrize the empirical transition matrix. In the infinite limit the matrix will be symmetric, but will diverge with statistical noise for short timescales. Forced symmetrization, by using the matrix T_sym = 1/2 (T + transpose(T)), removes problems like the existence of (small magnitude) negative eigenvalues.</dd>
-<dt><b>mininum-var-min: (100)</b></dt>
-<dd> The <b>min-variance</b> strategy (option of <b>lmc-stats</b> is only valid for larger number of samples, and can get stuck if too few samples are used at each state. <b>mininum-var-min</b> is the minimum number of samples that each state that are allowed before the <b>min-variance</b> strategy is activated if selected.</dd>
-<dt><b>init-lambda-weights: </b></dt>
-<dd>The initial weights (free energies) used for the expanded ensemble states. Default is a vector of zero weights. format is similar to the lambda vector settings in <b>fep-lambdas</b>, except the weights can be any floating point number. Units are kT. Its length must match the lambda vector lengths.</dd>
-<dt><b>lmc-weights-equil: (no)</b></dt>
-<dd><dl compact>
-<dt><b>no</b></dt>
-<dd>Expanded ensemble weights continue to be updated throughout the simulation.</dd>
-<dt><b>yes</b></dt>
-<dd>The input expanded ensemble weights are treated as equilibrated, and are not updated throughout the simulation.</dd>
-<dt><b>wl-delta</b></dt>
-<dd>Expanded ensemble weight updating is stopped when the Wang-Landau incrementor falls below the value specified by <b>weight-equil-wl-delta</b>.</dd>
-<dt><b>number-all-lambda</b></dt>
-<dd>Expanded ensemble weight updating is stopped when the number of samples at all of the lambda states is greater than the value specified by <b>weight-equil-number-all-lambda</b>.</dd>
-<dt><b>number-steps</b></dt>
-<dd>Expanded ensemble weight updating is stopped when the number of steps is greater than the level specified by <b>weight-equil-number-steps</b>.</dd>
-<dt><b>number-samples</b></dt>
-<dd>Expanded ensemble weight updating is stopped when the number of total samples across all lambda states is greater than the level specified by <b>weight-equil-number-samples</b>.</dd>
-<dt><b>count-ratio</b></dt>
-<dd>Expanded ensemble weight updating is stopped when the ratio of samples at the least sampled lambda state and most sampled lambda state greater than the value specified by <b>weight-equil-count-ratio</b>.</dd>
-</dl>
-<dt><b>simulated-tempering: (no)</b></dt>
-<dd>Turn simulated tempering on or off. Simulated tempering is implemented as expanded ensemble sampling with different temperatures instead of different Hamiltonians.</dd>
-<dt><b>sim-temp-low: (300)</b></dt>
-<dd>Low temperature for simulated tempering.</dd>
-<dt><b>sim-temp-high: (300)</b></dt>
-<dd>High temperature for simulated tempering.</dd>
-<dt><b>simulated-tempering-scaling: (linear)</b></dt>
-<dd>Controls the way that the temperatures at intermediate lambdas are calculated from the <b>temperature-lambda</b> part of the lambda vector.</dd>
-<dd><dl compact>
-<dt><b>linear</b></dt>
-<dd>Linearly interpolates the temperatures using the values of <b>temperature-lambda</b>,i.e. if <b>sim-temp-low</b>=300, <b>sim-temp-high</b>=400, then lambda=0.5 correspond to a temperature of 350. A nonlinear set of temperatures can always be implemented with uneven spacing in lambda.</dd>
-<dt><b>geometric</b></dt>
-<dd> Interpolates temperatures geometrically between <b>sim-temp-low</b> and <b>sim-temp-high</b>. The i:th state has temperature <b>sim-temp-low</b> * (<b>sim-temp-high</b>/<b>sim-temp-low</b>) raised to the power of (i/(ntemps-1)). This should give roughly equal exchange for constant heat capacity, though of course things simulations that involve protein folding have very high heat capacity peaks.</dd>
-<dt><b>exponential</b></dt>
-<dd> Interpolates temperatures exponentially between <b>sim-temp-low</b> and <b>sim-temp-high</b>. The ith state has temperature
-<b>sim-temp-low</b> + (<b>sim-temp-high</b>-<b>sim-temp-low</b>)*((exp(<b>temperature-lambdas</b>[i])-1)/(exp(1.0)-1)).</dd>
-</dl>
-</dl>
-
-<A NAME="neq"><br>
-<hr>
-<h3>Non-equilibrium MD<!--QuietIdx-->non-equilibrium MD<!--EQuietIdx--></h3>
-
-<dl>
-<dt><b>acc-grps: </b></dt>
-<dd>groups for constant acceleration (e.g.: <tt>Protein Sol</tt>)
-all atoms in groups Protein and Sol will experience constant acceleration
-as specified in the <b>accelerate</b> line</dd>
-<dt><b>accelerate: (0) [nm ps<sup>-2</sup>]</b></dt>
-<dd>acceleration for <b>acc-grps</b>; x, y and z for each group
-(e.g. <tt>0.1 0.0 0.0 -0.1 0.0 0.0</tt> means that first group has constant
-acceleration of 0.1 nm ps<sup>-2</sup> in X direction, second group the
-opposite).</dd>
-<dt><b>freezegrps: </b></dt>
-<dd>Groups that are to be frozen (i.e. their X, Y, and/or Z position will
-not be updated; e.g. <tt>Lipid SOL</tt>). <b>freezedim</b> specifies for
-which dimension the freezing applies.
-To avoid spurious contibrutions to the virial and pressure due to large
-forces between completely frozen atoms you need to use
-<A HREF="#egexcl">energy group exclusions</A>, this also saves computing time.
-Note that coordinates of frozen atoms are not scaled by pressure-coupling
-algorithms.</dd>
-<dt><b>freezedim: </b></dt>
-<dd>dimensions for which groups in <b>freezegrps</b> should be frozen,
-specify <tt>Y</tt> or <tt>N</tt> for X, Y and Z and for each group
-(e.g. <tt>Y Y N N N N</tt> means that particles in the first group
-can move only in Z direction. The particles in the second group can
-move in any direction).</dd>
-<dt><b>cos-acceleration: (0) [nm ps<sup>-2</sup>]</b></dt>
-<dd>the amplitude of the acceleration profile for calculating the
-<!--Idx-->viscosity<!--EIdx-->.
-The acceleration is in the X-direction and the magnitude is
-<b>cos-acceleration</b> cos(2 pi z/boxheight).
-Two terms are added to the energy file:
-the amplitude of the velocity profile and 1/viscosity.</dd>
-<dt><b><!--Idx-->deform<!--EIdx-->: (0 0 0 0 0 0) [nm ps<sup>-1</sup>]</b></dt>
-<dd>The velocities of deformation for the box elements:
-a(x) b(y) c(z) b(x) c(x) c(y). Each step the box elements
-for which <b>deform</b> is non-zero are calculated as:
-box(ts)+(t-ts)*deform, off-diagonal elements are corrected
-for periodicity. The coordinates are transformed accordingly.
-Frozen degrees of freedom are (purposely) also transformed.
-The time ts is set to t at the first step and at steps at which
-x and v are written to trajectory to ensure exact restarts.
-Deformation can be used together with semiisotropic or anisotropic
-pressure coupling when the appropriate compressibilities are set to zero.
-The diagonal elements can be used to <!--Idx-->strain<!--EIdx--> a solid.
-The off-diagonal elements can be used to <!--Idx-->shear<!--EIdx--> a solid
-or a liquid.</dd>
-</dl>
-
-<A NAME="ef"><br>
-<hr>
-<h3>Electric fields<!--QuietIdx-->electric field<!--EQuietIdx--></h3>
-
-<dl>
-<dt><b>E-x ; E-y ; E-z:</b></dt>
-<dd>If you want to use an electric field in a direction, enter 3 numbers
-after the appropriate <b>E-*</b>, the first number: the number of cosines,
-only 1 is implemented (with frequency 0) so enter 1,
-the second number: the strength of the electric field in
-<b>V nm<sup>-1</sup></b>,
-the third number: the phase of the cosine, you can enter any number here
-since a cosine of frequency zero has no phase.</dd>
-<dt><b>E-xt; E-yt; E-zt: </b></dt>
-<dd>not implemented yet</dd>
-</dl>
-<br>
-
-<hr>
-<A NAME="qmmm"><br>
-<h3>Mixed quantum/classical molecular dynamics<!--QuietIdx>QM/MM<!--EQuietIdx--></h3>
-
-<dl>
-<dt><b>QMMM:</b></dt>
-<dd><dl compact="compact">
-<dt><b>no</b></dt>
-<dd>No QM/MM.</dd>
-<dt><b>yes</b></dt>
-<dd>Do a QM/MM simulation. Several groups can be described at
-different QM levels separately. These are specified in
-the <b>QMMM-grps</b> field separated by spaces. The level of <i>ab
-initio</i> theory at which the groups are described is specified
-by <b>QMmethod</b> and <b>QMbasis</b> Fields. Describing the
-groups at different levels of theory is only possible with the ONIOM
-QM/MM scheme, specified by <b>QMMMscheme</b>.</dd>
-</dl></dd>
-
-<dt><b>QMMM-grps:</b></dt>
-<dd>groups to be descibed at the QM level</dd>
-
-<dt><b>QMMMscheme:</b></dt>
-<dd><dl compact="compact">
-<dt><b>normal</b></dt>
-<dd>normal QM/MM. There can only be one <b>QMMM-grps</b> that is modelled
-at the <b>QMmethod</b> and <b>QMbasis</b> level of <i>ab initio</i>
-theory. The rest of the system is described at the MM level. The QM
-and MM subsystems interact as follows: MM point charges are included
-in the QM one-electron hamiltonian and all Lennard-Jones interactions
-are described at the MM level.</dd>
-<dt><b>ONIOM</b></dt>
-<dd>The interaction between the subsystem is described using the ONIOM
-method by Morokuma and co-workers. There can be more than one <b>QMMM-grps</b> each modeled at a different level of QM theory
-(<b>QMmethod</b> and <b>QMbasis</b>).
-</dd></dl></dd>
-
-<dt><b>QMmethod: (RHF)</b></dt>
-<dd>Method used to compute the energy and gradients on the QM
-atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
-CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
-included in the active space is specified by <b>CASelectrons</b>
-and <b>CASorbitals</b>. </dd>
-
-<dt><b>QMbasis: (STO-3G)</b></dt>
-<dd>Basis set used to expand the electronic wavefuntion. Only Gaussian
-basis sets are currently available, <i>i.e.</i> STO-3G, 3-21G, 3-21G*,
-3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*, and 6-311G.</dd>
-
-<dt><b>QMcharge: (0) [integer]</b></dt>
-<dd>The total charge in <tt>e</tt> of the <b>QMMM-grps</b>. In case
-there are more than one <b>QMMM-grps</b>, the total charge of each
-ONIOM layer needs to be specified separately.</dd>
-
-<dt><b>QMmult: (1) [integer]</b></dt>
-<dd>The multiplicity of the <b>QMMM-grps</b>. In case there are more
-than one <b>QMMM-grps</b>, the multiplicity of each ONIOM layer needs
-to be specified separately.</dd>
-
-<dt><b>CASorbitals: (0) [integer]</b></dt>
-<dd>The number of orbitals to be included in the active space when
-doing a CASSCF computation.</dd>
-
-<dt><b>CASelectrons: (0) [integer]</b></dt>
-<dd>The number of electrons to be included in the active space when
-doing a CASSCF computation.</dd>
-
-<dt><b>SH:</b></dt>
-<dd><dl compact="compact">
-<dt><b>no</b></dt>
-<dd>No surface hopping. The system is always in the electronic
-ground-state.</dd>
-<dt><b>yes</b></dt>
-<dd>Do a QM/MM MD simulation on the excited state-potential energy
-surface and enforce a <i>diabatic</i> hop to the ground-state when the
-system hits the conical intersection hyperline in the course the
-simulation. This option only works in combination with the CASSCF
-method.</dd>
-</dl>
-</dl>
-
-<A NAME="gbsa"><br>
-<hr>
-<h3>Implicit solvent</h3>
-
-<dl>
-<dt><b>implicit-solvent:</b></dt>
-<dd><dl compact="compact">
-<dt><b>no</b></dt>
-<dd>No implicit solvent</dd>
-<dt><b>GBSA</b></dt>
-<dd>Do a simulation with implicit solvent using the Generalized Born formalism.
-Three different methods for calculating the Born radii are available, Still, HCT and
-OBC. These are specified with the <b>gb-algorithm</b> field. The non-polar solvation
-is specified with the <b>sa-algorithm</b> field.</dd>
-</dl>
-
-<dt><b>gb-algorithm:</b></dt>
-<dd><dl compact="compact">
-<dt><b>Still</b></dt>
-<dd>Use the Still method to calculate the Born radii</dd>
-<dt><b>HCT</b></dt>
-<dd>Use the Hawkins-Cramer-Truhlar method to calculate the Born radii</dd>
-<dt><b>OBC</b></dt>
-<dd>Use the Onufriev-Bashford-Case method to calculate the Born radii</dd>
-</dl>
-
-<dt><b>nstgbradii: (1) [steps]</b></dt>
-<dd>Frequency to (re)-calculate the Born radii. For most practial purposes,
-setting a value larger than 1 violates energy conservation and leads to
-unstable trajectories.</dd>
-
-<dt><b>rgbradii: (1.0) [nm]</b></dt>
-<dd>Cut-off for the calculation of the Born radii. Currently must be equal to rlist</dd>
-
-<dt><b>gb-epsilon-solvent: (80)</b></dt>
-<dd>Dielectric constant for the implicit solvent</dd>
-
-<dt><b>gb-saltconc: (0) [M]</b></dt>
-<dd>Salt concentration for implicit solvent models, currently not used</dd>
-
-<dt><b>gb-obc-alpha (1); gb-obc-beta (0.8); gb-obc-gamma (4.85);</b></dt>
-<dd>Scale factors for the OBC model. Default values are OBC(II).
-Values for OBC(I) are 0.8, 0 and 2.91 respectively</dd>
-
-<dt><b>gb-dielectric-offset: (0.009) [nm]</b></dt>
-<dd>Distance for the di-electric offset when calculating the Born radii. This is
-the offset between the center of each atom the center of the polarization energy
-for the corresponding atom</dd>
-
-<dt><b>sa-algorithm</b></dt>
-<dd><dl compact="compact">
-<dt><b>Ace-approximation</b></dt>
-<dd>Use an Ace-type approximation (default)</dd>
-<dt><b>None</b></dt>
-<dd>No non-polar solvation calculation done. For GBSA only the polar part gets
-calculated</dd>
-</dl>
-
-<dt><b>sa-surface-tension: [kJ mol<sup>-1</sup> nm<sup>-2</sup>]</b></dt>
-<dd>Default value for surface tension with SA algorithms. The default value is -1;
-Note that if this default value is not changed
-it will be overridden by <tt>grompp</tt> using values that are specific for the choice
-of radii algorithm (0.0049 kcal/mol/Angstrom<sup>2</sup> for Still, 0.0054 kcal/mol/Angstrom<sup>2</sup>
-for HCT/OBC)
-
-Setting it to 0 will while using an sa-algorithm other than None means
-no non-polar calculations are done.
-</dd>
-</dl>
-
-<A NAME="adress"><br>
-<hr>
-<h3>Adaptive Resolution Simulation</h3>
-
-<dl>
-<dt><b>adress: (no)</b></dt>
-<dd>Decide whether the AdResS feature is turned on.</dd>
-<dt><b>adress-type: (Off)</b></dt>
-<dd><dl compact>
-<dt><b>Off</b></dt>
-<dd>Do an AdResS simulation with weight equal 1, which is equivalent to an explicit (normal) MD simulation. The difference to disabled AdResS is that the AdResS variables are still read-in and hence are defined.</dd>
-<dt><b>Constant</b></dt>
-<dd>Do an AdResS simulation with a constant weight, <b>adress-const-wf</b> defines the value of the weight</dd>
-<dt><b>XSplit</b></dt>
-<dd>Do an AdResS simulation with simulation box split in x-direction, so basically the weight is only a function of the x coordinate and all distances are measured using the x coordinate only.</dd>
-<dt><b>Sphere</b></dt>
-<dd>Do an AdResS simulation with spherical explicit zone.</dd>
-</dl></dd>
-<dt><b>adress-const-wf: (1)</b></dt>
-<dd>Provides the weight for a constant weight simulation (<b>adress-type</b>=Constant)</dd>
-<dt><b>adress-ex-width: (0)</b></dt>
-<dd>Width of the explicit zone, measured from <b>adress-reference-coords</b>.</dd>
-<dt><b>adress-hy-width: (0)</b></dt>
-<dd>Width of the hybrid zone.</dd>
-<dt><b>adress-reference-coords: (0,0,0)</b></dt>
-<dd>Position of the center of the explicit zone. Periodic boundary conditions apply for measuring the distance from it.</dd>
-<dt><b>adress-cg-grp-names</b></dt>
-<dd>The names of the coarse-grained energy groups. All other energy groups are considered explicit and their interactions will be automatically excluded with the coarse-grained groups.</dd>
-<dt><b>adress-site: (COM)</b>The mapping point from which the weight is calculated.</dt>
-<dd><dl compact>
-<dt><b>COM</b></dt>
-<dd>The weight is calculated from the center of mass of each charge group.</dd>
-<dt><b>COG</b></dt>
-<dd>The weight is calculated from the center of geometry of each charge group.</dd>
-<dt><b>Atom</b></dt>
-<dd>The weight is calculated from the position of 1st atom of each charge group.</dd>
-<dt><b>AtomPerAtom</b></dt>
-<dd>The weight is calculated from the position of each individual atom.</dd>
-</dl></dd>
-<dt><b>adress-interface-correction: (Off)</b></dt>
-<dd><dl compact>
-<dt><b>Off</b></dt>
-<dd>Do not a apply any interface correction.</dd>
-<dt><b>thermoforce</b></dt>
-<dd>Apply thermodynamic force interface correction. The table can be specified using the <tt>-tabletf</tt> option of <tt>mdrun</tt>. The table should contain the potential and force (acting on molecules) as function of the distance from <b>adress-reference-coords</b>.</dd>
-</dl></dd>
-<dt><b>adress-tf-grp-names</b></dt>
-<dd>The names of the energy groups to which the <b>thermoforce</b> is applied if enabled in <b>adress-interface-correction</b>. If no group is given the default table is applied.</dd>
-<dt><b>adress-ex-forcecap: (0)</b></dt>
-<dd>Cap the force in the hybrid region, useful for big molecules. 0 disables force capping.</dd>
-</dl>
-
-<A NAME="user"><br>
-<hr>
-<h3>User defined thingies</h3>
-
-<dl>
-<dt><b>user1-grps; user2-grps: </b></dt>
-<dt><b>userint1 (0); userint2 (0); userint3 (0); userint4 (0)</b></dt>
-<dt><b>userreal1 (0); userreal2 (0); userreal3 (0); userreal4 (0)</b></dt>
-<dd>These you can use if you modify code. You can pass integers and
-reals to your subroutine. Check the inputrec definition in
-<tt>src/include/types/inputrec.h</tt></dd>
-
-</dl>
-
-<A NAME="idx"><br>
-<hr>
-<h3>Index</h3>
-
-<P>
-
-<multicol cols=4>
-<A HREF="#neq">acc-grps</A><br>
-<A HREF="#neq">accelerate</A><br>
-<A HREF="#sa">annealing</A><br>
-<A HREF="#sa">annealing-npoints</A><br>
-<A HREF="#sa">annealing-time</A><br>
-<A HREF="#sa">annealing-temp</A><br>
-<A HREF="#ld">bd-fric</A><br>
-<A HREF="#vdw">bDispCorr</A><br>
-<A HREF="#run">comm-mode</A><br>
-<A HREF="#run">comm-grps</A><br>
-<A HREF="#pc">compressibility</A><br>
-<A HREF="#bond">constraint-algorithm</A><br>
-<A HREF="#bond">constraints</A><br>
-<A HREF="#neq">cos-acceleration</A><br>
-<A HREF="#el">coulombtype</A><br>
-<A HREF="#el">coulomb-modifier</A><br>
-<A HREF="#free">couple-intramol</A><br>
-<A HREF="#free">couple-lambda0</A><br>
-<A HREF="#free">couple-lambda1</A><br>
-<A HREF="#free">couple-moltype</A><br>
-<A HREF="#nl">cutoff-scheme</A><br>
-<A HREF="#pp">define</A><br>
-<A HREF="#neq">deform</A><br>
-<A HREF="#free">delta-lambda</A><br>
-<A HREF="#nmr">disre</A><br>
-<A HREF="#nmr">disre-weighting</A><br>
-<A HREF="#nmr">disre-mixed</A><br>
-<A HREF="#nmr">disre-fc</A><br>
-<A HREF="#nmr">disre-tau</A><br>
-<A HREF="#run">dt</A><br>
-<A HREF="#em">emstep</A><br>
-<A HREF="#em">emtol</A><br>
-<A HREF="#egexcl">energygrp-excl</A><br>
-<A HREF="#table">energygrp-table</A><br>
-<A HREF="#out">energygrps</A><br>
-<A HREF="#el2">epsilon-r</A><br>
-<A HREF="#el2">epsilon-rf</A><br>
-<A HREF="#ewald">ewald-rtol</A><br>
-<A HREF="#ewald">ewald-geometry</A><br>
-<A HREF="#ewald">epsilon-surface</A><br>
-<A HREF="#ef">E-x</A><br>
-<A HREF="#ef">E-xt</A><br>
-<A HREF="#ef">E-y</A><br>
-<A HREF="#ef">E-yt</A><br>
-<A HREF="#ef">E-z</A><br>
-<A HREF="#ef">E-zt </A><br>
-<A HREF="#shellmd">fcstep</A><br>
-<A HREF="#ewald">fourier-nx</A><br>
-<A HREF="#ewald">fourier-ny</A><br>
-<A HREF="#ewald">fourier-nz</A><br>
-<A HREF="#ewald">fourierspacing</A><br>
-<A HREF="#free">free-energy</A><br>
-<A HREF="#neq">freezedim </A><br>
-<A HREF="#neq">freezegrps</A><br>
-<A HREF="#vel">gen-seed</A><br>
-<A HREF="#vel">gen-temp</A><br>
-<A HREF="#vel">gen-vel</A><br>
-<A HREF="#pp">include</A><br>
-<A HREF="#free">init-lambda</A><br>
-<A HREF="#expanded">init-lambda-weights</A><br>
-<A HREF="#run">init-step</A><br>
-<A HREF="#expanded">initial-wl-delta</A><br>
-<A HREF="#run">integrator</A><br>
-<A HREF="#ld">ld-seed</A><br>
-<A HREF="#bond2">lincs-iter</A><br>
-<A HREF="#bond2">lincs-order</A><br>
-<A HREF="#bond2">lincs-warnangle</A><br>
-<A HREF="#expanded">lmc-forced-nstart</A><br>
-<A HREF="#expanded">lmc-gibbsdelta</A><br>
-<A HREF="#expanded">lmc-mc-move</A><br>
-<A HREF="#expanded">lmc-seed</A><br>
-<A HREF="#expanded">lmc-stats</A><br>
-<A HREF="#expanded">lmc-weights-equil</A><br>
-<A HREF="#expanded">mc-temperature</A><br>
-<A HREF="#expanded">mininum-var-min</A><br>
-<A HREF="#bond2">morse</A><br>
-<A HREF="#em">nbfgscorr</A><br>
-<A HREF="#shellmd">niter</A><br>
-<A HREF="#tc">nh-chain-length</A><br>
-<A HREF="#em">nstcgsteep</A><br>
-<A HREF="#out">nstcalcenergy</A><br>
-<A HREF="#run">nstcomm</A><br>
-<A HREF="#nmr">nstdisreout</A><br>
-<A HREF="#out">nstenergy</A><br>
-<A HREF="#run">nsteps</A><br>
-<A HREF="#out">nstfout</A><br>
-<A HREF="#nl">nstlist</A><br>
-<A HREF="#out">nstlog</A><br>
-<A HREF="#pc">nstpcouple</A><br>
-<A HREF="#tc">nsttcouple</A><br>
-<A HREF="#out">nstvout</A><br>
-<A HREF="#out">nstxout</A><br>
-<A HREF="#out">nstxout-compressed</A><br>
-<A HREF="#expanded">nst-transition-matrix</A><br>
-<A HREF="#nl">ns-type</A><br>
-<A HREF="#wall">nwall</A><br>
-<A HREF="#nmr2">orire</A><br>
-<A HREF="#nmr2">orire-fc</A><br>
-<A HREF="#nmr2">orire-tau</A><br>
-<A HREF="#nmr2">orire-fitgrp</A><br>
-<A HREF="#nmr2">nstorireout</A><br>
-<A HREF="#nl">pbc</A><br>
-<A HREF="#pc">pcoupl</A><br>
-<A HREF="#pc">pcoupltype</A><br>
-<A HREF="#nl">periodic-molecules</A><br>
-<A HREF="#ewald">pme-order</A><br>
-<A HREF="#pull">pull</A><br>
-<A HREF="#pc">refcoord-scaling</A><br>
-<A HREF="#pc">ref-p</A><br>
-<A HREF="#tc">ref-t</A><br>
-<A HREF="#el2">rcoulomb-switch</A><br>
-<A HREF="#el2">rcoulomb</A><br>
-<A HREF="#nl">rlist</A><br>
-<A HREF="#nl">rlistlong</A><br>
-<A HREF="#tpi">rtpi</A><br>
-<A HREF="#vdw">rvdw-switch</A><br>
-<A HREF="#vdw">rvdw</A><br>
-<A HREF="#free">sc-alpha</A><br>
-<A HREF="#free">sc-power</A><br>
-<A HREF="#free">sc-sigma</A><br>
-<A HREF="#bond2">shake-tol</A><br>
-<A HREF="#expanded">sim-temp-low</A><br>
-<A HREF="#expanded">sim-temp-high</A><br>
-<A HREF="#expanded">simulated-tempering</A><br>
-<A HREF="#expanded">simulated-tempering-scaling</A><br>
-<A HREF="#expanded">symmetrized-transition-matrix</A><br>
-<A HREF="#table">table-extension</A><br>
-<A HREF="#pc">tau-p</A><br>
-<A HREF="#tc">tau-t</A><br>
-<A HREF="#tc">tc-grps</A><br>
-<A HREF="#tc">tcoupl</A><br>
-<A HREF="#run">tinit</A><br>
-<A HREF="#bond">continuation</A><br>
-<A HREF="#user">user1-grps</A><br>
-<A HREF="#user">user2-grps</A><br>
-<A HREF="#user">userint1</A><br>
-<A HREF="#user">userint2</A><br>
-<A HREF="#user">userint3</A><br>
-<A HREF="#user">userint4</A><br>
-<A HREF="#user">userreal1</A><br>
-<A HREF="#user">userreal2</A><br>
-<A HREF="#user">userreal3</A><br>
-<A HREF="#user">userreal4</A><br>
-<A HREF="#vdw">vdwtype</A><br>
-<A HREF="#vdw">vdw-modifier</A><br>
-<A HREF="#nl">verlet-buffer-tolerance</A><br>
-<A HREF="#out">compressed-x-grps</A><br>
-<A HREF="#out">compressed-x-precision</A><br>
-<A HREF="#sa">zero-temp-time</A><br>
-<A HREF="#walls">wall-atomtype</A><br>
-<A HREF="#walls">wall-density</A><br>
-<A HREF="#walls">wall-ewald-zfac</A><br>
-<A HREF="#walls">wall-r-linpot</A><br>
-<A HREF="#walls">wall-type</A><br>
-<A HREF="#expanded">weight-equil-count-ratio</A><br>
-<A HREF="#expanded">weight-equil-number-all-lambda</A><br>
-<A HREF="#expanded">weight-equil-number-samples</A><br>
-<A HREF="#expanded">weight-equil-number-steps</A><br>
-<A HREF="#expanded">weight-equil-wl-delta</A><br>
-<A HREF="#expanded">wl-ratio</A><br>
-<A HREF="#expanded">wl-scale</A><br>
-</multicol>
<title>mtx file format</title>
<H3>Description</H3>
Files with the mtx file extension contain a matrix.
-The file format is identical to the <a href="trj.html">trj</a> format.
+The file format is identical to the <a href="trr.html">trr</a> format.
Currently this file format is only used for hessian matrices,
which are produced with <a href="../programs/gmx-mdrun.html">gmx mdrun</a> and read by
<a href="../programs/gmx-nmeig.html">gmx nmeig</a>.
+++ /dev/null
-<TITLE>Options</TITLE>
-<UL>
-<LI>
-Optional files are not used unless the option is set, in contrast to
-non optional files, where the default file name is used when the
-option is not set.
-<P>
-All GROMACS programs will accept file options without a file extension
-or filename being specified. In such cases the default filenames will
-be used. With multiple input file types, such as generic structure
-format, the directory will be searched for files of each type with the
-supplied or default name. When no such file is found, or with output
-files the first file type will be used.
-<P>
-All GROMACS programs with the exception of <tt>mdrun</tt>,
-<tt>trjcat</tt> and <tt>eneconv</tt> check if the command line options
-are valid. If this is not the case, the program will be halted.
-<P>
-<LI>
-All GROMACS programs have 4 hidden options:
-<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
-<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]hidden</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> [hidden] Print hidden options </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]quiet</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> [hidden] Do not print help info </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-man</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>html</tt> </TD><TD> [hidden] Write manual and quit: no, html, tex, nroff, java, ascii or completion </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]debug</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> [hidden] Write file with debug information </TD></TD>
-</TABLE>
-<P>
-<LI>
-Enumerated options (enum) should be used with one of the arguments
-listed in the option description, the argument may be abbreviated.
-The first match to the shortest argument in the list will be selected.
-<P>
-<LI>
-Vector options can be used with 1 or 3 parameters. When only one
-parameter is supplied the two others are also set to this value.
-<P>
-<LI>
-All GROMACS programs can read compressed or g-zipped files. There
-might be a problem with reading compressed <tt>.xtc</tt>,
-<tt>.trr</tt> and <tt>.trj</tt> files, but these will not compress
-very well anyway.
-<P>
-<LI>
-Most GROMACS programs can process a trajectory with less atoms than
-the run input or structure file, but only if the trajectory consists
-of the first n atoms of the run input or structure file.
-</UL>
<H3>Description</H3>
The top file extension stands for topology. It is an ascii file which is
read by <a href="../programs/gmx-grompp.html">gmx grompp</a> which processes it
-and creates a binary topology (<a href="tpb.html">.tpb file</a>).<br>
+and creates a binary topology (<a href="tpr.html">.tpr file</a>).<br>
A sample file is included below:
<pre>
;
+++ /dev/null
-<title>tpa file format</title>
-<H3>Description</H3>
-The tpa file extension stands for binary run input file. This file contains
-the starting structure of your simulation, The molecular topology and
-all the simulation data. Because this file is in binary format it
-cannot be read with a normal editor. To read a binary run input file type:
-<PRE>
-% <a href="../programs/gmx-dump.html">gmx dump</a> -s topol.tpa
-</PRE>
-or if you're not such a fast reader:
-<PRE>
-% gmxdump -s topol.tpa | more
-</PRE>
-
-<p>
-You can also compare two tpa files using:
-<pre>
-% <a href="../programs/gmx-check.html">gmx check</a> -s1 top1 -s2 top2 | more
-</pre>
+++ /dev/null
-<title>tpb file format</title>
-<h3>Description</h3>
-The tpb file extension stands for binary run input file. This file contains
-the starting structure of your simulation, The molecular topology and
-all the simulation data. Because this file is in binary format it
-cannot be read with a normal editor. To read a binary run input file type:
-<PRE>
-% <a href="../programs/gmx-dump.html">gmx dump</a> -s topol.tpb
-</PRE>
-or if you're not such a fast reader:
-<PRE>
-% gmxdump -s topol.tpb | more
-</PRE>
-
-<p>
-You can also compare two tpb files using:
-<pre>
-% <a href="../programs/gmx-check.html">gmx check</a> -s1 top1 -s2 top2 | more
-</pre>
+++ /dev/null
-<title>trj file format</title>
-<h3>Description</h3>
-Files with the trj file extension contain the trajectory of a simulation.
-In this file all the coordinates, velocities, forces and energies are
-printed as you told GROMACS in your mdp file. This file is in binary
-format an can be read with <a href="../programs/gmx-dump.html">gmx dump</a>.
-<PRE>
-% <a href="../programs/gmx-dump.html">gmx dump</a> -f traj.trj
-</PRE>
-or if you're not such a fast reader:
-<PRE>
-% gmxdump -f traj.trj | more
-</PRE>
-
-<p>
-You can also get a quick look in the contents of the file (number of
-frames etc.) using:
-<PRE>
-% <a href="../programs/gmx-check.html">gmx check</a> -f traj.trj
-</PRE>
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014, by the GROMACS development team, led by
+# Copyright (c) 2014,2015, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
if(MARKDOWN_CONFIGURE_IS_POSSIBLE AND PANDOC_EXECUTABLE)
set(name "user-guide")
configure_markdown(main.md)
- make_markdown_html(${name} ${CMAKE_CURRENT_BINARY_DIR}/main.md)
- make_markdown_pdf(${name} ${CMAKE_CURRENT_BINARY_DIR}/main.md)
+ configure_markdown(references.md)
+
+ # TODO The concatenation of the markdown into a single document on
+ # the pandoc command line generated by CMake is not pretty, but
+ # there's no standard native include-file mechanism in
+ # Markdown. We should resolve this when we agree on a final
+ # generation platform.
+ list(APPEND list_of_markdown_files
+ ${CMAKE_CURRENT_SOURCE_DIR}/getting-started.md
+ ${CMAKE_CURRENT_SOURCE_DIR}/tools.md
+ ${CMAKE_CURRENT_SOURCE_DIR}/mdp-options.md
+ ${CMAKE_CURRENT_SOURCE_DIR}/cutoff-schemes.md
+ ${CMAKE_CURRENT_SOURCE_DIR}/mdrun-features.md
+ ${CMAKE_CURRENT_SOURCE_DIR}/mdrun-performance.md
+ ${CMAKE_CURRENT_SOURCE_DIR}/file-formats.md
+ ${CMAKE_CURRENT_SOURCE_DIR}/environment-variables.md
+ )
+
+ make_markdown_html(${name} ${CMAKE_CURRENT_BINARY_DIR}/main.md ${list_of_markdown_files} ${CMAKE_CURRENT_BINARY_DIR}/references.md)
+ make_markdown_pdf(${name} ${CMAKE_CURRENT_BINARY_DIR}/main.md ${list_of_markdown_files} ${CMAKE_CURRENT_BINARY_DIR}/references.md)
# Add a top-level target for the webpage build to hook onto
add_custom_target(${name}
--- /dev/null
+# Non-bonded cut-off schemes
+
+TODO in future patch
--- /dev/null
+
+# Environment Variables
+
+GROMACS programs may be influenced by the use of
+environment variables. First of all, the variables set in
+the `GMXRC` file are essential for running and
+compiling GROMACS. Some other useful environment variables are
+listed in the following sections. Most environment variables function
+by being set in your shell to any non-NULL value. Specific
+requirements are described below if other values need to be set. You
+should consult the documentation for your shell for instructions on
+how to set environment variables in the current shell, or in config
+files for future shells. Note that requirements for exporting
+environment variables to jobs run under batch control systems vary and
+you should consult your local documentation for details.
+
+## Output Control
+
+* `GMX_CONSTRAINTVIR`: print constraint virial and force virial energy terms.
+
+* `GMX_MAXBACKUP`: GROMACS automatically backs up old
+ copies of files when trying to write a new file of the same
+ name, and this variable controls the maximum number of
+ backups that will be made, default 99. If set to 0 it fails to
+ run if any output file already exists. And if set to -1 it
+ overwrites any output file without making a backup.
+
+* `GMX_NO_QUOTES`: if this is explicitly set, no cool quotes
+ will be printed at the end of a program.
+
+* `GMX_SUPPRESS_DUMP`: prevent dumping of step files during
+ (for example) blowing up during failure of constraint
+ algorithms.
+
+* `GMX_TPI_DUMP`: dump all configurations to a [.pdb]
+ file that have an interaction energy less than the value set
+ in this environment variable.
+
+* `GMX_VIEW_XPM`: `GMX_VIEW_XVG`, `GMX_VIEW_EPS` and `GMX_VIEW_PDB`, commands used to
+ automatically view [.xvg], [.xpm], [.eps]
+ and [.pdb] file types, respectively; they default to `xv`, `xmgrace`,
+ `ghostview` and `rasmol`. Set to empty to disable
+ automatic viewing of a particular file type. The command will
+ be forked off and run in the background at the same priority
+ as the GROMACS tool (which might not be what you want).
+ Be careful not to use a command which blocks the terminal
+ (e.g. `vi`), since multiple instances might be run.
+
+* `GMX_VIRIAL_TEMPERATURE`: print virial temperature energy term
+
+* `GMX_LOG_BUFFER`: the size of the buffer for file I/O. When set
+ to 0, all file I/O will be unbuffered and therefore very slow.
+ This can be handy for debugging purposes, because it ensures
+ that all files are always totally up-to-date.
+
+* `GMX_LOGO_COLOR`: set display color for logo in [gmx view].
+
+* `GMX_PRINT_LONGFORMAT`: use long float format when printing
+ decimal values.
+
+* `GMX_COMPELDUMP`: Applies for computational electrophysiology setups
+ only (see reference manual). The initial structure gets dumped to
+ [.pdb] file, which allows to check whether multimeric channels have
+ the correct PBC representation.
+
+## Debugging
+
+* `GMX_PRINT_DEBUG_LINES`: when set, print debugging info on line numbers.
+
+* `GMX_DD_NST_DUMP`: number of steps that elapse between dumping
+ the current DD to a PDB file (default 0). This only takes effect
+ during domain decomposition, so it should typically be
+ 0 (never), 1 (every DD phase) or a multiple of `nstlist`.
+
+* `GMX_DD_NST_DUMP_GRID`: number of steps that elapse between dumping
+ the current DD grid to a PDB file (default 0). This only takes effect
+ during domain decomposition, so it should typically be
+ 0 (never), 1 (every DD phase) or a multiple of `nstlist`.
+
+* `GMX_DD_DEBUG`: general debugging trigger for every domain
+ decomposition (default 0, meaning off). Currently only checks
+ global-local atom index mapping for consistency.
+
+* `GMX_DD_NPULSE`: over-ride the number of DD pulses used
+ (default 0, meaning no over-ride). Normally 1 or 2.
+
+* There are a number of extra environment variables like these
+ that are used in debugging - check the code!
+
+## Performance and Run Control
+
+* `GMX_DO_GALACTIC_DYNAMICS`: planetary simulations are made possible (just for fun) by setting
+ this environment variable, which allows setting `epsilon_r = -1` in the [.mdp]
+ file. Normally, `epsilon_r` must be greater than zero to prevent a fatal error.
+ See [wwwpage] for example input files for a planetary simulation.
+
+* `GMX_ALLOW_CPT_MISMATCH`: when set, runs will not exit if the
+ ensemble set in the [.tpr] file does not match that of the
+ [.cpt] file.
+
+* `GMX_CUDA_NB_EWALD_TWINCUT`: force the use of twin-range cutoff kernel even if `rvdw` =
+ `rcoulomb` after PP-PME load balancing. The switch to twin-range kernels is automated,
+ so this variable should be used only for benchmarking.
+
+* `GMX_CUDA_NB_ANA_EWALD`: force the use of analytical Ewald kernels. Should be used only for benchmarking.
+
+* `GMX_CUDA_NB_TAB_EWALD`: force the use of tabulated Ewald kernels. Should be used only for benchmarking.
+
+* `GMX_CUDA_STREAMSYNC`: force the use of cudaStreamSynchronize on ECC-enabled GPUs, which leads
+ to performance loss due to a known CUDA driver bug present in API v5.0 NVIDIA drivers (pre-30x.xx).
+ Cannot be set simultaneously with `GMX_NO_CUDA_STREAMSYNC`.
+
+* `GMX_CYCLE_ALL`: times all code during runs. Incompatible with threads.
+
+* `GMX_CYCLE_BARRIER`: calls MPI_Barrier before each cycle start/stop call.
+
+* `GMX_DD_ORDER_ZYX`: build domain decomposition cells in the order
+ (z, y, x) rather than the default (x, y, z).
+
+* `GMX_DD_USE_SENDRECV2`: during constraint and vsite communication, use a pair
+ of `MPI_SendRecv` calls instead of two simultaneous non-blocking calls
+ (default 0, meaning off). Might be faster on some MPI implementations.
+
+* `GMX_DLB_BASED_ON_FLOPS`: do domain-decomposition dynamic load balancing based on flop count rather than
+ measured time elapsed (default 0, meaning off).
+ This makes the load balancing reproducible, which can be useful for debugging purposes.
+ A value of 1 uses the flops; a value > 1 adds (value - 1)*5% of noise to the flops to increase the imbalance and the scaling.
+
+* `GMX_DLB_MAX_BOX_SCALING`: maximum percentage box scaling permitted per domain-decomposition
+ load-balancing step (default 10)
+
+* `GMX_DD_RECORD_LOAD`: record DD load statistics for reporting at end of the run (default 1, meaning on)
+
+* `GMX_DD_NST_SORT_CHARGE_GROUPS`: number of steps that elapse between re-sorting of the charge
+ groups (default 1). This only takes effect during domain decomposition, so should typically
+ be 0 (never), 1 (to mean at every domain decomposition), or a multiple of `nstlist`.
+
+* `GMX_DETAILED_PERF_STATS`: when set, print slightly more detailed performance information
+ to the [.log] file. The resulting output is the way performance summary is reported in versions
+ 4.5.x and thus may be useful for anyone using scripts to parse [.log] files or standard output.
+
+* `GMX_DISABLE_SIMD_KERNELS`: disables architecture-specific SIMD-optimized (SSE2, SSE4.1, AVX, etc.)
+ non-bonded kernels thus forcing the use of plain C kernels.
+
+* `GMX_DISABLE_CUDA_TIMING`: timing of asynchronously executed GPU operations can have a
+ non-negligible overhead with short step times. Disabling timing can improve performance in these cases.
+
+* `GMX_DISABLE_GPU_DETECTION`: when set, disables GPU detection even if [mdrun] was compiled
+ with GPU support.
+
+* `GMX_DISRE_ENSEMBLE_SIZE`: the number of systems for distance restraint ensemble
+ averaging. Takes an integer value.
+
+* `GMX_EMULATE_GPU`: emulate GPU runs by using algorithmically equivalent CPU reference code instead of
+ GPU-accelerated functions. As the CPU code is slow, it is intended to be used only for debugging purposes.
+ The behavior is automatically triggered if non-bonded calculations are turned off using `GMX_NO_NONBONDED`
+ case in which the non-bonded calculations will not be called, but the CPU-GPU transfer will also be skipped.
+
+* `GMX_ENX_NO_FATAL`: disable exiting upon encountering a corrupted frame in an [.edr]
+ file, allowing the use of all frames up until the corruption.
+
+* `GMX_FORCE_UPDATE`: update forces when invoking `mdrun -rerun`.
+
+* `GMX_GPU_ID`: set in the same way as `mdrun -gpu_id`, `GMX_GPU_ID`
+ allows the user to specify different GPU id-s, which can be useful for selecting different
+ devices on different compute nodes in a cluster. Cannot be used in conjunction with `mdrun -gpu_id`.
+
+* `GMX_IGNORE_FSYNC_FAILURE_ENV`: allow [mdrun] to continue even if
+ a file is missing.
+
+* `GMX_LJCOMB_TOL`: when set to a floating-point value, overrides the default tolerance of
+ 1e-5 for force-field floating-point parameters.
+
+* `GMX_MAX_MPI_THREADS`: sets the maximum number of MPI-threads that [mdrun]
+ can use.
+
+* `GMX_MAXCONSTRWARN`: if set to -1, [mdrun] will
+ not exit if it produces too many LINCS warnings.
+
+* `GMX_NB_GENERIC`: use the generic C kernel. Should be set if using
+ the group-based cutoff scheme and also sets `GMX_NO_SOLV_OPT` to be true,
+ thus disabling solvent optimizations as well.
+
+* `GMX_NB_MIN_CI`: neighbor list balancing parameter used when running on GPU. Sets the
+ target minimum number pair-lists in order to improve multi-processor load-balance for better
+ performance with small simulation systems. Must be set to a positive integer, the default value
+ is optimized for NVIDIA Fermi and Kepler GPUs, therefore changing it is not necessary for
+ normal usage, but it can be useful on future architectures.
+
+* `GMX_NBLISTCG`: use neighbor list and kernels based on charge groups.
+
+* `GMX_NBNXN_CYCLE`: when set, print detailed neighbor search cycle counting.
+
+* `GMX_NBNXN_EWALD_ANALYTICAL`: force the use of analytical Ewald non-bonded kernels,
+ mutually exclusive of `GMX_NBNXN_EWALD_TABLE`.
+
+* `GMX_NBNXN_EWALD_TABLE`: force the use of tabulated Ewald non-bonded kernels,
+ mutually exclusive of `GMX_NBNXN_EWALD_ANALYTICAL`.
+
+* `GMX_NBNXN_SIMD_2XNN`: force the use of 2x(N+N) SIMD CPU non-bonded kernels,
+ mutually exclusive of `GMX_NBNXN_SIMD_4XN`.
+
+* `GMX_NBNXN_SIMD_4XN`: force the use of 4xN SIMD CPU non-bonded kernels,
+ mutually exclusive of `GMX_NBNXN_SIMD_2XNN`.
+
+* `GMX_NO_ALLVSALL`: disables optimized all-vs-all kernels.
+
+* `GMX_NO_CART_REORDER`: used in initializing domain decomposition communicators. Rank reordering
+ is default, but can be switched off with this environment variable.
+
+* `GMX_NO_CUDA_STREAMSYNC`: the opposite of `GMX_CUDA_STREAMSYNC`. Disables the use of the
+ standard cudaStreamSynchronize-based GPU waiting to improve performance when using CUDA driver API
+ ealier than v5.0 with ECC-enabled GPUs.
+
+* `GMX_NO_INT`, `GMX_NO_TERM`, `GMX_NO_USR1`: disable signal handlers for SIGINT,
+ SIGTERM, and SIGUSR1, respectively.
+
+* `GMX_NO_NODECOMM`: do not use separate inter- and intra-node communicators.
+
+* `GMX_NO_NONBONDED`: skip non-bonded calculations; can be used to estimate the possible
+ performance gain from adding a GPU accelerator to the current hardware setup -- assuming that this is
+ fast enough to complete the non-bonded calculations while the CPU does bonded force and PME computation.
+
+* `GMX_NO_PULLVIR`: when set, do not add virial contribution to COM pull forces.
+
+* `GMX_NOCHARGEGROUPS`: disables multi-atom charge groups, i.e. each atom
+ in all non-solvent molecules is assigned its own charge group.
+
+* `GMX_NOPREDICT`: shell positions are not predicted.
+
+* `GMX_NO_SOLV_OPT`: turns off solvent optimizations; automatic if `GMX_NB_GENERIC`
+ is enabled.
+
+* `GMX_NSCELL_NCG`: the ideal number of charge groups per neighbor searching grid cell is hard-coded
+ to a value of 10. Setting this environment variable to any other integer value overrides this hard-coded
+ value.
+
+* `GMX_PME_NTHREADS`: set the number of OpenMP or PME threads (overrides the number guessed by
+ [mdrun].
+
+* `GMX_PME_P3M`: use P3M-optimized influence function instead of smooth PME B-spline interpolation.
+
+* `GMX_PME_THREAD_DIVISION`: PME thread division in the format "x y z" for all three dimensions. The
+ sum of the threads in each dimension must equal the total number of PME threads (set in
+ `GMX_PME_NTHREADS`).
+
+* `GMX_PMEONEDD`: if the number of domain decomposition cells is set to 1 for both x and y,
+ decompose PME in one dimension.
+
+* `GMX_REQUIRE_SHELL_INIT`: require that shell positions are initiated.
+
+* `GMX_REQUIRE_TABLES`: require the use of tabulated Coulombic
+ and van der Waals interactions.
+
+* `GMX_SCSIGMA_MIN`: the minimum value for soft-core sigma. **Note** that this value is set
+ using the `sc-sigma` keyword in the [.mdp] file, but this environment variable can be used
+ to reproduce pre-4.5 behavior with respect to this parameter.
+
+* `GMX_TPIC_MASSES`: should contain multiple masses used for test particle insertion into a cavity.
+ The center of mass of the last atoms is used for insertion into the cavity.
+
+* `GMX_USE_GRAPH`: use graph for bonded interactions.
+
+* `GMX_VERLET_BUFFER_RES`: resolution of buffer size in Verlet cutoff scheme. The default value is
+ 0.001, but can be overridden with this environment variable.
+
+* `MPIRUN`: the `mpirun` command used by [gmx tune_pme].
+
+* `MDRUN`: the [mdrun] command used by [gmx tune_pme].
+
+* `GMX_NSTLIST`: sets the default value for `nstlist`, preventing it from being tuned during
+ [mdrun] startup when using the Verlet cutoff scheme.
+
+* `GMX_USE_TREEREDUCE`: use tree reduction for nbnxn force reduction. Potentially faster for large number of
+ OpenMP threads (if memory locality is important).
+
+## Analysis and Core Functions
+
+* `GMX_QM_ACCURACY`: accuracy in Gaussian L510 (MC-SCF) component program.
+
+* `GMX_QM_ORCA_BASENAME`: prefix of [.tpr] files, used in Orca calculations
+ for input and output file names.
+
+* `GMX_QM_CPMCSCF`: when set to a nonzero value, Gaussian QM calculations will
+ iteratively solve the CP-MCSCF equations.
+
+* `GMX_QM_MODIFIED_LINKS_DIR`: location of modified links in Gaussian.
+
+* `DSSP`: used by [gmx do_dssp] to point to the `dssp`
+ executable (not just its path).
+
+* `GMX_QM_GAUSS_DIR`: directory where Gaussian is installed.
+
+* `GMX_QM_GAUSS_EXE`: name of the Gaussian executable.
+
+* `GMX_DIPOLE_SPACING`: spacing used by [gmx dipoles].
+
+* `GMX_MAXRESRENUM`: sets the maximum number of residues to be renumbered by
+ [gmx grompp]. A value of -1 indicates all residues should be renumbered.
+
+* `GMX_FFRTP_TER_RENAME`: Some force fields (like AMBER) use specific names for N- and C-
+ terminal residues (NXXX and CXXX) as [.rtp] entries that are normally renamed. Setting
+ this environment variable disables this renaming.
+
+* `GMX_PATH_GZIP`: `gunzip` executable, used by [gmx wham].
+
+* `GMX_FONT`: name of X11 font used by [gmx view].
+
+* `GMXTIMEUNIT`: the time unit used in output files, can be
+ anything in fs, ps, ns, us, ms, s, m or h.
+
+* `GMX_QM_GAUSSIAN_MEMORY`: memory used for Gaussian QM calculation.
+
+* `MULTIPROT`: name of the `multiprot` executable, used by the
+ contributed program `do_multiprot`.
+
+* `NCPUS`: number of CPUs to be used for Gaussian QM calculation
+
+* `GMX_ORCA_PATH`: directory where Orca is installed.
+
+* `GMX_QM_SA_STEP`: simulated annealing step size for Gaussian QM calculation.
+
+* `GMX_QM_GROUND_STATE`: defines state for Gaussian surface hopping calculation.
+
+* `GMX_TOTAL`: name of the `total` executable used by the contributed
+ `do_shift` program.
+
+* `GMX_ENER_VERBOSE`: make [gmx energy] and [gmx eneconv]
+ loud and noisy.
+
+* `VMD_PLUGIN_PATH`: where to find VMD plug-ins. Needed to be
+ able to read file formats recognized only by a VMD plug-in.
+
+* `VMDDIR`: base path of VMD installation.
+
+* `GMX_USE_XMGR`: sets viewer to `xmgr` (deprecated) instead of `xmgrace`.
--- /dev/null
+# GROMACS file formats
+
+TODO in future patch: gather information from
+docs/old-html/online/*html, convert to Markdown, update for accuracy,
+organize here.
--- /dev/null
+# Getting started with GROMACS
+
+In this chapter we assume the reader is familiar with Molecular Dynamics and
+familiar with Unix, including the use of a text editor such as `jot`, `emacs`
+or `vi`. We furthermore assume the GROMACS software is installed properly on
+your system. When you see a line like
+
+ ls -l
+
+you are supposed to type the contents of that line on your computer terminal.
+
+## Setting up your environment
+
+In order to check whether you have access to GROMACS, please
+start by entering the command:
+
+ gmx -version
+
+This command should print out information about the version of Gromacs
+installed. If this, in contrast, returns the phrase
+
+ gmx: command not found.
+
+then you have to find where your version of GROMACS is installed. In
+the default case, the binaries are located in
+`/usr/local/gromacs/bin`, however, you can ask your local system
+administrator for more information, and then follow the advice in the
+[install guide](install-guide.html#getting-access-to-gromacs-after-installation).
+
+## Flowchart of typical GROMACS simulation
+
+A typical simulation workflow with GROMACS is [illustrated here](online/flow.html).
+
+## Important GROMACS files
+
+Here is an overview of the most important GROMACS file types that you will
+encounter.
+
+### Molecular Topology file (`.top`)
+
+The molecular topology file is generated by the program [gmx pdb2gmx]. [gmx pdb2gmx] translates a [PDB] structure file of any peptide or protein to a molecular topology file. This topology file contains a complete description of all the interactions in your peptide or protein.
+
+### Molecular Structure file (`.gro`, `.pdb`)
+
+When [gmx pdb2gmx] is executed to generate a molecular topology, it also translates the structure file ([.pdb] file) to a GROMOS structure file ([.gro] file). The main difference between a [pdb] file and a gromos file is their format and that a [.gro] file can also hold velocities. However, if you do not need the velocities, you can also use a [PDB] file in all programs. To generate a box of solvent molecules around the peptide, the program [gmx solvate] is used. First the program [gmx editconf] should be used to define a box of appropriate size around the molecule. [gmx solvate] solvates a solute molecule (the peptide) into any solvent (in this case, water). The output of [gmx solvate] is a gromos structure file of the peptide solvated in water. [gmx solvate] also changes the molecular topology file (generated by [gmx pdb2gmx]) to add solvent to the topology.
+
+### Molecular Dynamics parameter file (`.mdp`)
+
+The Molecular Dynamics Parameter ([.mdp]) file contains all information about the Molecular Dynamics simulation itself e.g. time-step, number of steps, temperature, pressure etc. The easiest way of handling such a file is by adapting a sample [.mdp] file. A [sample mdp file](online/mdp.html) is available.
+
+### Index file (`.ndx`)
+
+Sometimes you may need an index file to specify actions on groups of atoms (e.g. temperature coupling, accelerations, freezing). Usually the default index groups will be sufficient, so for this demo we will not consider the use of index files.
+
+### Run input file (`.tpr`)
+
+The next step is to combine the molecular structure ([.gro] file), topology ([.top] file) MD-parameters ([.mdp] file) and (optionally) the index file ([.ndx]) to generate a run input file ([.tpr] extension). This file contains all information needed to start a simulation with GROMACS. The [gmx grompp] program processes all input files and generates the run input [.tpr] file.
+
+### Trajectory file (`.trr`)
+
+Once the run input file is available, we can start the simulation. The program which starts the simulation is called [gmx mdrun] (or sometimes just mdrun, or mdrun_mpi). The only input file of [gmx mdrun] that you usually need in order to start a run is the run input file ([.tpr] file). The typical output files of [gmx mdrun] are the trajectory file ([.trr] file), a logfile ( [.log] file),
+and perhaps a checkpoint file ([.cpt] file).
+
+## Tutorial material
+
+There are [many tutorials
+available](http://www.gromacs.org/Documentation/Tutorials) that cover
+aspects of using GROMACS.
+
+## Background reading
+
+> Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., Hermans, J. (1981)
+Intermolecular Forces, chapter Interaction models for water in relation to
+protein hydration, pp 331-342. Dordrecht: D. Reidel Publishing Company
+Dordrecht
+
+>
+
+> Kabsch, W., Sander, C. (1983). Dictionary of protein secondary
+structure: Pattern recognition of hydrogen-bonded and geometrical features.
+Biopolymers **22**, 2577--2637.
+
+>
+
+> Mierke, D.F., Kessler, H. (1991). Molecular dynamics with dimethyl
+sulfoxide as a solvent. Conformation of a cyclic hexapeptide. J. Am. Chem.
+Soc. **113**, 9446.
+
+>
+
+> Stryer, L. (1988). Biochemistry vol. 1, p. 211. New York: Freeman, 3
+edition.
# Introduction #
-Coming soon!
+This guide provides
+
+* material introducing GROMACS
+* practical advice for making effective use of GROMACS.
+
+For getting, building and installing GROMACS, see the [install
+guide]. For background on algorithms and implementations, see the
+[reference manual].
--- /dev/null
+# Molecular dynamics parameters (.mdp options)
+
+## General information
+
+Default values are given in parentheses. The first option in the list is always the default option. Units are given in square brackets The difference between a dash and an underscore is ignored.
+
+A [sample `.mdp` file](online/mdp.html) is available. This should be appropriate to start a normal simulation. Edit it to suit your specific needs and desires.
+
+
+### Preprocessing
+
+include:
+: directories to include in your topology. Format: `-I/home/john/mylib -I../otherlib`
+
+define:
+: defines to pass to the preprocessor, default is no defines. You can use any defines to control options in your customized topology files. Options that are already available by default are:
+ `-DFLEXIBLE` will use flexible water instead of rigid water into your topology, this can be useful for normal mode analysis.
+ `-DPOSRES` will trigger the inclusion of `posre.itp` into your topology, used for position restraints.
+
+
+### Run control
+
+integrator:
+: (Despite the name, this list includes algorithms that are not actually integrators. **steep** and all entries following it are in this category)
+
+ md
+ : A leap-frog algorithm for integrating Newton's equations of motion.
+
+ md-vv
+ : A velocity Verlet algorithm for integrating Newton's equations of motion. For constant NVE simulations started from corresponding points in the same trajectory, the trajectories are analytically, but not binary, identical to the **md** leap-frog integrator. The the kinetic energy, which is determined from the whole step velocities and is therefore slightly too high. The advantage of this integrator is more accurate, reversible Nose-Hoover and Parrinello-Rahman coupling integration based on Trotter expansion, as well as (slightly too small) full step velocity output. This all comes at the cost off extra computation, especially with constraints and extra communication in parallel. Note that for nearly all production simulations the **md** integrator is accurate enough.
+
+ md-vv-avek
+ : A velocity Verlet algorithm identical to **md-vv**, except that the kinetic energy is determined as the average of the two half step kinetic energies as in the **md** integrator, and this thus more accurate. With Nose-Hoover and/or Parrinello-Rahman coupling this comes with a slight increase in computational cost.
+
+ sd
+ : An accurate and efficient leap-frog stochastic dynamics integrator. With constraints, coordinates needs to be constrained twice per integration step. Depending on the computational cost of the force calculation, this can take a significant part of the simulation time. The temperature for one or more groups of atoms (**tc-grps**) is set with **ref-t**, the inverse friction constant for each group is set with **tau-t**. The parameter **tcoupl** is ignored. The random generator is initialized with **ld-seed**. When used as a thermostat, an appropriate value for **tau-t** is 2 ps, since this results in a friction that is lower than the internal friction of water, while it is high enough to remove excess heat NOTE: temperature deviations decay twice as fast as with a Berendsen thermostat with the same **tau-t**.
+
+ sd2
+ : This used to be the default sd integrator, but is now deprecated. Four Gaussian random numbers are required per coordinate per step. With constraints, the temperature will be slightly too high.
+
+ bd
+ : An Euler integrator for Brownian or position Langevin dynamics, the velocity is the force divided by a friction coefficient (**bd-fric**) plus random thermal noise (**ref-t**). When **bd-fric**`=0`, the friction coefficient for each particle is calculated as mass/**tau-t**, as for the integrator **sd**. The random generator is initialized with **ld-seed**.
+
+ steep
+ : A steepest descent algorithm for energy minimization. The maximum step size is **emstep**, the tolerance is **emtol**.
+
+ cg
+ : A conjugate gradient algorithm for energy minimization, the tolerance is **emtol**. CG is more efficient when a steepest descent step is done every once in a while, this is determined by **nstcgsteep**. For a minimization prior to a normal mode analysis, which requires a very high accuracy, GROMACS should be compiled in double precision.
+
+ l-bfgs
+ : A quasi-Newtonian algorithm for energy minimization according to the low-memory Broyden-Fletcher-Goldfarb-Shanno approach. In practice this seems to converge faster than Conjugate Gradients, but due to the correction steps necessary it is not (yet) parallelized.
+
+ nm
+ : Normal mode analysis is performed on the structure in the [.tpr] file. GROMACS should be compiled in double precision.
+
+ tpi
+ : Test particle insertion. The last molecule in the topology is the test particle. A trajectory must be provided to `mdrun -rerun`. This trajectory should not contain the molecule to be inserted. Insertions are performed **nsteps** times in each frame at random locations and with random orientiations of the molecule. When **nstlist** is larger than one, **nstlist** insertions are performed in a sphere with radius **rtpi** around a the same random location using the same neighborlist (and the same long-range energy when **rvdw** or **rcoulomb**>**rlist**, which is only allowed for single-atom molecules). Since neighborlist construction is expensive, one can perform several extra insertions with the same list almost for free. The random seed is set with **ld-seed**. The temperature for the Boltzmann weighting is set with **ref-t**, this should match the temperature of the simulation of the original trajectory. Dispersion correction is implemented correctly for TPI. All relevant quantities are written to the file specified with `mdrun -tpi`. The distribution of insertion energies is written to the file specified with `mdrun -tpid`. No trajectory or energy file is written. Parallel TPI gives identical results to single-node TPI. For charged molecules, using PME with a fine grid is most accurate and also efficient, since the potential in the system only needs to be calculated once per frame.
+
+ tpic
+ : Test particle insertion into a predefined cavity location. The procedure is the same as for **tpi**, except that one coordinate extra is read from the trajectory, which is used as the insertion location. The molecule to be inserted should be centered at 0,0,0. Gromacs does not do this for you, since for different situations a different way of centering might be optimal. Also **rtpi** sets the radius for the sphere around this location. Neighbor searching is done only once per frame, **nstlist** is not used. Parallel **tpic** gives identical results to single-rank **tpic**.
+
+tinit: (0) [ps]
+: starting time for your run (only makes sense for integrators **md**, **sd** and **bd**)
+
+dt: (0.001) [ps]
+: time step for integration (only makes sense for integrators **md**, **sd** and **bd**)
+
+nsteps: (0)
+: maximum number of steps to integrate or minimize, -1 is no maximum
+
+init-step: (0)
+: The starting step. The time at an step i in a run is calculated as: t = **tinit** + **dt** * (**init-step** + i). The free-energy lambda is calculated as: lambda = **init-lambda** + **delta-lambda** * (**init-step** + i). Also non-equilibrium MD parameters can depend on the step number. Thus for exact restarts or redoing part of a run it might be necessary to set **init-step** to the step number of the restart frame. [gmx convert-tpr] does this automatically.
+
+comm-mode:
+: + **Linear**
+ Remove center of mass translation
+
+ + **Angular**
+ Remove center of mass translation and rotation around the center of mass
+
+ + **None**
+ No restriction on the center of mass motion
+
+nstcomm: (100) [steps]
+: frequency for center of mass motion removal
+
+comm-grps:
+: group(s) for center of mass motion removal, default is the whole system
+
+
+### Langevin dynamics
+
+bd-fric: (0) [amu ps-1]
+: Brownian dynamics friction coefficient. When **bd-fric** =0, the friction coefficient for each particle is calculated as mass/**tau-t**.
+
+ld-seed: (-1) [integer]
+: used to initialize random generator for thermal noise for stochastic and Brownian dynamics. When **ld-seed** is set to -1, a pseudo random seed is used. When running BD or SD on multiple processors, each processor uses a seed equal to **ld-seed** plus the processor number.
+
+
+### Energy minimization
+
+emtol: (10.0) [kJ mol-1 nm-1]
+: the minimization is converged when the maximum force is smaller than this value
+
+emstep: (0.01) [nm]
+: initial step-size
+
+nstcgsteep: (1000) [steps]
+: frequency of performing 1 steepest descent step while doing conjugate gradient energy minimization.
+
+nbfgscorr: (10)
+: Number of correction steps to use for L-BFGS minimization. A higher number is (at least theoretically) more accurate, but slower.
+
+
+### Shell Molecular Dynamics
+
+When shells or flexible constraints are present in the system the positions of the shells and the lengths of the flexible constraints are optimized at every
+time step until either the RMS force on the shells and constraints is less than emtol, or a maximum number of iterations **niter** has been reached
+
+emtol: (10.0) [kJ mol-1 nm-1]
+: the minimization is converged when the maximum force is smaller than this value. For shell MD this value should be 1.0 at most, but since the variable is used for energy minimization as well the default is 10.0.
+
+niter: (20)
+: maximum number of iterations for optimizing the shell positions and the flexible constraints.
+
+fcstep: (0) [ps2]
+: the step size for optimizing the flexible constraints. Should be chosen as mu/(d2V/dq2) where mu is the reduced mass of two particles in a flexible constraint and d2V/dq2 is the second derivative of the potential in the constraint direction. Hopefully this number does not differ too much between the flexible constraints, as the number of iterations and thus the runtime is very sensitive to **fcstep**. Try several values!
+
+
+### Test particle insertion
+
+rtpi: (0.05) [nm]
+: the test particle insertion radius, see integrators **tpi** and **tpic**
+
+
+### Output control
+
+nstxout: (0) [steps]
+: number of steps that elapse between writing coordinates to output trajectory file, the last coordinates are always written
+
+nstvout: (0) [steps]
+: number of steps that elapse between writing velocities to output trajectory, the last velocities are always written
+
+nstfout: (0) [steps]
+: number of steps that elapse between writing forces to output trajectory.
+
+nstlog: (1000) [steps]
+: number of steps that elapse between writing energies to the log file, the last energies are always written
+
+nstcalcenergy: (100)
+: number of steps that elapse between calculating the energies, 0 is never. This option is only relevant with dynamics. With a twin-range cut-off setup **nstcalcenergy** should be equal to or a multiple of **nstlist**. This option affects the performance in parallel simulations, because calculating energies requires global communication between all processes which can become a bottleneck at high parallelization.
+
+nstenergy: (1000) [steps]
+: number of steps that else between writing energies to energy file, the last energies are always written, should be a multiple of **nstcalcenergy**. Note that the exact sums and fluctuations over all MD steps modulo **nstcalcenergy** are stored in the energy file, so [gmx energy] can report exact energy averages and fluctuations also when **nstenergy** >1
+
+nstxout-compressed: (0) [steps]
+: number of steps that elapse between writing position coordinates using lossy compression
+
+compressed-x-precision: (1000) [real]
+: precision with which to write to the compressed trajectory file
+
+compressed-x-grps:
+: group(s) to write to the compressed trajectory file, by default the whole system is written (if **nstxout-compressed** > 0)
+
+energygrps:
+: group(s) to write to energy file
+
+
+### Neighbor searching
+
+cutoff-scheme:
+: + **Verlet**
+ Generate a pair list with buffering. The buffer size is automatically set based on **verlet-buffer-tolerance**, unless this is set to -1, in which case **rlist** will be used. This option has an explicit, exact cut-off at **rvdw**=**rcoulomb**. Currently only cut-off, reaction-field, PME electrostatics and plain LJ are supported. Some [mdrun] functionality is not yet supported with the **Verlet** scheme, but [gmx grompp] checks for this. Native GPU acceleration is only supported with **Verlet**. With GPU-accelerated PME or with separate PME ranks, [mdrun] will automatically tune the CPU/GPU load balance by scaling **rcoulomb** and the grid spacing. This can be turned off with `mdrun -notunepme`. **Verlet** is faster than **group** when there is no water, or if **group** would use a pair-list buffer to conserve energy.
+
+ + **group**
+ Generate a pair list for groups of atoms. These groups correspond to the charge groups in the topology. This was the only cut-off treatment scheme before version 4.6, and is **deprecated in 5.0**. There is no explicit buffering of the pair list. This enables efficient force calculations for water, but energy is only conserved when a buffer is explicitly added.
+
+nstlist: (10) [steps]
+: + **>0**
+ Frequency to update the neighbor list (and the long-range forces, when using twin-range cut-offs). When this is 0, the neighbor list is made only once. With energy minimization the neighborlist will be updated for every energy evaluation when **nstlist** >0. With **cutoff-scheme=Verlet** and **verlet-buffer-tolerance** set, **nstlist** is actually a minimum value and [mdrun] might increase it, unless it is set to 1. With parallel simulations and/or non-bonded force calculation on the GPU, a value of 20 or 40 often gives the best performance. With **cutoff-scheme=Group** and non-exact cut-off's, **nstlist** will affect the accuracy of your simulation and it can not be chosen freely.
+
+ + **0**
+ The neighbor list is only constructed once and never updated. This is mainly useful for vacuum simulations in which all particles see each other.
+
+ + **<0**
+ Unused.
+
+nstcalclr: (-1) [steps]
+: Controls the period between calculations of long-range forces when using the group cut-off scheme.
+
+ + **1**
+ Calculate the long-range forces every single step. This is useful to have separate neighbor lists with buffers for electrostatics and Van der Waals interactions, and in particular it makes it possible to have the Van der Waals cutoff longer than electrostatics (useful _e.g._ with PME). However, there is no point in having identical long-range cutoffs for both interaction forms and update them every step - then it will be slightly faster to put everything in the short-range list.
+
+ + **>1**
+ Calculate the long-range forces every **nstcalclr** steps and use a multiple-time-step integrator to combine forces. This can now be done more frequently than **nstlist** since the lists are stored, and it might be a good idea _e.g._ for Van der Waals interactions that vary slower than electrostatics.
+
+ + **-1**
+ Calculate long-range forces on steps where neighbor searching is performed. While this is the default value, you might want to consider updating the long-range forces more frequently.
+
+ Note that twin-range force evaluation might be enabled automatically by PP-PME load balancing. This is done in order to maintain the chosen Van der Waals interaction radius even if the load balancing is changing the electrostatics cutoff. If the [.mdp] file already specifies twin-range interactions (_e.g._ to evaluate Lennard-Jones interactions with a longer cutoff than the PME electrostatics every 2-3 steps), the load balancing will have also a small effect on Lennard-Jones, since the short-range cutoff (inside which forces are evaluated every step) is changed.
+
+ns-type:
+: + **grid**
+ Make a grid in the box and only check atoms in neighboring grid cells when constructing a new neighbor list every **nstlist** steps. In large systems grid search is much faster than simple search.
+
+ + **simple**
+ Check every atom in the box when constructing a new neighbor list every **nstlist** steps (only with **cutoff-scheme=group**).
+
+pbc:
+: + **xyz**
+ Use periodic boundary conditions in all directions.
+
+ + **no**
+ Use no periodic boundary conditions, ignore the box. To simulate without cut-offs, set all cut-offs and **nstlist** to 0. For best performance without cut-offs on a single MPI rank, set **nstlist** to zero and `ns-type=simple`.
+
+ + **xy**
+ Use periodic boundary conditions in x and y directions only. This works only with `ns-type=grid` and can be used in combination with **walls**. Without walls or with only one wall the system size is infinite in the z direction. Therefore pressure coupling or Ewald summation methods can not be used. These disadvantages do not apply when two walls are used.
+
+periodic-molecules:
+: + **no**
+ molecules are finite, fast molecular PBC can be used
+
+ + **yes**
+ for systems with molecules that couple to themselves through the periodic boundary conditions, this requires a slower PBC algorithm and molecules are not made whole in the output
+
+verlet-buffer-tolerance: (0.005) [kJ/mol/ps]
+: Useful only with **cutoff-scheme**=**Verlet**. This sets the maximum allowed error for pair interactions per particle caused by the Verlet buffer, which indirectly sets **rlist**. As both **nstlist** and the Verlet buffer size are fixed (for performance reasons), particle pairs not in the pair list can occasionally get within the cut-off distance during **nstlist**-1 nsteps. This causes very small jumps in the energy. In a constant-temperature ensemble, these very small energy jumps can be estimated for a given cut-off and **rlist**. The estimate assumes a homogeneous particle distribution, hence the errors might be slightly underestimated for multi-phase systems. For longer pair-list life-time (**nstlist**-1)*dt the buffer is overestimated, because the interactions between particles are ignored. Combined with cancellation of errors, the actual drift of the total energy is usually one to two orders of magnitude smaller. Note that the generated buffer size takes into account that the GROMACS pair-list setup leads to a reduction in the drift by a factor 10, compared to a simple particle-pair based list. Without dynamics (energy minimization etc.), the buffer is 5% of the cut-off. For NVE simulations the initial temperature is used, unless this is zero, in which case a buffer of 10% is used. For NVE simulations the tolerance usually needs to be lowered to achieve proper energy conservation on the nanosecond time scale. To override the automated buffer setting, use **verlet-buffer-tolerance**=-1 and set **rlist** manually.
+
+rlist: (1) [nm]
+: Cut-off distance for the short-range neighbor list. With **cutoff-scheme**=**Verlet**, this is by default set by the **verlet-buffer-tolerance** option and the value of **rlist** is ignored.
+
+rlistlong: (-1) [nm]
+: Cut-off distance for the long-range neighbor list. This parameter is only relevant for a twin-range cut-off setup with switched potentials. In that case a buffer region is required to account for the size of charge groups. In all other cases this parameter is automatically set to the longest cut-off distance.
+
+
+### Electrostatics
+
+coulombtype:
+: + **Cut-off**
+ Twin range cut-offs with neighborlist cut-off **rlist** and Coulomb cut-off **rcoulomb**, where **rcoulomb**>=**rlist**.
+
+ + **Ewald**
+ Classical Ewald sum electrostatics. The real-space cut-off **rcoulomb** should be equal to **rlist**. Use _e.g._ **rlist** =0.9, **rcoulomb** =0.9. The highest magnitude of wave vectors used in reciprocal space is controlled by **fourierspacing**. The relative accuracy of direct/reciprocal space is controlled by **ewald-rtol**.
+ NOTE: Ewald scales as O(N3/2) and is thus extremely slow for large systems. It is included mainly for reference - in most cases PME will perform much better.
+
+ + **PME**
+ Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct space is similar to the Ewald sum, while the reciprocal part is performed with FFTs. Grid dimensions are controlled with **fourierspacing** and the interpolation order with **pme-order**. With a grid spacing of 0.1 nm and cubic interpolation the electrostatic forces have an accuracy of 2-3*10-4. Since the error from the vdw-cutoff is larger than this you might try 0.15 nm. When running in parallel the interpolation parallelizes better than the FFT, so try decreasing grid dimensions while increasing interpolation.
+
+ + **P3M-AD**
+ Particle-Particle Particle-Mesh algorithm with analytical derivative for for long range electrostatic interactions. The method and code is identical to SPME, except that the influence function is optimized for the grid. This gives a slight increase in accuracy.
+
+ + **Reaction-Field electrostatics**
+ Reaction field with Coulomb cut-off **rcoulomb**, where **rcoulomb** >= **rlist**. The dielectric constant beyond the cut-off is **epsilon-rf**. The dielectric constant can be set to infinity by setting **epsilon-rf**=0.
+
+ + **Generalized-Reaction-Field**
+ Generalized reaction field with Coulomb cut-off **rcoulomb**, where **rcoulomb** >= **rlist**. The dielectric constant beyond the cut-off is **epsilon-rf**. The ionic strength is computed from the number of charged (_i.e._ with non zero charge) charge groups. The temperature for the GRF potential is set with **ref-t**.
+
+ + **Reaction-Field-zero**
+ In GROMACS, normal reaction-field electrostatics with **cutoff-scheme****=group** leads to bad energy conservation. **Reaction-Field-zero** solves this by making the potential zero beyond the cut-off. It can only be used with an infinite dielectric constant (**epsilon-rf=0**), because only for that value the force vanishes at the cut-off. **rlist** should be 0.1 to 0.3 nm larger than **rcoulomb** to accommodate for the size of charge groups and diffusion between neighbor list updates. This, and the fact that table lookups are used instead of analytical functions make **Reaction-Field-zero** computationally more expensive than normal reaction-field.
+
+ + **Reaction-Field-nec**
+ The same as **Reaction-Field**, but implemented as in GROMACS versions before 3.3. No reaction-field correction is applied to excluded atom pairs and self pairs. The 1-4 interactions are calculated using a reaction-field. The missing correction due to the excluded pairs that do not have a 1-4 interaction is up to a few percent of the total electrostatic energy and causes a minor difference in the forces and the pressure.
+
+ + **Shift**
+ Analogous to **Shift** for **vdwtype**. You might want to use **Reaction-Field-zero** instead, which has a similar potential shape, but has a physical interpretation and has better energies due to the exclusion correction terms.
+
+ + **Encad-Shift**
+ The Coulomb potential is decreased over the whole range, using the definition from the Encad simulation package.
+
+ + **Switch**
+ Analogous to **Switch** for **vdwtype**. Switching the Coulomb potential can lead to serious artifacts, advice: use **Reaction-Field-zero** instead.
+
+ + **User**
+ [mdrun] will now expect to find a file `table.xvg` with user-defined potential functions for repulsion, dispersion and Coulomb. When pair interactions are present, [mdrun] also expects to find a file `tablep.xvg` for the pair interactions. When the same interactions should be used for non-bonded and pair interactions the user can specify the same file name for both table files. These files should contain 7 columns: the `x` value, `f(x)`, `-f'(x)`, `g(x)`, `-g'(x)`, `h(x)`, `-h'(x)`, where `f(x)` is the Coulomb function, `g(x)` the dispersion function and `h(x)` the repulsion function. When **vdwtype** is not set to **User** the values for `g`, `-g'`, `h` and `-h'` are ignored. For the non-bonded interactions `x` values should run from 0 to the largest cut-off distance + **table-extension** and should be uniformly spaced. For the pair interactions the table length in the file will be used. The optimal spacing, which is used for non-user tables, is `0.002 nm` when you run in mixed precision or `0.0005 nm` when you run in double precision. The function value at `x=0` is not important. More information is in the printed manual.
+
+ + **PME-Switch**
+ A combination of PME and a switch function for the direct-space part (see above). **rcoulomb** is allowed to be smaller than **rlist**. This is mainly useful constant energy simulations (note that using **PME** with **cutoff-scheme**=**Verlet** will be more efficient).
+
+ + **PME-User**
+ A combination of PME and user tables (see above). **rcoulomb** is allowed to be smaller than **rlist**. The PME mesh contribution is subtracted from the user table by [mdrun]. Because of this subtraction the user tables should contain about 10 decimal places.
+
+ + **PME-User-Switch**
+ A combination of PME-User and a switching function (see above). The switching function is applied to final particle-particle interaction, _i.e._ both to the user supplied function and the PME Mesh correction part.
+
+coulomb-modifier:
+: + **Potential-shift-Verlet**
+ Selects **Potential-shift** with the Verlet cutoff-scheme, as it is (nearly) free; selects **None** with the group cutoff-scheme.
+
+ + **Potential-shift**
+ Shift the Coulomb potential by a constant such that it is zero at the cut-off. This makes the potential the integral of the force. Note that this does not affect the forces or the sampling.
+
+ + **None**
+ Use an unmodified Coulomb potential. With the group scheme this means no exact cut-off is used, energies and forces are calculated for all pairs in the neighborlist.
+
+rcoulomb-switch: (0) [nm]
+: where to start switching the Coulomb potential, only relevant when force or potential switching is used
+
+rcoulomb: (1) [nm]
+: distance for the Coulomb cut-off
+
+epsilon-r: (1)
+: The relative dielectric constant. A value of 0 means infinity.
+
+epsilon-rf: (0)
+: The relative dielectric constant of the reaction field. This is only used with reaction-field electrostatics. A value of 0 means infinity.
+
+
+### VdW
+
+vdwtype:
+: + **Cut-off**
+ Twin range cut-offs with neighbor list cut-off **rlist** and VdW cut-off **rvdw**, where **rvdw** >= **rlist**.
+
+ + **PME**
+ Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The grid dimensions are controlled with **fourierspacing** in the same way as for electrostatics, and the interpolation order is controlled with **pme-order**. The relative accuracy of direct/reciprocal space is controlled by **ewald-rtol-lj**, and the specific combination rules that are to be used by the reciprocal routine are set using **lj-pme-comb-rule**.
+
+ + **Shift**
+ This functionality is deprecated and replaced by **vdw-modifier = Force-switch**. The LJ (not Buckingham) potential is decreased over the whole range and the forces decay smoothly to zero between **rvdw-switch** and **rvdw**. The neighbor search cut-off **rlist** should be 0.1 to 0.3 nm larger than **rvdw** to accommodate for the size of charge groups and diffusion between neighbor list updates.
+
+ + **Switch**
+ This functionality is deprecated and replaced by **vdw-modifier = Potential-switch**. The LJ (not Buckingham) potential is normal out to **rvdw-switch**, after which it is switched off to reach zero at **rvdw**. Both the potential and force functions are continuously smooth, but be aware that all switch functions will give rise to a bulge (increase) in the force (since we are switching the potential). The neighbor search cut-off **rlist** should be 0.1 to 0.3 nm larger than **rvdw** to accommodate for the size of charge groups and diffusion between neighbor list updates.
+
+ + **Encad-Shift**
+ The LJ (not Buckingham) potential is decreased over the whole range, using the definition from the Encad simulation package.
+
+ + **User**
+ See **user** for **coulombtype**. The function value at zero is not important. When you want to use LJ correction, make sure that **rvdw** corresponds to the cut-off in the user-defined function. When **coulombtype** is not set to **User** the values for `f` and `-f'` are ignored.
+
+vdw-modifier:
+: + **Potential-shift-Verlet**
+ Selects **Potential-shift** with the Verlet cutoff-scheme, as it is (nearly) free; selects **None** with the group cutoff-scheme.
+
+ + **Potential-shift**
+ Shift the Van der Waals potential by a constant such that it is zero at the cut-off. This makes the potential the integral of the force. Note that this does not affect the forces or the sampling.
+
+ + **None**
+ Use an unmodified Van der Waals potential. With the group scheme this means no exact cut-off is used, energies and forces are calculated for all pairs in the neighborlist.
+
+ + **Force-switch**
+ Smoothly switches the forces to zero between **rvdw-switch** and **rvdw**. This shifts the potential shift over the whole range and switches it to zero at the cut-off. Note that this is more expensive to calculate than a plain cut-off and it is not required for energy conservation, since **Potential-shift** conserves energy just as well.
+
+ + **Potential-switch**
+ Smoothly switches the potential to zero between **rvdw-switch** and **rvdw**. Note that this introduces articifically large forces in the switching region and is much more expensive to calculate. This option should only be used if the force field you are using requires this.
+
+rvdw-switch: (0) [nm]
+: where to start switching the LJ force and possibly the potential, only relevant when force or potential switching is used
+
+rvdw: (1) [nm]
+: distance for the LJ or Buckingham cut-off
+
+DispCorr:
+: + **no**
+ don't apply any correction
+
+ + **EnerPres**
+ apply long range dispersion corrections for Energy and Pressure
+
+ + **Ener**
+ apply long range dispersion corrections for Energy only
+
+
+### Tables
+
+table-extension: (1) [nm]
+: Extension of the non-bonded potential lookup tables beyond the largest cut-off distance. The value should be large enough to account for charge group sizes and the diffusion between neighbor-list updates. Without user defined potential the same table length is used for the lookup tables for the 1-4 interactions, which are always tabulated irrespective of the use of tables for the non-bonded interactions. The value of **table-extension** in no way affects the values of **rlist**, **rcoulomb**, or **rvdw**.
+
+energygrp-table:
+: When user tables are used for electrostatics and/or VdW, here one can give pairs of energy groups for which seperate user tables should be used. The two energy groups will be appended to the table file name, in order of their definition in **energygrps**, seperated by underscores. For example, if `energygrps = Na Cl Sol` and `energygrp-table = Na Na Na Cl`, [mdrun] will read `table_Na_Na.xvg` and `table_Na_Cl.xvg` in addition to the normal `table.xvg` which will be used for all other energy group pairs.
+
+
+### Ewald
+
+fourierspacing: (0.12) [nm]
+: For ordinary Ewald, the ratio of the box dimensions and the spacing determines a lower bound for the number of wave vectors to use in each (signed) direction. For PME and P3M, that ratio determines a lower bound for the number of Fourier-space grid points that will be used along that axis. In all cases, the number for each direction can be overridden by entering a non-zero value for **fourier_n[xyz]**. For optimizing the relative load of the particle-particle interactions and the mesh part of PME, it is useful to know that the accuracy of the electrostatics remains nearly constant when the Coulomb cut-off and the PME grid spacing are scaled by the same factor.
+
+fourier-nx (0) ; fourier-ny (0) ; fourier-nz: (0)
+: Highest magnitude of wave vectors in reciprocal space when using Ewald.
+ Grid size when using PME or P3M. These values override **fourierspacing** per direction. The best choice is powers of 2, 3, 5 and 7. Avoid large primes.
+
+pme-order (4)
+: Interpolation order for PME. 4 equals cubic interpolation. You might try 6/8/10 when running in parallel and simultaneously decrease grid dimension.
+
+ewald-rtol (1e-5)
+: The relative strength of the Ewald-shifted direct potential at **rcoulomb** is given by **ewald-rtol**. Decreasing this will give a more accurate direct sum, but then you need more wave vectors for the reciprocal sum.
+
+ewald-rtol-lj (1e-3)
+: When doing PME for VdW-interactions, **ewald-rtol-lj** is used to control the relative strength of the dispersion potential at **rvdw** in the same way as **ewald-rtol** controls the electrostatic potential.
+
+lj-pme-comb-rule (Geometric)
+: The combination rules used to combine VdW-parameters in the reciprocal part of LJ-PME. Geometric rules are much faster than Lorentz-Berthelot and usually the recommended choice, even when the rest of the force field uses the Lorentz-Berthelot rules.
+
+ + **Geometric**
+ Apply geometric combination rules
+
+ + **Lorentz-Berthelot**
+ Apply Lorentz-Berthelot combination rules
+
+ewald-geometry: (3d)
+: + **3d**
+ The Ewald sum is performed in all three dimensions.
+
+ + **3dc**
+ The reciprocal sum is still performed in 3D, but a force and potential correction applied in the `z` dimension to produce a pseudo-2D summation. If your system has a slab geometry in the `x-y` plane you can try to increase the `z`-dimension of the box (a box height of 3 times the slab height is usually ok) and use this option.
+
+epsilon-surface: (0)
+: This controls the dipole correction to the Ewald summation in 3D. The default value of zero means it is turned off. Turn it on by setting it to the value of the relative permittivity of the imaginary surface around your infinite system. Be careful - you shouldn't use this if you have free mobile charges in your system. This value does not affect the slab 3DC variant of the long range corrections.
+
+
+### Temperature coupling
+
+tcoupl:
+: + **no**
+ No temperature coupling.
+
+ + **berendsen**
+ Temperature coupling with a Berendsen-thermostat to a bath with temperature **ref-t**, with time constant **tau-t**. Several groups can be coupled separately, these are specified in the **tc-grps** field separated by spaces.
+
+ + **nose-hoover**
+ Temperature coupling using a Nose-Hoover extended ensemble. The reference temperature and coupling groups are selected as above, but in this case **tau-t** controls the period of the temperature fluctuations at equilibrium, which is slightly different from a relaxation time. For NVT simulations the conserved energy quantity is written to energy and log file.
+
+ + **andersen**
+ Temperature coupling by randomizing a fraction of the particles at each timestep. Reference temperature and coupling groups are selected as above. **tau-t** is the average time between randomization of each molecule. Inhibits particle dynamics somewhat, but little or no ergodicity issues. Currently only implemented with velocity Verlet, and not implemented with constraints.
+
+ + **andersen-massive**
+ Temperature coupling by randomizing all particles at infrequent timesteps. Reference temperature and coupling groups are selected as above. **tau-t** is the time between randomization of all molecules. Inhibits particle dynamics somewhat, but little or no ergodicity issues. Currently only implemented with velocity Verlet.
+
+ + **v-rescale**
+ Temperature coupling using velocity rescaling with a stochastic term (JCP 126, 014101). This thermostat is similar to Berendsen coupling, with the same scaling using **tau-t**, but the stochastic term ensures that a proper canonical ensemble is generated. The random seed is set with **ld-seed**. This thermostat works correctly even for **tau-t**=0. For NVT simulations the conserved energy quantity is written to the energy and log file.
+
+nsttcouple: (-1)
+: The frequency for coupling the temperature. The default value of -1 sets **nsttcouple** equal to **nstlist**, unless **nstlist**<=0, then a value of 10 is used. For velocity Verlet integrators **nsttcouple** is set to 1.
+
+nh-chain-length (10)
+: the number of chained Nose-Hoover thermostats for velocity Verlet integrators, the leap-frog **md** integrator only supports 1. Data for the NH chain variables is not printed to the .edr, but can be using the `GMX_NOSEHOOVER_CHAINS` environment variable
+
+tc-grps:
+: groups to couple to separate temperature baths
+
+tau-t: [ps]
+: time constant for coupling (one for each group in **tc-grps**), -1 means no temperature coupling
+
+ref-t: [K]
+: reference temperature for coupling (one for each group in **tc-grps**)
+
+
+### Pressure coupling
+
+pcoupl:
+: + **no**
+ No pressure coupling. This means a fixed box size.
+
+ + **berendsen**
+ Exponential relaxation pressure coupling with time constant **tau-p**. The box is scaled every timestep. It has been argued that this does not yield a correct thermodynamic ensemble, but it is the most efficient way to scale a box at the beginning of a run.
+
+ + **Parrinello-Rahman**
+ Extended-ensemble pressure coupling where the box vectors are subject to an equation of motion. The equation of motion for the atoms is coupled to this. No instantaneous scaling takes place. As for Nose-Hoover temperature coupling the time constant **tau-p** is the period of pressure fluctuations at equilibrium. This is probably a better method when you want to apply pressure scaling during data collection, but beware that you can get very large oscillations if you are starting from a different pressure. For simulations where the exact fluctation of the NPT ensemble are important, or if the pressure coupling time is very short it may not be appropriate, as the previous time step pressure is used in some steps of the GROMACS implementation for the current time step pressure.
+
+ + **MTTK**
+ Martyna-Tuckerman-Tobias-Klein implementation, only useable with **md-vv** or **md-vv-avek**, very similar to Parrinello-Rahman. As for Nose-Hoover temperature coupling the time constant **tau-p** is the period of pressure fluctuations at equilibrium. This is probably a better method when you want to apply pressure scaling during data collection, but beware that you can get very large oscillations if you are starting from a different pressure. Currently (as of version 5.1), it only supports isotropic scaling, and only works without constraints.
+
+pcoupltype:
+: + **isotropic**
+ Isotropic pressure coupling with time constant **tau-p**. The compressibility and reference pressure are set with **compressibility** and **ref-p**, one value is needed.
+
+ + **semiisotropic**
+ Pressure coupling which is isotropic in the `x` and `y` direction, but different in the `z` direction. This can be useful for membrane simulations. 2 values are needed for `x/y` and `z` directions respectively.
+
+ + **anisotropic**
+ Idem, but 6 values are needed for `xx`, `yy`, `zz`, `xy/yx`, `xz/zx` and `yz/zy` components, respectively. When the off-diagonal compressibilities are set to zero, a rectangular box will stay rectangular. Beware that anisotropic scaling can lead to extreme deformation of the simulation box.
+
+ + **surface-tension**
+ Surface tension coupling for surfaces parallel to the xy-plane. Uses normal pressure coupling for the `z`-direction, while the surface tension is coupled to the `x/y` dimensions of the box. The first **ref-p** value is the reference surface tension times the number of surfaces [bar nm], the second value is the reference `z`-pressure [bar]. The two **compressibility** values are the compressibility in the `x/y` and `z` direction respectively. The value for the `z`-compressibility should be reasonably accurate since it influences the convergence of the surface-tension, it can also be set to zero to have a box with constant height.
+
+nstpcouple: (-1)
+: The frequency for coupling the pressure. The default value of -1 sets **nstpcouple** equal to **nstlist**, unless **nstlist** <=0, then a value of 10 is used. For velocity Verlet integrators **nstpcouple** is set to 1.
+
+tau-p: (1) [ps]
+: time constant for coupling
+
+compressibility: [bar-1]
+: compressibility (NOTE: this is now really in bar-1) For water at 1 atm and 300 K the compressibility is 4.5e-5 [bar-1].
+
+ref-p: [bar]
+: reference pressure for coupling
+
+refcoord-scaling:
+: + **no**
+ The reference coordinates for position restraints are not modified. Note that with this option the virial and pressure will depend on the absolute positions of the reference coordinates.
+
+ + **all**
+ The reference coordinates are scaled with the scaling matrix of the pressure coupling.
+
+ + **com**
+ Scale the center of mass of the reference coordinates with the scaling matrix of the pressure coupling. The vectors of each reference coordinate to the center of mass are not scaled. Only one COM is used, even when there are multiple molecules with position restraints. For calculating the COM of the reference coordinates in the starting configuration, periodic boundary conditions are not taken into account.
+
+
+### Simulated annealing
+
+Simulated annealing is controlled separately for each temperature group in GROMACS. The reference temperature is a piecewise linear function, but you can use an arbitrary number of points for each group, and choose either a single sequence or a periodic behaviour for each group. The actual annealing is performed by dynamically changing the reference temperature used in the thermostat algorithm selected, so remember that the system will usually not instantaneously reach the reference temperature!
+
+annealing:
+: Type of annealing for each temperature group
+
+ + **no**
+ No simulated annealing - just couple to reference temperature value.
+
+ + **single**
+ A single sequence of annealing points. If your simulation is longer than the time of the last point, the temperature will be coupled to this constant value after the annealing sequence has reached the last time point.
+
+ + **periodic**
+ The annealing will start over at the first reference point once the last reference time is reached. This is repeated until the simulation ends.
+
+annealing-npoints:
+: A list with the number of annealing reference/control points used for each temperature group. Use 0 for groups that are not annealed. The number of entries should equal the number of temperature groups.
+
+annealing-time:
+: List of times at the annealing reference/control points for each group. If you are using periodic annealing, the times will be used modulo the last value, _i.e._ if the values are 0, 5, 10, and 15, the coupling will restart at the 0ps value after 15ps, 30ps, 45ps, etc. The number of entries should equal the sum of the numbers given in **annealing-npoints**.
+
+annealing-temp:
+: List of temperatures at the annealing reference/control points for each group. The number of entries should equal the sum of the numbers given in **annealing-npoints**.
+
+ Confused? OK, let's use an example. Assume you have two temperature groups, set the group selections to `annealing = single periodic`, the number of points of each group to `annealing-npoints = 3 4`, the times to `annealing-time = 0 3 6 0 2 4 6` and finally temperatures to `annealing-temp = 298 280 270 298 320 320 298`. The first group will be coupled to 298K at 0ps, but the reference temperature will drop linearly to reach 280K at 3ps, and then linearly between 280K and 270K from 3ps to 6ps. After this is stays constant, at 270K. The second group is coupled to 298K at 0ps, it increases linearly to 320K at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it decreases to 298K, and then it starts over with the same pattern again, _i.e._ rising linearly from 298K to 320K between 6ps and 8ps. Check the summary printed by [gmx grompp] if you are unsure!
+
+
+### Velocity generation
+
+gen-vel:
+: + **no**
+ Do not generate velocities. The velocities are set to zero when there are no velocities in the input structure file.
+
+ + **yes**
+ Generate velocities in [gmx grompp] according to a Maxwell distribution at temperature **gen-temp**, with random seed **gen-seed**. This is only meaningful with integrator **md**.
+
+gen-temp: (300) [K]
+: temperature for Maxwell distribution
+
+gen-seed: (-1) [integer]
+: used to initialize random generator for random velocities, when **gen-seed** is set to -1, a pseudo random seed is used.
+
+
+### Bonds
+
+constraints:
+: + **none**
+ No constraints except for those defined explicitly in the topology, _i.e._ bonds are represented by a harmonic (or other) potential or a Morse potential (depending on the setting of **morse**) and angles by a harmonic (or other) potential. **h-bonds**
+ Convert the bonds with H-atoms to constraints.
+
+ + **all-bonds**
+ Convert all bonds to constraints.
+
+ + **h-angles**
+ Convert all bonds and additionally the angles that involve H-atoms to bond-constraints.
+
+ + **all-angles**
+ Convert all bonds and angles to bond-constraints.
+
+constraint-algorithm:
+: + **LINCS**
+ LINear Constraint Solver. With domain decomposition the parallel version P-LINCS is used. The accuracy in set with **lincs-order**, which sets the number of matrices in the expansion for the matrix inversion. After the matrix inversion correction the algorithm does an iterative correction to compensate for lengthening due to rotation. The number of such iterations can be controlled with **lincs-iter**. The root mean square relative constraint deviation is printed to the log file every **nstlog** steps. If a bond rotates more than **lincs-warnangle** in one step, a warning will be printed both to the log file and to `stderr`. LINCS should not be used with coupled angle constraints.
+
+ + **SHAKE**
+ SHAKE is slightly slower and less stable than LINCS, but does work with angle constraints. The relative tolerance is set with **shake-tol**, 0.0001 is a good value for "normal" MD. SHAKE does not support constraints between atoms on different nodes, thus it can not be used with domain decompositon when inter charge-group constraints are present. SHAKE can not be used with energy minimization.
+
+continuation:
+: This option was formerly known as **unconstrained-start**.
+
+ + **no**
+ apply constraints to the start configuration and reset shells
+
+ + **yes**
+ do not apply constraints to the start configuration and do not reset shells, useful for exact coninuation and reruns
+
+shake-tol: (0.0001)
+: relative tolerance for SHAKE
+
+lincs-order: (4)
+: Highest order in the expansion of the constraint coupling matrix. When constraints form triangles, an additional expansion of the same order is applied on top of the normal expansion only for the couplings within such triangles. For "normal" MD simulations an order of 4 usually suffices, 6 is needed for large time-steps with virtual sites or BD. For accurate energy minimization an order of 8 or more might be required. With domain decomposition, the cell size is limited by the distance spanned by **lincs-order**+1 constraints. When one wants to scale further than this limit, one can decrease **lincs-order** and increase **lincs-iter**, since the accuracy does not deteriorate when (1+**lincs-iter**)***lincs-order** remains constant.
+
+lincs-iter: (1)
+: Number of iterations to correct for rotational lengthening in LINCS. For normal runs a single step is sufficient, but for NVE runs where you want to conserve energy accurately or for accurate energy minimization you might want to increase it to 2.
+
+lincs-warnangle: (30) [degrees]
+: maximum angle that a bond can rotate before LINCS will complain
+
+morse:
+: + **no**
+ bonds are represented by a harmonic potential
+
+ + **yes**
+ bonds are represented by a Morse potential
+
+
+### Energy group exclusions
+
+energygrp-excl:
+: Pairs of energy groups for which all non-bonded interactions are excluded. An example: if you have two energy groups `Protein` and `SOL`, specifying `energygrp-excl = Protein Protein SOL SOL` would give only the non-bonded interactions between the protein and the solvent. This is especially useful for speeding up energy calculations with `mdrun -rerun` and for excluding interactions within frozen groups.
+
+
+### Walls
+
+nwall: 0
+: When set to **1** there is a wall at `z=0`, when set to **2** there is also a wall at `z=z-box`. Walls can only be used with **pbc=xy**. When set to **2** pressure coupling and Ewald summation can be used (it is usually best to use semiisotropic pressure coupling with the `x/y` compressibility set to 0, as otherwise the surface area will change). Walls interact wit the rest of the system through an optional **wall-atomtype**. Energy groups `wall0` and `wall1` (for **nwall=2**) are added automatically to monitor the interaction of energy groups with each wall. The center of mass motion removal will be turned off in the `z`-direction.
+
+wall-atomtype:
+: the atom type name in the force field for each wall. By (for example) defining a special wall atom type in the topology with its own combination rules, this allows for independent tuning of the interaction of each atomtype with the walls.
+
+wall-type:
+: + **9-3**
+ LJ integrated over the volume behind the wall: 9-3 potential
+
+ + **10-4**
+ LJ integrated over the wall surface: 10-4 potential
+
+ + **12-6**
+ direct LJ potential with the `z` distance from the wall
+
+ + **table**
+ user defined potentials indexed with the `z` distance from the wall, the tables are read analogously to the **energygrp-table** option, where the first name is for a "normal" energy group and the second name is `wall0` or `wall1`, only the dispersion and repulsion columns are used
+
+wall-r-linpot: -1 (nm)
+: Below this distance from the wall the potential is continued linearly and thus the force is constant. Setting this option to a postive value is especially useful for equilibration when some atoms are beyond a wall. When the value is <=0 (<0 for **wall-type=table**), a fatal error is generated when atoms are beyond a wall.
+
+wall-density: [nm-3/nm-2]
+: the number density of the atoms for each wall for wall types **9-3** and **10-4**
+
+wall-ewald-zfac: 3
+: The scaling factor for the third box vector for Ewald summation only, the minimum is 2. Ewald summation can only be used with **nwall=2**, where one should use **ewald-geometry`=3dc`**. The empty layer in the box serves to decrease the unphysical Coulomb interaction between periodic images.
+
+
+### COM pulling
+
+pull:
+: + **no**
+ No center of mass pulling. All the following pull options will be ignored (and if present in the [.mdp] file, they unfortunately generate warnings)
+
+ + **umbrella**
+ Center of mass pulling using an umbrella potential between the reference group and one or more groups.
+
+ + **constraint**
+ Center of mass pulling using a constraint between the reference group and one or more groups. The setup is identical to the option **umbrella**, except for the fact that a rigid constraint is applied instead of a harmonic potential.
+
+ + **constant-force**
+ Center of mass pulling using a linear potential and therefore a constant force. For this option there is no reference position and therefore the parameters **pull-init** and **pull-rate** are not used.
+
+pull-geometry:
+: + **distance**
+ Pull along the vector connecting the two groups. Components can be selected with **pull-dim**.
+
+ + **direction**
+ Pull in the direction of **pull-vec**.
+
+ + **direction-periodic**
+ As **direction**, but allows the distance to be larger than half the box size. With this geometry the box should not be dynamic (_e.g._ no pressure scaling) in the pull dimensions and the pull force is not added to virial.
+
+ + **cylinder**
+ Designed for pulling with respect to a layer where the reference COM is given by a local cylindrical part of the reference group. The pulling is in the direction of **pull-vec**. From the reference group a cylinder is selected around the axis going through the pull group with direction **pull-vec** using two radii. The radius **pull-r1** gives the radius within which all the relative weights are one, between **pull-r1** and **pull-r0** the weights are switched to zero. Mass weighting is also used. Note that the radii should be smaller than half the box size. For tilted cylinders they should be even smaller than half the box size since the distance of an atom in the reference group from the COM of the pull group has both a radial and an axial component.
+
+pull-dim: (Y Y Y)
+: the distance components to be used with geometry **distance**, and also sets which components are printed to the output files
+
+pull-r1: (1) [nm]
+: the inner radius of the cylinder for geometry **cylinder**
+
+pull-r0: (1) [nm]
+: the outer radius of the cylinder for geometry **cylinder**
+
+pull-constr-tol: (1e-6)
+: the relative constraint tolerance for constraint pulling
+
+pull-start:
+: + **no**
+ do not modify **pull-init**
+
+ + **yes**
+ add the COM distance of the starting conformation to **pull-init**
+
+pull-print-reference: (10)
+: + **no**
+ do not print the COM of the first group in each pull coordinate
+
+ + **yes**
+ print the COM of the first group in each pull coordinate
+
+pull-nstxout: (10)
+: frequency for writing out the COMs of all the pull group
+
+pull-nstfout: (1)
+: frequency for writing out the force of all the pulled group
+
+pull-ngroups: (1)
+: The number of pull groups, not including the absolute reference group, when used. Pull groups can be reused in multiple pull coordinates. Below only the pull options for group 1 are given, further groups simply increase the group index number.
+
+pull-ncoords: (1)
+: The number of pull coordinates. Below only the pull options for coordinate 1 are given, further coordinates simply increase the coordinate index number.
+
+pull-group1-name:
+: The name of the pull group, is looked up in the index file or in the default groups to obtain the atoms involved.
+
+pull-group1-weights:
+: Optional relative weights which are multiplied with the masses of the atoms to give the total weight for the COM. The number should be 0, meaning all 1, or the number of atoms in the pull group.
+
+pull-group1-pbcatom: (0)
+: The reference atom for the treatment of periodic boundary conditions inside the group (this has no effect on the treatment of the pbc between groups). This option is only important when the diameter of the pull group is larger than half the shortest box vector. For determining the COM, all atoms in the group are put at their periodic image which is closest to **pull-group1-pbcatom**. A value of 0 means that the middle atom (number wise) is used. This parameter is not used with geometry **cylinder**. A value of -1 turns on cosine weighting, which is useful for a group of molecules in a periodic system, _e.g._ a water slab (see Engin et al. J. Chem. Phys. B 2010).
+
+pull-coord1-groups:
+: The two groups indices should be given on which this pull coordinate will operate. The first index can be 0, in which case an absolute reference of **pull-coord1-origin** is used. With an absolute reference the system is no longer translation invariant and one should think about what to do with the center of mass motion.
+
+pull-coord1-origin: (0.0 0.0 0.0)
+: The pull reference position for use with an absolute reference.
+
+pull-coord1-vec: (0.0 0.0 0.0)
+: The pull direction. [gmx grompp] normalizes the vector.
+
+pull-coord1-init: (0.0) [nm]
+: The reference distance at t=0.
+
+pull-coord1-rate: (0) [nm/ps]
+: The rate of change of the reference position.
+
+pull-coord1-k: (0) [kJ mol-1 nm-2] / [kJ mol-1 nm-1]
+: The force constant. For umbrella pulling this is the harmonic force constant in [kJ mol-1 nm-2]. For constant force pulling this is the force constant of the linear potential, and thus the negative (!) of the constant force in [kJ mol-1 nm-1].
+
+pull-coord1-kB: (pull-k1) [kJ mol-1 nm-2] / [kJ mol-1 nm-1]
+: As **pull-coord1-k**, but for state B. This is only used when **free-energy** is turned on. The force constant is then (1 - lambda) * **pull-coord1-k** + lambda * **pull-coord1-kB**.
+
+
+### NMR refinement
+
+disre:
+: + **no**
+ ignore distance restraint information in topology file
+
+ + **simple**
+ simple (per-molecule) distance restraints.
+
+ + **ensemble**
+ distance restraints over an ensemble of molecules in one simulation box. Normally, one would perform ensemble averaging over multiple subsystems, each in a separate box, using `mdrun -multi`. Supply `topol0.tpr`, `topol1.tpr`, ... with different coordinates and/or velocities. The environment variable `GMX_DISRE_ENSEMBLE_SIZE` sets the number of systems within each ensemble (usually equal to the `mdrun -multi` value).
+
+disre-weighting:
+: + **equal** (default)
+ divide the restraint force equally over all atom pairs in the restraint
+
+ + **conservative**
+ the forces are the derivative of the restraint potential, this results in an weighting of the atom pairs to the reciprocal seventh power of the displacement. The forces are conservative when **disre-tau** is zero.
+
+disre-mixed:
+: + **no**
+ the violation used in the calculation of the restraint force is the time-averaged violation
+
+ + **yes**
+ the violation used in the calculation of the restraint force is the square root of the product of the time-averaged violation and the instantaneous violation
+
+disre-fc: (1000) [kJ mol-1 nm-2]
+: force constant for distance restraints, which is multiplied by a (possibly) different factor for each restraint given in the `fac` column of the interaction in the topology file.
+
+disre-tau: (0) [ps]
+: time constant for distance restraints running average. A value of zero turns off time averaging.
+
+nstdisreout: (100) [steps]
+: period between steps when the running time-averaged and instantaneous distances of all atom pairs involved in restraints are written to the energy file (can make the energy file very large)
+
+orire:
+: + **no**
+ ignore orientation restraint information in topology file
+
+ + **yes**
+ use orientation restraints, ensemble averaging can be performed with `mdrun -multi`
+
+orire-fc: (0) [kJ mol]
+: force constant for orientation restraints, which is multiplied by a (possibly) different weight factor for each restraint, can be set to zero to obtain the orientations from a free simulation
+
+orire-tau: (0) [ps]
+: time constant for orientation restraints running average. A value of zero turns off time averaging.
+
+orire-fitgrp:
+: fit group for orientation restraining. This group of atoms is used to determine the rotation **R** of the system with respect to the reference orientation. The reference orientation is the starting conformation of the first subsystem. For a protein, backbone is a reasonable choice
+
+nstorireout: (100) [steps]
+: period between steps when the running time-averaged and instantaneous orientations for all restraints, and the molecular order tensor are written to the energy file (can make the energy file very large)
+
+
+### Free energy calculations
+
+free-energy:
+: + **no**
+ Only use topology A.
+
+ + **yes**
+ Interpolate between topology A (lambda=0) to topology B (lambda=1) and write the derivative of the Hamiltonian with respect to lambda (as specified with **dhdl-derivatives**), or the Hamiltonian differences with respect to other lambda values (as specified with **foreign-lambda**) to the energy file and/or to `dhdl.xvg`, where they can be processed by, for example [gmx bar]. The potentials, bond-lengths and angles are interpolated linearly as described in the manual. When **sc-alpha** is larger than zero, soft-core potentials are used for the LJ and Coulomb interactions.
+
+ + **expanded**
+ Turns on expanded ensemble simulation, where the alchemical state becomes a dynamic variable, allowing jumping between different Hamiltonians. See the expanded ensemble options for controlling how expanded ensemble simulations are performed. The different Hamiltonians used in expanded ensemble simulations are defined by the other free energy options.
+
+init-lambda: (-1)
+: starting value for lambda (float). Generally, this should only be used with slow growth (_i.e._ nonzero **delta-lambda**). In other cases, **init-lambda-state** should be specified instead. Must be greater than or equal to 0.
+
+delta-lambda: (0)
+: increment per time step for lambda
+
+init-lambda-state: (-1)
+: starting value for the lambda state (integer). Specifies which columm of the lambda vector (**coul-lambdas**, **vdw-lambdas**, **bonded-lambdas**, **restraint-lambdas**, **mass-lambdas**, **temperature-lambdas**, **fep-lambdas**) should be used. This is a zero-based index: **init-lambda-state** 0 means the first column, and so on.
+
+fep-lambdas: ()
+: Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every **nstdhdl** steps. Values must be between 0 and 1. Free energy differences between different lambda values can then be determined with [gmx bar]. **fep-lambdas** is different from the other `-lambdas` keywords because all components of the lambda vector that are not specified will use **fep-lambdas** (including restraint-lambdas and therefore the pull code restraints).
+
+coul-lambdas: ()
+: Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every **nstdhdl** steps. Values must be between 0 and 1. Only the electrostatic interactions are controlled with this component of the lambda vector (and only if the lambda=0 and lambda=1 states have differing electrostatic interactions).
+
+vdw-lambdas: ()
+: Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every **nstdhdl** steps. Values must be between 0 and 1. Only the van der Waals interactions are controlled with this component of the lambda vector.
+
+bonded-lambdas: ()
+: Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every **nstdhdl** steps. Values must be between 0 and 1. Only the bonded interactions are controlled with this component of the lambda vector.
+
+restraint-lambdas: ()
+: Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every **nstdhdl** steps. Values must be between 0 and 1. Only the restraint interactions: dihedral restraints, and the pull code restraints are controlled with this component of the lambda vector.
+
+mass-lambdas: ()
+: Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every **nstdhdl** steps. Values must be between 0 and 1. Only the particle masses are controlled with this component of the lambda vector.
+
+temperature-lambdas: ()
+: Zero, one or more lambda values for which Delta H values will be determined and written to dhdl.xvg every **nstdhdl** steps. Values must be between 0 and 1. Only the temperatures controlled with this component of the lambda vector. Note that these lambdas should not be used for replica exchange, only for simulated tempering.
+
+calc-lambda-neighbors (1)
+: Controls the number of lambda values for which Delta H values will be calculated and written out, if **init-lambda-state** has been set. A positive value will limit the number of lambda points calculated to only the nth neighbors of **init-lambda-state**: for example, if **init-lambda-state** is 5 and this parameter has a value of 2, energies for lambda points 3-7 will be calculated and writen out. A value of -1 means all lambda points will be written out. For normal BAR such as with [gmx bar], a value of 1 is sufficient, while for MBAR -1 should be used.
+
+sc-alpha: (0)
+: the soft-core alpha parameter, a value of 0 results in linear interpolation of the LJ and Coulomb interactions
+
+sc-r-power: (6)
+: the power of the radial term in the soft-core equation. Possible values are 6 and 48. 6 is more standard, and is the default. When 48 is used, then sc-alpha should generally be much lower (between 0.001 and 0.003).
+
+sc-coul: (no)
+: Whether to apply the soft core free energy interaction transformation to the Columbic interaction of a molecule. Default is no, as it is generally more efficient to turn off the Coulomic interactions linearly before turning off the van der Waals interactions.
+
+sc-power: (0)
+: the power for lambda in the soft-core function, only the values 1 and 2 are supported
+
+sc-sigma: (0.3) [nm]
+: the soft-core sigma for particles which have a C6 or C12 parameter equal to zero or a sigma smaller than **sc-sigma**
+
+couple-moltype:
+: Here one can supply a molecule type (as defined in the topology) for calculating solvation or coupling free energies. There is a special option **system** that couples all molecule types in the system. This can be useful for equilibrating a system starting from (nearly) random coordinates. **free-energy** has to be turned on. The Van der Waals interactions and/or charges in this molecule type can be turned on or off between lambda=0 and lambda=1, depending on the settings of **couple-lambda0** and **couple-lambda1**. If you want to decouple one of several copies of a molecule, you need to copy and rename the molecule definition in the topology.
+
+couple-lambda0:
+: + **vdw-q**
+ all interactions are on at lambda=0
+
+ + **vdw**
+ the charges are zero (no Coulomb interactions) at lambda=0
+
+ + **q**
+ the Van der Waals interactions are turned at lambda=0; soft-core interactions will be required to avoid singularities
+
+ + **none**
+ the Van der Waals interactions are turned off and the charges are zero at lambda=0; soft-core interactions will be required to avoid singularities.
+
+couple-lambda1:
+: analogous to **couple-lambda1**, but for lambda=1
+
+couple-intramol:
+: + **no**
+ All intra-molecular non-bonded interactions for moleculetype **couple-moltype** are replaced by exclusions and explicit pair interactions. In this manner the decoupled state of the molecule corresponds to the proper vacuum state without periodicity effects.
+
+ + **yes**
+ The intra-molecular Van der Waals and Coulomb interactions are also turned on/off. This can be useful for partitioning free-energies of relatively large molecules, where the intra-molecular non-bonded interactions might lead to kinetically trapped vacuum conformations. The 1-4 pair interactions are not turned off.
+
+* **nstdhdl: (100)**
+ the frequency for writing dH/dlambda and possibly Delta H to dhdl.xvg, 0 means no ouput, should be a multiple of **nstcalcenergy**.
+
+dhdl-derivatives: (yes)
+: If yes (the default), the derivatives of the Hamiltonian with respect to lambda at each **nstdhdl** step are written out. These values are needed for interpolation of linear energy differences with [gmx bar] (although the same can also be achieved with the right **foreign lambda** setting, that may not be as flexible), or with thermodynamic integration
+
+dhdl-print-energy: (no)
+: Include either the total or the potential energy in the dhdl file. Options are 'no', 'potential', or 'total'. This information is needed for later free energy analysis if the states of interest are at different temperatures. If all states are at the same temperature, this information is not needed. 'potential' is useful in case one is using `mdrun -rerun` to generate the `dhdl.xvg` file. When rerunning from an existing trajectory, the kinetic energy will often not be correct, and thus one must compute the residual free energy from the potential alone, with the kinetic energy component computed analytically.
+
+separate-dhdl-file: (yes)
+: + **yes**
+ the free energy values that are calculated (as specified with the **foreign-lambda** and **dhdl-derivatives** settings) are written out to a separate file, with the default name `dhdl.xvg`. This file can be used directly with [gmx bar].
+
+ + **no**
+ The free energy values are written out to the energy output file (`ener.edr`, in accumulated blocks at every **nstenergy** steps), where they can be extracted with [gmx energy] or used directly with [gmx bar].
+
+dh-hist-size: (0)
+: If nonzero, specifies the size of the histogram into which the Delta H values (specified with **foreign-lambda**) and the derivative dH/dl values are binned, and written to ener.edr. This can be used to save disk space while calculating free energy differences. One histogram gets written for each **foreign lambda** and two for the dH/dl, at every **nstenergy** step. Be aware that incorrect histogram settings (too small size or too wide bins) can introduce errors. Do not use histograms unless you're certain you need it.
+
+dh-hist-spacing (0.1)
+: Specifies the bin width of the histograms, in energy units. Used in conjunction with **dh-hist-size**. This size limits the accuracy with which free energies can be calculated. Do not use histograms unless you're certain you need it.
+
+
+### Expanded Ensemble calculations
+
+nstexpanded
+: The number of integration steps beween attempted moves changing the system Hamiltonian in expanded ensemble simulations. Must be a multiple of **nstcalcenergy**, but can be greater or less than **nstdhdl**.
+lmc-stats:
+: + **no**
+ No Monte Carlo in state space is performed.
+
+ + **metropolis-transition**
+ Uses the Metropolis weights to update the expanded ensemble weight of each state. Min{1,exp(-(beta_new u_new - beta_old u_old)}
+
+ + **barker-transition**
+ Uses the Barker transition critera to update the expanded ensemble weight of each state i, defined by exp(-beta_new u_new)/[exp(-beta_new u_new)+exp(-beta_old u_old)
+
+ + **wang-landau**
+ Uses the Wang-Landau algorithm (in state space, not energy space) to update the expanded ensemble weights.
+
+ + **min-variance**
+ Uses the minimum variance updating method of Escobedo et al. to update the expanded ensemble weights. Weights will not be the free energies, but will rather emphasize states that need more sampling to give even uncertainty.
+
+lmc-mc-move:
+: + **no**
+ No Monte Carlo in state space is performed.
+
+ + **metropolis-transition**
+ Randomly chooses a new state up or down, then uses the Metropolis critera to decide whether to accept or reject: Min{1,exp(-(beta_new u_new - beta_old u_old)}
+
+ + **barker-transition**
+ Randomly chooses a new state up or down, then uses the Barker transition critera to decide whether to accept or reject: exp(-beta_new u_new)/[exp(-beta_new u_new)+exp(-beta_old u_old)]
+
+ + **gibbs**
+ Uses the conditional weights of the state given the coordinate (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state to move to.
+
+ + **metropolized-gibbs**
+ Uses the conditional weights of the state given the coordinate (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state to move to, EXCLUDING the current state, then uses a rejection step to ensure detailed balance. Always more efficient that Gibbs, though only marginally so in many situations, such as when only the nearest neighbors have decent phase space overlap.
+
+lmc-seed: (-1)
+: random seed to use for Monte Carlo moves in state space. When **lmc-seed** is set to -1, a pseudo random seed is us
+
+mc-temperature:
+: Temperature used for acceptance/rejection for Monte Carlo moves. If not specified, the temperature of the simulation specified in the first group of **ref_t** is used.
+
+wl-ratio: (0.8)
+: The cutoff for the histogram of state occupancies to be reset, and the free energy incrementor to be changed from delta to delta * **wl-scale**. If we define the Nratio = (number of samples at each histogram) / (average number of samples at each histogram). **wl-ratio** of 0.8 means that means that the histogram is only considered flat if all Nratio > 0.8 AND simultaneously all 1/Nratio > 0.8.
+
+wl-scale: (0.8)
+: Each time the histogram is considered flat, then the current value of the Wang-Landau incrementor for the free energies is multiplied by **wl-scale**. Value must be between 0 and 1.
+
+init-wl-delta: (1.0)
+: The initial value of the Wang-Landau incrementor in kT. Some value near 1 kT is usually most efficient, though sometimes a value of 2-3 in units of kT works better if the free energy differences are large.
+
+wl-oneovert: (no)
+: Set Wang-Landau incrementor to scale with 1/(simulation time) in the large sample limit. There is significant evidence that the standard Wang-Landau algorithms in state space presented here result in free energies getting 'burned in' to incorrect values that depend on the initial state. when **wl-oneovert** is true, then when the incrementor becomes less than 1/N, where N is the mumber of samples collected (and thus proportional to the data collection time, hence '1 over t'), then the Wang-Lambda incrementor is set to 1/N, decreasing every step. Once this occurs, **wl-ratio** is ignored, but the weights will still stop updating when the equilibration criteria set in **lmc-weights-equil** is achieved.
+
+lmc-repeats: (1)
+: Controls the number of times that each Monte Carlo swap type is performed each iteration. In the limit of large numbers of Monte Carlo repeats, then all methods converge to Gibbs sampling. The value will generally not need to be different from 1.
+
+lmc-gibbsdelta: (-1)
+: Limit Gibbs sampling to selected numbers of neighboring states. For Gibbs sampling, it is sometimes inefficient to perform Gibbs sampling over all of the states that are defined. A positive value of **lmc-gibbsdelta** means that only states plus or minus **lmc-gibbsdelta** are considered in exchanges up and down. A value of -1 means that all states are considered. For less than 100 states, it is probably not that expensive to include all states.
+
+lmc-forced-nstart: (0)
+: Force initial state space sampling to generate weights. In order to come up with reasonable initial weights, this setting allows the simulation to drive from the initial to the final lambda state, with **lmc-forced-nstart** steps at each state before moving on to the next lambda state. If **lmc-forced-nstart** is sufficiently long (thousands of steps, perhaps), then the weights will be close to correct. However, in most cases, it is probably better to simply run the standard weight equilibration algorithms. **nst-transition-matrix: (-1)**
+ Frequency of outputting the expanded ensemble transition matrix. A negative number means it will only be printed at the end of the simulation.
+
+symmetrized-transition-matrix: (no)
+: Whether to symmetrize the empirical transition matrix. In the infinite limit the matrix will be symmetric, but will diverge with statistical noise for short timescales. Forced symmetrization, by using the matrix T_sym = 1/2 (T + transpose(T)), removes problems like the existence of (small magnitude) negative eigenvalues.
+
+mininum-var-min: (100)
+: The **min-variance** strategy (option of **lmc-stats** is only valid for larger number of samples, and can get stuck if too few samples are used at each state. **mininum-var-min** is the minimum number of samples that each state that are allowed before the **min-variance** strategy is activated if selected.
+
+init-lambda-weights:
+: The initial weights (free energies) used for the expanded ensemble states. Default is a vector of zero weights. format is similar to the lambda vector settings in **fep-lambdas**, except the weights can be any floating point number. Units are kT. Its length must match the lambda vector lengths.
+
+lmc-weights-equil: (no)
+: + **no**
+ Expanded ensemble weights continue to be updated throughout the simulation.
+
+ + **yes**
+ The input expanded ensemble weights are treated as equilibrated, and are not updated throughout the simulation.
+
+ + **wl-delta**
+ Expanded ensemble weight updating is stopped when the Wang-Landau incrementor falls below the value specified by **weight-equil-wl-delta**.
+
+ + **number-all-lambda**
+ Expanded ensemble weight updating is stopped when the number of samples at all of the lambda states is greater than the value specified by **weight-equil-number-all-lambda**.
+
+ + **number-steps**
+ Expanded ensemble weight updating is stopped when the number of steps is greater than the level specified by **weight-equil-number-steps**.
+
+ + **number-samples**
+ Expanded ensemble weight updating is stopped when the number of total samples across all lambda states is greater than the level specified by **weight-equil-number-samples**.
+
+ + **count-ratio**
+ Expanded ensemble weight updating is stopped when the ratio of samples at the least sampled lambda state and most sampled lambda state greater than the value specified by **weight-equil-count-ratio**.
+
+simulated-tempering: (no)
+: Turn simulated tempering on or off. Simulated tempering is implemented as expanded ensemble sampling with different temperatures instead of different Hamiltonians.
+
+sim-temp-low: (300) [K]
+: Low temperature for simulated tempering.
+
+sim-temp-high: (300) [K]
+: High temperature for simulated tempering.
+
+simulated-tempering-scaling: (linear)
+: Controls the way that the temperatures at intermediate lambdas are calculated from the **temperature-lambda** part of the lambda vector.
+
+ + **linear**
+ Linearly interpolates the temperatures using the values of **temperature-lambda**, _i.e._ if **sim-temp-low**=300, **sim-temp-high**=400, then lambda=0.5 correspond to a temperature of 350. A nonlinear set of temperatures can always be implemented with uneven spacing in lambda.
+
+ + **geometric**
+ Interpolates temperatures geometrically between **sim-temp-low** and **sim-temp-high**. The i:th state has temperature **sim-temp-low** * (**sim-temp-high**/**sim-temp-low**) raised to the power of (i/(ntemps-1)). This should give roughly equal exchange for constant heat capacity, though of course things simulations that involve protein folding have very high heat capacity peaks.
+
+ + **exponential**
+ Interpolates temperatures exponentially between **sim-temp-low** and **sim-temp-high**. The ith state has temperature **sim-temp-low** + (**sim-temp-high**-**sim-temp-low**)*((exp(**temperature-lambdas**[i])-1)/(exp(1.0)-1)).
+
+
+### Non-equilibrium MD
+
+acc-grps:
+: groups for constant acceleration (_e.g._ `Protein Sol`) all atoms in groups Protein and Sol will experience constant acceleration as specified in the **accelerate** line
+
+accelerate: (0) [nm ps-2]
+: acceleration for **acc-grps**; x, y and z for each group (_e.g._ `0.1 0.0 0.0 -0.1 0.0 0.0` means that first group has constant acceleration of 0.1 nm ps-2 in X direction, second group the opposite).
+
+freezegrps:
+: Groups that are to be frozen (_i.e._ their X, Y, and/or Z position will not be updated; _e.g._ `Lipid SOL`). **freezedim** specifies for which dimension the freezing applies. To avoid spurious contibrutions to the virial and pressure due to large forces between completely frozen atoms you need to use energy group exclusions, this also saves computing time. Note that coordinates of frozen atoms are not scaled by pressure-coupling algorithms.
+
+freezedim:
+: dimensions for which groups in **freezegrps** should be frozen, specify `Y` or `N` for X, Y and Z and for each group (_e.g._ `Y Y N N N N` means that particles in the first group can move only in Z direction. The particles in the second group can move in any direction).
+
+cos-acceleration: (0) [nm ps-2]
+: the amplitude of the acceleration profile for calculating the viscosity. The acceleration is in the X-direction and the magnitude is **cos-acceleration** cos(2 pi z/boxheight). Two terms are added to the energy file: the amplitude of the velocity profile and 1/viscosity.
+
+deform: (0 0 0 0 0 0) [nm ps-1]
+: The velocities of deformation for the box elements: a(x) b(y) c(z) b(x) c(x) c(y). Each step the box elements for which **deform** is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal elements are corrected for periodicity. The coordinates are transformed accordingly. Frozen degrees of freedom are (purposely) also transformed. The time ts is set to t at the first step and at steps at which x and v are written to trajectory to ensure exact restarts. Deformation can be used together with semiisotropic or anisotropic pressure coupling when the appropriate compressibilities are set to zero. The diagonal elements can be used to strain a solid. The off-diagonal elements can be used to shear a solid or a liquid.
+
+
+### Electric fields
+
+E-x ; E-y ; E-z:
+: If you want to use an electric field in a direction, enter 3 numbers after the appropriate **E-***, the first number: the number of cosines, only 1 is implemented (with frequency 0) so enter 1, the second number: the strength of the electric field in **V nm-1**, the third number: the phase of the cosine, you can enter any number here since a cosine of frequency zero has no phase.
+
+E-xt; E-yt; E-zt:
+: not implemented yet
+
+
+### Mixed quantum/classical molecular dynamics
+
+QMMM:
+: + **no**
+ No QM/MM.
+
+ + **yes**
+ Do a QM/MM simulation. Several groups can be described at different QM levels separately. These are specified in the **QMMM-grps** field separated by spaces. The level of _ab initio_ theory at which the groups are described is specified by **QMmethod** and **QMbasis** Fields. Describing the groups at different levels of theory is only possible with the ONIOM QM/MM scheme, specified by **QMMMscheme**.
+
+QMMM-grps:
+: groups to be descibed at the QM level
+
+QMMMscheme:
+: + **normal**
+ normal QM/MM. There can only be one **QMMM-grps** that is modelled at the **QMmethod** and **QMbasis** level of _ab initio_ theory. The rest of the system is described at the MM level. The QM and MM subsystems interact as follows: MM point charges are included in the QM one-electron hamiltonian and all Lennard-Jones interactions are described at the MM level.
+
+ + **ONIOM**
+ The interaction between the subsystem is described using the ONIOM method by Morokuma and co-workers. There can be more than one **QMMM-grps** each modeled at a different level of QM theory (**QMmethod** and **QMbasis**).
+
+QMmethod: (RHF)
+: Method used to compute the energy and gradients on the QM atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2, CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals included in the active space is specified by **CASelectrons** and **CASorbitals**.
+
+QMbasis: (STO-3G)
+: Basis set used to expand the electronic wavefuntion. Only Gaussian basis sets are currently available, _i.e._ `STO-3G, 3-21G, 3-21G*, 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*,` and `6-311G`.
+
+QMcharge: (0) [integer]
+: The total charge in `e` of the **QMMM-grps**. In case there are more than one **QMMM-grps**, the total charge of each ONIOM layer needs to be specified separately.
+
+QMmult: (1) [integer]
+: The multiplicity of the **QMMM-grps**. In case there are more than one **QMMM-grps**, the multiplicity of each ONIOM layer needs to be specified separately.
+
+CASorbitals: (0) [integer]
+: The number of orbitals to be included in the active space when doing a CASSCF computation.
+
+CASelectrons: (0) [integer]
+: The number of electrons to be included in the active space when doing a CASSCF computation.
+
+SH:
+: + **no**
+ No surface hopping. The system is always in the electronic ground-state.
+
+ + **yes**
+ Do a QM/MM MD simulation on the excited state-potential energy surface and enforce a _diabatic_ hop to the ground-state when the system hits the conical intersection hyperline in the course the simulation. This option only works in combination with the CASSCF method.
+
+
+### Implicit solvent
+
+implicit-solvent:
+: + **no**
+ No implicit solvent
+
+ + **GBSA**
+ Do a simulation with implicit solvent using the Generalized Born formalism. Three different methods for calculating the Born radii are available, Still, HCT and OBC. These are specified with the **gb-algorithm** field. The non-polar solvation is specified with the **sa-algorithm** field.
+
+gb-algorithm:
+: + **Still**
+ Use the Still method to calculate the Born radii
+
+ + **HCT**
+ Use the Hawkins-Cramer-Truhlar method to calculate the Born radii
+
+ + **OBC**
+ Use the Onufriev-Bashford-Case method to calculate the Born radii
+
+nstgbradii: (1) [steps]
+: Frequency to (re)-calculate the Born radii. For most practial purposes, setting a value larger than 1 violates energy conservation and leads to unstable trajectories.
+
+rgbradii: (1.0) [nm]
+: Cut-off for the calculation of the Born radii. Currently must be equal to rlist
+
+gb-epsilon-solvent: (80)
+: Dielectric constant for the implicit solvent
+
+gb-saltconc: (0) [M]
+: Salt concentration for implicit solvent models, currently not used
+
+gb-obc-alpha (1); gb-obc-beta (0.8); gb-obc-gamma (4.85);
+: Scale factors for the OBC model. Default values are OBC(II). Values for OBC(I) are 0.8, 0 and 2.91 respectively
+
+gb-dielectric-offset: (0.009) [nm]
+: Distance for the di-electric offset when calculating the Born radii. This is the offset between the center of each atom the center of the polarization energy for the corresponding atom
+
+sa-algorithm
+: + **Ace-approximation**
+ Use an Ace-type approximation (default)
+
+ + **None**
+ No non-polar solvation calculation done. For GBSA only the polar part gets calculated
+
+sa-surface-tension: [kJ mol-1 nm-2]
+: Default value for surface tension with SA algorithms. The default value is -1; Note that if this default value is not changed it will be overridden by [gmx grompp] using values that are specific for the choice of radii algorithm (0.0049 kcal/mol/Angstrom2 for Still, 0.0054 kcal/mol/Angstrom2 for HCT/OBC) Setting it to 0 will while using an sa-algorithm other than None means no non-polar calculations are done.
+
+
+### Adaptive Resolution Simulation
+
+adress: (no)
+: Decide whether the AdResS feature is turned on.
+
+adress-type: (Off)
+: + **Off**
+ Do an AdResS simulation with weight equal 1, which is equivalent to an explicit (normal) MD simulation. The difference to disabled AdResS is that the AdResS variables are still read-in and hence are defined.
+
+ + **Constant**
+ Do an AdResS simulation with a constant weight, **adress-const-wf** defines the value of the weight
+
+ + **XSplit**
+ Do an AdResS simulation with simulation box split in x-direction, so basically the weight is only a function of the x coordinate and all distances are measured using the x coordinate only.
+
+ + **Sphere**
+ Do an AdResS simulation with spherical explicit zone.
+
+adress-const-wf: (1)
+: Provides the weight for a constant weight simulation (**adress-type**=Constant)
+
+adress-ex-width: (0)
+: Width of the explicit zone, measured from **adress-reference-coords**.
+
+adress-hy-width: (0)
+: Width of the hybrid zone.
+
+adress-reference-coords: (0,0,0)
+: Position of the center of the explicit zone. Periodic boundary conditions apply for measuring the distance from it.
+
+adress-cg-grp-names
+: The names of the coarse-grained energy groups. All other energy groups are considered explicit and their interactions will be automatically excluded with the coarse-grained groups.
+* **adress-site: (COM)** The mapping point from which the weight is calculated.
+
+ + **COM**
+ The weight is calculated from the center of mass of each charge group.
+
+ + **COG**
+ The weight is calculated from the center of geometry of each charge group.
+
+ + **Atom**
+ The weight is calculated from the position of 1st atom of each charge group.
+
+ + **AtomPerAtom**
+ The weight is calculated from the position of each individual atom.
+
+adress-interface-correction: (Off)
+: + **Off**
+ Do not a apply any interface correction.
+
+ + **thermoforce**
+ Apply thermodynamic force interface correction. The table can be specified using the `-tabletf` option of [mdrun]. The table should contain the potential and force (acting on molecules) as function of the distance from **adress-reference-coords**.
+
+adress-tf-grp-names
+: The names of the energy groups to which the **thermoforce** is applied if enabled in **adress-interface-correction**. If no group is given the default table is applied.
+
+adress-ex-forcecap: (0)
+: Cap the force in the hybrid region, useful for big molecules. 0 disables force capping.
+
+
+### User defined thingies
+
+user1-grps; user2-grps; userint1 (0); userint2 (0); userint3 (0); userint4 (0); userreal1 (0); userreal2 (0); userreal3 (0); userreal4 (0)
+: These you can use if you modify code. You can pass integers and reals to your subroutine. Check the inputrec definition in `src/include/types/inputrec.h`
--- /dev/null
+# Useful `mdrun` features #
+
+This section discusses features in `mdrun` that don't fit well
+elsewhere.
+
+## Re-running a simulation
+
+The rerun feature allows you to take a trajectory file in any
+supported format and compute quantities based upon the coordinates in
+that file using the model physics supplied in the `topol.tpr` file. It
+can be used with command lines like `mdrun -s topol -rerun
+traj.trr`. That [.tpr] could be different from the one that generated
+the trajectory. This can be used to compute the energy or forces for
+exactly the coordinates supplied as input, or to extract quantities
+based on subsets of the molecular system (see [gmx convert-tpr] and
+[gmx trjconv]).
+
+Neighbour searching is normally performed for every frame in the
+trajectory, since [mdrun] can no longer assume anything about how the
+structures were generated. If `nstlist` is zero, then only one
+neighbour list will be constructed. Naturally, no update or constraint
+algorithms are ever used.
+
+## Running a simulation in reproducible mode
+
+It is generally difficult to run an efficient parallel MD simulation
+that is based primarily on floating-point arithmetic and is fully
+reproducible. By default, [mdrun] will observe how things are going
+and vary how the simulation is conducted in order to optimize
+throughput. However, there is a "reproducible mode" available with
+`mdrun -reprod` that will systematically eliminate all sources of
+variation within that run; repeated invocations on the same input and
+hardware will be binary identical. However, running in this mode on
+different hardware, or with a different compiler, etc. will not be
+reproducible. This should normally only be used when investigating
+possible problems.
+
+## Running multi-simulations
+
+There are numerous situations where running a related set of
+simulations within the same invocation of mdrun are necessary or
+useful. Running a replica-exchange simulation requires it, as do
+simulations using ensemble-based distance or orientation restraints.
+Running a related series of lambda points for a free-energy
+computation is also convenient to do this way.
+
+This feature requires [configuring GROMACS with an external MPI
+library](install-guide.html#mpi-support) so that the set of
+simulations can communicate. The `n` simulations within the set can
+use internal MPI parallelism also, so that `mpirun -np x mdrun_mpi`
+for `x` a multiple of `n` will use `x/n` ranks per simulation.
+
+There are two ways of organizing files when running such
+simulations. Most of the normal mechanisms work in either case,
+including `-deffnm`.
+
+`-multidir`
+ You must create a set of `n` directories for the `n` simulations,
+ place all the relevant input files in those directories (e.g. named
+ `topol.tpr`), and run with `mpirun -np x mdrun_mpi -s topol
+ -multidir <names-of-directories>`. If the order of the simulations
+ within the multi-simulation is significant, then you are responsible
+ for ordering their names when you provide them to `-multidir`. Be
+ careful with shells that do filename globbing dictionary-style, e.g.
+ `dir1 dir10 dir11 ... dir2 ...`. This option is generally the
+ most convenient to use. `mdrun -table` for the group cutoff-scheme
+ works only in this mode.
+
+`-multi`
+ You must organize that the filenames for each simulation in a set of
+ `n` simulations have an integer `0` through `n-1` appended to
+ the filename (e.g. `topol2.tpr`), and run with `mpirun -np x mdrun
+ -multi n -s input`. The order of simulations within the set is
+ determined by the integer appended.
+
+### Examples running multi-simulations
+
+ mpirun -np 32 mdrun_mpi -multi
+
+Starts a multi-simulation on 32 ranks with as many simulations `n` as
+there are files named `topol*.tpr` for integers `0` to `n-1`. Other
+input and output files are suffixed similarly.
+
+ mpirun -np 32 mdrun_mpi -multidir a b c d
+
+Starts a multi-simulation on 32 ranks with 4 simulations. The input
+and output files are found in directories `a`, `b`, `c`, and `d`.
+
+ mpirun -np 32 mdrun_mpi -multidir a b c d -gpu_id 0000000011111111
+
+Starts the same multi-simulation as before. On a machine with two
+physical nodes and two GPUs per node, there will be 16 MPI ranks per
+node, and 8 MPI ranks per simulation. The 16 MPI ranks doing PP work
+on a node are mapped to the GPUs with IDs 0 and 1, even though they
+come from more than one simulation. They are mapped in the order
+indicated, so that the PP ranks from each simulation use a single
+GPU. However, the order `0101010101010101` could run faster.
+
+### Running replica-exchange simulations
+
+When running a multi-simulation, using `mdrun -replex n` means that a
+replica exchange is attempted every given number of steps. The number
+of replicas is set with the `-multi` or `-multidir` option, described
+above. All run input files should use a different value for the
+coupling parameter (e.g. temperature), which ascends over the set of
+input files. The random seed for replica exchange is set with
+`-reseed`. After every exchange, The velocities are scaled and
+neighbor searching is performed. See the Reference Manual for more
+details on how replica exchange functions in GROMACS.
--- /dev/null
+# Getting good performance from `mdrun` #
+
+The GROMACS build system and the `mdrun` tool has a lot of built-in
+and configurable intelligence to detect your hardware and make pretty
+effective use of that hardware. For a lot of casual and serious use of
+`mdrun`, the automatic machinery works well enough. But to get the
+most from your hardware to maximise your scientific quality, read on!
+
+## Hardware background information ##
+
+Modern computer hardware is complex and heterogeneous, so we need to
+discuss a little bit of background information and set up some
+definitions. Experienced HPC users can skip this section.
+
+core
+: A hardware compute unit that actually executes instructions. There
+ is normally more than one core in a processor, often many more.
+
+cache
+: A special kind of memory local to core(s) that is much faster to
+ access than main memory, kind of like the top of a human's desk,
+ compared to their filing cabinet. There are often several layers
+ of caches associated with a core.
+
+socket
+: A group of cores that share some kind of locality, such as a shared
+ cache. This makes it more efficient to spread computational work
+ over cores within a socket than over cores in different
+ sockets. Modern processors often have more than one socket.
+
+node
+: A group of sockets that share coarser-level locality, such as shared
+ access to the same memory without requiring any network
+ hardware. A normal laptop or desktop computer is a node. A node
+ is often the smallest amount of a large compute cluster that a
+ user can request to use.
+
+thread
+: A stream of instructions for a core to execute. There are
+ many different programming abstractions that create and manage
+ spreading computation over multiple threads, such as OpenMP,
+ pthreads, winthreads, CUDA, OpenCL, and OpenACC. Some kinds of
+ hardware can map more than one software thread to a core; on Intel
+ x86 processors this is called "hyper-threading." Normally,
+ `mdrun` will not benefit from such mapping.
+
+affinity
+: On some kinds of hardware, software threads can migrate
+ between cores to help automatically balance workload. Normally,
+ the performance of `mdrun` will degrade dramatically if this is
+ permitted, so `mdrun` will by default set the affinity of its
+ threads to their cores, unless the user or software environment
+ has already done so. Setting thread affinity is sometimes called
+ "pinning" threads to cores.
+
+MPI
+: The dominant multi-node parallelization-scheme, which
+ provides a standardized language in which programs can be
+ written that work across more than one node.
+
+rank
+: In MPI, a rank is the smallest grouping of hardware
+ used in the multi-node parallelization scheme. That grouping can
+ be controlled by the user, and might correspond to a core, a
+ socket, a node, or a group of nodes. The best choice varies with
+ the hardware, software and compute task. Sometimes an MPI rank is
+ called an MPI process.
+
+GPU
+: A graphics processing unit, which is often faster
+ and more efficient than conventional processors for particular
+ kinds of compute workloads. A GPU is always associated with a
+ particular node, and often a particular socket within that node.
+
+OpenMP
+: A standardized technique supported by many compilers
+ to share a compute workload over multiple cores. Often
+ combined with MPI to achieve hybrid MPI/OpenMP parallelism.
+
+CUDA
+: A programming-language extension developed by Nvidia
+ for use in writing code for their GPUs.
+
+SIMD
+: Modern CPU cores have instructions that can execute
+ large numbers of floating-point instructions in a single
+ cycle.
+
+
+## GROMACS background information ##
+
+The algorithms in `mdrun` and their implementations are most relevant
+when choosing how to make good use of the hardware. For details,
+see the Reference Manual. The most important of these are
+
+Domain Decomposition (DD)
+: This algorithm decomposes the (short-ranged) component of the
+ non-bonded interactions into domains that share spatial locality,
+ which permits efficient code to be written. Each domain handles
+ all of the particle-particle (PP) interactions for its members,
+ and is mapped to a single rank. Within a PP rank, OpenMP threads
+ can share the workload, or the work can be off-loaded to a
+ GPU. The PP rank also handles any bonded interactions for the
+ members of its domain. A GPU may perform work for more than one PP
+ rank, but it is normally most efficient to use a single PP rank
+ per GPU and for that rank to have thousands of atoms. When the
+ work of a PP rank is done on the CPU, mdrun will make extensive
+ use of the SIMD capabilities of the core. There are various
+ [command-line options](#controlling-the-domain-decomposition-algorithm)
+ to control the behaviour of the DD algorithm.
+
+Particle-mesh Ewald (PME)
+: This algorithm treats the long-ranged components of the non-bonded
+ interactions (Coulomb and/or Lennard-Jones). Either all, or just
+ a subset of ranks may participate in the work for computing
+ long-ranged component (often inaccurately called simple the "PME"
+ component). Because the algorithm uses a 3D FFT that requires
+ global communication, its performance gets worse as more ranks
+ participate, which can mean it is fastest to use just a subset of
+ ranks (e.g. one-quarter to one-half of the ranks). If there are
+ separate PME ranks, then the remaining ranks handle the PP
+ work. Otherwise, all ranks do both PP and PME work.
+
+## Running mdrun within a single node ##
+
+`mdrun` can be configured and compiled in several different ways that
+are efficient to use within a single node. The default configuration
+using a suitable compiler will deploy a multi-level hybrid parallelism
+that uses CUDA, OpenMP and the threading platform native to the
+hardware. For programming convenience, in GROMACS, those native
+threads are used to implement on a single node the same MPI scheme as
+would be used between nodes, but much more efficient; this is called
+thread-MPI. From a user's perspective, real MPI and thread-MPI look
+almost the same, and GROMACS refers to MPI ranks to mean either kind,
+except where noted. A real external MPI can be used for `mdrun` within
+a single node, but runs more slowly than the thread-MPI version.
+
+By default, `mdrun` will inspect the hardware available at run time
+and do its best to make fairly efficient use of the whole node. The
+log file, stdout and stderr are used to print diagnostics that
+inform the user about the choices made and possible consequences.
+
+A number of command-line parameters are available to vary the default
+behaviour.
+
+`-nt`
+: The total number of threads to use. The default, 0, will start as
+ many threads as available cores. Whether the threads are
+ thread-MPI ranks, or OpenMP threads within such ranks depends on
+ other settings.
+
+`-ntmpi`
+: The total number of thread-MPI ranks to use. The default, 0,
+ will start one rank per GPU (if present), and otherwise one rank
+ per core.
+
+`-ntomp`
+: The total number of OpenMP threads per rank to start. The
+ default, 0, will start one thread on each available core.
+ Alternatively, mdrun will honour the appropriate system
+ environment variable (e.g. `OMP_NUM_THREADS`) if set.
+
+`-npme`
+: The total number of ranks to dedicate to the long-ranged
+ component of PME, if used. The default, -1, will dedicate ranks
+ only if the total number of threads is at least 12, and will use
+ around one-third of the ranks for the long-ranged component.
+
+`-ntomp_pme`
+: When using PME with separate PME ranks,
+ the total number of OpenMP threads per separate PME ranks.
+ The default, 0, copies the value from `-ntomp`.
+
+`-gpu_id`
+: A string that specifies the ID numbers of the GPUs to be
+ used by corresponding PP ranks on this node. For example,
+ "0011" specifies that the lowest two PP ranks use GPU 0,
+ and the other two use GPU 1.
+
+`-pin`
+: Can be set to "auto," "on" or "off" to control whether
+ mdrun will attempt to set the affinity of threads to cores.
+ Defaults to "auto," which means that if mdrun detects that all the
+ cores on the node are being used for mdrun, then it should behave
+ like "on," and attempt to set the affinities (unless they are
+ already set by something else).
+
+`-pinoffset`
+: If `-pin on`, specifies the logical core number to
+ which mdrun should pin the first thread. When running more than
+ one instance of mdrun on a node, use this option to to avoid
+ pinning threads from different mdrun instances to the same core.
+
+`-pinstride`
+: If `-pin on`, specifies the stride in logical core
+ numbers for the cores to which mdrun should pin its threads. When
+ running more than one instance of mdrun on a node, use this option
+ to to avoid pinning threads from different mdrun instances to the
+ same core. Use the default, 0, to minimize the number of threads
+ per physical core - this lets mdrun manage the hardware-, OS- and
+ configuration-specific details of how to map logical cores to
+ physical cores.
+
+`-ddorder`
+: Can be set to "interleave," "pp_pme" or "cartesian."
+ Defaults to "interleave," which means that any separate PME ranks
+ will be mapped to MPI ranks in an order like PP, PP, PME, PP, PP,
+ PME, ... etc. This generally makes the best use of the available
+ hardware. "pp_pme" maps all PP ranks first, then all PME
+ ranks. "cartesian" is a special-purpose mapping generally useful
+ only on special torus networks with accelerated global
+ communication for Cartesian communicators. Has no effect if there
+ are no separate PME ranks.
+
+`-nb`
+: Can be set to "auto", "cpu", "gpu", "cpu_gpu."
+ Defaults to "auto," which uses a compatible GPU if available.
+ Setting "cpu" requires that no GPU is used. Setting "gpu" requires
+ that a compatible GPU be available and will be used. Setting
+ "cpu_gpu" permits the CPU to execute a GPU-like code path, which
+ will run slowly on the CPU and should only be used for debugging.
+
+### Examples for mdrun on one node
+
+ mdrun
+Starts mdrun using all the available resources. mdrun
+will automatically choose a fairly efficient division
+into thread-MPI ranks, OpenMP threads and assign work
+to compatible GPUs. Details will vary with hardware
+and the kind of simulation being run.
+
+ mdrun -nt 8
+Starts mdrun using 8 threads, which might be thread-MPI
+or OpenMP threads depending on hardware and the kind
+of simulation being run.
+
+ mdrun -ntmpi 2 -ntomp 4
+Starts mdrun using eight total threads, with four thread-MPI
+ranks and two OpenMP threads per core. You should only use
+these options when seeking optimal performance, and
+must take care that the ranks you create can have
+all of their OpenMP threads run on the same socket.
+The number of ranks must be a multiple of the number of
+sockets, and the number of cores per node must be
+a multiple of the number of threads per rank.
+
+ mdrun -gpu_id 12
+Starts mdrun using GPUs with IDs 1 and 2 (e.g. because
+GPU 0 is dedicated to running a display). This requires
+two thread-MPI ranks, and will split the available
+CPU cores between them using OpenMP threads.
+
+ mdrun -ntmpi 4 -gpu_id "1122"
+Starts mdrun using four thread-MPI ranks, and maps them
+to GPUs with IDs 1 and 2. The CPU cores available will
+be split evenly between the ranks using OpenMP threads.
+
+ mdrun -nt 6 -pin on -pinoffset 0
+ mdrun -nt 6 -pin on -pinoffset 3
+Starts two mdrun processes, each with six total threads.
+Threads will have their affinities set to particular
+logical cores, beginning from the logical core
+with rank 0 or 3, respectively. The above would work
+well on an Intel CPU with six physical cores and
+hyper-threading enabled. Use this kind of setup only
+if restricting mdrun to a subset of cores to share a
+node with other processes.
+
+ mpirun_mpi -np 2
+When using an `mdrun_mpi` compiled with external MPI,
+this will start two ranks and as many OpenMP threads
+as the hardware and MPI setup will permit. If the
+MPI setup is restricted to one node, then the resulting
+`mdrun_mpi` will be local to that node.
+
+## Running mdrun on more than one node ##
+
+This requires configuring GROMACS to build with an external MPI
+library. By default, this mdrun executable will be named
+`mdrun_mpi`. All of the considerations for running single-node
+mdrun still apply, except that `-ntmpi` and `-nt` cause a fatal
+error, and instead the number of ranks is controlled by the
+MPI environment.
+Settings such as `-npme` are much more important when
+using multiple nodes. Configuring the MPI environment to
+produce one rank per core is generally good until one
+approaches the strong-scaling limit. At that point, using
+OpenMP to spread the work of an MPI rank over more than one
+core is needed to continue to improve absolute performance.
+The location of the scaling limit depends on the processor,
+presence of GPUs, network, and simulation algorithm, but
+it is worth measuring at around ~200 atoms/core if you
+need maximum throughput.
+
+There are further command-line parameters that are relevant in these
+cases.
+
+`-tunepme`
+: If "on," will optimize various aspects of the PME
+ and DD algorithms, shifting load between ranks and/or
+ GPUs to maximize throughput
+
+`-gcom`
+: Can be used to limit global communication every n steps. This can
+ improve performance for highly parallel simulations where this global
+ communication step becomes the bottleneck. For a global thermostat
+ and/or barostat, the temperature and/or pressure will also only be
+ updated every `-gcom` steps. By default, it is set to the
+ minimum of `nstcalcenergy` and `nstlist`.
+
+The [gmx tune_pme] utility is available to search a wider
+range of parameter space, including making safe
+modifications to the [.tpr] file, and varying `-npme`.
+It is only aware of the number of ranks created by
+the MPI environment, and does not explicitly manage
+any aspect of OpenMP during the optimization.
+
+### Examples for mdrun on more than one node ##
+
+The examples and explanations for for single-node mdrun are
+still relevant, but `-nt` is no longer the way
+to choose the number of MPI ranks.
+
+ mpirun -np 16 mdrun_mpi
+Starts `mdrun_mpi` with 16 ranks, which are mapped to
+the hardware by the MPI library, e.g. as specified
+in an MPI hostfile. The available cores will be
+automatically split among ranks using OpenMP threads,
+depending on the hardware and any environment settings
+such as `OMP_NUM_THREADS`.
+
+ mpirun -np 16 mdrun_mpi -npme 5
+Starts `mdrun_mpi` with 16 ranks, as above, and
+require that 5 of them are dedicated to the PME
+component.
+
+ mpirun -np 11 mdrun_mpi -ntomp 2 -npme 6 -ntomp_pme 1
+Starts `mdrun_mpi` with 11 ranks, as above, and
+require that six of them are dedicated to the PME
+component with one OpenMP thread each. The remaining
+five do the PP component, with two OpenMP threads
+each.
+
+ mpirun -np 4 mdrun -ntomp 6 -gpu_id 00
+Starts `mdrun_mpi` on a machine with two nodes, using
+four total ranks, each rank with six OpenMP threads,
+and both ranks on a node sharing GPU with ID 0.
+
+ mpirun -np 8 mdrun -ntomp 3 -gpu_id 0000
+Starts `mdrun_mpi` on a machine with two nodes, using
+eight total ranks, each rank with three OpenMP threads,
+and all four ranks on a node sharing GPU with ID 0.
+This may or may not be faster than the previous setup
+on the same hardware.
+
+ mpirun -np 20 mdrun_mpi -ntomp 4 -gpu_id 0
+Starts `mdrun_mpi` with 20 ranks, and assigns the CPU cores evenly
+across ranks each to one OpenMP thread. This setup is likely to be
+suitable when there are ten nodes, each with one GPU, and each node
+has two sockets.
+
+ mpirun -np 20 mdrun_mpi -gpu_id 00
+Starts `mdrun_mpi` with 20 ranks, and assigns the CPU cores evenly
+across ranks each to one OpenMP thread. This setup is likely to be
+suitable when there are ten nodes, each with one GPU, and each node
+has two sockets.
+
+ mpirun -np 20 mdrun_mpi -gpu_id 01
+Starts `mdrun_mpi` with 20 ranks. This setup is likely
+to be suitable when there are ten nodes, each with two
+GPUs.
+
+ mpirun -np 40 mdrun_mpi -gpu_id 0011
+Starts `mdrun_mpi` with 40 ranks. This setup is likely
+to be suitable when there are ten nodes, each with two
+GPUs, and OpenMP performs poorly on the hardware.
+
+## Controlling the domain decomposition algorithm
+
+This section lists all the options that affect how the domain
+decomposition algorithm decomposes the workload to the available
+parallel hardware.
+
+`-rdd`
+: Can be used to set the required maximum distance for inter
+ charge-group bonded interactions. Communication for two-body
+ bonded interactions below the non-bonded cut-off distance always
+ comes for free with the non-bonded communication. Atoms beyond
+ the non-bonded cut-off are only communicated when they have
+ missing bonded interactions; this means that the extra cost is
+ minor and nearly indepedent of the value of `-rdd`. With dynamic
+ load balancing, option `-rdd` also sets the lower limit for the
+ domain decomposition cell sizes. By default `-rdd` is determined
+ by [mdrun] based on the initial coordinates. The chosen value will
+ be a balance between interaction range and communication cost.
+
+`-ddcheck`
+: On by default. When inter charge-group bonded interactions are
+ beyond the bonded cut-off distance, [mdrun] terminates with an
+ error message. For pair interactions and tabulated bonds that do
+ not generate exclusions, this check can be turned off with the
+ option `-noddcheck`.
+
+`-rcon`
+: When constraints are present, option `-rcon` influences
+ the cell size limit as well.
+ Atoms connected by NC constraints, where NC is the LINCS order
+ plus 1, should not be beyond the smallest cell size. A error
+ message is generated when this happens, and the user should change
+ the decomposition or decrease the LINCS order and increase the
+ number of LINCS iterations. By default [mdrun] estimates the
+ minimum cell size required for P-LINCS in a conservative
+ fashion. For high parallelization, it can be useful to set the
+ distance required for P-LINCS with `-rcon`.
+
+`-dds`
+: Sets the minimum allowed x, y and/or z scaling of the cells with
+ dynamic load balancing. [mdrun] will ensure that the cells can
+ scale down by at least this factor. This option is used for the
+ automated spatial decomposition (when not using `-dd`) as well as
+ for determining the number of grid pulses, which in turn sets the
+ minimum allowed cell size. Under certain circumstances the value
+ of `-dds` might need to be adjusted to account for high or low
+ spatial inhomogeneity of the system.
+
+## Finding out how to run mdrun better
+
+TODO In future patch: red flags in log files, how to interpret wallcycle output
+
+TODO In future patch: import wiki page stuff on performance checklist; maybe here,
+maybe elsewhere
+
+## Running mdrun with GPUs
+
+TODO In future patch: any tips not covered above
--- /dev/null
+[/a/]: # (TODO when we decide on file formats and generation engine, resolve whether generating these should be automated, or whatever)
+
+[gmx bar]: programs/gmx-bar.html
+[gmx energy]: programs/gmx-energy.html
+[gmx convert-tpr]: programs/gmx-convert-tpr.html
+[gmx trjconv]: programs/gmx-trjconv.html
+[gmx dipoles]: programs/gmx-dipoles.html
+[gmx tune_pme]: programs/gmx-tune_pme.html
+[gmx do_dssp]: programs/gmx-do_dssp.html
+[gmx view]: programs/gmx-view.html
+[gmx eneconv]: programs/gmx-eneconv.html
+[gmx wham]: programs/gmx-wham.html
+[gmx grompp]: programs/gmx-grompp.html
+[gmx solvate]: programs/gmx-solvate.html
+[gmx editconf]: programs/gmx-editconf.html
+[gmx pdb2gmx]: programs/gmx-pdb2gmx.html
+[gmx mdrun]: programs/gmx-mdrun.html
+[mdrun]: programs/gmx-mdrun.html
+[trjcat]: programs/gmx-trjcat.html
+[eneconv]: programs/gmx-eneconv.html
+
+[pdb]: online/pdb.html
+[.pdb]: online/pdb.html
+[.gro]: online/gro.html
+[.top]: online/top.html
+[.cpt]: online/cpt.html
+[.trr]: online/trr.html
+[.xtc]: online/xtc.html
+[.tng]: online/tng.html
+[.tpr]: online/tpr.html
+[.ndx]: online/ndx.html
+[.mdp]: online/mdp.html
+
+[wwwpage]: http://www.gromacs.org
+[install guide]: install-guide.html
+[reference manual]: manual-@PROJECT_VERSION@.pdf
--- /dev/null
+# Command-line tools in GROMACS
+
+GROMACS includes many tools for preparing, running and analysing
+molecular dynamics simulations. These are all structured as part of
+the `gmx` binary, and invoked with commands like `gmx grompp`.
+[mdrun] is the only other binary that [can be
+built](install-guide.html#building-only-mdrun), but even it can be run
+with `gmx mdrun`. Documentation for these can be found at the links
+below.
+
+* Tools documentation [by name](programs/byname.html)
+* Tools documentation [by topic](programs/bytopic.html)
+
+## Common options and behaviour of GROMACS tools
+
+Optional files are not used unless the option is set, in contrast to
+non optional files, where the default file name is used when the
+option is not set.
+
+All GROMACS tools will accept file options without a file extension
+or filename being specified. In such cases the default filenames will
+be used. With multiple input file types, such as generic structure
+format, the directory will be searched for files of each type with the
+supplied or default name. When no such file is found, or with output
+files the first file type will be used.
+
+All GROMACS tools with the exception of [mdrun], [trjcat] and
+[eneconv] check if the command line options are valid. If this is not
+the case, the program will be halted.
+
+All GROMACS tools have 4 hidden options:
+
+ option type default description
+------------- ---- ------- ------------------
+`-[no]hidden` bool [`yes`] [hidden] Print description for hidden options
+`-[no]quiet` bool [` no`] [hidden] Do not print help info
+`-[no]debug` bool [` no`] [hidden] Write file with debug information
+
+Many tools accept enumerated options (enum), which should be used with
+one of the arguments listed in the option description. The argument
+may be abbreviated, and the first match to the shortest argument in
+the list will be selected.
+
+Many tools also use options that may accept a vector of values. Either
+1 or 3 parameters can be supplied; when only one parameter is supplied
+the two other values are also set to this value.
+
+All GROMACS tools can read compressed (`*.Z`) or g-zipped (`*.gz`)
+files. There might be a problem with reading compressed [.tng] or
+[.xtc] files, but these will not compress very well anyway.
+
+Most GROMACS tools can process a trajectory with fewer atoms than the
+run input or structure file, but only if the trajectory consists of
+the first n atoms of the run input or structure file.
+
+
GMXLDLIB=${GMXPREFIX}/@LIB_INSTALL_DIR@
GMXMAN=${GMXPREFIX}/@MAN_INSTALL_DIR@
GMXDATA=${GMXPREFIX}/@DATA_INSTALL_DIR@
+GROMACS_DIR=${GMXPREFIX}
LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH:+:}${LD_LIBRARY_PATH}
PKG_CONFIG_PATH=${GMXLDLIB}/pkgconfig${PKG_CONFIG_PATH:+:}${PKG_CONFIG_PATH}
MANPATH=${GMXMAN}:${MANPATH}
# export should be separate, so /bin/sh understands it
-export GMXBIN GMXLDLIB GMXMAN GMXDATA LD_LIBRARY_PATH PATH MANPATH PKG_CONFIG_PATH
+export GMXBIN GMXLDLIB GMXMAN GMXDATA LD_LIBRARY_PATH PATH MANPATH
+export PKG_CONFIG_PATH GROMACS_DIR
IFS="$old_IFS"
unset old_IFS
setenv GMXLDLIB ${GMXPREFIX}/@LIB_INSTALL_DIR@
setenv GMXMAN ${GMXPREFIX}/@MAN_INSTALL_DIR@
setenv GMXDATA ${GMXPREFIX}/@DATA_INSTALL_DIR@
+setenv GROMACS_DIR ${GMXPREFIX}
#make them begin with :
if ($?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ":${LD_LIBRARY_PATH}"
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2011,2012, by the GROMACS development team, led by
+# Copyright (c) 2011,2012,2014, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
DESTINATION ${DATA_INSTALL_DIR}/template
COMPONENT development)
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindGROMACS.cmakein
- ${CMAKE_CURRENT_BINARY_DIR}/cmake/FindGROMACS.cmake @ONLY)
-
-install(FILES ${CMAKE_CURRENT_BINARY_DIR}/cmake/FindGROMACS.cmake
+install(FILES cmake/FindGROMACS.cmake
DESTINATION ${DATA_INSTALL_DIR}/template/cmake
COMPONENT development)
-
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 2.8.8)
-project(template)
+project(template CXX)
-# Cmake modules/macros are in a subdirectory to keep this file cleaner
-set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
-
-if(NOT CMAKE_BUILD_TYPE)
+if (NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel." FORCE)
-endif(NOT CMAKE_BUILD_TYPE)
+endif()
-option(GMX_DOUBLE "Use double precision" OFF)
+# CMake modules are in a subdirectory to keep this file cleaner
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
-########################################################################
-# Fix stupid flags on MSVC
-########################################################################
-IF(CMAKE_GENERATOR MATCHES "Visual Studio")
- STRING(REPLACE /MD /MT CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE})
- SET(CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE} CACHE STRING "" FORCE)
- STRING(REPLACE /MD /MT CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG})
- SET(CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG} CACHE STRING "" FORCE)
-ENDIF(CMAKE_GENERATOR MATCHES "Visual Studio")
-
-########################################################################
-# Basic system tests (standard libraries, headers, functions, types) #
-########################################################################
-
-if (GMX_DOUBLE)
- set(LIBGROMACS "libgromacs_d")
-else(GMX_DOUBLE)
- set(LIBGROMACS "libgromacs")
-endif(GMX_DOUBLE)
-
-FIND_PACKAGE(GROMACS COMPONENTS ${LIBGROMACS} REQUIRED)
-message("GROMACS version ${GROMACS_VERSION_STRING} found")
-if ("${GROMACS_VERSION_STRING}" VERSION_LESS "5.0")
- message(FATAL_ERROR "This template works with GROMACS 5.0 (and possibly later versions)")
+# In principle, this could be deduced from GROMACS_IS_DOUBLE returned by
+# find_package(GROMACS) based on the suffix alone, but it is clearer that the
+# user explicitly sets what they want to get, and then need to provide a suffix
+# to match.
+option(GMX_DOUBLE "Use double precision" OFF)
+set(GMX_SUFFIX "" CACHE STRING "Suffix for the GROMACS installation to use (empty for default)")
+
+# This does not allow for a non-suffixed double-precision libgromacs, but
+# that should be rare enough for demonstration purposes.
+if (GMX_DOUBLE AND NOT GMX_SUFFIX)
+ set(GROMACS_SUFFIX "_d")
+else()
+ set(GROMACS_SUFFIX ${GMX_SUFFIX})
endif()
-add_definitions( ${GROMACS_DEFINITIONS} )
-include_directories( ${GROMACS_INCLUDE_DIRS} )
+find_package(GROMACS 5.1 REQUIRED)
+gromacs_check_double(GMX_DOUBLE)
+gromacs_check_compiler(CXX)
+include_directories(${GROMACS_INCLUDE_DIRS})
+add_definitions(${GROMACS_DEFINITIONS})
+
+# Use static linking on MSVC
+if (CMAKE_GENERATOR MATCHES "Visual Studio")
+ string(REPLACE /MD /MT CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE})
+ set(CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE} CACHE STRING "" FORCE)
+ string(REPLACE /MD /MT CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG})
+ set(CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG} CACHE STRING "" FORCE)
+endif()
add_executable(template template.cpp)
target_link_libraries(template ${GROMACS_LIBRARIES})
Once installed, this directory contains CMakelist.txt,
Makefile.pkg and a small program that you could use as
a template when writing your own analysis software.
+Further explanation for the template code can be found
+in the Doxygen documentation (link to the latest development
+version):
+ <http://jenkins.gromacs.org/job/Documentation_Gerrit_Nightly/javadoc/doxygen/html-user/page_analysistemplate.xhtml>
The CMakelist.txt can be used together with cmake to
build the template program:
to find a particular GROMACS installation.
The Makefile.pkg can be used if cmake is unavailable. It
-makes use of pkg-config only to build the template program:
+makes use of pkg-config to build the template program:
$ source /path/to/GMXRC
$ make -f Makefile.pkg
You will need to make sure that you use a sufficiently similar C++
compiler and C++ Standard Library as the one that was used for
-compiling GROMACS, preferably the same one. If you used any system
-libraries (e.g. Boost, FFTW, BLAS, LAPACK) when installing GROMACS,
-then you will need make them available to the template build system
-also. The easiest way to do this is to have pkg-config installed on
-your system, and to source GMXRC from the GROMACS installation before
-you attempt to configure the template. A subset of Boost is supposed
-to be installed with GROMACS, but currently the automatic machinery
-does not detect that installation, so you may need to install Boost
-(headers only) in order to use the GROMACS template program.
-
-If the compiler used for GROMACS was capable of some C++11 features
-then, by default, those will be required for compiling the
-template. To make that work, you can either configure GROMACS with
-$ cmake -DGMX_CXX11=off
-or configure the template with the appropriate
-$ cmake -DCMAKE_CXX_FLAGS="-flag-for-your-compiler"
-You can find out the necessary flags from your compiler's documentation,
-or by inspecting the src/buildinfo.h file in the GROMACS build tree.
+compiling GROMACS, preferably the same one. Boost headers used to
+compile GROMACS are also required, and are automatically added to
+the include path by both of the above build systems.
+See the Doxygen documentation for using GROMACS as a library for
+more details about the build system used to build the template, as
+well as its limitations (link to the latest development version):
+ <http://jenkins.gromacs.org/job/Documentation_Gerrit_Nightly/javadoc/doxygen/html-user/page_usinglibrary.xhtml>
----------------------------------------------------------
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+# This file should remain version-agnostic, with all things specific to a
+# particular GROMACS version remaining in the package configuration files.
+# This find module only provides some convenience functionality to manage the
+# suffixes etc.
+# That should allow using the same FindGROMACS.cmake file with multiple
+# different GROMACS installations on the same machine.
+
+# Propagate all flags passed to parent find_package() to the config call below.
+set(_gmx_find_args "")
+if (GROMACS_FIND_VERSION)
+ if (GROMACS_FIND_VERSION VERSION_LESS "5.1")
+ message(FATAL_ERROR
+ "This version of FindGROMACS.cmake requires GROMACS-provided "
+ "package configuration files, and only works to find "
+ "GROMACS 5.1 or later.")
+ endif()
+ list(APPEND _gmx_find_args ${GROMACS_FIND_VERSION})
+ if (GROMACS_FIND_VERSION_EXACT)
+ list(APPEND _gmx_find_args EXACT)
+ endif()
+endif()
+if (GROMACS_FIND_REQUIRED)
+ list(APPEND _gmx_find_args REQUIRED)
+endif()
+if (GROMACS_FIND_QUIETLY)
+ list(APPEND _gmx_find_args QUIET)
+endif()
+
+# Determine the actual name of the package configuration files.
+set(_gmx_pkg_name gromacs)
+if (DEFINED GROMACS_SUFFIX)
+ set(_gmx_pkg_name gromacs${GROMACS_SUFFIX})
+endif()
+# Delegate all the actual work to the package configuration files.
+# The CONFIGS option is not really necessary, but provides a bit better error
+# messages, since we actually know what the config file should be called.
+find_package(GROMACS ${_gmx_find_args} CONFIG
+ NAMES ${_gmx_pkg_name}
+ CONFIGS ${_gmx_pkg_name}-config.cmake)
+unset(_gmx_find_args)
+unset(_gmx_pkg_name)
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2009-2011, by the VOTCA Development Team (http://www.votca.org).
-# Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public License
-# as published by the Free Software Foundation; either version 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-# - Finds parts of GROMACS
-# Find the native GROMACS components headers and libraries.
-#
-# GROMACS_INCLUDE_DIRS - where to find GROMACS headers.
-# GROMACS_LIBRARIES - List of libraries when used by GROMACS.
-# GROMACS_FOUND - True if all GROMACS components were found.
-# GROMACS_DEFINITIONS - Extra definies needed by GROMACS
-# GROMACS_PKG - The name of the pkg-config package needed
-# GROMACS_VERSION - GROMACS lib interface version
-# GROMACS_MAJOR_VERSION - GROMACS lib interface major version
-# GROMACS_MINOR_VERSION - GROMACS lib interface minor version
-# GROMACS_PATCH_LEVEL - GROMACS lib interface patch level
-# GROMACS_VERSION_STRING - GROMACS lib interface version string (e.g. "4.5.3")
-#
-
-find_package(PkgConfig)
-list(LENGTH GROMACS_FIND_COMPONENTS GROMACS_NUM_COMPONENTS_WANTED)
-if(${GROMACS_NUM_COMPONENTS_WANTED} LESS 1)
- message(FATAL_ERROR "find_package(GROMACS) needs to be supplied with the name of a GROMACS component for which it can search")
-elseif(${GROMACS_NUM_COMPONENTS_WANTED} GREATER 1)
- message(FATAL_ERROR "We only support finding one GROMACS component at this point, go and implement it ;-)")
-elseif(${GROMACS_FIND_COMPONENTS} MATCHES "^lib(gmx|gromacs)(_d)?$")
- set(GROMACS_PKG "${GROMACS_FIND_COMPONENTS}")
- string(REGEX REPLACE "^lib(.*)" "\\1" GROMACS_LIBRARY_NAME "${GROMACS_PKG}")
-else()
- message(FATAL_ERROR "We do not support finding ${GROMACS_FIND_COMPONENTS}, go and implement it ;-)")
-endif()
-
-if(GMX_DOUBLE AND NOT "${GROMACS_PKG}" MATCHES "_d$")
- message(FATAL_ERROR "GMX_DOUBLE was true, but I was asked to find ${GROMACS_PKG} (without _d at the end) - illogical!")
-endif(GMX_DOUBLE AND NOT "${GROMACS_PKG}" MATCHES "_d$")
-if(NOT GMX_DOUBLE AND "${GROMACS_PKG}" MATCHES "_d$")
- message(FATAL_ERROR "GMX_DOUBLE was false, but I was asked to find ${GROMACS_PKG} (with _d at the end) - illogical!")
-endif(NOT GMX_DOUBLE AND "${GROMACS_PKG}" MATCHES "_d$")
-
-pkg_check_modules(PC_GROMACS ${GROMACS_PKG})
-if (GMX_DOUBLE)
- list(APPEND GMX_DEFS "-DGMX_DOUBLE")
-endif(GMX_DOUBLE)
-if (PC_GROMACS_CFLAGS_OTHER)
- foreach(DEF ${PC_GROMACS_CFLAGS_OTHER})
- if (${DEF} MATCHES "^-D")
- list(APPEND GMX_DEFS ${DEF})
- endif (${DEF} MATCHES "^-D")
- endforeach(DEF)
- list(REMOVE_DUPLICATES GMX_DEFS)
-endif (PC_GROMACS_CFLAGS_OTHER)
-set(GROMACS_DEFINITIONS "${GMX_DEFS}" CACHE STRING "extra GROMACS definitions")
-
-find_library(GROMACS_LIBRARY NAMES ${GROMACS_LIBRARY_NAME}
- HINTS ${PC_GROMACS_LIBRARY_DIRS} @CMAKE_INSTALL_PREFIX@/@LIB_INSTALL_DIR@)
-if (GROMACS_LIBRARY)
- if("${GROMACS_LIBRARY}" MATCHES "lib(gmx|gromacs)[^;]*\\.a")
- if(PC_GROMACS_LIBRARIES)
- list(REMOVE_ITEM PC_GROMACS_LIBRARIES ${GROMACS_LIBRARY_NAME})
- foreach (LIB ${PC_GROMACS_LIBRARIES})
- find_library(GROMACS_${LIB} NAMES ${LIB}
- HINTS ${PC_GROMACS_LIBRARY_DIRS} @CMAKE_INSTALL_PREFIX@/@LIB_INSTALL_DIR@)
- list(APPEND GMX_DEP_LIBRARIES ${GROMACS_${LIB}})
- unset(GROMACS_${LIB} CACHE)
- endforeach(LIB)
- endif(PC_GROMACS_LIBRARIES)
- if(PC_GROMACS_CFLAGS_OTHER)
- foreach(LIB ${PC_GROMACS_CFLAGS_OTHER})
- if (${LIB} MATCHES "thread")
- find_package(Threads REQUIRED)
- list(APPEND GMX_DEP_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
- endif (${LIB} MATCHES "thread")
- endforeach(LIB)
- endif(PC_GROMACS_CFLAGS_OTHER)
- set(GROMACS_DEP_LIBRARIES "${GMX_DEP_LIBRARIES}" CACHE FILEPATH "GROMACS depency libs (only needed for static (.a) ${GROMACS_LIBRARY}")
- endif("${GROMACS_LIBRARY}" MATCHES "lib(gmx|gromacs)[^;]*\\.a")
- include(CheckLibraryExists)
- check_library_exists("${GROMACS_LIBRARY};${GROMACS_DEP_LIBRARIES}" GromacsVersion "" FOUND_GROMACS_VERSION)
- if(NOT FOUND_GROMACS_VERSION)
- message(FATAL_ERROR "Could not find GromacsVersion in ${GROMACS_LIBRARY};${GROMACS_DEP_LIBRARIES}, take look at the error message in ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log to find out what was going wrong. If you don't have pkg-config installed you will most likely have to set GROMACS_LIBRARY and GROMACS_DEP_LIBRARY by hand which sets the GROMACS lib and its depencies (e.g. -DGROMACS_LIBRARY='/path/to/libgmx.so' -DGROMACS_DEP_LIBRARIES='/path/to/libblas.so;/path/to/libm.so') !")
- endif(NOT FOUND_GROMACS_VERSION)
- check_library_exists("${GROMACS_LIBRARY};${GROMACS_DEP_LIBRARIES}" init_mtop "" FOUND_GROMACS_INIT_MTOP)
- if(NOT FOUND_GROMACS_INIT_MTOP)
- message(FATAL_ERROR "Could not find init_mtop in the GROMACS library, take look at the error message in ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log to find out what was going wrong. This most likely means that your GROMACS version is too old, we need at least GROMACS 4.0.7.")
- endif(NOT FOUND_GROMACS_INIT_MTOP)
- set(GROMACS_VERSION 40000)
- check_library_exists("${GROMACS_LIBRARY};${GROMACS_DEP_LIBRARIES}" output_env_done "" FOUND_GROMACS_OUTPUT_ENV_DONE)
- if(FOUND_GROMACS_OUTPUT_ENV_DONE)
- set(GROMACS_VERSION 40500)
- endif(FOUND_GROMACS_OUTPUT_ENV_DONE)
- check_library_exists("${GROMACS_LIBRARY};${GROMACS_DEP_LIBRARIES}" gmx_nonbonded_setup "" FOUND_GROMACS_GMX_NONBONDED_SETUP)
- if(FOUND_GROMACS_GMX_NONBONDED_SETUP)
- set(GROMACS_VERSION 40600)
- endif(FOUND_GROMACS_GMX_NONBONDED_SETUP)
- check_library_exists("${GROMACS_LIBRARY};${GROMACS_DEP_LIBRARIES}" init_domdec_vsites "" FOUND_GROMACS_INIT_DOMDEC_VSITES)
- if(FOUND_GROMACS_INIT_DOMDEC_VSITES)
- set(GROMACS_VERSION 50000)
- endif(FOUND_GROMACS_INIT_DOMDEC_VSITES)
- set(GROMACS_VERSION ${GROMACS_VERSION} CACHE STRING "GROMACS lib interface version")
-else(GROMACS_LIBRARY)
- set(GROMACS_VERSION 40500)
-endif (GROMACS_LIBRARY)
-
-math(EXPR GROMACS_MAJOR_VERSION "${GROMACS_VERSION} / 10000")
-math(EXPR GROMACS_MINOR_VERSION "${GROMACS_VERSION} / 100 % 100")
-math(EXPR GROMACS_PATCH_LEVEL "${GROMACS_VERSION} % 100")
-set(GROMACS_VERSION_STRING "${GROMACS_MAJOR_VERSION}.${GROMACS_MINOR_VERSION}.${GROMACS_PATCH_LEVEL}")
-
-if ("${GROMACS_PKG}" MATCHES "libgmx")
- if (${GROMACS_VERSION} EQUAL 40000)
- find_path(GROMACS_INCLUDE_DIR tpxio.h HINTS ${PC_GROMACS_INCLUDE_DIRS} @CMAKE_INSTALL_PREFIX@/@INCL_INSTALL_DIR@)
- else(${GROMACS_VERSION} EQUAL 40000)
- find_path(GROMACS_INCLUDE_DIR gromacs/tpxio.h HINTS ${PC_GROMACS_INCLUDE_DIRS} @CMAKE_INSTALL_PREFIX@/@INCL_INSTALL_DIR@)
- endif(${GROMACS_VERSION} EQUAL 40000)
-elseif("${GROMACS_PKG}" MATCHES "libgromacs")
- find_path(GROMACS_INCLUDE_DIR gromacs/version.h HINTS ${PC_GROMACS_INCLUDE_DIRS} @CMAKE_INSTALL_PREFIX@/@INCL_INSTALL_DIR@)
-endif("${GROMACS_PKG}" MATCHES "libgmx")
-
-set(GROMACS_LIBRARIES "${GROMACS_LIBRARY};${GROMACS_DEP_LIBRARIES}" )
-set(GROMACS_INCLUDE_DIRS ${GROMACS_INCLUDE_DIR} )
-if (PC_GROMACS_INCLUDE_DIRS)
- list(APPEND GROMACS_INCLUDE_DIRS ${PC_GROMACS_INCLUDE_DIRS})
-endif(PC_GROMACS_INCLUDE_DIRS)
-
-if(NOT ${GROMACS_MAJOR_VERSION} LESS 5)
- include(CheckIncludeFile)
- # Let find_package find the subset of Boost installed with
- # GROMACS, by appending the relevant subdirectory, unless
- # pkg-config already took care of it.
- if(PC_GROMACS_INCLUDE_DIRS)
- set(BOOST_INCLUDEDIR ${GROMACS_INCLUDE_DIRS})
- else()
- set(BOOST_INCLUDEDIR ${GROMACS_INCLUDE_DIRS}/gromacs/external/boost)
- endif()
- find_package(Boost 1.44.0 REQUIRED)
- if(Boost_FOUND)
- list(APPEND GROMACS_INCLUDE_DIRS ${Boost_INCLUDE_DIRS})
- else()
- message(FATAL_ERROR "Boost not found, compiling the GROMACS template will not work")
- endif()
-endif()
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set GROMACS_FOUND to TRUE
-# if all listed variables are TRUE
-find_package_handle_standard_args(GROMACS DEFAULT_MSG GROMACS_LIBRARY GROMACS_INCLUDE_DIR)
-
-mark_as_advanced(GROMACS_INCLUDE_DIR GROMACS_LIBRARY GROMACS_DEFINITIONS GROMACS_PKG GROMACS_VERSION GROMACS_DEP_LIBRARIES)
-413
+525
If You Want Something Done You Have to Do It Yourself_(Highlander II)
I Live the Life They Wish They Did_(Tricky)
Jesus Built My Hotrod_(Ministry)
It was something to at least have a choice of nightmares_(Joseph Conrad)
You fight, work, sweat, nearly kill yourself, sometimes you do kill yourself, trying to accomplish something - and you can't._(Joseph Conrad)
And after some more talk we agreed that the wisdom of rats had been grossly overrated, being in fact no greater than that of men_(Joseph Conrad)
+It's an easy game, just don't let the ball past!_(Szilard Pall)
The soul? There's nothing but chemistry here_(Breaking Bad)
You got one part of that wrong. This is not meth._(Breaking Bad)
It's easy to remember: a half a kT is equal to five fourths of a kJ/mol._(Anders Gabrielsson)
... and that dream of dreams, a computational model that predicts everything accurately._(Roald Hoffmann)
You see it through a charmed medium: you can not discern that the gilding is slime and the silk draperies cobwebs; that the marble is sordid slate, and the polished woods mere refuse chips and scale bark._(Mr. Rochester in Jane Eyre by Charlotte Bronte)
I know poetry is not dead, nor genius lost; nor has Mammon gained power over either, to bind or slay; they will both assert their existence, their presence, their liberty and strength again one day._(Jane Eyre in Jane Eyre by Charlotte Bronte)
-
+Parallel programming is not about elegance!_(Bill Gropp)
+In a talk you have a choice: You can make one point or no points._(Paul Sigler)
+Where all think alike, no one thinks very much._(Walter Lippmann)
+The scientist is not the person who always gives the right answers, he is the one who asks the right questions._(Claude Levi-Strauss)
+A curious aspect of the theory of evolution is that everybody thinks he understands it._(Jacques Monod)
+When a distinguished but elderly scientist states that something is possible, he is almost certainly right. When he states that something is impossible, he is very probably wrong._(Arthur C. Clarke)
+Energy is a very subtle concept. It is very, very difficult to get right._(Richard Feynman)
+The determined Real Programmer can write FORTRAN programs in any language._(Ed Post)
+FORTRAN was the language of choice for the same reason that three-legged races are popular._(Ken Thompson)
+A computer without COBOL and FORTRAN is like a piece of chocolate cake without ketchup or mustard._(Unix fortune program)
+Consistently separating words by spaces became a general custom about the tenth century A.D., and lasted until about 1957, when FORTRAN abandoned the practice._(Sun FORTRAN Reference Manual)
+Ludwig Boltzmann, who spent much of his life studying statistical mechanics, died in 1906, by his own hand. Paul Ehrenfest, carrying on the same work, died similarly in 1933. Now it is our turn to study statistical mechanics. Perhaps it will be wise to approach the subject cautiously._(David Goodstein)
+It all works because Avogadro's number is closer to infinity than to 10._(Ralph Baierlein)
+In this house, we OBEY the laws of thermodynamics!_(Homer Simpson)
+We mathematicians are all a bit crazy._(Lev Landau)
+There is no such thing as free energy. Anyone who advocates it does not know what he is talking about._(Alireza Haghighat)
+In science it often happens that scientists say, 'You know that's a really good argument; my position is mistaken,' and then they would actually change their minds and you never hear that old view from them again. They really do it. It doesn't happen as often as it should, because scientists are human and change is sometimes painful. But it happens every day. I cannot recall the last time something like that happened in politics or religion._(Carl Sagan)
+There is nothing new to be discovered in physics now. All that remains is more and more precise measurement._(Lord Kelvin, 1900)
+I love fools' experiments. I am always making them._(Charles Darwin)
+If you want to save your child from polio, you can pray or you can inoculate... choose science._(Carl Sagan)
+Molecular biology is essentially the practice of biochemistry without a license._(Edwin Chargaff)
+If at one time or another I have brushed a few colleagues the wrong way, I must apologize: I had not realized that they were covered with fur._(Edwin Chargaff)
+It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material._(Watson & Crick)
+The researcher's art is first of all to find himself a good boss._(Andre Lwoff)
+What about my nose?_(Aneesur Rahman, responding to an Argonne manager arguing the long hair of Charles Bennett in his group was disreputing the lab; Retold by Michael Klein)
+Science, my lad, is made up of mistakes, but they are mistakes which it is useful to make, because they lead little by little to the truth._(Jules Verne)
+Don't be afraid of hard work. Nothing worthwhile comes easily. Don't let others discourage you or tell you that you can't do it. In my day I was told women didn't go into chemistry. I saw no reason why we couldn't._(Gertrude Elion)
+The Nobel Prize is fine, but the drugs I've developed are rewards in themselves._(Gertrude Elion)
+...sometimes a scream is better than a thesis._(Ralph Waldo Emerson)
+The great tragedy of science - the slaying of a beautiful hypothesis by an ugly fact._(Thomas Henry Huxley)
+Dr Pauling, how do you have so many good ideas? Well David, I have a lot of ideas and throw away the bad ones._(Linus Pauling)
+I try to identify myself with the atoms... I ask what I would do If I were a carbon atom or a sodium atom._(Linus Pauling)
+I admired Bohr very much. We had long talks together, long talks in which Bohr did practically all the talking._(Paul Dirac)
+Predictions can be very difficult - especially about the future._(Niels Bohr)
+For those who want some proof that physicists are human, the proof is in the idiocy of all the different units which they use for measuring energy._(Richard Feynman)
+Dreams seldom materialize on their own._(Dian Fossey)
+Above all, don't fear difficult moments. The best comes from them._(Rita Levi-Montalcini)
+Our struggle today is not to have a female Einstein get appointed as an assistant professor. It is for a woman schlemiel to get as quickly promoted as a male schlemiel._(Bella Abzug)
+I never thought of stopping, and I just hated sleeping. I can't imagine having a better life._(Barbara McClintock)
+The farther the experiment is from theory, the closer it is to the Nobel Prize._(Irene Joliot-Curie)
+I never see what has been done; I only see what remains to be done._(Marie Curie)
+There is no reason for any individual to have a computer in his home._(Ken Olsen, head of Digital Equipment Corp.)
+People disagree with me. I just ignore them._(Linus Torvalds on the use of C++ in the kernel)
+Beware of bugs in the above code; I have only proved it correct, not tried it._(Donald Knuth)
+My greatest contribution to the field of science is that I never entered it._(Colin Powell)
+We are perhaps not far removed from the time when we shall be able to submit the bulk of chemical phenomena to calculation._(Joseph Gay-Lussac, 1808)
+If mathematical analysis should ever hold a prominent place in chemistry - an aberration which is happily almost impossible - it would occasion a rapid and widespread degeneration of that science._(Aguste Comte, 1830)
+Almost without exception, the talented women I have known have believed they had less ability than they actually had. And almost without exception, the talented men I have known believed they had more._(Gregory Petsko)
+The first 90% of the code accounts for the first 90% of the development time. The remaining 10% of the code accounts for the other 90% of the development time._(Tom Cargill)
+The Internet? We are not interested in it._(Bill Gates, 1993)
+Perl: The only language that looks the same before and after RSA encryption._(Keith Bostic)
+There are only two things wrong with C++: The initial concept and the implementation._(Bertrand Meyer)
+XML is not a language in the sense of a programming language any more than sketches on a napkin are a language._(Charles Simonyi)
+It has been discovered that C++ provides a remarkable facility for concealing the trivial details of a program - such as where its bugs are._(David Keppel)
+UNIX is basically a simple operating system. It just takes a genius to understand its simplicity._(Dennis Ritchie)
+There are two major products that come out of Berkeley: LSD and UNIX. We don't believe this to be a coincidence._(Jeremy Anderson)
+There are only two kinds of programming languages: those people always bitch about and those nobody uses._(Bjarne Stroustrup)
+If Java had true garbage collection, most programs would delete themselves upon execution._(Robert Sewell)
+Documentation is like sex: When it's good it's great, and when it's bad it's better than nothing._(Linus Torvalds)
+C has the power of assembly language and the convenience of... assembly language._(Dennis Ritchie)
+The last good thing written in C was Franz Schubert's Symphony Number 9._(Erwin Dieterich)
+User-friendly, adj.: Programmer-hostile._(New Hacker's Dictionary)
+First off, I'd suggest printing out a copy of the GNU coding standards, and NOT read it. Burn them, it's a great symbolic gesture._(Linus Torvalds)
+I invented the term 'Object-Oriented', and I can tell you I did not have C++ in mind._(Alay Kay, author of Smalltalk)
+FORTRAN, the infantile disorder, by now nearly 20 years old, is hopelessly inadequate for whatever computer application you have in mind today: it is now too clumsy, too risky, and too expensive to use._(Edsger Dijkstra, 1970)
+Do you know what cations don't like? Dog-ions. Do you know what they like? Pie._(Tom Cheatham)
+The most exciting phrase to hear in science, the one that heralds new discoveries, is not "Eureka" but "That's funny..."._(Isaac Asimov)
+Those people who think they know everything are a great annoyance to those of us who do._(Isaac Asimov)
+No great discovery was ever made without a bold guess._(Marie Curie)
+Chance favors the prepared mind._(Louis Pasteur)
+I love deadlines. I like the whooshing sound they make as they fly by._(Douglas Adams)
+Good judgement is the result of experience; experience is the result of bad judgement._(Mark Twain)
+No matter how important you are, you are not as important as lunch._(Randy Pausch)
+There is just one thing I can promise you about the outer-space program: your tax dollar will go farther._(Wernher von Braun)
+Harvard makes mistakes too, you know. Kissinger taught there._(Woody Allen)
+Nothing in biology makes sense except in the light of evolution._(Theodosius Dobzhansky)
+I have a hunch that the unknown sequences of DNA will decode into copyright notices and patent protections._(Donald Knuth)
+It always takes longer than you think even when you take Hofstadter's Law into account._(Hofstadter's Law)
+A ship in port is safe, but that is not what ships are for. Sail out to sea and do new things._(Grace Hopper, developer of COBOL)
+I was told I'd never make it to VP rank because I was too outspoken. Maybe so, but I think men will always find an excuse for keeping women in their 'place.' So, let's make that place the executive suite and start more of our own companies._(Jean Bartik, ENIAC developer)
+If it's a good idea, go ahead and do it. It's much easier to apologize than it is to get permission._(Grace Hopper, developer of COBOL)
+This isn't right. This isn't even wrong._(Wolfgang Pauli)
+Louis Pasteur's theory of germs is ridicolous fiction._(Pierre Pachet, Professor of Physiology at Toulouse, 1872)
+Research ! A mere excuse for idleness; it has never achieved, and will never achieve any results of the slightest value._(Benjamin Jowett, British theologian, 1817-93)
+Problems worthy of attack prove their worth by hitting back._(Piet Hein)
+You should never bet against anything in science at odds of more than about 10^12 to 1._(Ernest Rutherford)
+X-rays will prove to be a hoax._(Lord Kelvin, while president of the Royal Society)
+If you're doing I/O, you're doing it wrong!_(Cannada "Drew" Lewis)
+The easiest way to scale well is to have bad single-core performance_(Blind Freddie)
+Heard a talk introducing a new language called Swift, from a guy named Wozniak, and it had nothing to do with Apple!_(Adam Cadien)
+When doing HPC, don't communica_(Jim Demmel)
+Today we're not going to optimize our CUDA code, cause that's just a rabbit hole of misery!_(Tim Warburton)
+Big Data is like teenage sex: everyone talks about it, nobody really knows how to do it, everyone thinks everyone else is doing it, so everyone claims they are doing it..._(Dan Ariely)
+It seems likely that significant software contributions to existing scientific software projects are not likely to be rewarded through the traditional reputation economy of science. Together these factors provide a reason to expect the over-production of independent scientific software packages, and the underproduction of collaborative projects in which later academics build on the work of earlier ones._(Howison & Herbsleb)
+On average, it takes twenty years for the world's largest super computer to shrink down to the size of your laptop._(Pete Beckman)
+When using an abacus, a human can achieve about 0.1 flops/watt. Super-computers achieve about 2 gigaflops/watt._(John Linford)
+Try to calculate the numbers that have been_(The Smoke Fairies)
+Please implement proper hep writing_(GROMACS)
+The three principal virtues of a programmer are Laziness, Impatience, and Hubris_(Larry Wall)
+You're like them scientists on TV explaining black holes. More you talk, less I get_(Jess Walter)
+Wedged as we are between two eternities of idleness, there is no excuse for being idle now_(Anthony Burgess)
+Even the *healthy* people move in clouds of cigarette smoke, women straining polyester, men in raggedly cutoffs slathering mayonnaise on foot-long hot dogs. It's as if the hotel were hosting a conference on adult onset diabetes_(Jess Walter)
+In practice, throwing traditional norms and values overboard results not in perfect freedom and relationships based on reason, but in chaos and fear_(Paul Verhaeghe)
+When I asked a younger colleague at the university how he had been able to change his research field several times within a decade or so, he answered: "It's just a question of new software"_(Paul Verhaeghe)
+Never mind, death professor, your structure's fine_(TV on the Radio)
+Come and play on the hospital roof, I got something that's yours_(Sherlock)
+Njuta men inte frossa, springa men inte fly_(Paganus)
+Misslycka kan man med all kod_(Mats Nylen)
+Two guys can move very fast when they're motivated enough and unemployed_(Eric Betzig)
+A protein is a chain of letters._(Julie Bernauer)
+The best way to obtain plausible negative examples is to run a docking program with a biophysics-based function._(Julie Bernauer)
Fe2+ 55.847 ; Iron. See Chem. Phys. Lett. 449, 144 (2007).
; Added by DvdS 05/2005 copied from GROMACS force field.
SI 28.080 ; Silicium in Glass etc.
+; tip4p-EW
+HW_tip4pew 1.008
+OW_tip4pew 16.00
Fe2+ Fe2+ 26 55.84700 2.000 A 2.59400e-01 5.43920e-02
; Added by DvdS 05/2005 copied from GROMACS force field.
SI SI 14 28.08000 0.000 A 3.38550e-01 2.44704e+00
+; tip4p-EW
+HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
+OW_tip4pew 8 16.00 0.0000 A 3.16435e-01 6.80946e-01
--- /dev/null
+
+; Horn et al. (2004). J. Chem. Phys.120, 9665-9678
+; http://dx.doi.org/10.1063/1.1683075
+
+[ moleculetype ]
+; molname nrexcl
+SOL 2
+
+[ atoms ]
+; id at type res nr res name at name cg nr charge mass
+ 1 OW_tip4pew 1 SOL OW 1 0 16.00000
+ 2 HW_tip4pew 1 SOL HW1 1 0.52422 1.00800
+ 3 HW_tip4pew 1 SOL HW2 1 0.52422 1.00800
+ 4 MW 1 SOL MW 1 -1.04844 0.00000
+
+#ifndef FLEXIBLE
+
+[ settles ]
+; i funct doh dhh
+1 1 0.09572 0.15139
+
+#else
+[ bonds ]
+; i j funct length force.c.
+1 2 1 0.09572 502416.0 0.09572 502416.0
+1 3 1 0.09572 502416.0 0.09572 502416.0
+
+[ angles ]
+; i j k funct angle force.c.
+2 1 3 1 104.52 628.02 104.52 628.02
+
+#endif
+
+
+[ virtual_sites3 ]
+; Vsite from funct a b
+4 1 2 3 1 0.106676721 0.106676721
+
+
+[ exclusions ]
+1 2 3 4
+2 1 3 4
+3 1 2 4
+4 1 2 3
+
+
+; The position of the virtual site is computed as follows:
+;
+; O
+;
+; V
+;
+; H H
+;
+; Ewald tip4p:
+; const = distance (OV) / [ cos (angle(VOH)) * distance (OH) ]
+; 0.0125 nm / [ cos (52.26 deg) * 0.09572 nm ]
+; then a = b = 0.5 * const = 0.106676721
+;
+; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
tip4p TIP4P TIP 4-point, recommended
+tip4pew TIP4PEW TIP 4-point with Ewald
tip3p TIP3P TIP 3-point
tip5p TIP5P TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues)
tip5pe TIP5P TIP 5-point improved for Ewald sums
K Ion
NA Ion
CA Ion
-MK Ion
+MG Ion
CL Ion
ZN Ion
CU1 Ion
endif()
configure_file(config.h.cmakein config.h)
+configure_file(gmxpre-config.h.cmakein gmxpre-config.h)
configure_file(buildinfo.h.cmakein buildinfo.h ESCAPE_QUOTES)
if (BUILD_TESTING)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#ifndef GMX_CONFIG_H
#define GMX_CONFIG_H
-#include "gromacs/utility/gmx_header_config.h"
/* TODO: For now, disable Doxygen warnings from here */
/*! \cond */
-/* Default location of data files */
-#define GMXLIB_SEARCH_DIR "@GMXLIB_SEARCH_DIR@"
-
-/* Default location of data files */
-#define GMXLIB_FALLBACK "@GMXLIB_FALLBACK@"
-
/* Binary suffix for the created binaries */
#define GMX_BINARY_SUFFIX "@GMX_BINARY_SUFFIX@"
+/* Installation prefix (default location of data files) */
+#define CMAKE_INSTALL_PREFIX "@CMAKE_INSTALL_PREFIX@"
+
+/* Location of data files in the installation directory */
+#define DATA_INSTALL_DIR "@DATA_INSTALL_DIR@"
+
/* Source directory for the build */
#cmakedefine CMAKE_SOURCE_DIR "@CMAKE_SOURCE_DIR@"
/* Binary directory for the build */
#cmakedefine CMAKE_BINARY_DIR "@CMAKE_BINARY_DIR@"
-/* Turn off water-water neighborlist optimization only - not used right now */
-#cmakedefine DISABLE_WATERWATER_NLIST
-
-/* Turn off all water neighborlist optimization - not used right now */
-#cmakedefine DISABLE_WATER_NLIST
-
/* IEEE754 floating-point format. Memory layout is defined by macros
* GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER and GMX_IEEE754_BIG_ENDIAN_WORD_ORDER.
*/
/* Target platform is BlueGene/Q */
#cmakedefine GMX_TARGET_BGQ
+/** Define if we are building natively on Windows */
+#cmakedefine GMX_NATIVE_WINDOWS
+
+/** Define if we are building for Cygwin */
+#cmakedefine GMX_CYGWIN
+
+/** Define if we have sufficient C++11 support */
+#cmakedefine GMX_CXX11
+
/* GCC bug in AVX maskload/maskstore arguments - worked around internally */
#cmakedefine GMX_SIMD_X86_AVX_GCC_MASKLOAD_BUG
/* AVX2 256-bit SIMD instruction set level was selected */
#cmakedefine GMX_SIMD_X86_AVX2_256
+/* MIC (Xeon Phi) SIMD instruction set level was selected */
+#cmakedefine GMX_SIMD_X86_MIC
+
+/* 32-bit ARM NEON SIMD instruction set level was selected */
+#cmakedefine GMX_SIMD_ARM_NEON
+
+/* ARM (AArch64) NEON Advanced SIMD instruction set level was selected */
+#cmakedefine GMX_SIMD_ARM_NEON_ASIMD
+
/* IBM QPX was selected as SIMD instructions (e.g. BlueGene/Q) */
#cmakedefine GMX_SIMD_IBM_QPX
+/* IBM VMX was selected as SIMD instructions (Power 6 and later) */
+#cmakedefine GMX_SIMD_IBM_VMX
+
+/* IBM VSX was selected as SIMD instructions (Power 7 and later) */
+#cmakedefine GMX_SIMD_IBM_VSX
+
/* Fujitsu Sparc64 HPC-ACE SIMD acceleration */
#cmakedefine GMX_SIMD_SPARC64_HPC_ACE
/* Use MPI (with mpicc) for parallelization */
#cmakedefine GMX_LIB_MPI
-/* MPI_IN_PLACE exists for collective operations */
-#cmakedefine MPI_IN_PLACE_EXISTS
+/* Use threads_mpi for parallelization */
+#cmakedefine GMX_THREAD_MPI
+#if defined GMX_LIB_MPI || defined GMX_THREAD_MPI
/* Make a parallel version of GROMACS using message passing
(MPI or thread_mpi) */
-#cmakedefine GMX_MPI
+#define GMX_MPI
+#endif
-/* Use threads_mpi for parallelization */
-#cmakedefine GMX_THREAD_MPI
+/* MPI_IN_PLACE exists for collective operations */
+#cmakedefine MPI_IN_PLACE_EXISTS
/* Use OpenMP multithreading */
#cmakedefine GMX_OPENMP
-/* Ignore calls to nice(3) */
-#cmakedefine GMX_NO_NICE
+/* Can and should use nice(3) to set priority */
+#cmakedefine GMX_USE_NICE
+
+/* Maximum number of OpenMP threads supported */
+#define GMX_OPENMP_MAX_THREADS @GMX_OPENMP_MAX_THREADS@
/* Use if can't rename checkpoints */
#cmakedefine GMX_NO_RENAME
-/* Ignore calls to system(3) */
-#cmakedefine GMX_NO_SYSTEM
-
/* Use (modified) Gamess-UK for QM-MM calculations */
#cmakedefine GMX_QMMM_GAMESS
#cmakedefine TMPI_ATOMICS
/* Define for busy wait option */
+/* See gmxpre-config.h.cmakein for explanation for the #ifdef */
+#ifndef TMPI_WAIT_FOR_NO_ONE
#cmakedefine TMPI_WAIT_FOR_NO_ONE
+#endif
/* Define for copy buffer option */
#cmakedefine TMPI_COPY_BUFFER
/* Use GPU native acceleration */
#cmakedefine GMX_GPU
+/* Use NVML */
+#cmakedefine HAVE_NVML
+
/* Define to 1 if fseeko (and presumably ftello) exists and is declared. */
#cmakedefine HAVE_FSEEKO
/* Define if SIGUSR1 is present */
#cmakedefine HAVE_SIGUSR1
-/* Define to 1 to make fseeko visible on some hosts (e.g. glibc 2.2). */
-#cmakedefine _LARGEFILE_SOURCE
-
-/* Define for large files, on AIX-style hosts. */
-#cmakedefine _LARGE_FILES
-
-/* Some systems requires this to be set to 64 for large file support */
-#cmakedefine _FILE_OFFSET_BITS @_FILE_OFFSET_BITS@
-
-/* Build special-purpose mdrun library */
-#cmakedefine GMX_FAHCORE
-
/* Enable gromacs quotes */
#cmakedefine GMX_COOL_QUOTES
-#ifdef GMX_FAHCORE
-#define FULLINDIRECT 1
-#define USE_FAH_XDR 1
-#include "swindirect.h"
-#endif
-
/* default name mangling maybe wrong on exotic plattforms */
#define F77_FUNC(name,NAME) name ## _
/* Define if we have pipes */
#cmakedefine HAVE_PIPES
+/* Define if we have feenableexcept */
+#cmakedefine HAVE_FEENABLEEXCEPT
+
/* Define if we have zlib */
#cmakedefine HAVE_ZLIB
-#endif
-
/*! \endcond */
+
+#endif
#include <stdio.h>
#include <string.h>
#include <math.h>
-#include "main.h"
+
#include "macros.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "copyrite.h"
-#include "sysstuff.h"
#include "txtdump.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/fileio/xtcio.h"
#include "gromacs/fileio/enxio.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trnio.h"
#include "txtdump.h"
-#include "vec.h"
+#include "gromacs/math/vec.h"
static char *nm[5] = { "OW", "HW1", "HW2", "DW", "SW" };
int main(int argc,char *argv[])
{
static char *desc[] = {
- "[TT]gmxdump[tt] reads a run input file ([TT].tpa[tt]/[TT].tpr[tt]/[TT].tpb[tt]),",
- "a trajectory ([TT].trj[tt]/[TT].trr[tt]/[TT].xtc[tt]) or an energy",
- "file ([TT].ene[tt]/[TT].edr[tt]) and prints that to standard",
+ "[TT]gmxdump[tt] reads a run input file ([TT].tpr[tt]),",
+ "a trajectory ([TT].trr[tt]/[TT].xtc[tt]) or an energy",
+ "file ([TT].edr[tt]) and prints that to standard",
"output in a readable format. This program is essential for",
"checking your run input file in case of problems.[PAR]"
};
#endif
#include "typedefs.h"
-#include "main.h"
-#include "vec.h"
+#include "gromacs/math/vec.h"
#include "txtdump.h"
void calc_force(int natom,rvec f[],rvec fff[])
#include "ns.h"
#include "gromacs/utility/smalloc.h"
#include "wnblist.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "macros.h"
#include "gromacs/commandline/pargs.h"
#include "copyrite.h"
#include "gromacs/fileio/confio.h"
-#include "pbc.h"
-#include "vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/math/vec.h"
int main(int argc,char *argv[])
{
#include <config.h>
#endif
-#include "sysstuff.h"
#include "typedefs.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "mshift.h"
#include "gromacs/commandline/pargs.h"
#include "copyrite.h"
#include "gromacs/fileio/pdbio.h"
-#include "gmx_fatal.h"
-#include "xvgr.h"
-#include "gromacs/fileio/matio.h"
-#include "index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/topology/index.h"
#include "gstat.h"
#include "gromacs/fileio/tpxio.h"
#include "viewit.h"
#include "gbutil.h"
-#include "vec.h"
+#include "gromacs/math/vec.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT | PCA_BE_NICE ,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT,
NFILE,fnm, asize(pa),pa, asize(desc),desc,
asize(bugs),bugs,&oenv
);
out=gmx_ffopen(TrjoutFile,filemode);
break;
}
- if (outftp == efG87)
- fprintf(gmx_fio_getfp(trx_get_fileio(trxout)),"Generated by %s. #atoms=%d, a BOX is"
- " stored in this file.\n",ShortProgram(),nout);
}
if (natoms > atoms->nr) {
#include <stdlib.h>
#include "errno.h"
-#include "sysstuff.h"
#include "typedefs.h"
#include "gromacs/utility/cstringutil.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "mshift.h"
#include "gromacs/commandline/pargs.h"
#include "copyrite.h"
#include "gromacs/fileio/confio.h"
-#include "gmx_fatal.h"
-#include "xvgr.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/xvgr.h"
#include "gstat.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
#include "gromacs/fileio/pdbio.h"
void cat(FILE *out,char *fn,real t)
#define NFILE asize(fnm)
CopyRight(stdout,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE ,NFILE,fnm,
+ parse_common_args(&argc,argv,PCA_CAN_TIME,NFILE,fnm,
asize(pa),pa,asize(desc),desc,asize(bugs),bugs);
top=read_top(ftp2fn(efTPX,NFILE,fnm));
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "random.h"
#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/futil.h"
-#include "physics.h"
-#include "xvgr.h"
-#include "vec.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/math/units.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/math/vec.h"
#include "names.h"
#include "ehdata.h"
#include "gromacs/fileio/pdbio.h"
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "random.h"
#include "gromacs/fileio/strdb.h"
-#include "gromacs/fileio/futil.h"
-#include "physics.h"
+#include "gromacs/utility/futil.h"
#include "ehdata.h"
typedef struct {
#include "macros.h"
#include "copyrite.h"
#include "gromacs/commandline/pargs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "random.h"
#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/futil.h"
-#include "physics.h"
-#include "xvgr.h"
-#include "vec.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
#include "names.h"
#include "ehdata.h"
int seed;
CopyRight(stdout,argv[0]);
- parse_common_args(&argc,argv,PCA_BE_NICE,NFILE,fnm,
+ parse_common_args(&argc,argv,0,NFILE,fnm,
NPA,pa,asize(desc),desc,0,NULL);
please_cite(stdout,"Timneanu2004a");
#include <config.h>
#endif
-#include "sysstuff.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "gromacs/commandline/pargs.h"
#include "random.h"
#include "names.h"
#include "gromacs/fileio/matio.h"
-#include "physics.h"
-#include "vec.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/futil.h"
#include "copyrite.h"
-#include "xvgr.h"
-#include "index.h"
#include "gromacs/fileio/tpxio.h"
int main(int argc,char *argv[])
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE ,NFILE,fnm,
+ parse_common_args(&argc,argv,PCA_CAN_TIME,NFILE,fnm,
asize(pa),pa,asize(desc),desc,0,NULL);
top = read_top(ftp2fn(efTPX,NFILE,fnm));
#include "copyrite.h"
#include "typedefs.h"
#include "macros.h"
-#include "vec.h"
+#include "gromacs/math/vec.h"
#include "gromacs/commandline/pargs.h"
#include "coulomb.h"
int eel=0,m=0;
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL);
if (strcmp(opt[0],"cut") == 0)
#include <math.h>
-#include "sysstuff.h"
#include "typedefs.h"
#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "rmpbc.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
#include "copyrite.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/tpxio.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
#include "gromacs/utility/smalloc.h"
#include "nrnb.h"
#include "gstat.h"
-#include "gromacs/fileio/matio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#define G_REF1 0
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE,
+ parse_common_args(&argc,argv,PCA_CAN_TIME,
NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL,&oenv);
#include <stdio.h>
#include "typedefs.h"
#include "gromacs/utility/smalloc.h"
-#include "vec.h"
+#include "gromacs/math/vec.h"
#include "gmx_random.h"
#include "gmx_statistics.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/confio.h"
-#include "symtab.h"
#include "gromacs/utility/smalloc.h"
-#include "symtab.h"
+#include "gromacs/topology/symtab.h"
#include "macros.h"
#include "copyrite.h"
#include "gromacs/commandline/pargs.h"
-#include "index.h"
-#include "vec.h"
+#include "gromacs/math/vec.h"
#include "typedefs.h"
#include "gbutil.h"
-#include "physics.h"
-#include "atomprop.h"
+#include "gromacs/math/units.h"
void copy_atom(t_symtab *tab,t_atoms *a1,int i1,t_atoms *a2,int i2,
rvec xin[],rvec xout[],rvec vin[],rvec vout[])
#include "macros.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/fileio/confio.h"
-#include "vec.h"
+#include "gromacs/math/vec.h"
#include "gromacs/commandline/pargs.h"
#include "copyrite.h"
#include "gromacs/fileio/pdbio.h"
#include "typedefs.h"
#include "gromacs/commandline/pargs.h"
#include "copyrite.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/fileio/pdbio.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "pbc.h"
-#include "physics.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/math/units.h"
#include "names.h"
#include "txtdump.h"
#include "gromacs/fileio/trnio.h"
-#include "symtab.h"
+#include "gromacs/topology/symtab.h"
#include "gromacs/fileio/strdb.h"
-#include "atomprop.h"
#include "gromacs/fileio/confio.h"
#define TET 109.47
#include "typedefs.h"
#include "gromacs/commandline/pargs.h"
#include "copyrite.h"
-#include "gmx_fatal.h"
-#include "xvgr.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/xvgr.h"
+#include "viewit.h"
#include "gromacs/fileio/pdbio.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "pbc.h"
-#include "physics.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/units.h"
#include "names.h"
#include "txtdump.h"
#include "gromacs/fileio/trnio.h"
-#include "symtab.h"
#include "gromacs/fileio/confio.h"
real pot(real x,real qq,real c6,real c12)
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
void my_func(char *msg)
{
#include "typedefs.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "complex.h"
#include "fftgrid.h"
#include "mdrun.h"
#include <math.h>
#include <string.h>
#include "typedefs.h"
-#include "vec.h"
-#include "physics.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/units.h"
#include "macros.h"
#include "names.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/writeps.h"
#include "copyrite.h"
-#include "xvgr.h"
-#include "minvert.h"
#include "pppm.h"
#include "readinp.h"
-#include "main.h"
#include "force.h"
#include "nrnb.h"
#include "coulomb.h"
-#include "mshift.h"
+#include "gromacs/pbcutil/mshift.h"
#include "poisson.h"
#include "mdatoms.h"
#include "typedefs.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
-#include "xvgr.h"
+#include "gromacs/fileio/xvgr.h"
#include "copyrite.h"
#include "mdrun.h"
#include "main.h"
cr = init_par(&argc,&argv);
if (MASTER(cr))
CopyRight(stdout,argv[0]);
- parse_common_args(&argc,argv,
- PCA_CAN_SET_DEFFNM | (MASTER(cr) ? 0 : PCA_QUIET),
+ parse_common_args(&argc,argv, PCA_CAN_SET_DEFFNM,
NFILE,fnm,asize(pa),pa,0,NULL,0,NULL);
gmx_log_open(ftp2fn(efLOG,NFILE,fnm),cr,1,0,&fplog);
-* !filter
+# Only recent versions of git support pattern matching rules that would allow
+# the first to be conveniently specified in the main .gitattributes file.
+* -filter -gmx-doxygen
gmock-1.7.0/CMakeLists.txt filter=copyright
#include <assert.h>
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/utility/basedefinitions.h"
/* We only use the C interface of ThreeFry and r123array2x64. This file is a
replacment for the original from the Random123 distribution. It sets all
/* For "inline" use the Gromacs own gmx_inline */
#define R123_STATIC_INLINE static gmx_inline
/* force_inline isn't used in Gromacs - if it matters for a compiler it probably
- not only matters here and should be defined in simple.h */
+ not only matters here and should be defined in basedefinitions.h */
#define R123_FORCE_INLINE(decl) decl
/* We assume in Gromacs that assert is available outside of Cuda */
#define R123_ASSERT assert
1) Download Boost (current minimal version is derived from 1.55.0)
2) Extract
3) Edit Boost files to uncomment unnessary includes (search for GMX in minimal version and copy all changes)
+ Alternative make a patch by diffing against unmodified version and applying patch. Such as
+ diff /path/to/boost_1_55_0 . -rwu |grep -v ^"Only in" > patch && patch -p? < patch
4) Make sure our subset works even with compilers not listed
among the boost ones (in particular, Fujistu in native mode):
- Edit config/select_compiler_config.hpp to add the fallback
to a generic compiler capability file at the end.
- Add the generic compiler capability file config/compiler/generic.hpp
-5) run bcp with required files (currently exception/all.hpp, scoped_ptr.hpp)
+5) run bcp with required files (currently boost/exception/all.hpp boost/scoped_ptr.hpp)
6) delete source files which are not required. Currently:
- - libs/smart_ptr/src/sp_collector.cpp
- - libs/smart_ptr/src/sp_debug_hooks.cpp
- Make sure that they are really not needed.If any source files are added make sure to add them to cmake.
+ - libs/smart_ptr/
+ - libs/exception/
+ Make sure that they are really not needed. If any source files are added make sure to add them to cmake.
************************************************************/
-#include "types/simple.h"
-
#ifndef _fftpack_h
#define _fftpack_h
+#include "gromacs/utility/real.h"
+
#ifdef __cplusplus
extern "C" {
#endif
#ifdef __cplusplus
}
#endif
+
#endif
include(gmxGetGmockTupleWorkaround)
get_gmock_tuple_workaround(GMOCK_COMPILE_DEFINITIONS)
-set(GMOCK_COMPILE_DEFINITIONS "_GNU_SOURCE=1;${GMOCK_COMPILE_DEFINITIONS}")
-set(GMOCK_COMPILE_DEFINITIONS ${GMOCK_COMPILE_DEFINITIONS} PARENT_SCOPE)
# GTest/GMock suggest linking with pthreads when available for thread safety
set(CMAKE_THREAD_PREFER_PTHREAD 1)
endif()
add_library(gmock STATIC ${UNITTEST_TARGET_OPTIONS} ${GMOCK_SOURCES} ${GTEST_SOURCES})
-set_property(TARGET gmock APPEND PROPERTY COMPILE_DEFINITIONS "${GMOCK_COMPILE_DEFINITIONS};GTEST_CAN_STREAM_RESULTS=0")
+set_property(TARGET gmock APPEND PROPERTY COMPILE_DEFINITIONS
+ "_GNU_SOURCE=1;${GMOCK_COMPILE_DEFINITIONS};GTEST_CAN_STREAM_RESULTS=0")
set(GMOCK_LIBRARIES gmock ${PTHREADS_LIBRARIES} PARENT_SCOPE)
set(GTEST_LIBRARIES ${GMOCK_LIBRARIES} PARENT_SCOPE)
set(GMOCK_INCLUDE_DIRS ${GMOCK_INCLUDE_DIRS} PARENT_SCOPE)
set(GTEST_INCLUDE_DIRS ${GTEST_INCLUDE_DIRS} PARENT_SCOPE)
+set(GMOCK_COMPILE_DEFINITIONS ${GMOCK_COMPILE_DEFINITIONS} PARENT_SCOPE)
# pragma warning(push) // Saves the current warning state.
# pragma warning(disable:4389) // Temporarily disables warning on
// signed/unsigned mismatch.
+# pragma warning(disable:4805) // Temporarily disables warning on
+ // unsafe mix of types
#endif
if (expected == actual) {
--- /dev/null
+This directory contains only the barebone version of the
+lmfit package, version 5.1. Full version is available from
+http://apps.jcns.fz-juelich.de/doku/sc/lmfit
+
+License in gromacs root directory in file COPYING
--- /dev/null
+/*
+ * Library: lmfit (Levenberg-Marquardt least squares fitting)
+ *
+ * File: lmcurve.c
+ *
+ * Contents: Levenberg-Marquardt curve-fitting
+ *
+ * Copyright: Joachim Wuttke, Forschungszentrum Juelich GmbH (2004-2013)
+ *
+ * License: see ../COPYING (FreeBSD)
+ *
+ * Homepage: apps.jcns.fz-juelich.de/lmfit
+ */
+
+#include "lmmin.h"
+#include "gromacs/utility/basedefinitions.h"
+
+typedef struct {
+ const double *t;
+ const double *y;
+ double (*f)(double t, const double *par);
+} lmcurve_data_struct;
+
+
+void lmcurve_evaluate( const double *par, int m_dat, const void *data,
+ double *fvec, gmx_unused int *info )
+{
+ int i;
+ for (i = 0; i < m_dat; i++)
+ {
+ fvec[i] =
+ ((lmcurve_data_struct*)data)->y[i] -
+ ((lmcurve_data_struct*)data)->f(
+ ((lmcurve_data_struct*)data)->t[i], par );
+ }
+}
+
+
+void lmcurve( int n_par, double *par, int m_dat,
+ const double *t, const double *y,
+ double (*f)( double t, const double *par ),
+ const lm_control_struct *control,
+ lm_status_struct *status )
+{
+ lmcurve_data_struct data;
+ data.t = t;
+ data.y = y;
+ data.f = f;
+
+ lmmin( n_par, par, m_dat, (const void*) &data,
+ lmcurve_evaluate, control, status );
+}
--- /dev/null
+/*
+ * Library: lmfit (Levenberg-Marquardt least squares fitting)
+ *
+ * File: lmcurve.h
+ *
+ * Contents: Declarations for Levenberg-Marquardt curve fitting.
+ *
+ * Copyright: Joachim Wuttke, Forschungszentrum Juelich GmbH (2004-2013)
+ *
+ * License: see ../COPYING (FreeBSD)
+ *
+ * Homepage: apps.jcns.fz-juelich.de/lmfit
+ */
+
+#ifndef LMCURVE_H
+#define LMCURVE_H
+#undef __BEGIN_DECLS
+#undef __END_DECLS
+#ifdef __cplusplus
+# define __BEGIN_DECLS extern "C" {
+# define __END_DECLS }
+#else
+# define __BEGIN_DECLS /* empty */
+# define __END_DECLS /* empty */
+#endif
+
+#include "lmstruct.h"
+
+__BEGIN_DECLS
+
+void lmcurve( int n_par, double *par, int m_dat,
+ const double *t, const double *y,
+ double (*f)( double t, const double *par ),
+ const lm_control_struct *control,
+ lm_status_struct *status );
+
+__END_DECLS
+#endif /* LMCURVE_H */
--- /dev/null
+/*
+ * Library: lmfit (Levenberg-Marquardt least squares fitting)
+ *
+ * File: lmmin.c
+ *
+ * Contents: Levenberg-Marquardt minimization.
+ *
+ * Copyright: MINPACK authors, The University of Chikago (1980-1999)
+ * Joachim Wuttke, Forschungszentrum Juelich GmbH (2004-2013)
+ *
+ * License: see ../COPYING (FreeBSD)
+ *
+ * Homepage: apps.jcns.fz-juelich.de/lmfit
+ */
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+#include <float.h>
+#include "lmmin.h"
+
+#define MIN(a, b) (((a) <= (b)) ? (a) : (b))
+#define MAX(a, b) (((a) >= (b)) ? (a) : (b))
+#define SQR(x) (x)*(x)
+
+/* function declarations (implemented below). */
+void lm_lmpar( int n, double *r, int ldr, int *ipvt, double *diag,
+ double *qtb, double delta, double *par, double *x,
+ double *sdiag, double *aux, double *xdi );
+void lm_qrfac( int m, int n, double *a, int *ipvt,
+ double *rdiag, double *acnorm, double *wa );
+void lm_qrsolv( int n, double *r, int ldr, int *ipvt, double *diag,
+ double *qtb, double *x, double *sdiag, double *wa );
+
+
+/*****************************************************************************/
+/* Numeric constants */
+/*****************************************************************************/
+
+/* machine-dependent constants from float.h */
+#define LM_MACHEP DBL_EPSILON /* resolution of arithmetic */
+#define LM_DWARF DBL_MIN /* smallest nonzero number */
+#define LM_SQRT_DWARF sqrt(DBL_MIN) /* square should not underflow */
+#define LM_SQRT_GIANT sqrt(DBL_MAX) /* square should not overflow */
+#define LM_USERTOL 30*LM_MACHEP /* users are recommended to require this */
+
+/* If the above values do not work, the following seem good for an x86:
+ LM_MACHEP .555e-16
+ LM_DWARF 9.9e-324
+ LM_SQRT_DWARF 1.e-160
+ LM_SQRT_GIANT 1.e150
+ LM_USER_TOL 1.e-14
+ The following values should work on any machine:
+ LM_MACHEP 1.2e-16
+ LM_DWARF 1.0e-38
+ LM_SQRT_DWARF 3.834e-20
+ LM_SQRT_GIANT 1.304e19
+ LM_USER_TOL 1.e-14
+ */
+
+const lm_control_struct lm_control_double = {
+ LM_USERTOL, LM_USERTOL, LM_USERTOL, LM_USERTOL, 100., 100, 1,
+ NULL, 0, -1, -1
+};
+const lm_control_struct lm_control_float = {
+ 1.e-7, 1.e-7, 1.e-7, 1.e-7, 100., 100, 1,
+ NULL, 0, -1, -1
+};
+
+
+/*****************************************************************************/
+/* Message texts (indexed by status.info) */
+/*****************************************************************************/
+
+const char *lm_infmsg[] = {
+ "found zero (sum of squares below underflow limit)",
+ "converged (the relative error in the sum of squares is at most tol)",
+ "converged (the relative error of the parameter vector is at most tol)",
+ "converged (both errors are at most tol)",
+ "trapped (by degeneracy; increasing epsilon might help)",
+ "exhausted (number of function calls exceeding preset patience)",
+ "failed (ftol<tol: cannot reduce sum of squares any further)",
+ "failed (xtol<tol: cannot improve approximate solution any further)",
+ "failed (gtol<tol: cannot improve approximate solution any further)",
+ "crashed (not enough memory)",
+ "exploded (fatal coding error: improper input parameters)",
+ "stopped (break requested within function evaluation)"
+};
+
+const char *lm_shortmsg[] = {
+ "found zero",
+ "converged (f)",
+ "converged (p)",
+ "converged (2)",
+ "degenerate",
+ "call limit",
+ "failed (f)",
+ "failed (p)",
+ "failed (o)",
+ "no memory",
+ "invalid input",
+ "user break"
+};
+
+
+/*****************************************************************************/
+/* Monitoring auxiliaries. */
+/*****************************************************************************/
+
+void lm_print_pars( int nout, const double *par, double fnorm, FILE* fout )
+{
+ int i;
+ for (i = 0; i < nout; ++i)
+ {
+ fprintf( fout, " %16.9g", par[i] );
+ }
+ fprintf( fout, " => %18.11g\n", fnorm );
+}
+
+
+/*****************************************************************************/
+/* lmmin (main minimization routine) */
+/*****************************************************************************/
+
+void lmmin( int n, double *x, int m, const void *data,
+ void (*evaluate) (const double *par, int m_dat, const void *data,
+ double *fvec, int *userbreak),
+ const lm_control_struct *C, lm_status_struct *S )
+{
+ double *fvec, *diag, *fjac, *qtf, *wa1, *wa2, *wa3, *wf;
+ int *ipvt;
+ int j, i;
+ double actred, dirder, fnorm, fnorm1, gnorm, pnorm,
+ prered, ratio, step, sum, temp, temp1, temp2, temp3;
+ static double p0001 = 1.0e-4;
+
+ int maxfev = C->patience * (n+1);
+
+ int outer, inner; /* loop counters, for monitoring */
+ int inner_success; /* flag for loop control */
+ double lmpar = 0; /* Levenberg-Marquardt parameter */
+ double delta = 0;
+ double xnorm = 0;
+ double eps = sqrt(MAX(C->epsilon, LM_MACHEP)); /* for forward differences */
+
+ int nout = C->n_maxpri == -1 ? n : MIN( C->n_maxpri, n );
+
+ /* The workaround msgfile=NULL is needed for default initialization */
+ FILE* msgfile = C->msgfile ? C->msgfile : stdout;
+
+ /* Default status info; must be set ahead of first return statements */
+ S->outcome = 0; /* status code */
+ S->userbreak = 0;
+ S->nfev = 0; /* function evaluation counter */
+
+/*** Check input parameters for errors. ***/
+
+ if (n <= 0)
+ {
+ fprintf( stderr, "lmmin: invalid number of parameters %i\n", n );
+ S->outcome = 10; /* invalid parameter */
+ return;
+ }
+ if (m < n)
+ {
+ fprintf( stderr, "lmmin: number of data points (%i) "
+ "smaller than number of parameters (%i)\n", m, n );
+ S->outcome = 10;
+ return;
+ }
+ if (C->ftol < 0. || C->xtol < 0. || C->gtol < 0.)
+ {
+ fprintf( stderr,
+ "lmmin: negative tolerance (at least one of %g %g %g)\n",
+ C->ftol, C->xtol, C->gtol );
+ S->outcome = 10;
+ return;
+ }
+ if (maxfev <= 0)
+ {
+ fprintf( stderr, "lmmin: nonpositive function evaluations limit %i\n",
+ maxfev );
+ S->outcome = 10;
+ return;
+ }
+ if (C->stepbound <= 0.)
+ {
+ fprintf( stderr, "lmmin: nonpositive stepbound %g\n", C->stepbound );
+ S->outcome = 10;
+ return;
+ }
+ if (C->scale_diag != 0 && C->scale_diag != 1)
+ {
+ fprintf( stderr, "lmmin: logical variable scale_diag=%i, "
+ "should be 0 or 1\n", C->scale_diag );
+ S->outcome = 10;
+ return;
+ }
+
+/*** Allocate work space. ***/
+ fvec = diag = fjac = qtf = wa1 = wa2 = wa3 = wf = NULL;
+ ipvt = NULL;
+ if ( (fvec = (double *) malloc(m * sizeof(double))) == NULL ||
+ (diag = (double *) malloc(n * sizeof(double))) == NULL ||
+ (qtf = (double *) malloc(n * sizeof(double))) == NULL ||
+ (fjac = (double *) malloc(n*m*sizeof(double))) == NULL ||
+ (wa1 = (double *) malloc(n * sizeof(double))) == NULL ||
+ (wa2 = (double *) malloc(n * sizeof(double))) == NULL ||
+ (wa3 = (double *) malloc(n * sizeof(double))) == NULL ||
+ (wf = (double *) malloc(m * sizeof(double))) == NULL ||
+ (ipvt = (int *) malloc(n * sizeof(int) )) == NULL)
+ {
+ S->outcome = 9;
+ if (NULL != fvec)
+ {
+ free(fvec);
+ }
+ if (NULL != diag)
+ {
+ free(diag);
+ }
+ if (NULL != qtf)
+ {
+ free(qtf);
+ }
+ if (NULL != fjac)
+ {
+ free(fjac);
+ }
+ if (NULL != wa1)
+ {
+ free(wa1);
+ }
+ if (NULL != wa2)
+ {
+ free(wa2);
+ }
+ if (NULL != wa3)
+ {
+ free(wa3);
+ }
+ if (NULL != wf)
+ {
+ free(wf);
+ }
+ if (NULL != ipvt)
+ {
+ free(ipvt);
+ }
+ return;
+ }
+
+ if (!C->scale_diag)
+ {
+ for (j = 0; j < n; j++)
+ {
+ diag[j] = 1.;
+ }
+ }
+
+/*** Evaluate function at starting point and calculate norm. ***/
+
+ (*evaluate)( x, m, data, fvec, &(S->userbreak) );
+ S->nfev = 1;
+ if (S->userbreak)
+ {
+ goto terminate;
+ }
+ fnorm = lm_enorm(m, fvec);
+ if (C->verbosity)
+ {
+ fprintf( msgfile, "lmmin start " );
+ lm_print_pars( nout, x, fnorm, msgfile );
+ }
+ if (fnorm <= LM_DWARF)
+ {
+ S->outcome = 0; /* sum of squares almost zero, nothing to do */
+ goto terminate;
+ }
+
+/*** The outer loop: compute gradient, then descend. ***/
+
+ for (outer = 0;; ++outer)
+ {
+
+/*** [outer] Calculate the Jacobian. ***/
+
+ for (j = 0; j < n; j++)
+ {
+ temp = x[j];
+ step = MAX(eps*eps, eps * fabs(temp));
+ x[j] += step; /* replace temporarily */
+ (*evaluate)( x, m, data, wf, &(S->userbreak) );
+ ++(S->nfev);
+ if (S->userbreak)
+ {
+ goto terminate;
+ }
+ for (i = 0; i < m; i++)
+ {
+ fjac[j*m+i] = (wf[i] - fvec[i]) / step;
+ }
+ x[j] = temp; /* restore */
+ }
+ if (C->verbosity >= 10)
+ {
+ /* print the entire matrix */
+ printf("\nlmmin Jacobian\n");
+ for (i = 0; i < m; i++)
+ {
+ printf(" ");
+ for (j = 0; j < n; j++)
+ {
+ printf("%.5e ", fjac[j*m+i]);
+ }
+ printf("\n");
+ }
+ }
+
+/*** [outer] Compute the QR factorization of the Jacobian. ***/
+
+/* fjac is an m by n array. The upper n by n submatrix of fjac
+ * is made to contain an upper triangular matrix r with diagonal
+ * elements of nonincreasing magnitude such that
+ *
+ * p^T*(jac^T*jac)*p = r^T*r
+ *
+ * (NOTE: ^T stands for matrix transposition),
+ *
+ * where p is a permutation matrix and jac is the final calculated
+ * Jacobian. Column j of p is column ipvt(j) of the identity matrix.
+ * The lower trapezoidal part of fjac contains information generated
+ * during the computation of r.
+ *
+ * ipvt is an integer array of length n. It defines a permutation
+ * matrix p such that jac*p = q*r, where jac is the final calculated
+ * Jacobian, q is orthogonal (not stored), and r is upper triangular
+ * with diagonal elements of nonincreasing magnitude. Column j of p
+ * is column ipvt(j) of the identity matrix.
+ */
+
+ lm_qrfac(m, n, fjac, ipvt, wa1, wa2, wa3);
+ /* return values are ipvt, wa1=rdiag, wa2=acnorm */
+
+/*** [outer] Form q^T * fvec and store first n components in qtf. ***/
+
+ for (i = 0; i < m; i++)
+ {
+ wf[i] = fvec[i];
+ }
+
+ for (j = 0; j < n; j++)
+ {
+ temp3 = fjac[j*m+j];
+ if (temp3 != 0.)
+ {
+ sum = 0;
+ for (i = j; i < m; i++)
+ {
+ sum += fjac[j*m+i] * wf[i];
+ }
+ temp = -sum / temp3;
+ for (i = j; i < m; i++)
+ {
+ wf[i] += fjac[j*m+i] * temp;
+ }
+ }
+ fjac[j*m+j] = wa1[j];
+ qtf[j] = wf[j];
+ }
+
+/*** [outer] Compute norm of scaled gradient and detect degeneracy. ***/
+
+ gnorm = 0;
+ for (j = 0; j < n; j++)
+ {
+ if (wa2[ipvt[j]] == 0)
+ {
+ continue;
+ }
+ sum = 0.;
+ for (i = 0; i <= j; i++)
+ {
+ sum += fjac[j*m+i] * qtf[i];
+ }
+ gnorm = MAX( gnorm, fabs( sum / wa2[ipvt[j]] / fnorm ) );
+ }
+
+ if (gnorm <= C->gtol)
+ {
+ S->outcome = 4;
+ goto terminate;
+ }
+
+/*** [outer] Initialize / update diag and delta. ***/
+
+ if (!outer)
+ {
+ /* first iteration only */
+ if (C->scale_diag)
+ {
+ /* diag := norms of the columns of the initial Jacobian */
+ for (j = 0; j < n; j++)
+ {
+ diag[j] = wa2[j] ? wa2[j] : 1;
+ }
+ /* xnorm := || D x || */
+ for (j = 0; j < n; j++)
+ {
+ wa3[j] = diag[j] * x[j];
+ }
+ xnorm = lm_enorm(n, wa3);
+ if (C->verbosity >= 2)
+ {
+ fprintf( msgfile, "lmmin diag " );
+ lm_print_pars( nout, x, xnorm, msgfile );
+ }
+ /* only now print the header for the loop table */
+ if (C->verbosity >= 3)
+ {
+ fprintf( msgfile, " o i lmpar prered"
+ " ratio dirder delta"
+ " pnorm fnorm" );
+ for (i = 0; i < nout; ++i)
+ {
+ fprintf( msgfile, " p%i", i );
+ }
+ fprintf( msgfile, "\n" );
+ }
+ }
+ else
+ {
+ xnorm = lm_enorm(n, x);
+ }
+ /* initialize the step bound delta. */
+ if (xnorm)
+ {
+ delta = C->stepbound * xnorm;
+ }
+ else
+ {
+ delta = C->stepbound;
+ }
+ }
+ else
+ {
+ if (C->scale_diag)
+ {
+ for (j = 0; j < n; j++)
+ {
+ diag[j] = MAX( diag[j], wa2[j] );
+ }
+ }
+ }
+
+/*** The inner loop. ***/
+ inner = 0;
+ do
+ {
+
+/*** [inner] Determine the Levenberg-Marquardt parameter. ***/
+
+ lm_lmpar( n, fjac, m, ipvt, diag, qtf, delta, &lmpar,
+ wa1, wa2, wf, wa3 );
+ /* used return values are fjac (partly), lmpar, wa1=x, wa3=diag*x */
+
+ /* predict scaled reduction */
+ pnorm = lm_enorm(n, wa3);
+ temp2 = lmpar * SQR( pnorm / fnorm );
+ for (j = 0; j < n; j++)
+ {
+ wa3[j] = 0;
+ for (i = 0; i <= j; i++)
+ {
+ wa3[i] -= fjac[j*m+i] * wa1[ipvt[j]];
+ }
+ }
+ temp1 = SQR( lm_enorm(n, wa3) / fnorm );
+ prered = temp1 + 2 * temp2;
+ dirder = -temp1 + temp2; /* scaled directional derivative */
+
+ /* at first call, adjust the initial step bound. */
+ if (!outer && pnorm < delta)
+ {
+ delta = pnorm;
+ }
+
+/*** [inner] Evaluate the function at x + p. ***/
+
+ for (j = 0; j < n; j++)
+ {
+ wa2[j] = x[j] - wa1[j];
+ }
+
+ (*evaluate)( wa2, m, data, wf, &(S->userbreak) );
+ ++(S->nfev);
+ if (S->userbreak)
+ {
+ goto terminate;
+ }
+ fnorm1 = lm_enorm(m, wf);
+
+/*** [inner] Evaluate the scaled reduction. ***/
+
+ /* actual scaled reduction */
+ actred = 1 - SQR(fnorm1/fnorm);
+
+ /* ratio of actual to predicted reduction */
+ ratio = prered ? actred/prered : 0;
+
+ if (C->verbosity == 2)
+ {
+ fprintf( msgfile, "lmmin (%i:%i) ", outer, inner );
+ lm_print_pars( nout, wa2, fnorm1, msgfile );
+ }
+ else if (C->verbosity >= 3)
+ {
+ printf( "%3i %2i %9.2g %9.2g %14.6g"
+ " %9.2g %10.3e %10.3e %21.15e",
+ outer, inner, lmpar, prered, ratio,
+ dirder, delta, pnorm, fnorm1 );
+ for (i = 0; i < nout; ++i)
+ {
+ fprintf( msgfile, " %16.9g", wa2[i] );
+ }
+ fprintf( msgfile, "\n" );
+ }
+
+ /* update the step bound */
+ if (ratio <= 0.25)
+ {
+ if (actred >= 0)
+ {
+ temp = 0.5;
+ }
+ else if (actred > -99) /* -99 = 1-1/0.1^2 */
+ {
+ temp = MAX( dirder / (2*dirder + actred), 0.1 );
+ }
+ else
+ {
+ temp = 0.1;
+ }
+ delta = temp * MIN(delta, pnorm / 0.1);
+ lmpar /= temp;
+ }
+ else if (ratio >= 0.75)
+ {
+ delta = 2*pnorm;
+ lmpar *= 0.5;
+ }
+ else if (!lmpar)
+ {
+ delta = 2*pnorm;
+ }
+
+/*** [inner] On success, update solution, and test for convergence. ***/
+
+ inner_success = ratio >= p0001;
+ if (inner_success)
+ {
+
+ /* update x, fvec, and their norms */
+ if (C->scale_diag)
+ {
+ for (j = 0; j < n; j++)
+ {
+ x[j] = wa2[j];
+ wa2[j] = diag[j] * x[j];
+ }
+ }
+ else
+ {
+ for (j = 0; j < n; j++)
+ {
+ x[j] = wa2[j];
+ }
+ }
+ for (i = 0; i < m; i++)
+ {
+ fvec[i] = wf[i];
+ }
+ xnorm = lm_enorm(n, wa2);
+ fnorm = fnorm1;
+ }
+
+ /* convergence tests */
+ S->outcome = 0;
+ if (fnorm <= LM_DWARF)
+ {
+ goto terminate; /* success: sum of squares almost zero */
+ }
+ /* test two criteria (both may be fulfilled) */
+ if (fabs(actred) <= C->ftol && prered <= C->ftol && ratio <= 2)
+ {
+ S->outcome = 1; /* success: x almost stable */
+ }
+ if (delta <= C->xtol * xnorm)
+ {
+ S->outcome += 2; /* success: sum of squares almost stable */
+ }
+ if (S->outcome != 0)
+ {
+ goto terminate;
+ }
+
+/*** [inner] Tests for termination and stringent tolerances. ***/
+
+ if (S->nfev >= maxfev)
+ {
+ S->outcome = 5;
+ goto terminate;
+ }
+ if (fabs(actred) <= LM_MACHEP &&
+ prered <= LM_MACHEP && ratio <= 2)
+ {
+ S->outcome = 6;
+ goto terminate;
+ }
+ if (delta <= LM_MACHEP*xnorm)
+ {
+ S->outcome = 7;
+ goto terminate;
+ }
+ if (gnorm <= LM_MACHEP)
+ {
+ S->outcome = 8;
+ goto terminate;
+ }
+
+/*** [inner] End of the loop. Repeat if iteration unsuccessful. ***/
+
+ ++inner;
+ }
+ while (!inner_success);
+
+/*** [outer] End of the loop. ***/
+
+ }
+ ;
+
+terminate:
+ S->fnorm = lm_enorm(m, fvec);
+ if (C->verbosity >= 2)
+ {
+ printf("lmmin outcome (%i) xnorm %g ftol %g xtol %g\n",
+ S->outcome, xnorm, C->ftol, C->xtol );
+ }
+ if (C->verbosity & 1)
+ {
+ fprintf( msgfile, "lmmin final " );
+ lm_print_pars( nout, x, S->fnorm, msgfile );
+ }
+ if (S->userbreak) /* user-requested break */
+ {
+ S->outcome = 11;
+ }
+
+/*** Deallocate the workspace. ***/
+ free(fvec);
+ free(diag);
+ free(qtf);
+ free(fjac);
+ free(wa1);
+ free(wa2);
+ free(wa3);
+ free(wf);
+ free(ipvt);
+
+} /*** lmmin. ***/
+
+
+/*****************************************************************************/
+/* lm_lmpar (determine Levenberg-Marquardt parameter) */
+/*****************************************************************************/
+
+void lm_lmpar(int n, double *r, int ldr, int *ipvt, double *diag,
+ double *qtb, double delta, double *par, double *x,
+ double *sdiag, double *aux, double *xdi)
+{
+/* Given an m by n matrix a, an n by n nonsingular diagonal
+ * matrix d, an m-vector b, and a positive number delta,
+ * the problem is to determine a value for the parameter
+ * par such that if x solves the system
+ *
+ * a*x = b and sqrt(par)*d*x = 0
+ *
+ * in the least squares sense, and dxnorm is the euclidean
+ * norm of d*x, then either par=0 and (dxnorm-delta) < 0.1*delta,
+ * or par>0 and abs(dxnorm-delta) < 0.1*delta.
+ *
+ * Using lm_qrsolv, this subroutine completes the solution of the problem
+ * if it is provided with the necessary information from the
+ * qr factorization, with column pivoting, of a. That is, if
+ * a*p = q*r, where p is a permutation matrix, q has orthogonal
+ * columns, and r is an upper triangular matrix with diagonal
+ * elements of nonincreasing magnitude, then lmpar expects
+ * the full upper triangle of r, the permutation matrix p,
+ * and the first n components of qT*b. On output
+ * lmpar also provides an upper triangular matrix s such that
+ *
+ * p^T*(a^T*a + par*d*d)*p = s^T*s.
+ *
+ * s is employed within lmpar and may be of separate interest.
+ *
+ * Only a few iterations are generally needed for convergence
+ * of the algorithm. If, however, the limit of 10 iterations
+ * is reached, then the output par will contain the best
+ * value obtained so far.
+ *
+ * parameters:
+ *
+ * n is a positive integer input variable set to the order of r.
+ *
+ * r is an n by n array. on input the full upper triangle
+ * must contain the full upper triangle of the matrix r.
+ * on OUTPUT the full upper triangle is unaltered, and the
+ * strict lower triangle contains the strict upper triangle
+ * (transposed) of the upper triangular matrix s.
+ *
+ * ldr is a positive integer input variable not less than n
+ * which specifies the leading dimension of the array r.
+ *
+ * ipvt is an integer input array of length n which defines the
+ * permutation matrix p such that a*p = q*r. column j of p
+ * is column ipvt(j) of the identity matrix.
+ *
+ * diag is an input array of length n which must contain the
+ * diagonal elements of the matrix d.
+ *
+ * qtb is an input array of length n which must contain the first
+ * n elements of the vector (q transpose)*b.
+ *
+ * delta is a positive input variable which specifies an upper
+ * bound on the euclidean norm of d*x.
+ *
+ * par is a nonnegative variable. on input par contains an
+ * initial estimate of the levenberg-marquardt parameter.
+ * on OUTPUT par contains the final estimate.
+ *
+ * x is an OUTPUT array of length n which contains the least
+ * squares solution of the system a*x = b, sqrt(par)*d*x = 0,
+ * for the output par.
+ *
+ * sdiag is an array of length n needed as workspace; on OUTPUT
+ * it contains the diagonal elements of the upper triangular matrix s.
+ *
+ * aux is a multi-purpose work array of length n.
+ *
+ * xdi is a work array of length n. On OUTPUT: diag[j] * x[j].
+ *
+ */
+ int i, iter, j, nsing;
+ double dxnorm, fp, fp_old, gnorm, parc, parl, paru;
+ double sum, temp;
+ static double p1 = 0.1;
+
+/*** lmpar: compute and store in x the gauss-newton direction. if the
+ jacobian is rank-deficient, obtain a least squares solution. ***/
+
+ nsing = n;
+ for (j = 0; j < n; j++)
+ {
+ aux[j] = qtb[j];
+ if (r[j * ldr + j] == 0 && nsing == n)
+ {
+ nsing = j;
+ }
+ if (nsing < n)
+ {
+ aux[j] = 0;
+ }
+ }
+ for (j = nsing - 1; j >= 0; j--)
+ {
+ aux[j] = aux[j] / r[j + ldr * j];
+ temp = aux[j];
+ for (i = 0; i < j; i++)
+ {
+ aux[i] -= r[j * ldr + i] * temp;
+ }
+ }
+
+ for (j = 0; j < n; j++)
+ {
+ x[ipvt[j]] = aux[j];
+ }
+
+/*** lmpar: initialize the iteration counter, evaluate the function at the
+ origin, and test for acceptance of the gauss-newton direction. ***/
+
+ for (j = 0; j < n; j++)
+ {
+ xdi[j] = diag[j] * x[j];
+ }
+ dxnorm = lm_enorm(n, xdi);
+ fp = dxnorm - delta;
+ if (fp <= p1 * delta)
+ {
+#ifdef LMFIT_DEBUG_MESSAGES
+ printf("debug lmpar nsing %d n %d, terminate (fp<p1*delta)\n",
+ nsing, n);
+#endif
+ *par = 0;
+ return;
+ }
+
+/*** lmpar: if the jacobian is not rank deficient, the newton
+ step provides a lower bound, parl, for the 0. of
+ the function. otherwise set this bound to 0.. ***/
+
+ parl = 0;
+ if (nsing >= n)
+ {
+ for (j = 0; j < n; j++)
+ {
+ aux[j] = diag[ipvt[j]] * xdi[ipvt[j]] / dxnorm;
+ }
+
+ for (j = 0; j < n; j++)
+ {
+ sum = 0.;
+ for (i = 0; i < j; i++)
+ {
+ sum += r[j * ldr + i] * aux[i];
+ }
+ aux[j] = (aux[j] - sum) / r[j + ldr * j];
+ }
+ temp = lm_enorm(n, aux);
+ parl = fp / delta / temp / temp;
+ }
+
+/*** lmpar: calculate an upper bound, paru, for the 0. of the function. ***/
+
+ for (j = 0; j < n; j++)
+ {
+ sum = 0;
+ for (i = 0; i <= j; i++)
+ {
+ sum += r[j * ldr + i] * qtb[i];
+ }
+ aux[j] = sum / diag[ipvt[j]];
+ }
+ gnorm = lm_enorm(n, aux);
+ paru = gnorm / delta;
+ if (paru == 0.)
+ {
+ paru = LM_DWARF / MIN(delta, p1);
+ }
+
+/*** lmpar: if the input par lies outside of the interval (parl,paru),
+ set par to the closer endpoint. ***/
+
+ *par = MAX(*par, parl);
+ *par = MIN(*par, paru);
+ if (*par == 0.)
+ {
+ *par = gnorm / dxnorm;
+ }
+
+/*** lmpar: iterate. ***/
+
+ for (iter = 0;; iter++)
+ {
+
+ /** evaluate the function at the current value of par. **/
+
+ if (*par == 0.)
+ {
+ *par = MAX(LM_DWARF, 0.001 * paru);
+ }
+ temp = sqrt(*par);
+ for (j = 0; j < n; j++)
+ {
+ aux[j] = temp * diag[j];
+ }
+
+ lm_qrsolv( n, r, ldr, ipvt, aux, qtb, x, sdiag, xdi );
+ /* return values are r, x, sdiag */
+
+ for (j = 0; j < n; j++)
+ {
+ xdi[j] = diag[j] * x[j]; /* used as output */
+ }
+ dxnorm = lm_enorm(n, xdi);
+ fp_old = fp;
+ fp = dxnorm - delta;
+
+ /** if the function is small enough, accept the current value
+ of par. Also test for the exceptional cases where parl
+ is zero or the number of iterations has reached 10. **/
+
+ if (fabs(fp) <= p1 * delta
+ || (parl == 0. && fp <= fp_old && fp_old < 0.)
+ || iter == 10)
+ {
+#ifdef LMFIT_DEBUG_MESSAGES
+ printf("debug lmpar nsing %d iter %d "
+ "par %.4e [%.4e %.4e] delta %.4e fp %.4e\n",
+ nsing, iter, *par, parl, paru, delta, fp);
+#endif
+ break; /* the only exit from the iteration. */
+ }
+
+ /** compute the Newton correction. **/
+
+ for (j = 0; j < n; j++)
+ {
+ aux[j] = diag[ipvt[j]] * xdi[ipvt[j]] / dxnorm;
+ }
+
+ for (j = 0; j < n; j++)
+ {
+ aux[j] = aux[j] / sdiag[j];
+ for (i = j + 1; i < n; i++)
+ {
+ aux[i] -= r[j * ldr + i] * aux[j];
+ }
+ }
+ temp = lm_enorm(n, aux);
+ parc = fp / delta / temp / temp;
+
+ /** depending on the sign of the function, update parl or paru. **/
+
+ if (fp > 0)
+ {
+ parl = MAX(parl, *par);
+ }
+ else if (fp < 0)
+ {
+ paru = MIN(paru, *par);
+ }
+ /* the case fp==0 is precluded by the break condition */
+
+ /** compute an improved estimate for par. **/
+
+ *par = MAX(parl, *par + parc);
+
+ }
+
+} /*** lm_lmpar. ***/
+
+/*****************************************************************************/
+/* lm_qrfac (QR factorization, from lapack) */
+/*****************************************************************************/
+
+void lm_qrfac(int m, int n, double *a, int *ipvt,
+ double *rdiag, double *acnorm, double *wa)
+{
+/*
+ * This subroutine uses Householder transformations with column
+ * pivoting (optional) to compute a qr factorization of the
+ * m by n matrix a. That is, qrfac determines an orthogonal
+ * matrix q, a permutation matrix p, and an upper trapezoidal
+ * matrix r with diagonal elements of nonincreasing magnitude,
+ * such that a*p = q*r. The Householder transformation for
+ * column k, k = 1,2,...,min(m,n), is of the form
+ *
+ * i - (1/u(k))*u*uT
+ *
+ * where u has zeroes in the first k-1 positions. The form of
+ * this transformation and the method of pivoting first
+ * appeared in the corresponding linpack subroutine.
+ *
+ * Parameters:
+ *
+ * m is a positive integer input variable set to the number
+ * of rows of a.
+ *
+ * n is a positive integer input variable set to the number
+ * of columns of a.
+ *
+ * a is an m by n array. On input a contains the matrix for
+ * which the qr factorization is to be computed. On OUTPUT
+ * the strict upper trapezoidal part of a contains the strict
+ * upper trapezoidal part of r, and the lower trapezoidal
+ * part of a contains a factored form of q (the non-trivial
+ * elements of the u vectors described above).
+ *
+ * ipvt is an integer OUTPUT array of length lipvt. This array
+ * defines the permutation matrix p such that a*p = q*r.
+ * Column j of p is column ipvt(j) of the identity matrix.
+ *
+ * rdiag is an OUTPUT array of length n which contains the
+ * diagonal elements of r.
+ *
+ * acnorm is an OUTPUT array of length n which contains the
+ * norms of the corresponding columns of the input matrix a.
+ * If this information is not needed, then acnorm can coincide
+ * with rdiag.
+ *
+ * wa is a work array of length n.
+ *
+ */
+ int i, j, k, kmax, minmn;
+ double ajnorm, sum, temp;
+
+/*** qrfac: compute initial column norms and initialize several arrays. ***/
+
+ for (j = 0; j < n; j++)
+ {
+ acnorm[j] = lm_enorm(m, &a[j*m]);
+ rdiag[j] = acnorm[j];
+ wa[j] = rdiag[j];
+ ipvt[j] = j;
+ }
+#ifdef LMFIT_DEBUG_MESSAGES
+ printf("debug qrfac\n");
+#endif
+
+/*** qrfac: reduce a to r with Householder transformations. ***/
+
+ minmn = MIN(m, n);
+ for (j = 0; j < minmn; j++)
+ {
+
+ /** bring the column of largest norm into the pivot position. **/
+
+ kmax = j;
+ for (k = j + 1; k < n; k++)
+ {
+ if (rdiag[k] > rdiag[kmax])
+ {
+ kmax = k;
+ }
+ }
+ if (kmax == j)
+ {
+ goto pivot_ok;
+ }
+
+ for (i = 0; i < m; i++)
+ {
+ temp = a[j*m+i];
+ a[j*m+i] = a[kmax*m+i];
+ a[kmax*m+i] = temp;
+ }
+ rdiag[kmax] = rdiag[j];
+ wa[kmax] = wa[j];
+ k = ipvt[j];
+ ipvt[j] = ipvt[kmax];
+ ipvt[kmax] = k;
+
+pivot_ok:
+ /** compute the Householder transformation to reduce the
+ j-th column of a to a multiple of the j-th unit vector. **/
+
+ ajnorm = lm_enorm(m-j, &a[j*m+j]);
+ if (ajnorm == 0.)
+ {
+ rdiag[j] = 0;
+ continue;
+ }
+
+ if (a[j*m+j] < 0.)
+ {
+ ajnorm = -ajnorm;
+ }
+ for (i = j; i < m; i++)
+ {
+ a[j*m+i] /= ajnorm;
+ }
+ a[j*m+j] += 1;
+
+ /** apply the transformation to the remaining columns
+ and update the norms. **/
+
+ for (k = j + 1; k < n; k++)
+ {
+ sum = 0;
+
+ for (i = j; i < m; i++)
+ {
+ sum += a[j*m+i] * a[k*m+i];
+ }
+
+ temp = sum / a[j + m * j];
+
+ for (i = j; i < m; i++)
+ {
+ a[k*m+i] -= temp * a[j*m+i];
+ }
+
+ if (rdiag[k] != 0.)
+ {
+ temp = a[m * k + j] / rdiag[k];
+ temp = MAX(0., 1 - temp * temp);
+ rdiag[k] *= sqrt(temp);
+ temp = rdiag[k] / wa[k];
+ if (0.05 * SQR(temp) <= LM_MACHEP)
+ {
+ rdiag[k] = lm_enorm(m-j-1, &a[m*k+j+1]);
+ wa[k] = rdiag[k];
+ }
+ }
+ }
+
+ rdiag[j] = -ajnorm;
+ }
+} /*** lm_qrfac. ***/
+
+
+/*****************************************************************************/
+/* lm_qrsolv (linear least-squares) */
+/*****************************************************************************/
+
+void lm_qrsolv(int n, double *r, int ldr, int *ipvt, double *diag,
+ double *qtb, double *x, double *sdiag, double *wa)
+{
+/*
+ * Given an m by n matrix a, an n by n diagonal matrix d,
+ * and an m-vector b, the problem is to determine an x which
+ * solves the system
+ *
+ * a*x = b and d*x = 0
+ *
+ * in the least squares sense.
+ *
+ * This subroutine completes the solution of the problem
+ * if it is provided with the necessary information from the
+ * qr factorization, with column pivoting, of a. That is, if
+ * a*p = q*r, where p is a permutation matrix, q has orthogonal
+ * columns, and r is an upper triangular matrix with diagonal
+ * elements of nonincreasing magnitude, then qrsolv expects
+ * the full upper triangle of r, the permutation matrix p,
+ * and the first n components of (q transpose)*b. The system
+ * a*x = b, d*x = 0, is then equivalent to
+ *
+ * r*z = q^T*b, p^T*d*p*z = 0,
+ *
+ * where x = p*z. If this system does not have full rank,
+ * then a least squares solution is obtained. On output qrsolv
+ * also provides an upper triangular matrix s such that
+ *
+ * p^T *(a^T *a + d*d)*p = s^T *s.
+ *
+ * s is computed within qrsolv and may be of separate interest.
+ *
+ * Parameters
+ *
+ * n is a positive integer input variable set to the order of r.
+ *
+ * r is an n by n array. On input the full upper triangle
+ * must contain the full upper triangle of the matrix r.
+ * On OUTPUT the full upper triangle is unaltered, and the
+ * strict lower triangle contains the strict upper triangle
+ * (transposed) of the upper triangular matrix s.
+ *
+ * ldr is a positive integer input variable not less than n
+ * which specifies the leading dimension of the array r.
+ *
+ * ipvt is an integer input array of length n which defines the
+ * permutation matrix p such that a*p = q*r. Column j of p
+ * is column ipvt(j) of the identity matrix.
+ *
+ * diag is an input array of length n which must contain the
+ * diagonal elements of the matrix d.
+ *
+ * qtb is an input array of length n which must contain the first
+ * n elements of the vector (q transpose)*b.
+ *
+ * x is an OUTPUT array of length n which contains the least
+ * squares solution of the system a*x = b, d*x = 0.
+ *
+ * sdiag is an OUTPUT array of length n which contains the
+ * diagonal elements of the upper triangular matrix s.
+ *
+ * wa is a work array of length n.
+ *
+ */
+ int i, kk, j, k, nsing;
+ double qtbpj, sum, temp;
+ double _sin, _cos, _tan, _cot; /* local variables, not functions */
+
+/*** qrsolv: copy r and q^T*b to preserve input and initialize s.
+ in particular, save the diagonal elements of r in x. ***/
+
+ for (j = 0; j < n; j++)
+ {
+ for (i = j; i < n; i++)
+ {
+ r[j * ldr + i] = r[i * ldr + j];
+ }
+ x[j] = r[j * ldr + j];
+ wa[j] = qtb[j];
+ }
+/*** qrsolv: eliminate the diagonal matrix d using a Givens rotation. ***/
+
+ for (j = 0; j < n; j++)
+ {
+
+/*** qrsolv: prepare the row of d to be eliminated, locating the
+ diagonal element using p from the qr factorization. ***/
+
+ if (diag[ipvt[j]] == 0.)
+ {
+ goto L90;
+ }
+ for (k = j; k < n; k++)
+ {
+ sdiag[k] = 0.;
+ }
+ sdiag[j] = diag[ipvt[j]];
+
+/*** qrsolv: the transformations to eliminate the row of d modify only
+ a single element of qT*b beyond the first n, which is initially 0. ***/
+
+ qtbpj = 0.;
+ for (k = j; k < n; k++)
+ {
+
+ /** determine a Givens rotation which eliminates the
+ appropriate element in the current row of d. **/
+
+ if (sdiag[k] == 0.)
+ {
+ continue;
+ }
+ kk = k + ldr * k;
+ if (fabs(r[kk]) < fabs(sdiag[k]))
+ {
+ _cot = r[kk] / sdiag[k];
+ _sin = 1 / sqrt(1 + SQR(_cot));
+ _cos = _sin * _cot;
+ }
+ else
+ {
+ _tan = sdiag[k] / r[kk];
+ _cos = 1 / sqrt(1 + SQR(_tan));
+ _sin = _cos * _tan;
+ }
+
+ /** compute the modified diagonal element of r and
+ the modified element of ((q^T)*b,0). **/
+
+ r[kk] = _cos * r[kk] + _sin * sdiag[k];
+ temp = _cos * wa[k] + _sin * qtbpj;
+ qtbpj = -_sin * wa[k] + _cos * qtbpj;
+ wa[k] = temp;
+
+ /** accumulate the tranformation in the row of s. **/
+
+ for (i = k + 1; i < n; i++)
+ {
+ temp = _cos * r[k * ldr + i] + _sin * sdiag[i];
+ sdiag[i] = -_sin * r[k * ldr + i] + _cos * sdiag[i];
+ r[k * ldr + i] = temp;
+ }
+ }
+
+L90:
+ /** store the diagonal element of s and restore
+ the corresponding diagonal element of r. **/
+
+ sdiag[j] = r[j * ldr + j];
+ r[j * ldr + j] = x[j];
+ }
+
+/*** qrsolv: solve the triangular system for z. if the system is
+ singular, then obtain a least squares solution. ***/
+
+ nsing = n;
+ for (j = 0; j < n; j++)
+ {
+ if (sdiag[j] == 0. && nsing == n)
+ {
+ nsing = j;
+ }
+ if (nsing < n)
+ {
+ wa[j] = 0;
+ }
+ }
+
+ for (j = nsing - 1; j >= 0; j--)
+ {
+ sum = 0;
+ for (i = j + 1; i < nsing; i++)
+ {
+ sum += r[j * ldr + i] * wa[i];
+ }
+ wa[j] = (wa[j] - sum) / sdiag[j];
+ }
+
+/*** qrsolv: permute the components of z back to components of x. ***/
+
+ for (j = 0; j < n; j++)
+ {
+ x[ipvt[j]] = wa[j];
+ }
+
+} /*** lm_qrsolv. ***/
+
+
+/*****************************************************************************/
+/* lm_enorm (Euclidean norm) */
+/*****************************************************************************/
+
+double lm_enorm(int n, const double *x)
+{
+/* Given an n-vector x, this function calculates the
+ * euclidean norm of x.
+ *
+ * The euclidean norm is computed by accumulating the sum of
+ * squares in three different sums. The sums of squares for the
+ * small and large components are scaled so that no overflows
+ * occur. Non-destructive underflows are permitted. Underflows
+ * and overflows do not occur in the computation of the unscaled
+ * sum of squares for the intermediate components.
+ * The definitions of small, intermediate and large components
+ * depend on two constants, LM_SQRT_DWARF and LM_SQRT_GIANT. The main
+ * restrictions on these constants are that LM_SQRT_DWARF**2 not
+ * underflow and LM_SQRT_GIANT**2 not overflow.
+ *
+ * Parameters
+ *
+ * n is a positive integer input variable.
+ *
+ * x is an input array of length n.
+ */
+ int i;
+ double agiant, s1, s2, s3, xabs, x1max, x3max, temp;
+
+ s1 = 0;
+ s2 = 0;
+ s3 = 0;
+ x1max = 0;
+ x3max = 0;
+ agiant = LM_SQRT_GIANT / n;
+
+ /** sum squares. **/
+
+ for (i = 0; i < n; i++)
+ {
+ xabs = fabs(x[i]);
+ if (xabs > LM_SQRT_DWARF)
+ {
+ if (xabs < agiant)
+ {
+ s2 += xabs * xabs;
+ }
+ else if (xabs > x1max)
+ {
+ temp = x1max / xabs;
+ s1 = 1 + s1 * SQR(temp);
+ x1max = xabs;
+ }
+ else
+ {
+ temp = xabs / x1max;
+ s1 += SQR(temp);
+ }
+ }
+ else if (xabs > x3max)
+ {
+ temp = x3max / xabs;
+ s3 = 1 + s3 * SQR(temp);
+ x3max = xabs;
+ }
+ else if (xabs != 0.)
+ {
+ temp = xabs / x3max;
+ s3 += SQR(temp);
+ }
+ }
+
+ /** calculation of norm. **/
+
+ if (s1 != 0)
+ {
+ return x1max * sqrt(s1 + (s2 / x1max) / x1max);
+ }
+ else if (s2 != 0)
+ {
+ if (s2 >= x3max)
+ {
+ return sqrt(s2 * (1 + (x3max / s2) * (x3max * s3)));
+ }
+ else
+ {
+ return sqrt(x3max * ((s2 / x3max) + (x3max * s3)));
+ }
+ }
+ else
+ {
+ return x3max * sqrt(s3);
+ }
+
+} /*** lm_enorm. ***/
--- /dev/null
+/*
+ * Library: lmfit (Levenberg-Marquardt least squares fitting)
+ *
+ * File: lmmin.h
+ *
+ * Contents: Declarations for Levenberg-Marquardt minimization.
+ *
+ * Copyright: Joachim Wuttke, Forschungszentrum Juelich GmbH (2004-2013)
+ *
+ * License: see ../COPYING (FreeBSD)
+ *
+ * Homepage: apps.jcns.fz-juelich.de/lmfit
+ */
+
+#ifndef LMMIN_H
+#define LMMIN_H
+#undef __BEGIN_DECLS
+#undef __END_DECLS
+#ifdef __cplusplus
+# define __BEGIN_DECLS extern "C" {
+# define __END_DECLS }
+#else
+# define __BEGIN_DECLS /* empty */
+# define __END_DECLS /* empty */
+#endif
+
+#include "lmstruct.h"
+
+__BEGIN_DECLS
+
+/*! \brief
+ * Levenberg-Marquardt minimization.
+ *
+ * This routine contains the core algorithm of our library.
+ *
+ * It minimizes the sum of the squares of m nonlinear functions
+ * in n variables by a modified Levenberg-Marquardt algorithm.
+ * The function evaluation is done by the user-provided routine 'evaluate'.
+ * The Jacobian is then calculated by a forward-difference approximation.
+ *
+ * Parameters:
+ *
+ * \param[in] n_par The number of variables (INPUT, positive integer).
+ * \param par The parameters to be fitted
+ * x is the solution vector (INPUT/OUTPUT, array of length n).
+ * On input it must be set to an estimated solution.
+ * On output it yields the final estimate of the solution.
+ *
+ * m is the number of functions to be minimized (INPUT, positive integer).
+ * It must fulfill m>=n.
+ *
+ * data is a pointer that is ignored by lmmin; it is however forwarded
+ * to the user-supplied functions evaluate and printout.
+ * In a typical application, it contains experimental data to be fitted.
+ *
+ * evaluate is a user-supplied function that calculates the m functions.
+ * Parameters:
+ * n, x, m, data as above.
+ * fvec is an array of length m; on OUTPUT, it must contain the
+ * m function values for the parameter vector x.
+ * userbreak is an integer pointer. When *userbreak is set to a
+ * nonzero value, lmmin will terminate.
+ *
+ * control contains INPUT variables that control the fit algorithm,
+ * as declared and explained in lmstruct.h
+ *
+ * status contains OUTPUT variables that inform about the fit result,
+ * as declared and explained in lmstruct.h
+ */
+void lmmin( int n_par, double *par, int m_dat, const void *data,
+ void (*evaluate) (const double *par, int m_dat, const void *data,
+ double *fvec, int *userbreak),
+ const lm_control_struct *control, lm_status_struct *status );
+
+/* Refined calculation of Eucledian norm. */
+double lm_enorm( int, const double * );
+
+__END_DECLS
+#endif /* LMMIN_H */
--- /dev/null
+/*
+ * Library: lmfit (Levenberg-Marquardt least squares fitting)
+ *
+ * File: lmstruct.h
+ *
+ * Contents: Declarations of parameter records, used in lmmin.h and lmcurve.h
+ *
+ * Copyright: Joachim Wuttke, Forschungszentrum Juelich GmbH (2004-2013)
+ *
+ * License: see ../COPYING (FreeBSD)
+ *
+ * Homepage: apps.jcns.fz-juelich.de/lmfit
+ */
+
+#ifndef LMSTRUCT_H
+#define LMSTRUCT_H
+#undef __BEGIN_DECLS
+#undef __END_DECLS
+#ifdef __cplusplus
+# define __BEGIN_DECLS extern "C" {
+# define __END_DECLS }
+#else
+# define __BEGIN_DECLS /* empty */
+# define __END_DECLS /* empty */
+#endif
+__BEGIN_DECLS
+
+#include <stdio.h>
+
+/* Collection of input parameters for fit control. */
+typedef struct {
+ double ftol; /* Relative error desired in the sum of squares.
+ Termination occurs when both the actual and
+ predicted relative reductions in the sum of squares
+ are at most ftol. */
+ double xtol; /* Relative error between last two approximations.
+ Termination occurs when the relative error between
+ two consecutive iterates is at most xtol. */
+ double gtol; /* Orthogonality desired between fvec and its derivs.
+ Termination occurs when the cosine of the angle
+ between fvec and any column of the Jacobian is at
+ most gtol in absolute value. */
+ double epsilon; /* Step used to calculate the Jacobian, should be
+ slightly larger than the relative error in the
+ user-supplied functions. */
+ double stepbound; /* Used in determining the initial step bound. This
+ bound is set to the product of stepbound and the
+ Euclidean norm of diag*x if nonzero, or else to
+ stepbound itself. In most cases stepbound should lie
+ in the interval (0.1,100.0). Generally, the value
+ 100.0 is recommended. */
+ int patience; /* Used to set the maximum number of function evaluations
+ to patience*(number_of_parameters+1). */
+ int scale_diag; /* If 1, the variables will be rescaled internally.
+ Recommended value is 1. */
+ FILE* msgfile; /* Progress messages will be written to this file. */
+ int verbosity; /* OR'ed: 1: print some messages; 2: print Jacobian. */
+ int n_maxpri; /* -1, or max number of parameters to print. */
+ int m_maxpri; /* -1, or max number of residuals to print. */
+} lm_control_struct;
+
+/* Collection of output parameters for status info. */
+typedef struct {
+ double fnorm; /* norm of the residue vector fvec. */
+ int nfev; /* actual number of iterations. */
+ int outcome; /* Status indicator. Nonnegative values are used as index
+ for the message text lm_infmsg, set in lmmin.c. */
+ int userbreak; /* Set when function evaluation requests termination. */
+} lm_status_struct;
+
+/* Preset (and recommended) control parameter settings. */
+extern const lm_control_struct lm_control_double;
+extern const lm_control_struct lm_control_float;
+
+/* Preset message texts. */
+
+extern const char *lm_infmsg[];
+extern const char *lm_shortmsg[];
+
+__END_DECLS
+#endif /* LMSTRUCT_H */
#ifndef TMPI_MPI_BINDINGS_H_
#define TMPI_MPI_BINDINGS_H_
+#include "tmpi.h"
+
/** \file
\brief MPI bindings for thread_mpi/tmpi.h
CPU_ZERO(&set);
CPU_SET(nr, &set);
return pthread_setaffinity_np(thread->th, sizeof(set), &set);
-#endif
+#else
return 0;
+#endif
}
if("${CMAKE_C_COMPILER_ID}" STREQUAL "GNU")
set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -Wall")
-elseif(WIN32 AND NOT CYGWIN)
+elseif(WIN32)
set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} /W2")
endif()
#ifndef PRId64
# define PRId64 __PRI64_PREFIX "d"
#endif
+#ifndef PRIu64
+# define PRIu64 __PRI64_PREFIX "u"
+#endif
#endif
#else
/* Define storage for little-endian or both types of CPUs. */
md5_word_t xbuf[16];
- /* cppcheck-suppress unassignedVariable */
const md5_word_t *X;
#endif
sizeof(struct tng_molecule));
if(!tng_data->molecules)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
tng_data->n_molecules * sizeof(struct tng_molecule),
__FILE__, __LINE__);
return(TNG_CRITICAL);
tng_data->n_molecules);
if(!tng_data->molecule_cnt_list)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
tng_data->n_molecules * sizeof(struct tng_molecule),
__FILE__, __LINE__);
return(TNG_CRITICAL);
sizeof(struct tng_chain));
if(!molecule->chains)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
molecule->n_chains * sizeof(struct tng_chain),
__FILE__, __LINE__);
return(TNG_CRITICAL);
sizeof(struct tng_residue));
if(!molecule->residues)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
molecule->n_residues * sizeof(struct tng_residue),
__FILE__, __LINE__);
if(molecule->chains)
sizeof(struct tng_atom));
if(!molecule->atoms)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
molecule->n_atoms * sizeof(struct tng_atom),
__FILE__, __LINE__);
if(molecule->chains)
sizeof(struct tng_bond));
if(!molecule->bonds)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
molecule->n_bonds * sizeof(struct tng_bond),
__FILE__, __LINE__);
if(molecule->chains)
if(!frame_set->molecule_cnt_list)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(int64_t) * tng_data->n_molecules,
__FILE__, __LINE__);
return(TNG_CRITICAL);
temp_name = realloc(block->name, name_len + 1);
if(!temp_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%u bytes). %s: %d\n",
name_len+1, __FILE__, __LINE__);
free(block->name);
block->name = 0;
sizeof(int64_t));
if(!mapping->real_particle_numbers)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
mapping->n_particles * sizeof(int64_t), __FILE__, __LINE__);
return(TNG_CRITICAL);
}
temp_name = realloc(block->name, name_len + 1);
if(!temp_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%u bytes). %s: %d\n",
name_len+1, __FILE__, __LINE__);
free(block->name);
block->name = 0;
dest = malloc(max_len);
if(!dest)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ld bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%lu bytes). %s: %d\n",
max_len, __FILE__, __LINE__);
return(TNG_CRITICAL);
}
n_particles);
if(!data->strings[i])
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(union data_values *) * n_particles,
__FILE__, __LINE__);
return(TNG_CRITICAL);
n_values_per_frame);
if(!data->strings[i][j])
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(union data_values) * n_values_per_frame,
__FILE__, __LINE__);
return(TNG_CRITICAL);
temp_name = realloc(block->name, len);
if(!temp_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n", len+1,
+ fprintf(stderr, "TNG library: Cannot allocate memory (%u bytes). %s: %d\n", len+1,
__FILE__, __LINE__);
free(block->name);
block->name = 0;
if(!new_molecules)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(struct tng_molecule) * (tng_data->n_molecules + 1),
__FILE__, __LINE__);
free(tng_data->molecules);
if(!new_molecule_cnt_list)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(int64_t) * (tng_data->n_molecules + 1),
__FILE__, __LINE__);
free(tng_data->molecule_cnt_list);
if(!new_molecules)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(struct tng_molecule) * (tng_data->n_molecules + 1),
__FILE__, __LINE__);
free(tng_data->molecules);
if(!new_molecule_cnt_list)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(int64_t) * (tng_data->n_molecules + 1),
__FILE__, __LINE__);
free(tng_data->molecule_cnt_list);
sizeof(struct tng_molecule) * tng_data_src->n_molecules);
if(!molecule_temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(struct tng_molecule) * tng_data_src->n_molecules,
__FILE__, __LINE__);
free(tng_data_dest->molecules);
sizeof(int64_t) * tng_data_src->n_molecules);
if(!list_temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(int64_t) * tng_data_src->n_molecules,
__FILE__, __LINE__);
free(tng_data_dest->molecule_cnt_list);
molecule->n_bonds);
if(!bond_temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(struct tng_bond) * molecule->n_bonds,
__FILE__, __LINE__);
free(molecule_temp->bonds);
if(!new_chains)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(struct tng_chain) * (molecule->n_chains + 1),
__FILE__, __LINE__);
free(molecule->chains);
if(!new_bonds)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(struct tng_bond) * (molecule->n_bonds + 1),
__FILE__, __LINE__);
*bond = 0;
if(!new_residues)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(struct tng_residue) * (molecule->n_residues + 1),
__FILE__, __LINE__);
free(molecule->residues);
if(!new_atoms)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(struct tng_atom) * (molecule->n_atoms + 1),
__FILE__, __LINE__);
free(molecule->atoms);
*from_atoms = malloc(sizeof(int64_t) * (*n_bonds));
if(!*from_atoms)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(int64_t) * (*n_bonds), __FILE__, __LINE__);
return(TNG_CRITICAL);
}
*to_atoms = malloc(sizeof(int64_t) * (*n_bonds));
if(!*to_atoms)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(int64_t) * (*n_bonds), __FILE__, __LINE__);
free(*from_atoms);
*from_atoms = 0;
if(!mapping)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(struct tng_particle_mapping)*frame_set->n_mapping_blocks,
__FILE__, __LINE__);
free(frame_set->mappings);
frame_set->mappings[frame_set->n_mapping_blocks - 1].real_particle_numbers = malloc(sizeof(int64_t) * n_particles);
if(!frame_set->mappings[frame_set->n_mapping_blocks - 1].real_particle_numbers)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(int64_t) * n_particles, __FILE__, __LINE__);
return(TNG_CRITICAL);
}
*values = malloc(sizeof(union data_values *) * n_frames);
if(!*values)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(union data_values **) * n_frames,
__FILE__, __LINE__);
return(TNG_CRITICAL);
n_values_per_frame);
if(!(*values)[i])
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(union data_values) * n_values_per_frame,
__FILE__, __LINE__);
free(values);
*values = malloc(sizeof(union data_values **) * n_frames);
if(!*values)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(union data_values **) * n_frames,
__FILE__, __LINE__);
return(TNG_CRITICAL);
n_particles);
if(!(*values)[i])
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(union data_values *) * n_particles,
__FILE__, __LINE__);
free(*values);
n_values_per_frame);
if(!(*values)[i][j])
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(union data_values *) * n_particles,
__FILE__, __LINE__);
tng_particle_data_values_free(tng_data, *values, n_frames,
temp = realloc(*data_block_ids_in_next_frame, size);
if(!temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(int64_t) * (*n_data_blocks_in_next_frame),
__FILE__, __LINE__);
free(*data_block_ids_in_next_frame);
temp = realloc(*data_block_ids_in_next_frame, size);
if(!temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(int64_t) * (*n_data_blocks_in_next_frame),
__FILE__, __LINE__);
free(*data_block_ids_in_next_frame);
temp = realloc(*data_block_ids_in_next_frame, size);
if(!temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
sizeof(int64_t) * (*n_data_blocks_in_next_frame),
__FILE__, __LINE__);
free(*data_block_ids_in_next_frame);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2012, The GROMACS development team.
- * Copyright (c) 2012,2014, by the GROMACS development team, led by
+ * Copyright (c) 2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \libinternal \file
+ * \brief
+ * Configuration macros from the build system for gmxpre.h.
+ *
+ * This header is an internal implementation detail of gmxpre.h, and should not
+ * be included from anywhere else.
+ *
+ * \see gmxpre.h
+ */
-#ifndef _fatal_collective_h
-#define _fatal_collective_h
-
-#include "typedefs.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
+/* Define to 1 to make fseeko visible on some hosts (e.g. glibc 2.2). */
+#cmakedefine _LARGEFILE_SOURCE
+/* Define for large files, on AIX-style hosts. */
+#cmakedefine _LARGE_FILES
-void
-gmx_fatal_collective(int f_errno, const char *file, int line,
- const t_commrec *cr, gmx_domdec_t *dd,
- const char *fmt, ...);
-/* As gmx_fatal declared in gmx_fatal.h,
- * but only the master process prints the error message.
- * This should only be called one of the following two situations:
- * 1) On all nodes in cr->mpi_comm_mysim, with cr!=NULL,dd==NULL.
- * 2) On all nodes in dd->mpi_comm_all, with cr==NULL,dd!=NULL.
- * This will call MPI_Finalize instead of MPI_Abort when possible,
- * This is useful for handling errors in code that is executed identically
- * for all processes.
- */
+/* Some systems requires this to be set to 64 for large file support */
+#cmakedefine _FILE_OFFSET_BITS @_FILE_OFFSET_BITS@
+/* Build special-purpose mdrun library */
+#cmakedefine GMX_FAHCORE
-#ifdef __cplusplus
-}
-#endif
+/* This is here for simplicity, since the layout for some thread-MPI structs
+ * declared in headers depend on this being consistently defined.
+ * But thread-MPI itself does not include gmxpre.h, so the same define is also
+ * set in config.h (which gets included by thread-MPI, but only in the source
+ * files). There are some other config.h defines that appear in thread-MPI
+ * headers, but currently Gromacs does not use any code that would depend on
+ * those, and for thread-MPI, config.h provides the definitions wherever
+ * required. */
+/* Define for busy wait option */
+#cmakedefine TMPI_WAIT_FOR_NO_ONE
-#endif /* _fatal_collective_h */
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Prerequisite header file for \Gromacs build.
+ *
+ * This header should be included as the first header in all source files, but
+ * not in header files. It is intended to contain definitions that must appear
+ * before any other code to work properly (e.g., macro definitions that
+ * influence behavior of system headers). This frees other code from include
+ * order dependencies that may raise from requirements of getting these
+ * definitions from some header.
+ *
+ * The definitions here should be kept to a minimum, and should be as static as
+ * possible (typically not change as a result of user choices in the build
+ * system), as any change will trigger a full rebuild. Avoid including any
+ * actual headers to not hide problems with include-what-you-use, and to keep
+ * build times to a minimum. Also, installer headers should avoid relying on
+ * the definitions from here (if possible), as this header will not be
+ * available to the user.
+ *
+ * \inlibraryapi
+ */
+//! \cond
+#ifdef HAVE_CONFIG_H
+#include "gmxpre-config.h"
+#endif
+
+/* We use a few GNU functions for thread affinity and other low-level stuff.
+ * However, all such uses should be accompanied by #ifdefs and a feature test
+ * at CMake level, so that the actual uses will be compiled only when available.
+ * But since the define affects system headers, it should be defined before
+ * including any system headers, and this is a robust location to do that.
+ * If this were defined only in source files that needed it, it would clutter
+ * the list of includes somewhere close to the beginning and make automatic
+ * sorting of the includes more difficult.
+ */
+#ifndef _GNU_SOURCE
+#define _GNU_SOURCE 1
+#endif
+
+/* Some C++(?) compilers require these to be defined to get the integer limits
+ * and format specifier macros from stdint.h and inttypes.h, respectively.
+ * The macros are in C99 and C++11, but not in C++98...
+ * As with _GNU_SOURCE, these need to be defined before these headers get first
+ * included. Unlike _GNU_SOURCE, these headers are included indirectly in most
+ * header and source files (even though the macros are not used that often), so
+ * there is no easy alternative to defining them here, either.
+ * If someone happens to use such a compiler to compile against the installed
+ * Gromacs headers, they need for now take care to define the macros themselves
+ * (as there is no way Gromacs can do that consistently).
+ */
+#define __STDC_LIMIT_MACROS
+#define __STDC_FORMAT_MACROS
+
+#ifdef GMX_FAHCORE
+#define FULLINDIRECT 1
+#define USE_FAH_XDR 1
+#include "swindirect.h"
+#endif
+//! \endcond
set(LIBGROMACS_SOURCES)
-function (gmx_install_headers DESTINATION)
+set_property(GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
+
+function (gmx_install_headers)
if (NOT GMX_BUILD_MDRUN_ONLY)
- if (DESTINATION)
- set(DESTINATION ${INCL_INSTALL_DIR}/gromacs/${DESTINATION})
+ file(RELATIVE_PATH _dest ${PROJECT_SOURCE_DIR}/src ${CMAKE_CURRENT_LIST_DIR})
+ install(FILES ${ARGN}
+ DESTINATION "${INCL_INSTALL_DIR}/${_dest}"
+ COMPONENT development)
+ endif()
+ foreach (_file ${ARGN})
+ if (IS_ABSOLUTE "${_file}")
+ set_property(GLOBAL APPEND PROPERTY GMX_INSTALLED_HEADERS ${_file})
else()
- set(DESTINATION ${INCL_INSTALL_DIR}/gromacs)
+ set_property(GLOBAL APPEND PROPERTY GMX_INSTALLED_HEADERS
+ ${CMAKE_CURRENT_LIST_DIR}/${_file})
endif()
- install(FILES ${ARGN} DESTINATION ${DESTINATION} COMPONENT development)
- endif()
+ endforeach()
endfunction ()
+function (gmx_write_installed_header_list)
+ get_property(_list GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
+ string(REPLACE ";" "\n" _list "${_list}")
+ # TODO: Make this only update the file timestamp if the contents actually change.
+ file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/installed-headers.txt "${_list}")
+endfunction()
+
if(GMX_USE_TNG)
option(GMX_EXTERNAL_TNG "Use external TNG instead of compiling the version shipped with GROMACS."
OFF)
add_subdirectory(gmxlib)
add_subdirectory(mdlib)
add_subdirectory(gmxpreprocess)
+add_subdirectory(listed-forces)
add_subdirectory(commandline)
+add_subdirectory(domdec)
+add_subdirectory(ewald)
add_subdirectory(fft)
add_subdirectory(linearalgebra)
add_subdirectory(math)
add_subdirectory(random)
add_subdirectory(onlinehelp)
add_subdirectory(options)
+add_subdirectory(pbcutil)
add_subdirectory(timing)
+add_subdirectory(topology)
add_subdirectory(utility)
add_subdirectory(fileio)
add_subdirectory(swap)
if (NOT GMX_BUILD_MDRUN_ONLY)
add_subdirectory(legacyheaders)
add_subdirectory(gmxana)
+ add_subdirectory(correlationfunctions)
add_subdirectory(statistics)
add_subdirectory(analysisdata)
add_subdirectory(selection)
tmpi_get_source_list(THREAD_MPI_SOURCES ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/src)
list(APPEND LIBGROMACS_SOURCES ${THREAD_MPI_SOURCES})
-file(GLOB LIBGROMACS_HEADERS *.h)
configure_file(version.h.cmakein version.h)
-gmx_install_headers("" ${LIBGROMACS_HEADERS})
-gmx_install_headers("" ${CMAKE_CURRENT_BINARY_DIR}/version.h)
-
-# Add target that generates baseversion-gen.c every time make is run
-# if git version info is requested, or create it statically.
-# This code is here instead of utility/CMakeLists.txt because CMake
-# ignores set_source_file_properties from subdirectories.
-set(GENERATED_VERSION_FILE
- ${CMAKE_CURRENT_BINARY_DIR}/utility/baseversion-gen.c)
-set(GENERATED_VERSION_FILE_SOURCE
- ${CMAKE_CURRENT_SOURCE_DIR}/utility/baseversion-gen.c.cmakein)
-if (GMX_GIT_VERSION_INFO)
- add_custom_target(gmx-version ALL
- COMMAND ${CMAKE_COMMAND}
- -D GIT_EXECUTABLE="${GIT_EXECUTABLE}"
- -D PROJECT_VERSION="${PROJECT_VERSION}"
- -D PROJECT_SOURCE_DIR="${PROJECT_SOURCE_DIR}"
- -D VERSION_CMAKEIN=${GENERATED_VERSION_FILE_SOURCE}
- -D VERSION_OUT=${GENERATED_VERSION_FILE}
- -P ${CMAKE_SOURCE_DIR}/cmake/gmxGenerateVersionInfo.cmake
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
- DEPENDS ${GENERATED_VERSION_FILE_SOURCE}
- COMMENT "Generating git version information")
- set_source_files_properties(${GENERATED_VERSION_FILE}
- PROPERTIES GENERATED true)
-else()
- set(GMX_PROJECT_VERSION_STR ${PROJECT_VERSION})
- configure_file(${GENERATED_VERSION_FILE_SOURCE} ${GENERATED_VERSION_FILE})
-endif()
+gmx_install_headers(
+ analysisdata.h
+ commandline.h
+ options.h
+ selection.h
+ trajectoryanalysis.h
+ utility.h
+ ${CMAKE_CURRENT_BINARY_DIR}/version.h
+ )
+
+# This code is here instead of utility/CMakeLists.txt, because CMake
+# custom commands and source file properties can only be set in the directory
+# that contains the target that uses them.
+# TODO: Generate a header instead that can be included from baseversion.c.
+# That probably simplifies things somewhat.
+set(GENERATED_VERSION_FILE utility/baseversion-gen.c)
+gmx_configure_version_file(
+ utility/baseversion-gen.c.cmakein ${GENERATED_VERSION_FILE}
+ REMOTE_HASH SOURCE_FILE)
list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE})
# apply gcc 4.4.x bug workaround
if(GMX_USE_GCC44_BUG_WORKAROUND)
include(gmxGCC44O3BugWorkaround)
- gmx_apply_gcc44_bug_workaround("gmxlib/bondfree.c")
+ gmx_apply_gcc44_bug_workaround("listed-forces/bonded.cpp")
gmx_apply_gcc44_bug_workaround("mdlib/force.c")
gmx_apply_gcc44_bug_workaround("mdlib/constr.c")
endif()
-add_library(libgromacs ${LIBGROMACS_SOURCES})
-if (GMX_GIT_VERSION_INFO)
- add_dependencies(libgromacs gmx-version)
+if (GMX_GPU)
+ cuda_add_library(libgromacs ${LIBGROMACS_SOURCES}
+ OPTIONS
+ RELWITHDEBINFO -g
+ DEBUG -g -D_DEBUG_=1)
+else()
+ add_library(libgromacs ${LIBGROMACS_SOURCES})
endif()
# Recent versions of gcc and clang give warnings on scanner.cpp, which
target_link_libraries(libgromacs
${EXTRAE_LIBRARIES}
- ${GMX_GPU_LIBRARIES}
${GMX_EXTRA_LIBRARIES}
${TNG_IO_LIBRARIES}
${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
VERSION ${LIBRARY_VERSION}
COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+gmx_write_installed_header_list()
+
# Only install the library in mdrun-only mode if it is actually necessary
# for the binary
if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
install(TARGETS libgromacs
- LIBRARY DESTINATION ${LIB_INSTALL_DIR}
- RUNTIME DESTINATION ${BIN_INSTALL_DIR}
- ARCHIVE DESTINATION ${LIB_INSTALL_DIR}
- COMPONENT libraries)
+ EXPORT libgromacs
+ LIBRARY DESTINATION ${LIB_INSTALL_DIR}
+ RUNTIME DESTINATION ${BIN_INSTALL_DIR}
+ ARCHIVE DESTINATION ${LIB_INSTALL_DIR}
+ COMPONENT libraries)
endif()
if (NOT GMX_BUILD_MDRUN_ONLY)
- configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libgromacs.pc.cmakein
- ${CMAKE_CURRENT_BINARY_DIR}/libgromacs.pc @ONLY)
- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgromacs.pc
- DESTINATION ${LIB_INSTALL_DIR}/pkgconfig
- RENAME "libgromacs${GMX_LIBS_SUFFIX}.pc"
- COMPONENT development)
+ include(InstallLibInfo.cmake)
endif()
if (INSTALL_CUDART_LIB) #can be set manual by user
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+function (do_pkgconfig)
+ set(PKG_CFLAGS "")
+ foreach (_dir ${INSTALLED_HEADER_INCLUDE_DIRS})
+ if (IS_ABSOLUTE ${_dir})
+ set(PKG_CFLAGS "${PKG_CFLAGS} -I${_dir}")
+ else()
+ set(PKG_CFLAGS "${PKG_CFLAGS} -I${CMAKE_INSTALL_PREFIX}/${_dir}")
+ endif()
+ endforeach()
+ if (INSTALLED_HEADER_DEFINITIONS)
+ foreach (_def ${INSTALLED_HEADER_DEFINITIONS})
+ set(PKG_CFLAGS "${PKG_CFLAGS} ${_def}")
+ endforeach()
+ endif()
+ set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
+
+ configure_file(libgromacs.pc.cmakein
+ libgromacs.pc @ONLY)
+ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libgromacs.pc
+ DESTINATION ${PKGCONFIG_INSTALL_DIR}
+ RENAME "libgromacs${GMX_LIBS_SUFFIX}.pc"
+ COMPONENT development)
+endfunction()
+
+function (do_cmake_config)
+ # Install everything into a subdirectory, because
+ # 1. CMake expects things to be there for CMAKE_PREFIX_PATH to work, and
+ # 2. This nicely isolates files for different suffixes from each other.
+ set(CMAKE_PACKAGE_DIR ${CMAKE_INSTALL_DIR}/gromacs${GMX_LIBS_SUFFIX})
+
+ # Install import definitions that take care of the library locations and
+ # library dependencies.
+ set(EXPORT_FILE_NAME libgromacs.cmake)
+ if (NOT BUILD_SHARED_LIBS)
+ set(EXPORT_FILE_NAME libgromacs_static.cmake)
+ endif()
+ install(EXPORT libgromacs
+ FILE ${EXPORT_FILE_NAME}
+ DESTINATION ${CMAKE_PACKAGE_DIR}
+ COMPONENT libraries)
+
+ get_filename_component(GROMACS_CXX_COMPILER ${CMAKE_CXX_COMPILER} REALPATH)
+ configure_file(gromacs-config.cmake.cmakein
+ gromacs-config.cmake @ONLY)
+ configure_file(gromacs-config-version.cmake.cmakein
+ gromacs-config-version.cmake @ONLY)
+ # The configuration files are also installed with the suffix, even though
+ # the directory already contains the suffix. This allows simple
+ # find_package(GROMACS NAMES gromacs_d) to find them, without also
+ # specifying CONFIGS.
+ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/gromacs-config.cmake
+ DESTINATION ${CMAKE_PACKAGE_DIR}
+ RENAME "gromacs${GMX_LIBS_SUFFIX}-config.cmake"
+ COMPONENT development)
+ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/gromacs-config-version.cmake
+ DESTINATION ${CMAKE_PACKAGE_DIR}
+ RENAME "gromacs${GMX_LIBS_SUFFIX}-config-version.cmake"
+ COMPONENT development)
+endfunction()
+
+do_pkgconfig()
+do_cmake_config()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* that process frames in parallel: the functionality in this module takes care
* of necessary synchronization and communication such that output from the
* frames is collected and output in the correct order.
+ * See \ref page_analysisdata for an overview of the high-level functionality
+ * and the terminology used.
*
* This module consists of two main parts. The first is formed by the
* gmx::AbstractAnalysisData class and classes that derive from it:
* process and store raw data as produced by the analysis tool. They also
* provide an interface to attach data modules that implement
* gmx::AnalysisDataModuleInterface.
- * Modules that implement this interface form the second part of the module,
- * and they provide functionality to do processing operations on the data.
+ *
+ * Modules that implement gmx::AnalysisDataModuleInterface form the second part
+ * of the module, and they provide functionality to do processing on the data.
* These modules can also derive from gmx::AbstractAnalysisData, allowing other
* modules to be attached to them to form a processing chain that best suits
* the analysis tool. Typically, such a processing chain ends in a plotting
* provide direct access to the processed data, allowing the analysis tool to
* do custom postprocessing outside the module framework.
*
- * The sequence chart below shows an overview of how analysis data objects
- * and modules interact (currently, multipoint data is an exception to this
- * diagram).
- * \msc
- * caller,
- * data [ label="AnalysisData", URL="\ref gmx::AnalysisData" ],
- * module1 [ label="data module", URL="\ref gmx::AnalysisDataModuleInterface" ];
- *
- * caller box module1 [ label="caller creates and initializes all objects" ];
- * caller => data [ label="addModule(module1)",
- * URL="\ref gmx::AbstractAnalysisData::addModule() " ];
- * caller => data [ label="startData()",
- * URL="\ref gmx::AnalysisData::startData()" ];
- * data => module1 [ label="dataStarted()",
- * URL="\ref gmx::AnalysisDataModuleInterface::dataStarted()" ];
- * caller << data [ label="handle",
- * URL="\ref gmx::AnalysisDataHandle" ];
- * caller => data [ label="handle->startFrame(0)",
- * URL="\ref gmx::AnalysisDataHandle::startFrame()" ];
- * caller => data [ label="add data for frame 0",
- * URL="\ref gmx::AnalysisDataHandle" ];
- * caller => data [ label="handle->finishFrame() (frame 0)",
- * URL="\ref gmx::AnalysisDataHandle::finishFrame()" ];
- * data => module1 [ label="frameStarted(0)",
- * URL="\ref gmx::AnalysisDataModuleInterface::frameStarted()" ];
- * data => module1 [ label="pointsAdded()",
- * URL="\ref gmx::AnalysisDataModuleInterface::pointsAdded()" ];
- * data => module1 [ label="frameFinished(0)",
- * URL="\ref gmx::AnalysisDataModuleInterface::frameFinished()" ];
- * caller => data [ label="handle->startFrame(1)",
- * URL="\ref gmx::AnalysisDataHandle::startFrame()" ];
- * caller => data [ label="add data for frame 1",
- * URL="\ref gmx::AnalysisDataHandle" ];
- * caller => data [ label="handle2->finishFrame() (frame 1)",
- * URL="\ref gmx::AnalysisDataHandle::finishFrame()" ];
- * data => module1 [ label="process frame 1" ];
- * ... [ label="add more frames" ];
- * caller => data [ label="handle->finishData()",
- * URL="\ref gmx::AnalysisDataHandle::finishData()" ];
- * data => module1 [ label="dataFinished()",
- * URL="\ref gmx::AnalysisDataModuleInterface::dataFinished()" ];
- * \endmsc
- *
- * The second sequence chart below shows the interaction in the case of two
- * gmx::AnalysisDataHandle objects, which can be used to insert data
- * concurrently for multiple frames. The gmx::AnalysisData object and the
- * handles take care to notify the module such that it always receives the
- * frames in the correct order.
- * \msc
- * caller,
- * handle1 [ label="handle1", URL="\ref gmx::AnalysisDataHandle" ],
- * handle2 [ label="handle2", URL="\ref gmx::AnalysisDataHandle" ],
- * module1 [ label="data module", URL="\ref gmx::AnalysisDataModuleInterface" ];
- *
- * caller box handle2 [ label="caller has created both handles using startData()" ];
- * caller => handle1 [ label="startFrame(0)",
- * URL="\ref gmx::AnalysisDataHandle::startFrame()" ];
- * caller => handle2 [ label="startFrame(1)",
- * URL="\ref gmx::AnalysisDataHandle::startFrame()" ];
- * caller => handle1 [ label="add data for frame 0",
- * URL="\ref gmx::AnalysisDataHandle" ];
- * caller => handle2 [ label="add data for frame 1",
- * URL="\ref gmx::AnalysisDataHandle" ];
- * caller => handle2 [ label="finishFrame() (frame 1)",
- * URL="\ref gmx::AnalysisDataHandle::finishFrame()" ];
- * caller => handle2 [ label="startFrame(2)",
- * URL="\ref gmx::AnalysisDataHandle::startFrame()" ];
- * caller => handle1 [ label="finishFrame() (frame 0)",
- * URL="\ref gmx::AnalysisDataHandle::finishFrame()" ];
- * handle1 => module1 [ label="process frame 0" ];
- * handle1 => module1 [ label="process frame 1" ];
- * caller => handle2 [ label="add data for frame 2",
- * URL="\ref gmx::AnalysisDataHandle" ];
- * caller => handle2 [ label="finishFrame() (frame 2)",
- * URL="\ref gmx::AnalysisDataHandle::finishFrame()" ];
- * handle2 => module1 [ label="process frame 2" ];
- * ...;
- * caller => handle1 [ label="finishData()",
- * URL="\ref gmx::AnalysisDataHandle::finishData()" ];
- * caller => handle2 [ label="finishData()",
- * URL="\ref gmx::AnalysisDataHandle::finishData()" ];
- * handle2 => module1 [ label="dataFinished()",
- * URL="\ref gmx::AnalysisDataModuleInterface::dataFinished()" ];
- * \endmsc
- *
* <H3>Using Data Objects and Modules</H3>
*
* To use the functionality in this module, you typically declare one or more
* one another using gmx::AbstractAnalysisData::addModule(). Then you add the
* actual data values to the gmx::AnalysisData object, which automatically
* passes it on to the modules.
- * After all data is added, you may optionally access some
- * results directly from the module objects. However, in many cases it is
- * sufficient to initially add a plotting module to the processing chain, which
- * will then automatically write the results into a file.
+ * After all data is added, you may optionally access some results directly
+ * from the module objects or from the gmx::AnalysisData object itself.
+ * However, in many cases it is sufficient to initially add a plotting module
+ * to the processing chain, which will then automatically write the results
+ * into a file.
*
* For simple processing needs with a small amount of data, an
* gmx::AnalysisArrayData class is also provided, which keeps all the data in an
* in-memory array and allows you to manipulate the data as you wish before you
* pass the data to the attached modules.
*
+ * <H3>Data Modules</H3>
+ *
+ * Modules that derive from gmx::AnalysisDataModuleInterface can operate in two
+ * modes:
+ * - In _serial_ mode, the frames are presented to the module always in the
+ * order of increasing indices, even if they become ready in a different
+ * order in the attached data.
+ * - In _parallel_ mode, the frames are presented in the order that they
+ * become available in the input data, which may not be sequential.
+ * This mode allows the input data to optimize its behavior if it does not
+ * need to store and sort the frames.
+ *
+ * The figure below shows the sequence of callbacks that the module receives.
+ * Arrows show a dependency between callbacks: the event at the start of the
+ * arrow always occurs before the event at the end. The events in the box are
+ * repeated for each frame. Dashed lines within this box show dependencies
+ * between these frames:
+ * - In serial mode, all the events are called in a deterministic order, with
+ * each frame completely processed before the next starts.
+ * - In parallel mode, multiple frames can be in progress simultaneously, and
+ * the events for different frames can occur even concurrently on different
+ * threads. However, frameFinishSerial() events will always occur in
+ * deterministic, sequential order for the frames. Also, the number of
+ * concurrent frames is limited by the parallelization factor passed to
+ * parallelDataStarted(): only M frames after the last frame for which
+ * frameFinishSerial() has been called can be in progress
+ *
+ * \dot
+ * digraph datamodule_events {
+ * rankdir = LR
+ * node [ shape=box ]
+ *
+ * start [ label="dataStarted()",
+ * URL="\ref gmx::AnalysisDataModuleInterface::dataStarted()" ]
+ * pstart [ label="parallelDataStarted()",
+ * URL="\ref gmx::AnalysisDataModuleInterface::parallelDataStarted()" ]
+ * subgraph cluster_frame {
+ * label = "for each frame"
+ * framestart [ label="frameStarted()",
+ * URL="\ref gmx::AnalysisDataModuleInterface::frameStarted()" ]
+ * pointsadd [ label="pointsAdded()",
+ * URL="\ref gmx::AnalysisDataModuleInterface::pointsAdded()" ]
+ * framefinish [ label="frameFinished()",
+ * URL="\ref gmx::AnalysisDataModuleInterface::frameFinished()" ]
+ * serialfinish [ label="frameFinishedSerial()",
+ * URL="\ref gmx::AnalysisDataModuleInterface::frameFinishedSerial()" ]
+ * }
+ * finish [ label="dataFinished()",
+ * URL="\ref gmx::AnalysisDataModuleInterface::dataFinished()" ]
+ *
+ * start -> framestart
+ * pstart -> framestart
+ * framestart -> pointsadd
+ * pointsadd -> pointsadd [ label="0..*", dir=back ]
+ * pointsadd -> framefinish
+ * framefinish -> serialfinish
+ * serialfinish -> finish
+ *
+ * framestart:se -> serialfinish:sw [ dir=back, style=dashed, weight=0,
+ * label="serial: frame n+1\nparallel: frame n+M" ]
+ * serialfinish -> serialfinish [ dir=back, style=dashed,
+ * label="frame n+1" ]
+ * }
+ * \enddot
+ *
+ * If the input data supports parallel mode, it calls parallelDataStarted().
+ * If the module returns `true` from this method, then it will process the
+ * frames in the parallel mode. If the module returns `false`, it will get the
+ * frames in serial order.
+ * If the input data does not support parallel mode, it calls dataStarted(),
+ * and the module will always get the frames in order.
+ *
+ * The sequence of when the module methods are called with respect to when data
+ * is added to the data object depends on the type of the module and the type
+ * of the data. However, generally the modules do not need to know the details
+ * of how this happens, as long as they work with the above state diagram.
+ *
+ * For parallel processing, the gmx::AnalysisData object itself only provides
+ * the infrastructure to support all of the above, including the reordering of
+ * the frames for serial processing. However, the caller is still responsible
+ * of the actual thread synchronization, and must call
+ * gmx::AnalysisData::finishFrameSerial() for each frame from a suitable
+ * context where the serial processing for that frame can be done. When using
+ * the data objects as part of the trajectory analysis framework
+ * (\ref page_analysisframework), these calls are handled by the framework.
+ *
* \if libapi
* <H3>Writing New Data and Module Objects</H3>
*
#ifndef GMX_ANALYSISDATA_H
#define GMX_ANALYSISDATA_H
-#include "analysisdata/analysisdata.h"
-#include "analysisdata/arraydata.h"
-#include "analysisdata/dataframe.h"
-#include "analysisdata/modules/average.h"
-#include "analysisdata/modules/displacement.h"
-#include "analysisdata/modules/histogram.h"
-#include "analysisdata/modules/lifetime.h"
-#include "analysisdata/modules/plot.h"
+#include "gromacs/analysisdata/analysisdata.h"
+#include "gromacs/analysisdata/arraydata.h"
+#include "gromacs/analysisdata/dataframe.h"
+#include "gromacs/analysisdata/modules/average.h"
+#include "gromacs/analysisdata/modules/displacement.h"
+#include "gromacs/analysisdata/modules/histogram.h"
+#include "gromacs/analysisdata/modules/lifetime.h"
+#include "gromacs/analysisdata/modules/plot.h"
#endif
file(GLOB ANALYSISDATA_SOURCES *.cpp modules/*.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${ANALYSISDATA_SOURCES} PARENT_SCOPE)
-set(ANALYSISDATA_PUBLIC_HEADERS
+gmx_install_headers(
abstractdata.h
analysisdata.h
arraydata.h
dataframe.h
- datamodule.h)
-gmx_install_headers(analysisdata ${ANALYSISDATA_PUBLIC_HEADERS})
+ datamodule.h
+ )
add_subdirectory(modules)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
-#include "gromacs/analysisdata/abstractdata.h"
+#include "gmxpre.h"
+
+#include "abstractdata.h"
#include <vector>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <boost/shared_ptr.hpp>
-#include "../legacyheaders/types/simple.h"
-
-#include "../utility/common.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
-#include "gromacs/analysisdata/analysisdata.h"
+#include "gmxpre.h"
+
+#include "analysisdata.h"
#include "gromacs/analysisdata/dataframe.h"
#include "gromacs/analysisdata/datastorage.h"
}
+void
+AnalysisData::finishFrameSerial(int frameIndex)
+{
+ impl_->storage_.finishFrameSerial(frameIndex);
+}
+
+
void
AnalysisData::finishData(AnalysisDataHandle handle)
{
#ifndef GMX_ANALYSISDATA_ANALYSISDATA_H
#define GMX_ANALYSISDATA_ANALYSISDATA_H
-#include "abstractdata.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/utility/real.h"
namespace gmx
{
* AnalysisDataHandle objects can be created using startData(). Each data
* handle can then be independently used to provide data frames (each frame
* must be provided by a single handle, but different frames can be freely
- * mixed between the handles). When all data has been provided, the handles
+ * mixed between the handles). The finishFrameSerial() method must be called
+ * in serial for each frame, after one of the handles has been used to provide
+ * the data for that frame. When all data has been provided, the handles
* are destroyed using finishData() (or AnalysisDataHandle::finishData()).
- * The AnalysisData object takes care of internally sorting the frames and
- * passing them to the attached modules in the order in which the modules
- * expect them.
+ *
+ * When used through the trajectory analysis framework, calls to startData(),
+ * finishFrameSerial(), and finishData() are handled by the framework.
*
* \todo
* Parallel implementation is not complete.
virtual int frameCount() const;
/*! \brief
- * Create a handle for adding data.
+ * Creates a handle for adding data.
*
* \param[in] opt Options for setting how this handle will be
* used.
*/
AnalysisDataHandle startData(const AnalysisDataParallelOptions &opt);
/*! \brief
- * Destroy a handle after all data has been added.
+ * Performs in-order sequential processing for the next frame.
+ *
+ * \param[in] frameIndex Index of the frame that has been finished.
+ * \throws unspecified Any exception thrown by attached data modules
+ * in AnalysisDataModuleInterface::frameFinishedSerial().
+ *
+ * This method should be called sequentially for each frame, after data
+ * for that frame has been produced. It is not necessary to call this
+ * method if there is no parallelism, i.e., if only a single data
+ * handle is created and the parallelization options provided at that
+ * time do not indicate parallelism.
+ */
+ void finishFrameSerial(int frameIndex);
+ /*! \brief
+ * Destroys a handle after all data has been added.
*
* \param[in] handle Handle to destroy.
* \throws unspecified Any exception thrown by attached data modules
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
-#include "gromacs/analysisdata/arraydata.h"
+#include "gmxpre.h"
+
+#include "arraydata.h"
#include <algorithm>
#include <vector>
-#include "../utility/gmxassert.h"
-
-#include "abstractdata.h"
-#include "dataframe.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/analysisdata/dataframe.h"
+#include "gromacs/utility/gmxassert.h"
namespace gmx
{
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
+#include "gmxpre.h"
+
#include "dataframe.h"
#include "gromacs/utility/gmxassert.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
-#include "../legacyheaders/types/simple.h"
-
-#include "../utility/arrayref.h"
-#include "../utility/flags.h"
-#include "../utility/gmxassert.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/flags.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
-#include "gromacs/analysisdata/datamodule.h"
+#include "gmxpre.h"
+
+#include "datamodule.h"
#include "gromacs/analysisdata/paralleloptions.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ANALYSISDATA_DATAMODULE_H
#define GMX_ANALYSISDATA_DATAMODULE_H
-#include "../legacyheaders/types/simple.h"
-
namespace gmx
{
* parallelDataStarted() methods (see below).
* All other methods in the interface are callbacks that are called by the
* data object to which the module is attached to describe the data.
- *
- * The modules can operate in two modes: serial or parallel.
- * In serial mode, the frames are presented to the module always in the order
- * of increasing indices, even if they become ready in a different order in the
- * attached data.
- * In parallel mode, the frames are presented in the order that they become
- * available in the input data, which may not be sequential. This mode allows
- * the input data to optimize its behavior if it does not need to store and
- * sort the frames.
- * If the input data supports parallel mode, it calls parallelDataStarted().
- * If the module returns true from this method, then it will process the frames
- * in the parallel mode. If the module returns false, it will get the frames
- * in serial order.
- * If the input data does not support parallel mode, it calls dataStarted().
+ * See \ref module_analysisdata for an overview of the notifications the
+ * modules receive, and \ref page_analysisdata for overview of the terminology.
*
* Concrete modules typically do not directly derive from this interface, but
* from either AnalysisDataModuleSerial or AnalysisDataModuleParallel.
* implementing class to report errors.
*/
virtual void frameFinished(const AnalysisDataFrameHeader &header) = 0;
+ /*! \brief
+ * Called in sequential order for each frame after they are finished.
+ *
+ * \param[in] frameIndex Index of the next finished frame.
+ * \throws unspecified Can throw any exception required by the
+ * implementing class to report errors.
+ *
+ * This method is called after frameFinished(), but with an additional
+ * constraint that it is always called in serial and with an increasing
+ * \p frameIndex. Parallel data modules need this to serialize their
+ * data for downsteam serial modules; AnalysisDataModuleSerial provides
+ * an empty implementation, as there frameFinished() can be used for
+ * the same purpose.
+ */
+ virtual void frameFinishedSerial(int frameIndex) = 0;
/*! \brief
* Called (once) when no more data is available.
*
virtual bool parallelDataStarted(
AbstractAnalysisData *data,
const AnalysisDataParallelOptions &options);
+ virtual void frameFinishedSerial(int /*frameIndex*/) {}
};
/*! \brief
virtual void frameStarted(const AnalysisDataFrameHeader &frame) = 0;
virtual void pointsAdded(const AnalysisDataPointSetRef &points) = 0;
virtual void frameFinished(const AnalysisDataFrameHeader &header) = 0;
- virtual void dataFinished() = 0;
+ virtual void frameFinishedSerial(int index) = 0;
+ virtual void dataFinished() = 0;
private:
virtual void dataStarted(AbstractAnalysisData *data);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
-#include "gromacs/analysisdata/datamodulemanager.h"
+#include "gmxpre.h"
+
+#include "datamodulemanager.h"
#include <vector>
module->pointsAdded(frame.pointSet(j));
}
module->frameFinished(frame.header());
+ module->frameFinishedSerial(frame.header().index());
}
if (state_ == eFinished)
{
}
}
}
+ Impl::ModuleList::const_iterator i;
+ for (i = impl_->modules_.begin(); i != impl_->modules_.end(); ++i)
+ {
+ i->module->frameFinishedSerial(header.index());
+ }
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ANALYSISDATA_DATAMODULEMANAGER_H
#define GMX_ANALYSISDATA_DATAMODULEMANAGER_H
-#include "abstractdata.h"
-
-#include "../utility/common.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
/*! \libinternal \brief
* Encapsulates handling of data modules attached to AbstractAnalysisData.
*
+ * See AnalysisDataModuleInterface and \ref module_analysisdata for more
+ * details on the notifications and the order in which they should be raised.
+ *
* \inlibraryapi
* \ingroup module_analysisdata
*/
* notifyPointsAdd() calls for the frame.
* \p header should be identical to that used in the corresponding
* notifyFrameStart() call.
+ *
+ * This method also notifies parallel modules about serial end of frame.
*/
void notifyFrameFinish(const AnalysisDataFrameHeader &header) const;
/*! \brief
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
+#include "gmxpre.h"
+
#include "dataproxy.h"
#include "gromacs/analysisdata/dataframe.h"
}
}
+void
+AnalysisDataProxy::frameFinishedSerial(int frameIndex)
+{
+ if (bParallel_)
+ {
+ // The x and dx values are unused in this case.
+ AnalysisDataFrameHeader header(frameIndex, 0.0, 0.0);
+ moduleManager().notifyFrameFinish(header);
+ }
+}
+
void
AnalysisDataProxy::dataFinished()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ANALYSISDATA_DATAPROXY_H
#define GMX_ANALYSISDATA_DATAPROXY_H
-#include "abstractdata.h"
-#include "datamodule.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/analysisdata/datamodule.h"
namespace gmx
{
virtual void frameStarted(const AnalysisDataFrameHeader &frame);
virtual void pointsAdded(const AnalysisDataPointSetRef &points);
virtual void frameFinished(const AnalysisDataFrameHeader &header);
+ virtual void frameFinishedSerial(int frameIndex);
virtual void dataFinished();
private:
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
+#include "gmxpre.h"
+
#include "datastorage.h"
#include <algorithm>
{
return storageLimit_ > 0 || (pendingLimit_ > 1 && modules_->hasSerialModules());
}
- /*! \brief
- * Calls notification methods for new frames.
- *
- * \param[in] firstLocation First frame to consider.
- * \throws unspecified Any exception thrown by frame notification
- * methods in AbstractAnalysisData.
- *
- * Notifies \a data_ of new frames (from \p firstLocation and after
- * that) if all previous frames have already been notified.
- * Also rotates the \a frames_ buffer as necessary.
- */
- void notifyNextFrames(size_t firstLocation);
//! Implementation for AnalysisDataStorage::finishFrame().
void finishFrame(int index);
+ /*! \brief
+ * Implementation for AnalysisDataStorage::finishFrameSerial().
+ */
+ void finishFrameSerial(int index);
//! Parent data object to access data dimensionality etc.
}
-void
-AnalysisDataStorageImpl::notifyNextFrames(size_t firstLocation)
-{
- if (frames_[firstLocation]->frameIndex() != firstUnnotifiedIndex_)
- {
- return;
- }
- size_t i = firstLocation;
- size_t end = endStorageLocation();
- while (i != end)
- {
- AnalysisDataStorageFrameData &storedFrame = *frames_[i];
- if (!storedFrame.isFinished())
- {
- break;
- }
- if (!storedFrame.isNotified())
- {
- // Increment before the notifications to make the frame available
- // in the module callbacks.
- ++firstUnnotifiedIndex_;
- modules_->notifyFrameStart(storedFrame.header());
- for (int j = 0; j < storedFrame.pointSetCount(); ++j)
- {
- modules_->notifyPointsAdd(storedFrame.pointSet(j));
- }
- modules_->notifyFrameFinish(storedFrame.header());
- storedFrame.markNotified();
- if (storedFrame.frameIndex() >= storageLimit_)
- {
- rotateBuffer();
- }
- }
- ++i;
- if (!storeAll() && i >= frames_.size())
- {
- i = 0;
- }
- }
-}
-
-
void
AnalysisDataStorageImpl::finishFrame(int index)
{
"Inconsistent internal frame indexing");
builders_.push_back(storedFrame.finishFrame(isMultipoint()));
modules_->notifyParallelFrameFinish(storedFrame.header());
+ if (pendingLimit_ == 1)
+ {
+ finishFrameSerial(index);
+ }
+}
+
+
+void
+AnalysisDataStorageImpl::finishFrameSerial(int index)
+{
+ GMX_RELEASE_ASSERT(index == firstUnnotifiedIndex_,
+ "Out of order finisFrameSerial() calls");
+ const int storageIndex = computeStorageLocation(index);
+ GMX_RELEASE_ASSERT(storageIndex >= 0, "Out of bounds frame index");
+
+ AnalysisDataStorageFrameData &storedFrame = *frames_[storageIndex];
+ GMX_RELEASE_ASSERT(storedFrame.frameIndex() == index,
+ "Inconsistent internal frame indexing");
+ GMX_RELEASE_ASSERT(storedFrame.isFinished(),
+ "finishFrameSerial() called before finishFrame()");
+ GMX_RELEASE_ASSERT(!storedFrame.isNotified(),
+ "finishFrameSerial() called twice for the same frame");
+ // Increment before the notifications to make the frame available
+ // in the module callbacks.
+ ++firstUnnotifiedIndex_;
if (shouldNotifyImmediately())
{
- ++firstUnnotifiedIndex_;
modules_->notifyFrameFinish(storedFrame.header());
- if (storedFrame.frameIndex() >= storageLimit_)
+ }
+ else
+ {
+ modules_->notifyFrameStart(storedFrame.header());
+ for (int j = 0; j < storedFrame.pointSetCount(); ++j)
{
- rotateBuffer();
+ modules_->notifyPointsAdd(storedFrame.pointSet(j));
}
+ modules_->notifyFrameFinish(storedFrame.header());
}
- else
+ storedFrame.markNotified();
+ if (storedFrame.frameIndex() >= storageLimit_)
{
- notifyNextFrames(storageIndex);
+ rotateBuffer();
}
}
AnalysisDataModuleManager *modules,
const AnalysisDataParallelOptions &options)
{
- const int pendingLimit = 2 * options.parallelizationFactor() - 1;
+ const int pendingLimit = options.parallelizationFactor();
impl_->pendingLimit_ = pendingLimit;
modules->notifyParallelDataStart(data, options);
// Data needs to be set before calling extendBuffer()
impl_->finishFrame(index);
}
+void
+AnalysisDataStorage::finishFrameSerial(int index)
+{
+ if (impl_->pendingLimit_ > 1)
+ {
+ impl_->finishFrameSerial(index);
+ }
+}
+
void
AnalysisDataStorage::finishDataStorage()
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
-#include "../legacyheaders/types/simple.h"
-
-#include "../utility/common.h"
-#include "../utility/gmxassert.h"
-
-#include "dataframe.h"
+#include "gromacs/analysisdata/dataframe.h"
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
namespace gmx
{
* forwarded to frameCount(), tryGetDataFrame() and requestStorage().
* Storage properties should be set up, and then startDataStorage() or
* startParallelDataStorage() called.
- * New frames can then be added using startFrame(), currentFrame() and
- * finishFrame() methods. When all frames are ready, finishDataStorage() must
- * be called. These methods (and AnalysisDataStorageFrame::finishPointSet())
- * take the responsibility of calling all the notification methods in
- * AnalysisDataModuleManager,
+ * New frames can then be added using startFrame(), currentFrame(),
+ * finishFrame(), and finishFrameSerial() methods (the last is only necessary
+ * if startParallelDataStorage() is used). When all frames are ready,
+ * finishDataStorage() must be called. These methods (and
+ * AnalysisDataStorageFrame::finishPointSet()) take the responsibility of
+ * calling all the notification methods in AnalysisDataModuleManager,
*
* \todo
* Proper multi-threaded implementation.
* far in the future:
* If \c i is the index of the last frame such that all frames from
* 0, ..., \c i have been finished, then \p header().index() should be
- * at most \c 2*parallelizationFactor-1 larger than \c i, where
+ * at most \c parallelizationFactor larger than \c i, where
* parallelizationFactor is the parallelization factor passed to
* setParallelOptions().
* Throws APIError if this constraint is violated.
*/
AnalysisDataStorageFrame &startFrame(int index, real x, real dx);
/*! \brief
- * Obtain a frame object for an in-progress frame.
+ * Obtains a frame object for an in-progress frame.
*
* \param[in] index Frame index.
* \retval Frame object corresponding to \p index.
* \see AnalysisDataStorageFrame::finishFrame()
*/
void finishFrame(int index);
+ /*! \brief
+ * Performs in-order sequential processing for a data frame.
+ *
+ * \param[in] index Frame index.
+ *
+ * If startParallelDataStorage() has been called with options that
+ * indicate parallelism, this method must be called after
+ * `finishFrame(index)` (or the equivalent call in
+ * AnalysisDataStorageFrame), such that it is called in the correct
+ * order sequentially for each frame.
+ *
+ * If there is no parallelism, this method does nothing; the equivalent
+ * processing is done already during finishFrame().
+ */
+ void finishFrameSerial(int index);
/*! \brief
* Finishes storing data.
*
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Defines gmx::AnalysisDataFrameLocalData and supporting types.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_analysisdata
+ */
+#ifndef GMX_ANALYSISDATA_FRAMELOCALDATA_H
+#define GMX_ANALYSISDATA_FRAMELOCALDATA_H
+
+#include <algorithm>
+#include <numeric>
+#include <vector>
+
+#include "gromacs/analysisdata/paralleloptions.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/gmxassert.h"
+
+namespace gmx
+{
+
+//! \addtogroup module_analysisdata
+//! \{
+
+/*! \internal
+ * \brief
+ * Handle to a single data set within frame-local data array.
+ *
+ * Methods in this class do not throw.
+ *
+ * \see AnalysisDataFrameLocalData
+ */
+template<typename ValueType>
+class AnalysisDataFrameLocalDataSetHandle
+{
+ public:
+ //! Constructs a handle from an array of values.
+ explicit AnalysisDataFrameLocalDataSetHandle(ArrayRef<ValueType> values)
+ : values_(values)
+ {
+ }
+
+ //! Clears all values in the data set.
+ void clear()
+ {
+ std::fill(values_.begin(), values_.end(), ValueType());
+ }
+
+ //! Accesses a single value in the data set.
+ ValueType &value(int column)
+ {
+ GMX_ASSERT(column >= 0 && column < static_cast<int>(values_.size()),
+ "Invalid column index");
+ return values_[column];
+ }
+
+ private:
+ ArrayRef<ValueType> values_;
+};
+
+/*! \internal
+ * \brief
+ * Handle to a single frame data within frame-local data array.
+ *
+ * Methods in this class do not throw.
+ *
+ * \see AnalysisDataFrameLocalData
+ */
+template<typename ValueType>
+class AnalysisDataFrameLocalDataHandle
+{
+ public:
+ //! Shorthand for the internal array of values.
+ typedef std::vector<ValueType> ValueArray;
+ //! Shorthand for a handle to a single data set.
+ typedef AnalysisDataFrameLocalDataSetHandle<ValueType> DataSetHandle;
+
+ //! Constructs a handle from specified frame data.
+ AnalysisDataFrameLocalDataHandle(const std::vector<int> *dataSetIndices,
+ ValueArray *values)
+ : dataSetIndices_(dataSetIndices), values_(values)
+ {
+ }
+
+ //! Returns the number of data sets in the array.
+ int dataSetCount() const
+ {
+ return dataSetIndices_->size() - 1;
+ }
+ //! Clears all values in the frame.
+ void clear()
+ {
+ std::fill(values_->begin(), values_->end(), ValueType());
+ }
+
+ //! Returns a handle for a single data set.
+ DataSetHandle dataSet(int dataSet)
+ {
+ GMX_ASSERT(dataSet >= 0 && dataSet < dataSetCount(),
+ "Invalid data set index");
+ const int firstIndex = (*dataSetIndices_)[dataSet];
+ const int lastIndex = (*dataSetIndices_)[dataSet + 1];
+ typename ValueArray::iterator begin = values_->begin() + firstIndex;
+ typename ValueArray::iterator end = values_->begin() + lastIndex;
+ return DataSetHandle(arrayRefFromVector<ValueType>(begin, end));
+ }
+ //! Accesses a single value in the frame.
+ ValueType &value(int dataSet, int column)
+ {
+ GMX_ASSERT(dataSet >= 0 && dataSet < dataSetCount(),
+ "Invalid data set index");
+ const int firstIndex = (*dataSetIndices_)[dataSet];
+ GMX_ASSERT(column >= 0
+ && column < (*dataSetIndices_)[dataSet+1] - firstIndex,
+ "Invalid column index");
+ return (*values_)[firstIndex + column];
+ }
+
+ private:
+ const std::vector<int> *dataSetIndices_;
+ ValueArray *values_;
+};
+
+/*! \internal \brief
+ * Container for an array of frame-local values that supports parallel data
+ * processing.
+ *
+ * \tparam ValueType Type of values to store.
+ *
+ * This class provides a convenient interface to create an array of frame-local
+ * data for use in analysis data modules that support parallel processing.
+ * The object is initialized by setting the desired dimensionality with
+ * setDataSetCount() and setColumnCount(), followed by a call to init(),
+ * typically in AnalysisDataModuleInterface::parallelDataStarted(),
+ *
+ * After initialization, frameData() can be used to access the data for a given
+ * frame, independently from other frames. This works if the assumptions about
+ * parallelism hold: if `N` is the parallelization factor given for init() with
+ * AnalysisDataParallelOptions::parallelizationFactor(), then frame `i+N` must
+ * not be accessed before all processing for frame `i` is finished.
+ * Technically, the data for different frames is kept in a ring buffer of size
+ * `N`.
+ *
+ * The data for a frame is not cleared after it is reused for a new frame (but
+ * is initially cleared). This allows using the data for accumulating values
+ * over all frames in a lock-free manner.
+ *
+ * frameDataSet() is provided for convenience when only a single data set
+ * needs to be accessed (typically in AnalysisDataModuleInterface::pointsAdded()).
+ *
+ * Methods in this class do not throw except where indicated.
+ *
+ * \see AnalysisDataFrameLocalData
+ */
+template<typename ValueType>
+class AnalysisDataFrameLocalData
+{
+ public:
+ //! Shorthand for the internal array of values for a frame.
+ typedef std::vector<ValueType> ValueArray;
+ //! Shorthand for a handle to a single frame.
+ typedef AnalysisDataFrameLocalDataHandle<ValueType> FrameHandle;
+ //! Shorthand for a handle to a single data set.
+ typedef AnalysisDataFrameLocalDataSetHandle<ValueType> DataSetHandle;
+
+ //! Constructs an empty container with a single data set.
+ AnalysisDataFrameLocalData()
+ {
+ dataSetColumns_.resize(2);
+ }
+
+ //! Whether init() has been called.
+ bool isInitialized() const { return !values_.empty(); }
+ /*! \brief
+ * Returns number of independent data frames in this object.
+ *
+ * This supports looping over all the frame arrays to, e.g., sum them
+ * up at the end in accumulation scenarios.
+ */
+ int frameCount() const { return values_.size(); }
+
+ /*! \brief
+ * Sets the number of data sets stored for each frame.
+ *
+ * \throws std::bad_alloc if out of memory.
+ *
+ * If not called, there is a single data set in the object.
+ * Cannot be called after init().
+ */
+ void setDataSetCount(int dataSetCount)
+ {
+ GMX_RELEASE_ASSERT(!isInitialized(),
+ "Cannot change value count after init()");
+ GMX_RELEASE_ASSERT(dataSetCount >= 0,
+ "Invalid data set count");
+ dataSetColumns_.resize(dataSetCount + 1);
+ }
+ /*! \brief
+ * Sets the number of columns stored for a data set.
+ *
+ * Must be called for each data set that needs to have values,
+ * otherwise there will be zero columns for that data set.
+ * Cannot be called after init().
+ */
+ void setColumnCount(int dataSet, int columnCount)
+ {
+ GMX_RELEASE_ASSERT(!isInitialized(),
+ "Cannot change value count after init()");
+ GMX_RELEASE_ASSERT(dataSet >= 0 && dataSet < static_cast<int>(dataSetColumns_.size()) - 1,
+ "Invalid data set index");
+ GMX_RELEASE_ASSERT(columnCount >= 0,
+ "Invalid column count");
+ dataSetColumns_[dataSet + 1] = columnCount;
+ }
+
+ /*! \brief
+ * Initializes the storage to support specified parallelism.
+ *
+ * \throws std::bad_alloc if out of memory.
+ */
+ void init(const AnalysisDataParallelOptions &opt)
+ {
+ GMX_RELEASE_ASSERT(!isInitialized(), "init() called multiple times");
+ std::partial_sum(dataSetColumns_.begin(), dataSetColumns_.end(),
+ dataSetColumns_.begin());
+ values_.resize(opt.parallelizationFactor());
+ typename std::vector<ValueArray>::iterator i;
+ for (i = values_.begin(); i != values_.end(); ++i)
+ {
+ i->resize(dataSetColumns_.back());
+ }
+ }
+
+ //! Returns a handle to access data for a frame.
+ FrameHandle frameData(int frameIndex)
+ {
+ GMX_ASSERT(frameIndex >= 0, "Invalid frame index");
+ GMX_ASSERT(isInitialized(), "Cannot access data before init()");
+ return FrameHandle(&dataSetColumns_,
+ &values_[frameIndex % values_.size()]);
+ }
+ //! Returns a handle to access a single data set within a frame.
+ DataSetHandle frameDataSet(int frameIndex, int dataSet)
+ {
+ return frameData(frameIndex).dataSet(dataSet);
+ }
+
+ private:
+ /*! \brief
+ * Index to find data sets within a per-frame array in `values_`.
+ *
+ * The first entry is always zero, followed by one entry for each data
+ * set. Before init(), the data set entries hold the numbers set with
+ * setColumnCount(). After init(), the data set entries hold the
+ * indices of the first column for that data set in the per-frame
+ * arrays in `values_`.
+ */
+ std::vector<int> dataSetColumns_;
+ /*! \brief
+ * Data array for each frame.
+ *
+ * This is a ring buffer whose size is specified by the desired
+ * parallelism level. For each frame, there is a single array of
+ * values, where the individual data sets are indexed with
+ * `dataSetColumns_`.
+ */
+ std::vector<ValueArray> values_;
+};
+
+//! \}
+
+} // namespace gmx
+
+#endif
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2013, by the GROMACS development team, led by
+# Copyright (c) 2010,2013,2014, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-set(ANALYSISDATA_MODULES_PUBLIC_HEADERS
+gmx_install_headers(
average.h
displacement.h
histogram.h
lifetime.h
- plot.h)
-gmx_install_headers(analysisdata/modules ${ANALYSISDATA_MODULES_PUBLIC_HEADERS})
+ plot.h
+ )
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
+#include "gmxpre.h"
+
#include "average.h"
#include <cmath>
#include <vector>
-#include "../abstractdata.h"
-#include "../arraydata.h"
-#include "../datamodule.h"
-#include "../../utility/common.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/analysisdata/arraydata.h"
+#include "gromacs/analysisdata/datamodule.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
-#include "gromacs/analysisdata/modules/displacement.h"
+#include "gmxpre.h"
+
+#include "displacement.h"
#include "gromacs/analysisdata/dataframe.h"
#include "gromacs/analysisdata/datamodulemanager.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ANALYSISDATA_MODULES_DISPLACEMENT_H
#define GMX_ANALYSISDATA_MODULES_DISPLACEMENT_H
-#include "../abstractdata.h"
-#include "../datamodule.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/analysisdata/datamodule.h"
+#include "gromacs/utility/real.h"
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
+#include "gmxpre.h"
+
#include "frameaverager.h"
#include "gromacs/analysisdata/dataframe.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
-#include "../../legacyheaders/types/simple.h"
-
-#include "../../utility/gmxassert.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
-#include "gromacs/analysisdata/modules/histogram.h"
+#include "gmxpre.h"
+
+#include "histogram.h"
#include <cmath>
#include "gromacs/analysisdata/dataframe.h"
#include "gromacs/analysisdata/datastorage.h"
+#include "gromacs/analysisdata/framelocaldata.h"
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
AverageHistogramPointer dest(
new StaticAverageHistogram(
- histogramFromBins(xstart(), nbins, 2*xstep())
+ histogramFromBins(settings().firstEdge(), nbins, 2*xstep())
.integerBins(bIntegerBins)));
dest->setColumnCount(columnCount());
dest->allocateValues();
{
AverageHistogramPointer dest(new StaticAverageHistogram());
copyContents(this, dest.get());
+ dest->settings_ = settings_;
return dest;
}
{
for (int c = 0; c < columnCount(); ++c)
{
- real sum = 0;
+ double sum = 0;
for (int i = 0; i < rowCount(); ++i)
{
sum += value(i, c).value();
}
}
+void
+AbstractAverageHistogram::makeCumulative()
+{
+ for (int c = 0; c < columnCount(); ++c)
+ {
+ double sum = 0;
+ for (int i = 0; i < rowCount(); ++i)
+ {
+ sum += value(i, c).value();
+ // Clear the error, as we don't cumulate that.
+ value(i, c).clear();
+ value(i, c).setValue(sum);
+ }
+ }
+ setXAxis(settings().firstEdge() + settings().binWidth(),
+ settings().binWidth());
+}
+
void
AbstractAverageHistogram::scaleSingle(int index, real factor)
* BasicHistogramImpl
*/
-/*! \internal \brief
- * Private implementation class for AnalysisDataSimpleHistogramModule and
- * AnalysisDataWeightedHistogramModule.
+/*! \internal
+ * \brief
+ * Base class for private implementation classes for histogram modules.
+ *
+ * Actual implementation classes are derived from this and add an accumulation
+ * data member that is specific to the histogram type in question.
+ * This is done like this to keep implementation details out of the header, and
+ * to not unnecessarily duplicate code.
*
* \ingroup module_analysisdata
*/
BasicHistogramImpl();
//! Creates an histogram impl with defined bin parameters.
explicit BasicHistogramImpl(const AnalysisHistogramSettings &settings);
- ~BasicHistogramImpl();
+ // Virtual only for simplicity.
+ virtual ~BasicHistogramImpl();
/*! \brief
* (Re)initializes the histogram from settings.
*/
void init(const AnalysisHistogramSettings &settings);
- /*! \brief
- * Initializes data storage frame when a new frame starts.
- */
- void initFrame(int dataSetCount, AnalysisDataStorageFrame *frame);
//! Storage implementation object.
AnalysisDataStorage storage_;
averager_->init(settings);
}
-
-void
-BasicHistogramImpl::initFrame(int dataSetCount, AnalysisDataStorageFrame *frame)
-{
- for (int s = 0; s < dataSetCount; ++s)
- {
- frame->selectDataSet(s);
- for (int i = 0; i < frame->columnCount(); ++i)
- {
- frame->setValue(i, 0.0);
- }
- }
- frame->selectDataSet(0);
-}
-
} // namespace internal
* AnalysisDataSimpleHistogramModule
*/
+/*! \internal \brief
+ * Private implementation class for AnalysisDataSimpleHistogramModule.
+ *
+ * \ingroup module_analysisdata
+ */
+class AnalysisDataSimpleHistogramModule::Impl : public internal::BasicHistogramImpl
+{
+ public:
+ //! Shorthand for the per-frame accumulation data structure type.
+ typedef AnalysisDataFrameLocalData<gmx_int64_t> FrameLocalData;
+
+ Impl() {}
+ //! Creates an histogram impl with defined bin parameters.
+ explicit Impl(const AnalysisHistogramSettings &settings)
+ : BasicHistogramImpl(settings)
+ {
+ }
+
+ //! Accumulates the histogram within a frame.
+ FrameLocalData accumulator_;
+};
+
AnalysisDataSimpleHistogramModule::AnalysisDataSimpleHistogramModule()
- : impl_(new internal::BasicHistogramImpl())
+ : impl_(new Impl())
{
}
AnalysisDataSimpleHistogramModule::AnalysisDataSimpleHistogramModule(
const AnalysisHistogramSettings &settings)
- : impl_(new internal::BasicHistogramImpl(settings))
+ : impl_(new Impl(settings))
{
}
const AnalysisDataParallelOptions &options)
{
addModule(impl_->averager_);
- setDataSetCount(data->dataSetCount());
- for (int i = 0; i < data->dataSetCount(); ++i)
+ const int dataSetCount = data->dataSetCount();
+ const int columnCount = settings().binCount();
+ setDataSetCount(dataSetCount);
+ impl_->accumulator_.setDataSetCount(dataSetCount);
+ for (int i = 0; i < dataSetCount; ++i)
{
- setColumnCount(i, settings().binCount());
+ setColumnCount(i, columnCount);
+ impl_->accumulator_.setColumnCount(i, columnCount);
}
+ impl_->accumulator_.init(options);
impl_->storage_.startParallelDataStorage(this, &moduleManager(), options);
return true;
}
void
AnalysisDataSimpleHistogramModule::frameStarted(const AnalysisDataFrameHeader &header)
{
- AnalysisDataStorageFrame &frame = impl_->storage_.startFrame(header);
- impl_->initFrame(dataSetCount(), &frame);
+ impl_->accumulator_.frameData(header.index()).clear();
}
void
AnalysisDataSimpleHistogramModule::pointsAdded(const AnalysisDataPointSetRef &points)
{
- AnalysisDataStorageFrame &frame =
- impl_->storage_.currentFrame(points.frameIndex());
- frame.selectDataSet(points.dataSetIndex());
+ Impl::FrameLocalData::DataSetHandle handle
+ = impl_->accumulator_.frameDataSet(points.frameIndex(), points.dataSetIndex());
for (int i = 0; i < points.columnCount(); ++i)
{
if (points.present(i))
const int bin = settings().findBin(points.y(i));
if (bin != -1)
{
- frame.value(bin) += 1;
+ handle.value(bin) += 1;
}
}
}
void
AnalysisDataSimpleHistogramModule::frameFinished(const AnalysisDataFrameHeader &header)
{
- impl_->storage_.finishFrame(header.index());
+ Impl::FrameLocalData::FrameHandle handle
+ = impl_->accumulator_.frameData(header.index());
+ AnalysisDataStorageFrame &frame = impl_->storage_.startFrame(header);
+ const int columnCount = settings().binCount();
+ for (int s = 0; s < dataSetCount(); ++s)
+ {
+ Impl::FrameLocalData::DataSetHandle dataSet = handle.dataSet(s);
+ frame.selectDataSet(s);
+ for (int i = 0; i < columnCount; ++i)
+ {
+ frame.setValue(i, dataSet.value(i));
+ }
+ }
+ frame.finishFrame();
+}
+
+
+void
+AnalysisDataSimpleHistogramModule::frameFinishedSerial(int frameIndex)
+{
+ impl_->storage_.finishFrameSerial(frameIndex);
}
* AnalysisDataWeightedHistogramModule
*/
+/*! \internal \brief
+ * Private implementation class for AnalysisDataWeightedHistogramModule.
+ *
+ * \ingroup module_analysisdata
+ */
+class AnalysisDataWeightedHistogramModule::Impl : public internal::BasicHistogramImpl
+{
+ public:
+ //! Shorthand for the per-frame accumulation data structure type.
+ typedef AnalysisDataFrameLocalData<double> FrameLocalData;
+
+ Impl() {}
+ //! Creates an histogram impl with defined bin parameters.
+ explicit Impl(const AnalysisHistogramSettings &settings)
+ : BasicHistogramImpl(settings)
+ {
+ }
+
+ //! Accumulates the histogram within a frame.
+ FrameLocalData accumulator_;
+};
+
AnalysisDataWeightedHistogramModule::AnalysisDataWeightedHistogramModule()
- : impl_(new internal::BasicHistogramImpl())
+ : impl_(new Impl())
{
}
AnalysisDataWeightedHistogramModule::AnalysisDataWeightedHistogramModule(
const AnalysisHistogramSettings &settings)
- : impl_(new internal::BasicHistogramImpl(settings))
+ : impl_(new Impl(settings))
{
}
const AnalysisDataParallelOptions &options)
{
addModule(impl_->averager_);
- setDataSetCount(data->dataSetCount());
- for (int i = 0; i < data->dataSetCount(); ++i)
+ const int dataSetCount = data->dataSetCount();
+ const int columnCount = settings().binCount();
+ setDataSetCount(dataSetCount);
+ impl_->accumulator_.setDataSetCount(dataSetCount);
+ for (int i = 0; i < dataSetCount; ++i)
{
- setColumnCount(i, settings().binCount());
+ setColumnCount(i, columnCount);
+ impl_->accumulator_.setColumnCount(i, columnCount);
}
+ impl_->accumulator_.init(options);
impl_->storage_.startParallelDataStorage(this, &moduleManager(), options);
return true;
}
void
AnalysisDataWeightedHistogramModule::frameStarted(const AnalysisDataFrameHeader &header)
{
- AnalysisDataStorageFrame &frame = impl_->storage_.startFrame(header);
- impl_->initFrame(dataSetCount(), &frame);
+ impl_->accumulator_.frameData(header.index()).clear();
}
int bin = settings().findBin(points.y(0));
if (bin != -1)
{
- AnalysisDataStorageFrame &frame =
- impl_->storage_.currentFrame(points.frameIndex());
- frame.selectDataSet(points.dataSetIndex());
+ Impl::FrameLocalData::DataSetHandle handle
+ = impl_->accumulator_.frameDataSet(points.frameIndex(), points.dataSetIndex());
for (int i = 1; i < points.columnCount(); ++i)
{
- frame.value(bin) += points.y(i);
+ handle.value(bin) += points.y(i);
}
}
}
void
AnalysisDataWeightedHistogramModule::frameFinished(const AnalysisDataFrameHeader &header)
{
- impl_->storage_.finishFrame(header.index());
+ Impl::FrameLocalData::FrameHandle handle
+ = impl_->accumulator_.frameData(header.index());
+ AnalysisDataStorageFrame &frame = impl_->storage_.startFrame(header);
+ const int columnCount = settings().binCount();
+ for (int s = 0; s < dataSetCount(); ++s)
+ {
+ Impl::FrameLocalData::DataSetHandle dataSet = handle.dataSet(s);
+ frame.selectDataSet(s);
+ for (int i = 0; i < columnCount; ++i)
+ {
+ frame.setValue(i, dataSet.value(i));
+ }
+ }
+ frame.finishFrame();
+}
+
+
+void
+AnalysisDataWeightedHistogramModule::frameFinishedSerial(int frameIndex)
+{
+ impl_->storage_.finishFrameSerial(frameIndex);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ANALYSISDATA_MODULES_HISTOGRAM_H
#define GMX_ANALYSISDATA_MODULES_HISTOGRAM_H
-#include "../abstractdata.h"
-#include "../arraydata.h"
-#include "../datamodule.h"
-#include "../../utility/uniqueptr.h"
+#include <boost/shared_ptr.hpp>
+
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/analysisdata/arraydata.h"
+#include "gromacs/analysisdata/datamodule.h"
namespace gmx
{
};
-namespace internal
-{
-
-class BasicHistogramImpl;
-
-} // namespace internal
-
class AbstractAverageHistogram;
//! Smart pointer to manage an AbstractAverageHistogram object.
-typedef gmx_unique_ptr<AbstractAverageHistogram>::type
+typedef boost::shared_ptr<AbstractAverageHistogram>
AverageHistogramPointer;
/*! \brief
*
* This class can represent multiple histograms in one object: each column in
* the data is an independent histogram.
+ * The X values correspond to center of the bins, except for a cumulative
+ * histogram made with makeCumulative().
*
* \inpublicapi
* \ingroup module_analysisdata
/*! \brief
* Creates a copy of the histogram with double the bin width.
*
+ * \param[in] bIntegerBins If `true`, the first bin in the result will
+ * cover the first bin from the source. Otherwise, the first bin
+ * will cover first two bins from the source.
* \throws std::bad_alloc if out of memory.
*
* The caller is responsible of deleting the returned object.
AverageHistogramPointer clone() const;
//! Normalizes the histogram such that the integral over it is one.
void normalizeProbability();
+ /*! \brief
+ * Makes the histograms cumulative by summing up each bin to all bins
+ * after it.
+ *
+ * The X values in the data are adjusted such that they match the right
+ * edges of bins instead of bin centers.
+ */
+ void makeCumulative();
//! Scales a single histogram by a uniform scaling factor.
void scaleSingle(int index, real factor);
//! Scales all histograms by a uniform scaling factor.
* The number of columns for all data sets equals the number of bins in the
* histogram.
*
+ * The histograms are accumulated as 64-bit integers within a frame and summed
+ * in double precision across frames, even if the output data is in single
+ * precision.
+ *
* \inpublicapi
* \ingroup module_analysisdata
*/
virtual void frameStarted(const AnalysisDataFrameHeader &header);
virtual void pointsAdded(const AnalysisDataPointSetRef &points);
virtual void frameFinished(const AnalysisDataFrameHeader &header);
+ virtual void frameFinishedSerial(int frameIndex);
virtual void dataFinished();
private:
virtual AnalysisDataFrameRef tryGetDataFrameInternal(int index) const;
virtual bool requestStorageInternal(int nframes);
- PrivateImplPointer<internal::BasicHistogramImpl> impl_;
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
// Copy and assign disallowed by base.
};
* The number of columns for all data sets equals the number of bins in the
* histogram.
*
+ * The histograms are accumulated in double precision, even if the output data
+ * is in single precision.
+ *
* \inpublicapi
* \ingroup module_analysisdata
*/
virtual void frameStarted(const AnalysisDataFrameHeader &header);
virtual void pointsAdded(const AnalysisDataPointSetRef &points);
virtual void frameFinished(const AnalysisDataFrameHeader &header);
+ virtual void frameFinishedSerial(int frameIndex);
virtual void dataFinished();
private:
virtual AnalysisDataFrameRef tryGetDataFrameInternal(int index) const;
virtual bool requestStorageInternal(int nframes);
- PrivateImplPointer<internal::BasicHistogramImpl> impl_;
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
// Copy and assign disallowed by base.
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
+#include "gmxpre.h"
+
#include "lifetime.h"
#include <cmath>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ANALYSISDATA_MODULES_LIFETIME_H
#define GMX_ANALYSISDATA_MODULES_LIFETIME_H
-#include "../arraydata.h"
-#include "../datamodule.h"
-#include "../../utility/common.h"
+#include "gromacs/analysisdata/arraydata.h"
+#include "gromacs/analysisdata/datamodule.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
* \ingroup module_analysisdata
* \author Teemu Murtola <teemu.murtola@gmail.com>
*/
-#include "gromacs/analysisdata/modules/plot.h"
+#include "gmxpre.h"
-#include <string>
-#include <vector>
+#include "plot.h"
#include <cstdio>
#include <cstring>
-#include <boost/shared_ptr.hpp>
+#include <string>
+#include <vector>
-#include "gromacs/legacyheaders/oenv.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "gromacs/legacyheaders/xvgr.h"
+#include <boost/shared_ptr.hpp>
#include "gromacs/analysisdata/dataframe.h"
#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/math/vec.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
#include "gromacs/options/timeunitmanager.h"
impl_->title_ = title;
}
+void
+AbstractPlotModule::setTitle(const std::string &title)
+{
+ impl_->title_ = title;
+}
+
void
AbstractPlotModule::setSubtitle(const char *subtitle)
}
+void
+AbstractPlotModule::setSubtitle(const std::string &subtitle)
+{
+ impl_->subtitle_ = subtitle;
+}
+
+
void
AbstractPlotModule::setXLabel(const char *label)
{
? static_cast<xvg_format_t>(impl_->settings_.plotFormat())
: exvgNONE);
output_env_t oenv;
- output_env_init(&oenv, getProgramContext(), time_unit, FALSE, xvg_format, 0, 0);
+ output_env_init(&oenv, getProgramContext(), time_unit, FALSE, xvg_format, 0);
boost::shared_ptr<output_env> oenvGuard(oenv, &output_env_done);
impl_->fp_ = xvgropen(impl_->filename_.c_str(), impl_->title_.c_str(),
impl_->xlabel_.c_str(), impl_->ylabel_.c_str(),
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <boost/shared_ptr.hpp>
-#include "../datamodule.h"
-#include "../../options/timeunitmanager.h"
-#include "../../utility/common.h"
+#include "gromacs/analysisdata/datamodule.h"
+#include "gromacs/options/timeunitmanager.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
* Set plot title.
*/
void setTitle(const char *title);
+ //! \copydoc setTitle(const char *)
+ void setTitle(const std::string &title);
/*! \brief
* Set plot subtitle.
*/
void setSubtitle(const char *subtitle);
+ //! \copydoc setSubtitle(const char *)
+ void setSubtitle(const std::string &subtitle);
/*! \brief
* Set X axis label.
*/
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
+#include "gmxpre.h"
+
+#include "gromacs/analysisdata/analysisdata.h"
+
#include <gmock/gmock.h>
#include <gtest/gtest.h>
-#include "gromacs/analysisdata/analysisdata.h"
#include "gromacs/analysisdata/paralleloptions.h"
#include "gromacs/utility/exceptions.h"
ASSERT_NO_THROW_GMX(handle2 = this->data_.startData(options));
ASSERT_NO_THROW_GMX(AnalysisDataTest::presentDataFrame(this->input_, 1, handle1));
ASSERT_NO_THROW_GMX(AnalysisDataTest::presentDataFrame(this->input_, 0, handle2));
+ ASSERT_NO_THROW_GMX(this->data_.finishFrameSerial(0));
+ ASSERT_NO_THROW_GMX(this->data_.finishFrameSerial(1));
ASSERT_NO_THROW_GMX(AnalysisDataTest::presentDataFrame(this->input_, 2, handle1));
+ ASSERT_NO_THROW_GMX(this->data_.finishFrameSerial(2));
ASSERT_NO_THROW_GMX(handle1.finishData());
ASSERT_NO_THROW_GMX(handle2.finishData());
}
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
-#include <gtest/gtest.h>
+#include "gmxpre.h"
#include "gromacs/analysisdata/arraydata.h"
+#include <gtest/gtest.h>
+
#include "gromacs/analysisdata/tests/datatest.h"
#include "testutils/testasserts.h"
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
+#include "gmxpre.h"
+
+#include "gromacs/analysisdata/modules/average.h"
+
#include <gtest/gtest.h>
#include "gromacs/analysisdata/analysisdata.h"
-#include "gromacs/analysisdata/modules/average.h"
#include "gromacs/analysisdata/tests/datatest.h"
#include "testutils/testasserts.h"
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
+#include "gmxpre.h"
+
#include "datatest.h"
#include <gmock/gmock.h>
#include <gtest/gtest.h>
-#include "gromacs/legacyheaders/types/simple.h"
-
#include "gromacs/analysisdata/dataframe.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
#include "testutils/refdata.h"
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
+#include "gmxpre.h"
+
+#include "gromacs/analysisdata/modules/histogram.h"
+
#include <gtest/gtest.h>
#include "gromacs/analysisdata/analysisdata.h"
-#include "gromacs/analysisdata/modules/histogram.h"
#include "gromacs/analysisdata/tests/datatest.h"
#include "testutils/testasserts.h"
}
+TEST_F(AbstractAverageHistogramTest, ComputesCumulativeHistogram)
+{
+ const AnalysisDataTestInput &input = AverageInputData::get();
+ MockAverageHistogram data(
+ gmx::histogramFromBins(1.0, input.frameCount(), 0.5).integerBins());
+ setupArrayData(input, &data);
+
+ ASSERT_NO_THROW_GMX(addStaticCheckerModule(input, &data));
+ ASSERT_NO_THROW_GMX(addReferenceCheckerModule("InputData", &data));
+ ASSERT_NO_THROW_GMX(data.done());
+
+ gmx::AverageHistogramPointer cumulative(data.clone());
+ cumulative->makeCumulative();
+ ASSERT_NO_THROW_GMX(addReferenceCheckerModule("CumulativeHistogram", cumulative.get()));
+ ASSERT_NO_THROW_GMX(cumulative->done());
+}
+
+
TEST_F(AbstractAverageHistogramTest, ResamplesAtDoubleBinWidth)
{
const AnalysisDataTestInput &input = AverageInputData::get();
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
+#include "gmxpre.h"
+
+#include "gromacs/analysisdata/modules/lifetime.h"
+
#include <gtest/gtest.h>
#include "gromacs/analysisdata/analysisdata.h"
-#include "gromacs/analysisdata/modules/lifetime.h"
#include "gromacs/analysisdata/tests/datatest.h"
#include "testutils/testasserts.h"
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_analysisdata
*/
+#include "gmxpre.h"
+
#include "mock_datamodule.h"
#include <gmock/gmock.h>
* Callback used to check frame finish against reference data.
*
* Called to check parameters and order of calls to frameFinished().
- * \a frameIndex_ is incremented here.
*/
void finishReferenceFrame(const AnalysisDataFrameHeader &header);
+ /*! \brief
+ * Callback used to check serial frame finish with reference data.
+ *
+ * Called to check parameters and order of calls to
+ * frameFinishedSerial().
+ * \a frameIndex_ is incremented here.
+ */
+ void finishReferenceFrameSerial(int frameIndex);
/*! \brief
* Reference data checker to use for checking frames.
{
EXPECT_TRUE(frameChecker_.get() != NULL);
EXPECT_EQ(frameIndex_, header.index());
- ++frameIndex_;
frameChecker_.reset();
}
+void
+MockAnalysisDataModule::Impl::finishReferenceFrameSerial(int frameIndex)
+{
+ EXPECT_TRUE(frameChecker_.get() == NULL);
+ EXPECT_EQ(frameIndex_, frameIndex);
+ ++frameIndex_;
+}
+
+
/********************************************************************
* MockAnalysisDataModule
*/
EXPECT_CALL(*this, parallelDataStarted(source, _))
.WillOnce(Return(true));
::testing::ExpectationSet framesFinished;
+ ::testing::Expectation prevFinish;
for (int row = 0; row < data.frameCount(); ++row)
{
::testing::InSequence frameSequence;
EXPECT_CALL(*this, pointsAdded(Property(&AnalysisDataPointSetRef::frameIndex, row)))
.WillOnce(Invoke(checker));
}
- framesFinished +=
- EXPECT_CALL(*this, frameFinished(Property(&AnalysisDataFrameHeader::index, row)))
- .WillOnce(Invoke(StaticDataFrameHeaderChecker(&frame)));
+ EXPECT_CALL(*this, frameFinished(Property(&AnalysisDataFrameHeader::index, row)))
+ .WillOnce(Invoke(StaticDataFrameHeaderChecker(&frame)));
+ ::testing::Expectation finish;
+ if (row > 0)
+ {
+ finish = EXPECT_CALL(*this, frameFinishedSerial(row))
+ .After(prevFinish);
+ }
+ else
+ {
+ finish = EXPECT_CALL(*this, frameFinishedSerial(row));
+ }
+ framesFinished += finish;
+ prevFinish = finish;
}
EXPECT_CALL(*this, dataFinished())
.After(framesFinished);
}
EXPECT_CALL(*this, frameFinished(_))
.WillOnce(Invoke(StaticDataFrameHeaderChecker(&frame)));
+ EXPECT_CALL(*this, frameFinishedSerial(row));
}
EXPECT_CALL(*this, dataFinished());
}
}
EXPECT_CALL(*this, frameFinished(_))
.WillOnce(Invoke(StaticDataFrameHeaderChecker(&frame)));
+ EXPECT_CALL(*this, frameFinishedSerial(row));
}
EXPECT_CALL(*this, dataFinished());
}
}
EXPECT_CALL(*this, frameFinished(_))
.WillOnce(Invoke(StaticDataFrameHeaderChecker(&frame)));
+ EXPECT_CALL(*this, frameFinishedSerial(row));
}
EXPECT_CALL(*this, dataFinished());
}
Expectation frameFinish = EXPECT_CALL(*this, frameFinished(_))
.After(dataStart)
.WillRepeatedly(Invoke(impl_.get(), &Impl::finishReferenceFrame));
+ Expectation frameFinishSerial = EXPECT_CALL(*this, frameFinishedSerial(_))
+ .After(dataStart)
+ .WillRepeatedly(Invoke(impl_.get(), &Impl::finishReferenceFrameSerial));
EXPECT_CALL(*this, dataFinished())
- .After(frameStart, pointsAdd, frameFinish);
+ .After(frameStart, pointsAdd, frameFinish, frameFinishSerial);
}
} // namespace test
#include "gromacs/analysisdata/dataframe.h"
#include "gromacs/analysisdata/datamodule.h"
#include "gromacs/analysisdata/paralleloptions.h"
-#include "gromacs/utility/common.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
MOCK_METHOD1(frameStarted, void(const AnalysisDataFrameHeader &header));
MOCK_METHOD1(pointsAdded, void(const AnalysisDataPointSetRef &points));
MOCK_METHOD1(frameFinished, void(const AnalysisDataFrameHeader &header));
+ MOCK_METHOD1(frameFinishedSerial, void(int frameIndex));
MOCK_METHOD0(dataFinished, void());
void setupStaticCheck(const AnalysisDataTestInput &data,
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <AnalysisData Name="InputData">
+ <DataFrame Name="Frame0">
+ <Real Name="X">1</Real>
+ <DataValues>
+ <Int Name="Count">1</Int>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ <Real Name="Error">1</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ <DataFrame Name="Frame1">
+ <Real Name="X">1.5</Real>
+ <DataValues>
+ <Int Name="Count">1</Int>
+ <DataValue>
+ <Real Name="Value">1</Real>
+ <Real Name="Error">1</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ <DataFrame Name="Frame2">
+ <Real Name="X">2</Real>
+ <DataValues>
+ <Int Name="Count">1</Int>
+ <DataValue>
+ <Real Name="Value">3</Real>
+ <Real Name="Error">2</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ <DataFrame Name="Frame3">
+ <Real Name="X">2.5</Real>
+ <DataValues>
+ <Int Name="Count">1</Int>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ <Real Name="Error">2</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ <DataFrame Name="Frame4">
+ <Real Name="X">3</Real>
+ <DataValues>
+ <Int Name="Count">1</Int>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ <Real Name="Error">1</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ <DataFrame Name="Frame5">
+ <Real Name="X">3.5</Real>
+ <DataValues>
+ <Int Name="Count">1</Int>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ <Real Name="Error">3</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ <DataFrame Name="Frame6">
+ <Real Name="X">4</Real>
+ <DataValues>
+ <Int Name="Count">1</Int>
+ <DataValue>
+ <Real Name="Value">1</Real>
+ <Real Name="Error">3</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ </AnalysisData>
+ <AnalysisData Name="CumulativeHistogram">
+ <DataFrame Name="Frame0">
+ <Real Name="X">1.25</Real>
+ <DataValues>
+ <Int Name="Count">1</Int>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ <DataFrame Name="Frame1">
+ <Real Name="X">1.75</Real>
+ <DataValues>
+ <Int Name="Count">1</Int>
+ <DataValue>
+ <Real Name="Value">3</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ <DataFrame Name="Frame2">
+ <Real Name="X">2.25</Real>
+ <DataValues>
+ <Int Name="Count">1</Int>
+ <DataValue>
+ <Real Name="Value">6</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ <DataFrame Name="Frame3">
+ <Real Name="X">2.75</Real>
+ <DataValues>
+ <Int Name="Count">1</Int>
+ <DataValue>
+ <Real Name="Value">10</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ <DataFrame Name="Frame4">
+ <Real Name="X">3.25</Real>
+ <DataValues>
+ <Int Name="Count">1</Int>
+ <DataValue>
+ <Real Name="Value">12</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ <DataFrame Name="Frame5">
+ <Real Name="X">3.75</Real>
+ <DataValues>
+ <Int Name="Count">1</Int>
+ <DataValue>
+ <Real Name="Value">12</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ <DataFrame Name="Frame6">
+ <Real Name="X">4.25</Real>
+ <DataValues>
+ <Int Name="Count">1</Int>
+ <DataValue>
+ <Real Name="Value">13</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ </AnalysisData>
+</ReferenceData>
</AnalysisData>
<AnalysisData Name="ResampledHistogram">
<DataFrame Name="Frame0">
- <Real Name="X">1.5</Real>
+ <Real Name="X">1.25</Real>
<DataValues>
<Int Name="Count">1</Int>
<DataValue>
</DataValues>
</DataFrame>
<DataFrame Name="Frame1">
- <Real Name="X">2.5</Real>
+ <Real Name="X">2.25</Real>
<DataValues>
<Int Name="Count">1</Int>
<DataValue>
</DataValues>
</DataFrame>
<DataFrame Name="Frame2">
- <Real Name="X">3.5</Real>
+ <Real Name="X">3.25</Real>
<DataValues>
<Int Name="Count">1</Int>
<DataValue>
</AnalysisData>
<AnalysisData Name="ResampledHistogram">
<DataFrame Name="Frame0">
- <Real Name="X">1</Real>
+ <Real Name="X">0.75</Real>
<DataValues>
<Int Name="Count">1</Int>
<DataValue>
</DataValues>
</DataFrame>
<DataFrame Name="Frame1">
- <Real Name="X">2</Real>
+ <Real Name="X">1.75</Real>
<DataValues>
<Int Name="Count">1</Int>
<DataValue>
</DataValues>
</DataFrame>
<DataFrame Name="Frame2">
- <Real Name="X">3</Real>
+ <Real Name="X">2.75</Real>
<DataValues>
<Int Name="Count">1</Int>
<DataValue>
</DataValues>
</DataFrame>
<DataFrame Name="Frame3">
- <Real Name="X">4</Real>
+ <Real Name="X">3.75</Real>
<DataValues>
<Int Name="Count">1</Int>
<DataValue>
* - Helper classes/functions for implementing the %main() function.
* See \ref page_usinglibrary for an overview of those available for user
* programs. These are declared in cmdlineinit.h
- * (gmx::CommandLineModuleInterface is declared in cmdlinemodule.h).
+ * (gmx::CommandLineModuleInterface is declared in cmdlinemodule.h and
+ * gmx::CommandLineOptionsInterface in cmdlineoptionsmodule.h).
* \if libapi
*
* Additionally, for internal \Gromacs use, gmx::CommandLineModuleManager
#ifndef GMX_COMMANDLINE_H
#define GMX_COMMANDLINE_H
-#include "commandline/cmdlinehelpwriter.h"
-#include "commandline/cmdlineinit.h"
-#include "commandline/cmdlinemodule.h"
-#include "commandline/cmdlineparser.h"
-#include "commandline/pargs.h"
+#include "gromacs/commandline/cmdlinehelpwriter.h"
+#include "gromacs/commandline/cmdlineinit.h"
+#include "gromacs/commandline/cmdlinemodule.h"
+#include "gromacs/commandline/cmdlineoptionsmodule.h"
+#include "gromacs/commandline/cmdlineparser.h"
+#include "gromacs/commandline/pargs.h"
#endif
file(GLOB COMMANDLINE_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${COMMANDLINE_SOURCES} PARENT_SCOPE)
-set(COMMANDLINE_PUBLIC_HEADERS
+gmx_install_headers(
cmdlinehelpwriter.h
cmdlineinit.h
cmdlinemodule.h
+ cmdlineoptionsmodule.h
cmdlineparser.h
cmdlineprogramcontext.h
- pargs.h)
-gmx_install_headers(commandline ${COMMANDLINE_PUBLIC_HEADERS})
+ pargs.h
+ )
if (BUILD_TESTING)
add_subdirectory(tests)
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_commandline
*/
+#include "gmxpre.h"
+
#include "cmdlinehelpcontext.h"
-#include "gromacs/commandline/shellcompletions.h"
#include "gromacs/utility/gmxassert.h"
+#include "shellcompletions.h"
+
namespace gmx
{
#ifndef GMX_COMMANDLINE_CMDLINEHELPCONTEXT_H
#define GMX_COMMANDLINE_CMDLINEHELPCONTEXT_H
-#include "../onlinehelp/helpwritercontext.h"
-#include "../utility/common.h"
+#include "gromacs/onlinehelp/helpwritercontext.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_commandline
*/
-#include "gromacs/commandline/cmdlinehelpmodule.h"
+#include "gmxpre.h"
+
+#include "cmdlinehelpmodule.h"
#include <string>
#include <vector>
#include "gromacs/commandline/cmdlinehelpcontext.h"
#include "gromacs/commandline/cmdlinehelpwriter.h"
#include "gromacs/commandline/cmdlineparser.h"
-#include "gromacs/commandline/shellcompletions.h"
#include "gromacs/onlinehelp/helpformat.h"
#include "gromacs/onlinehelp/helpmanager.h"
#include "gromacs/onlinehelp/helptopic.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/stringutil.h"
+#include "shellcompletions.h"
+
namespace gmx
{
*
* Does not throw.
*/
- explicit RootHelpTopic(const std::string &binaryName)
- : binaryName_(binaryName)
+ explicit RootHelpTopic(const CommandLineHelpModuleImpl &helpModule)
+ : helpModule_(helpModule)
{
}
virtual void writeHelp(const HelpWriterContext &context) const;
private:
- std::string binaryName_;
+ const CommandLineHelpModuleImpl &helpModule_;
GMX_DISALLOW_COPY_AND_ASSIGN(RootHelpTopic);
};
}
{
CommandLineCommonOptionsHolder optionsHolder;
- CommandLineHelpContext cmdlineContext(context);
+ CommandLineHelpContext cmdlineContext(*helpModule_.context_);
+ cmdlineContext.setModuleDisplayName(helpModule_.binaryName_);
optionsHolder.initOptions();
- cmdlineContext.setModuleDisplayName(binaryName_);
// TODO: Add <command> [<args>] into the synopsis.
- // TODO: Propagate the -hidden option here.
CommandLineHelpWriter(*optionsHolder.options())
.writeHelp(cmdlineContext);
}
const std::string &binaryName,
const CommandLineModuleMap &modules,
const CommandLineModuleGroupList &groups)
- : rootTopic_(new RootHelpTopic(binaryName)), programContext_(programContext),
+ : rootTopic_(new RootHelpTopic(*this)), programContext_(programContext),
binaryName_(binaryName), modules_(modules), groups_(groups),
context_(NULL), moduleOverride_(NULL), bHidden_(false),
outputOverride_(NULL)
#ifndef GMX_COMMANDLINE_CMDLINEHELPMODULE_H
#define GMX_COMMANDLINE_CMDLINEHELPMODULE_H
-#include "cmdlinemodule.h"
-#include "cmdlinemodulemanager-impl.h"
-
+#include "gromacs/commandline/cmdlinemodule.h"
#include "gromacs/onlinehelp/helptopicinterface.h"
-#include "gromacs/utility/common.h"
+#include "gromacs/utility/classhelpers.h"
+
+#include "cmdlinemodulemanager-impl.h"
namespace gmx
{
return "Print help information";
}
+ virtual void init(CommandLineModuleSettings *settings)
+ {
+ settings->setDefaultNiceLevel(0);
+ }
virtual int run(int argc, char *argv[]);
virtual void writeHelp(const CommandLineHelpContext &context) const;
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_commandline
*/
+#include "gmxpre.h"
+
#include "cmdlinehelpwriter.h"
#include <cstring>
#include <boost/scoped_ptr.hpp>
#include "gromacs/commandline/cmdlinehelpcontext.h"
-#include "gromacs/commandline/shellcompletions.h"
#include "gromacs/onlinehelp/helpformat.h"
#include "gromacs/onlinehelp/helpwritercontext.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/utility/file.h"
#include "gromacs/utility/stringutil.h"
+#include "shellcompletions.h"
+
namespace gmx
{
#ifndef GMX_COMMANDLINE_CMDLINEHELPWRITER_H
#define GMX_COMMANDLINE_CMDLINEHELPWRITER_H
-#include "../utility/common.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_commandline
*/
-#include "gromacs/commandline/cmdlineinit.h"
+#include "gmxpre.h"
+
+#include "cmdlineinit.h"
+
+#include "config.h"
#include <cstring>
#include <boost/scoped_ptr.hpp>
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-
#include "gromacs/commandline/cmdlinemodulemanager.h"
+#include "gromacs/commandline/cmdlineoptionsmodule.h"
#include "gromacs/commandline/cmdlineprogramcontext.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/utility/datafilefinder.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/init.h"
#include "gromacs/utility/programcontext.h"
//! Global context instance initialized in initForCommandLine().
boost::scoped_ptr<CommandLineProgramContext> g_commandLineContext;
+//! Global library data file finder that respects GMXLIB.
+boost::scoped_ptr<DataFileFinder> g_libFileFinder;
#ifdef GMX_LIB_MPI
void broadcastArguments(const t_commrec *cr, int *argc, char ***argv)
{
g_commandLineContext.reset(new CommandLineProgramContext(*argc, *argv));
setProgramContext(g_commandLineContext.get());
+ g_libFileFinder.reset(new DataFileFinder());
+ g_libFileFinder->setSearchPathFromEnv("GMXLIB");
+ setLibraryFileFinder(g_libFileFinder.get());
}
catch (const std::exception &ex)
{
void finalizeForCommandLine()
{
gmx::finalize();
+ setLibraryFileFinder(NULL);
+ g_libFileFinder.reset();
setProgramContext(NULL);
g_commandLineContext.reset();
}
+int processExceptionAtExitForCommandLine(const std::exception &ex)
+{
+ int rc = processExceptionAtExit(ex); //Currently this aborts for GMX_LIB_MPI
+ finalizeForCommandLine(); //thus this MPI_Finalize doesn't matter
+ return rc;
+}
+
int runCommandLineModule(int argc, char *argv[],
CommandLineModuleInterface *module)
{
- return gmx::CommandLineModuleManager::runAsMainSingleModule(argc, argv, module);
+ return CommandLineModuleManager::runAsMainSingleModule(argc, argv, module);
+}
+
+int runCommandLineModule(int argc, char *argv[],
+ const char *name, const char *description,
+ CommandLineOptionsModuleInterface *(*factory)())
+{
+ return CommandLineOptionsModuleInterface::runAsMain(
+ argc, argv, name, description, factory);
}
} // namespace gmx
// Forward declaration of class CommandLineProgramContext is not sufficient for
// MSVC if the return value of initForCommandLine() is ignored(!)
-#include "cmdlineprogramcontext.h"
+#include "gromacs/commandline/cmdlineprogramcontext.h"
namespace gmx
{
class CommandLineModuleInterface;
+class CommandLineOptionsModuleInterface;
/*! \brief
* Initializes the \Gromacs library for command-line use.
* \ingroup module_commandline
*/
void finalizeForCommandLine();
-
+/*! \brief
+ * Handles an exception and deinitializes after initForCommandLine.
+ *
+ * \param[in] ex Exception that is the cause for terminating the program.
+ * \returns Return code to return from main().
+ *
+ * This method should be called as the last thing before terminating the
+ * program because of an exception. See processExceptionAtExit() for details.
+ * Additionally this method undoes the work done by initForCommandLine.
+ *
+ * Does not throw.
+ */
+int processExceptionAtExitForCommandLine(const std::exception &ex);
/*! \brief
* Implements a main() method that runs a single module.
*
*/
int runCommandLineModule(int argc, char *argv[],
CommandLineModuleInterface *module);
+/*! \brief
+ * Implements a main() method that runs a single module.
+ *
+ * \param argc \c argc passed to main().
+ * \param argv \c argv passed to main().
+ * \param[in] name Name for the module.
+ * \param[in] description Short description for the module.
+ * \param factory Factory method that creates the module to run.
+ *
+ * This method allows for uniform behavior for binaries that only
+ * contain a single module without duplicating any of the
+ * implementation from CommandLineModuleManager (startup headers,
+ * common options etc.).
+ *
+ * Usage:
+ * \code
+ class CustomCommandLineOptionsModule : public CommandLineOptionsModuleInterface
+ {
+ // <...>
+ };
+
+ static CommandLineOptionsModuleInterface *create()
+ {
+ return new CustomCommandLineOptionsModule();
+ }
+
+ int main(int argc, char *argv[])
+ {
+ return gmx::runCommandLineModule(
+ argc, argv, "mymodule", "short description", &create);
+ }
+ \endcode
+ *
+ * Does not throw. All exceptions are caught and handled internally.
+ */
+int runCommandLineModule(int argc, char *argv[],
+ const char *name, const char *description,
+ CommandLineOptionsModuleInterface *(*factory)());
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/*! \file
+/*! \internal \file
* \brief
- * Include file for configuration macros that affect installed headers.
+ * Implements classes from cmdlinemodule.h.
*
- * This include file (or rather, one that it includes) will configured by CMake
- * and installed with GROMACS header files so that they can refer to a central
- * location for \#defines that will be available for builds of projects that
- * depend on GROMACS.
- *
- * The actual defines are in gmx_header_config_gen.h to allow usage of relative
- * include paths before installation.
- *
- * \todo
- * It would be better to have the defines here such that they are not generated
- * from CMake, but instead detected using \#ifdefs (possible for some of the
- * macros currently used).
- * Even better would be to not have these defines at all.
- *
- * \inlibraryapi
- * \ingroup module_utility
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_commandline
*/
-#include "gmx_header_config_gen.h"
+#include "gmxpre.h"
+
+#include "cmdlinemodule.h"
+
+#include "gromacs/commandline/cmdlinehelpcontext.h"
+
+namespace gmx
+{
+
+class CommandLineModuleSettings::Impl
+{
+ public:
+ Impl() : defaultNiceLevel_(19) {}
+
+ int defaultNiceLevel_;
+};
+
+CommandLineModuleSettings::CommandLineModuleSettings()
+ : impl_(new Impl)
+{
+}
+
+CommandLineModuleSettings::~CommandLineModuleSettings()
+{
+}
+
+int CommandLineModuleSettings::defaultNiceLevel() const
+{
+ return impl_->defaultNiceLevel_;
+}
+
+void CommandLineModuleSettings::setDefaultNiceLevel(int niceLevel)
+{
+ impl_->defaultNiceLevel_ = niceLevel;
+}
+
+//! \cond libapi
+void writeCommandLineHelpCMain(
+ const CommandLineHelpContext &context, const char *name,
+ int (*mainFunction)(int argc, char *argv[]))
+{
+ char *argv[2];
+ int argc = 1;
+ // TODO: The constness should not be cast away.
+ argv[0] = const_cast<char *>(name);
+ argv[1] = NULL;
+ GlobalCommandLineHelpContext global(context);
+ mainFunction(argc, argv);
+}
+//! \endcond
+
+} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
/*! \file
* \brief
- * Declares gmx::CommandLineModuleInterface.
+ * Declares gmx::CommandLineModuleInterface and supporting classes.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \inpublicapi
#ifndef GMX_COMMANDLINE_CMDLINEMODULE_H
#define GMX_COMMANDLINE_CMDLINEMODULE_H
+#include "gromacs/utility/classhelpers.h"
+
namespace gmx
{
class CommandLineHelpContext;
+/*! \brief
+ * Settings to pass information between a module and the general runner.
+ *
+ * Methods in this class do not throw, except that construction may throw
+ * std::bad_alloc.
+ *
+ * \inpublicapi
+ * \ingroup module_commandline
+ */
+class CommandLineModuleSettings
+{
+ public:
+ CommandLineModuleSettings();
+ ~CommandLineModuleSettings();
+
+ //! Returns the default nice level for this module.
+ int defaultNiceLevel() const;
+
+ /*! \brief
+ * Sets the default nice level for this module.
+ *
+ * If not called, the module will be niced.
+ */
+ void setDefaultNiceLevel(int niceLevel);
+
+ private:
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
+};
+
/*! \brief
* Module that can be run from command line using CommandLineModuleManager.
*
* \see CommandLineModuleManager
+ * \see CommandLineOptionsModule
*
* \inpublicapi
* \ingroup module_commandline
//! Returns a one-line description of the module.
virtual const char *shortDescription() const = 0;
+ /*! \brief
+ * Initializes the module and provides settings for the runner.
+ *
+ * This will be called before run(), and can be used to adjust
+ * initialization that the runner does.
+ *
+ * This method is currently not called when writing the help.
+ */
+ virtual void init(CommandLineModuleSettings *settings) = 0;
/*! \brief
* Runs the module with the given arguments.
*
* \param[in] context Context object for writing the help.
* \throws std::bad_alloc if out of memory.
* \throws FileIOError on any I/O error.
+ *
+ * Note that for MPI-enabled builds, this is called only on the master
+ * rank.
*/
virtual void writeHelp(const CommandLineHelpContext &context) const = 0;
};
+//! \cond libapi
+/*! \libinternal \brief
+ * Helper to implement CommandLineModuleInterface::writeHelp() with a C-like
+ * main() function that calls parse_common_args().
+ *
+ * \param[in] context Context object for writing the help.
+ * \param[in] name Name of the module.
+ * \param[in] mainFunction C-like main() function that calls parse_common_args().
+ *
+ * \ingroup module_commandline
+ */
+void writeCommandLineHelpCMain(
+ const CommandLineHelpContext &context, const char *name,
+ int (*mainFunction)(int argc, char *argv[]));
+//! \endcond
+
} // namespace gmx
#endif
#include <string>
#include <vector>
-#include "cmdlinemodule.h"
-#include "cmdlinemodulemanager.h"
-
+#include "gromacs/commandline/cmdlinemodule.h"
+#include "gromacs/commandline/cmdlinemodulemanager.h"
#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/options/options.h"
-#include "gromacs/utility/common.h"
+#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/uniqueptr.h"
*/
bool finishOptions();
+ //! Adjust defaults based on module settings.
+ void adjustFromSettings(const CommandLineModuleSettings &settings);
+
//! Returns the internal Options object.
Options *options() { return &options_; }
//! Returns the settings for printing startup information.
{
return bQuiet_ && !bVersion_;
}
+ //! Returns whether backups should be made.
+ bool shouldBackup() const { return bBackup_; }
+
+ //! Returns the nice level.
+ int niceLevel() const { return niceLevel_; }
+ //! Returns whether floating-point exception should be enabled
+ bool enableFPExceptions() const { return bFpexcept_; }
+ //! Returns the debug level.
+ int debugLevel() const { return debugLevel_; }
//! Returns the file to which startup information should be printed.
FILE *startupInfoFile() const { return (bVersion_ ? stdout : stderr); }
bool bQuiet_;
bool bVersion_;
bool bCopyright_;
+ int niceLevel_;
+ bool bBackup_;
+ bool bFpexcept_;
+ int debugLevel_;
GMX_DISALLOW_COPY_AND_ASSIGN(CommandLineCommonOptionsHolder);
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_commandline
*/
+#include "gmxpre.h"
+
#include "cmdlinemodulemanager.h"
#include <cstdio>
#include <string>
#include <utility>
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/network.h"
-
#include "gromacs/commandline/cmdlinehelpcontext.h"
-#include "gromacs/commandline/cmdlinehelpmodule.h"
#include "gromacs/commandline/cmdlineinit.h"
#include "gromacs/commandline/cmdlinemodule.h"
-#include "gromacs/commandline/cmdlinemodulemanager-impl.h"
#include "gromacs/commandline/cmdlineparser.h"
#include "gromacs/commandline/cmdlineprogramcontext.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
+#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/sysinfo.h"
-// For GMX_BINARY_SUFFIX
-#include "config.h"
+#include "cmdlinehelpmodule.h"
+#include "cmdlinemodulemanager-impl.h"
namespace gmx
{
return shortDescription_;
}
+ virtual void init(CommandLineModuleSettings * /*settings*/)
+ {
+ }
virtual int run(int argc, char *argv[])
{
return mainFunction_(argc, argv);
}
virtual void writeHelp(const CommandLineHelpContext &context) const
{
- char *argv[2];
- int argc = 1;
- // TODO: The constness should not be cast away.
- argv[0] = const_cast<char *>(name_);
- argv[1] = NULL;
- GlobalCommandLineHelpContext global(context);
- mainFunction_(argc, argv);
+ writeCommandLineHelpCMain(context, name_, mainFunction_);
}
private:
const char *name_;
const char *shortDescription_;
CMainFunction mainFunction_;
-
};
//! \}
CommandLineCommonOptionsHolder::CommandLineCommonOptionsHolder()
: options_(NULL, NULL), bHelp_(false), bHidden_(false),
- bQuiet_(false), bVersion_(false), bCopyright_(true)
+ bQuiet_(false), bVersion_(false), bCopyright_(true),
+ niceLevel_(19), bBackup_(true), bFpexcept_(false), debugLevel_(0)
{
binaryInfoSettings_.copyright(true);
}
.description("Print extended version information and quit"));
options_.addOption(BooleanOption("copyright").store(&bCopyright_)
.description("Print copyright information on startup"));
+ options_.addOption(IntegerOption("nice").store(&niceLevel_)
+ .description("Set the nicelevel (default depends on command)"));
+ options_.addOption(BooleanOption("backup").store(&bBackup_)
+ .description("Write backups if output files exist"));
+ options_.addOption(BooleanOption("fpexcept").store(&bFpexcept_)
+ .hidden().description("Enable floating-point exceptions"));
+ options_.addOption(IntegerOption("debug").store(&debugLevel_)
+ .hidden().defaultValueIfSet(1)
+ .description("Write file with debug information, "
+ "1: short (default), 2: also x and f"));
}
bool CommandLineCommonOptionsHolder::finishOptions()
return !bVersion_;
}
+void CommandLineCommonOptionsHolder::adjustFromSettings(
+ const CommandLineModuleSettings &settings)
+{
+ if (!options_.isSet("nice"))
+ {
+ niceLevel_ = settings.defaultNiceLevel();
+ }
+}
+
/********************************************************************
* CommandLineModuleManager::Impl
*/
*/
CommandLineModuleMap::const_iterator
findModuleByName(const std::string &name) const;
- /*! \brief
- * Finds a module that the name of the binary.
- *
- * \param[in] invokedName Name by which the program was invoked.
- * \throws std::bad_alloc if out of memory.
- * \returns Iterator to the found module, or
- * \c modules_.end() if not found.
- *
- * Checks whether the program is invoked through a symlink whose name
- * is different from \a binaryName_, and if so, checks
- * if a module name matches the name of the symlink.
- *
- * Note that the \p invokedName parameter is currently not necessary
- * (as the program context object is also available and provides this
- * value), but it clarifies the control flow.
- */
- CommandLineModuleMap::const_iterator
- findModuleFromBinaryName(const char *invokedName) const;
/*! \brief
* Processes command-line options for the wrapper binary.
return modules_.find(name);
}
-CommandLineModuleMap::const_iterator
-CommandLineModuleManager::Impl::findModuleFromBinaryName(
- const char *invokedName) const
-{
- std::string moduleName = invokedName;
-#ifdef GMX_BINARY_SUFFIX
- moduleName = stripSuffixIfPresent(moduleName, GMX_BINARY_SUFFIX);
-#endif
- if (moduleName == binaryName_)
- {
- return modules_.end();
- }
- if (startsWith(moduleName, "g_"))
- {
- moduleName.erase(0, 2);
- }
- if (startsWith(moduleName, "gmx"))
- {
- moduleName.erase(0, 3);
- }
- return findModuleByName(moduleName);
-}
-
CommandLineModuleInterface *
CommandLineModuleManager::Impl::processCommonOptions(
CommandLineCommonOptionsHolder *optionsHolder, int *argc, char ***argv)
{
// Check if we are directly invoking a certain module.
CommandLineModuleInterface *module = singleModule_;
- if (module == NULL)
- {
- // Also check for invokation through named symlinks.
- CommandLineModuleMap::const_iterator moduleIter
- = findModuleFromBinaryName(programContext_.programName());
- if (moduleIter != modules_.end())
- {
- module = moduleIter->second.get();
- }
- }
// TODO: It would be nice to propagate at least the -quiet option to
// the modules so that they can also be quiet in response to this.
int CommandLineModuleManager::run(int argc, char *argv[])
{
CommandLineModuleInterface *module;
- const bool bMaster = (!gmx_mpi_initialized() || gmx_node_rank() == 0);
+ const bool bMaster = (gmx_node_rank() == 0);
bool bQuiet = impl_->bQuiet_ || !bMaster;
CommandLineCommonOptionsHolder optionsHolder;
try
{
return 0;
}
- int rc = module->run(argc, argv);
+
+ CommandLineModuleSettings settings;
+ module->init(&settings);
+ optionsHolder.adjustFromSettings(settings);
+
+ gmx_set_max_backup_count(optionsHolder.shouldBackup() ? -1 : 0);
+
+ // Open the debug file.
+ if (optionsHolder.debugLevel() > 0)
+ {
+ std::string filename(impl_->programContext_.programName());
+ if (gmx_node_num() > 1)
+ {
+ filename.append(formatString("%d", gmx_node_rank()));
+ }
+ filename.append(".debug");
+
+ fprintf(stderr, "Will write debug log file: %s\n", filename.c_str());
+ gmx_init_debug(optionsHolder.debugLevel(), filename.c_str());
+ }
+ // Set the nice level unless disabled in the configuration.
+ if (optionsHolder.niceLevel() != 0)
+ {
+ static bool bNiceSet = false; // Only set it once.
+ if (!bNiceSet)
+ {
+ // TODO: Diagnostic if this fails and the user explicitly requested it.
+ gmx_set_nice(optionsHolder.niceLevel());
+ bNiceSet = true;
+ }
+ }
+ if (optionsHolder.enableFPExceptions())
+ {
+ //TODO: currently it is always enabled for mdrun (verlet) and tests.
+ gmx_feenableexcept();
+ }
+
+ int rc = 0;
+ if (!(module == impl_->helpModule_ && !bMaster))
+ {
+ rc = module->run(argc, argv);
+ }
if (!bQuiet)
{
gmx_thanx(stderr);
catch (const std::exception &ex)
{
printFatalErrorMessage(stderr, ex);
- return processExceptionAtExit(ex);
+ return processExceptionAtExitForCommandLine(ex);
}
}
#ifndef GMX_COMMANDLINE_CMDLINEMODULEMANAGER_H
#define GMX_COMMANDLINE_CMDLINEMODULEMANAGER_H
-#include "../onlinehelp/helptopicinterface.h"
-#include "../utility/common.h"
-#include "../utility/uniqueptr.h"
+#include "gromacs/onlinehelp/helptopicinterface.h"
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/uniqueptr.h"
namespace gmx
{
catch (const std::exception &ex)
{
gmx::printFatalErrorMessage(stderr, ex);
- return gmx::processExceptionAtExit(ex);
+ return gmx::processExceptionAtExitForCommandLine(ex);
}
}
* \endcode
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements supporting routines for gmx::CommandLineOptionsModuleInterface.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_commandline
+ */
+#include "gmxpre.h"
+
+#include "cmdlineoptionsmodule.h"
+
+#include <boost/scoped_ptr.hpp>
+
+#include "gromacs/commandline/cmdlinehelpwriter.h"
+#include "gromacs/commandline/cmdlinemodulemanager.h"
+#include "gromacs/commandline/cmdlineparser.h"
+#include "gromacs/options/filenameoptionmanager.h"
+#include "gromacs/options/options.h"
+#include "gromacs/utility/gmxassert.h"
+
+namespace gmx
+{
+
+namespace
+{
+
+/********************************************************************
+ * CommandLineOptionsModule
+ */
+
+class CommandLineOptionsModule : public CommandLineModuleInterface
+{
+ public:
+ //! Shorthand for the factory function pointer type.
+ typedef CommandLineOptionsModuleInterface::FactoryMethod FactoryMethod;
+
+ CommandLineOptionsModule(const char *name, const char *description,
+ FactoryMethod factory)
+ : name_(name), description_(description), factory_(factory)
+ {
+ }
+ virtual const char *name() const { return name_; }
+ virtual const char *shortDescription() const { return description_; }
+
+ virtual void init(CommandLineModuleSettings *settings);
+ virtual int run(int argc, char *argv[]);
+ virtual void writeHelp(const CommandLineHelpContext &context) const;
+
+ private:
+ void parseOptions(int argc, char *argv[]);
+
+ const char *name_;
+ const char *description_;
+ FactoryMethod factory_;
+ boost::scoped_ptr<CommandLineOptionsModuleInterface> module_;
+};
+
+void CommandLineOptionsModule::init(CommandLineModuleSettings *settings)
+{
+ module_.reset(factory_());
+ module_->init(settings);
+}
+
+int CommandLineOptionsModule::run(int argc, char *argv[])
+{
+ GMX_RELEASE_ASSERT(module_, "init() has not been called");
+ parseOptions(argc, argv);
+ return module_->run();
+}
+
+void CommandLineOptionsModule::writeHelp(const CommandLineHelpContext &context) const
+{
+ boost::scoped_ptr<CommandLineOptionsModuleInterface> module(factory_());
+ Options options(name(), shortDescription());
+ module->initOptions(&options);
+ CommandLineHelpWriter(options)
+ .setShowDescriptions(true)
+ .writeHelp(context);
+}
+
+void CommandLineOptionsModule::parseOptions(int argc, char *argv[])
+{
+ FileNameOptionManager fileoptManager;
+ Options options(name_, description_);
+
+ options.addManager(&fileoptManager);
+
+ module_->initOptions(&options);
+ {
+ CommandLineParser parser(&options);
+ parser.parse(&argc, argv);
+ options.finish();
+ }
+ module_->optionsFinished(&options);
+}
+
+} // namespace
+
+/********************************************************************
+ * CommandLineOptionsModuleInterface
+ */
+
+CommandLineOptionsModuleInterface::~CommandLineOptionsModuleInterface()
+{
+}
+
+// static
+CommandLineModuleInterface *
+CommandLineOptionsModuleInterface::createModule(
+ const char *name, const char *description, FactoryMethod factory)
+{
+ return new CommandLineOptionsModule(name, description, factory);
+}
+
+// static
+int CommandLineOptionsModuleInterface::runAsMain(
+ int argc, char *argv[], const char *name, const char *description,
+ FactoryMethod factory)
+{
+ CommandLineOptionsModule module(name, description, factory);
+ return CommandLineModuleManager::runAsMainSingleModule(argc, argv, &module);
+}
+
+// static
+void CommandLineOptionsModuleInterface::registerModule(
+ CommandLineModuleManager *manager, const char *name,
+ const char *description, FactoryMethod factory)
+{
+ CommandLineModulePointer module(createModule(name, description, factory));
+ manager->addModule(move(module));
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Declares gmx::CommandLineOptionsModuleInterface and supporting routines.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inpublicapi
+ * \ingroup module_commandline
+ */
+#ifndef GMX_COMMANDLINE_CMDLINEOPTIONSMODULE_H
+#define GMX_COMMANDLINE_CMDLINEOPTIONSMODULE_H
+
+#include "gromacs/commandline/cmdlinemodule.h"
+
+namespace gmx
+{
+
+class CommandLineModuleInterface;
+class CommandLineModuleManager;
+class Options;
+
+/*! \brief
+ * Module that can be run from a command line and uses gmx::Options for
+ * argument processing.
+ *
+ * This class provides a higher-level interface on top of
+ * gmx::CommandLineModuleInterface for cases where gmx::Options will be used
+ * for declaring the command-line arguments. The module only needs to declare
+ * the options it uses, and the framework takes care of command-line parsing
+ * and help output. The module typically consists of the following parts:
+ * - init() allows for some interaction between the module and the framework
+ * when running the module; see CommandLineModuleInterface::init(). If no
+ * such customization is necessary, an empty implementation is sufficient.
+ * - initOptions() is called both for running the module and for printing help
+ * for the module, and it should add the options that the module
+ * understands. Values provided for the options are typically stored in
+ * member variables.
+ * - optionsFinished() can be implemented in case additional processing is
+ * needed (e.g., checking whether an option was set by the user).
+ * - run() is called when running the module, after command-line options have
+ * been parsed and their values stored in the corresponding member
+ * variables.
+ *
+ * registerModule(), runAsMain(), or createModule() can be used to use modules
+ * of this type in all contexts where a gmx::CommandLineModuleInterface is
+ * expected. These methods create a gmx::CommandLineModuleInterface
+ * implementation that contains the common code needed to parse command-line
+ * options and write help, based on the information provided from the methods
+ * in this class.
+ *
+ * \inpublicapi
+ * \ingroup module_commandline
+ */
+class CommandLineOptionsModuleInterface
+{
+ public:
+ /*! \brief
+ * Function pointer to a factory method that returns an interface of
+ * this type.
+ *
+ * \returns Module to run (should be allocated with `new`).
+ * \throws std::bad_alloc if out of memory.
+ *
+ * The caller takes responsibility to `delete` the returned pointer.
+ */
+ typedef CommandLineOptionsModuleInterface *(*FactoryMethod)();
+
+ /*! \brief
+ * Creates a CommandLineModuleInterface to run the specified module.
+ *
+ * \param[in] name Name for the module.
+ * \param[in] description Short description for the module.
+ * \param[in] factory Factory that returns the module to run.
+ * \returns CommandLineModuleInterface object that runs the module
+ * returned by \p factory. Caller must `delete` the object.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * This is mainly used by unit tests that want to bypass
+ * CommandLineModuleManager.
+ */
+ static CommandLineModuleInterface *
+ createModule(const char *name, const char *description,
+ FactoryMethod factory);
+ /*! \brief
+ * Implements a main() method that runs a single module.
+ *
+ * \param argc \c argc passed to main().
+ * \param argv \c argv passed to main().
+ * \param[in] name Name for the module.
+ * \param[in] description Short description for the module.
+ * \param[in] factory Factory that returns the module to run.
+ *
+ * This method allows for uniform behavior for binaries that only
+ * contain a single module without duplicating any of the
+ * implementation from CommandLineModuleManager (startup headers,
+ * common options etc.).
+ *
+ * \see runCommandLineModule()
+ */
+ static int
+ runAsMain(int argc, char *argv[], const char *name,
+ const char *description, FactoryMethod factory);
+ /*! \brief
+ * Registers a module of a certain type to this manager.
+ *
+ * \param manager Manager to register to.
+ * \param[in] name Name for the module.
+ * \param[in] description Short description for the module.
+ * \param[in] factory Factory that returns the module to register.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * This method internally creates a CommandLineModuleInterface module
+ * with the given \p name and \p description, and adds that to
+ * \p manager. When run or asked to write the help, the module calls
+ * \p factory to get the actual module, and forwards the necessary
+ * calls.
+ */
+ static void
+ registerModule(CommandLineModuleManager *manager,
+ const char *name, const char *description,
+ FactoryMethod factory);
+
+ virtual ~CommandLineOptionsModuleInterface();
+
+ //! \copydoc gmx::CommandLineModuleInterface::init()
+ virtual void init(CommandLineModuleSettings *settings) = 0;
+ /*! \brief
+ * Initializes command-line arguments understood by the module.
+ *
+ * \param[in,out] options Options object to add the options to.
+ *
+ * When running the module, this method is called after init().
+ * When printing help, there is no call to init(), and this is the only
+ * method called.
+ * In both cases, the implementation should add options understood by
+ * the module to \p options. Output values from options should be
+ * stored in member variables.
+ */
+ virtual void initOptions(Options *options) = 0;
+ /*! \brief
+ * Called after all option values have been set.
+ *
+ * \param[in,out] options Options object in which options are stored.
+ *
+ * When running the module, this method is called after all
+ * command-line arguments have been parsed, but while the Options
+ * object still exists.
+ *
+ * If the module needs to call, e.g., Options::isSet(), this is the
+ * place to do that.
+ */
+ virtual void optionsFinished(Options *options) = 0;
+
+ /*! \brief
+ * Runs the module.
+ *
+ * \throws unspecified May throw exceptions to indicate errors.
+ * \returns Exit code for the program.
+ * \retval 0 on successful termination.
+ *
+ * This method is called after optionsFinished() when running the
+ * module, and should do all the processing for the module.
+ */
+ virtual int run() = 0;
+};
+
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_commandline
*/
+#include "gmxpre.h"
+
#include "cmdlineparser.h"
#include <cstdlib>
#include <vector>
#include "gromacs/options/optionsassigner.h"
-#include "gromacs/utility/common.h"
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/exceptions.h"
namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
#include <vector>
-#include "../utility/common.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_commandline
*/
+#include "gmxpre.h"
+
#include "cmdlineprogramcontext.h"
-#ifdef HAVE_CONFIG_H
#include "config.h"
-#endif
#include <cstdlib>
#include <cstring>
#include "thread_mpi/mutex.h"
-#include "gromacs/fileio/path.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/file.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/path.h"
#include "gromacs/utility/stringutil.h"
namespace gmx
* Returns whether given path prefix contains files from `share/top/`.
*
* \param[in] path Path prefix to check.
- * \param[out] result If return value is `true`, the pointee is set to the
- * actual data directory. Otherwise, the pointee is not modified.
* \returns `true` if \p path contains the data files.
*
* Checks whether \p path could be the installation prefix where `share/top/`
* files have been installed: appends the relative installation path of the
* data files and calls isAcceptableLibraryPath().
*/
-bool isAcceptableLibraryPathPrefix(const std::string &path, std::string *result)
+bool isAcceptableLibraryPathPrefix(const std::string &path)
{
- std::string testPath = Path::join(path, GMXLIB_SEARCH_DIR);
+ std::string testPath = Path::join(path, DATA_INSTALL_DIR, "top");
if (isAcceptableLibraryPath(testPath))
{
- *result = testPath;
return true;
}
return false;
}
/*! \brief
- * Returns a fallback data path.
+ * Returns a fallback installation prefix path.
*
* Checks a few standard locations for the data files before returning a
* configure-time hard-coded path. The hard-coded path is preferred if it
* actually contains the data files, though.
*/
-std::string findFallbackLibraryDataPath()
+std::string findFallbackInstallationPrefixPath()
{
#ifndef GMX_NATIVE_WINDOWS
- if (!isAcceptableLibraryPath(GMXLIB_FALLBACK))
+ if (!isAcceptableLibraryPathPrefix(CMAKE_INSTALL_PREFIX))
{
- std::string foundPath;
- if (isAcceptableLibraryPathPrefix("/usr/local", &foundPath))
+ if (isAcceptableLibraryPathPrefix("/usr/local"))
{
- return foundPath;
+ return "/usr/local";
}
- if (isAcceptableLibraryPathPrefix("/usr", &foundPath))
+ if (isAcceptableLibraryPathPrefix("/usr"))
{
- return foundPath;
+ return "/usr";
}
- if (isAcceptableLibraryPathPrefix("/opt", &foundPath))
+ if (isAcceptableLibraryPathPrefix("/opt"))
{
- return foundPath;
+ return "/opt";
}
}
#endif
- return GMXLIB_FALLBACK;
+ return CMAKE_INSTALL_PREFIX;
}
/*! \brief
* Finds the library data files based on path of the binary.
*
- * \param[in] binaryPath Absolute path to the binary.
+ * \param[in] binaryPath Absolute path to the binary.
+ * \param[out] bSourceLayout Set to `true` if the binary is run from
+ * the build tree and the original source directory can be found.
* \returns Path to the `share/top/` data files.
*
* The search based on the path only works if the binary is in the same
* Extra logic is present to allow running binaries from the build tree such
* that they use up-to-date data files from the source tree.
*/
-std::string findDefaultLibraryDataPath(const std::string &binaryPath)
+std::string findInstallationPrefixPath(const std::string &binaryPath,
+ bool *bSourceLayout)
{
+ *bSourceLayout = false;
// If the input path is not absolute, the binary could not be found.
// Don't search anything.
if (Path::isAbsolute(binaryPath))
// If running directly from the build tree, try to use the source
// directory.
#if (defined CMAKE_SOURCE_DIR && defined CMAKE_BINARY_DIR)
- if (Path::startsWith(searchPath, CMAKE_BINARY_DIR))
+ std::string buildBinPath;
+#ifdef CMAKE_INTDIR
+ buildBinPath = Path::join(CMAKE_BINARY_DIR, "bin", CMAKE_INTDIR);
+#else
+ buildBinPath = Path::join(CMAKE_BINARY_DIR, "bin");
+#endif
+ if (Path::isEquivalent(searchPath, buildBinPath))
{
std::string testPath = Path::join(CMAKE_SOURCE_DIR, "share/top");
if (isAcceptableLibraryPath(testPath))
{
- return testPath;
+ *bSourceLayout = true;
+ return CMAKE_SOURCE_DIR;
}
}
#endif
// Use the executable path to (try to) find the library dir.
+ // TODO: Consider only going up exactly the required number of levels.
while (!searchPath.empty())
{
- std::string testPath = Path::join(searchPath, GMXLIB_SEARCH_DIR);
- if (isAcceptableLibraryPath(testPath))
+ if (isAcceptableLibraryPathPrefix(searchPath))
{
- return testPath;
+ return searchPath;
}
searchPath = Path::getParentPath(searchPath);
}
// End of smart searching. If we didn't find it in our parent tree,
// or if the program name wasn't set, return a fallback.
- return findFallbackLibraryDataPath();
+ return findFallbackInstallationPrefixPath();
}
//! \}
std::string displayName_;
std::string commandLine_;
mutable std::string fullBinaryPath_;
- mutable std::string defaultLibraryDataPath_;
+ mutable std::string installationPrefix_;
+ mutable bool bSourceLayout_;
mutable tMPI::mutex binaryPathMutex_;
};
CommandLineProgramContext::Impl::Impl()
- : programName_("GROMACS")
+ : programName_("GROMACS"), bSourceLayout_(false)
{
}
CommandLineProgramContext::Impl::Impl(int argc, const char *const argv[],
ExecutableEnvironmentPointer env)
- : executableEnv_(move(env))
+ : executableEnv_(env), bSourceLayout_(false)
{
invokedName_ = (argc != 0 ? argv[0] : "");
programName_ = Path::getFilename(invokedName_);
CommandLineProgramContext::CommandLineProgramContext(
int argc, const char *const argv[], ExecutableEnvironmentPointer env)
- : impl_(new Impl(argc, argv, move(env)))
+ : impl_(new Impl(argc, argv, env))
{
}
return impl_->fullBinaryPath_.c_str();
}
-const char *CommandLineProgramContext::defaultLibraryDataPath() const
+InstallationPrefixInfo CommandLineProgramContext::installationPrefix() const
{
tMPI::lock_guard<tMPI::mutex> lock(impl_->binaryPathMutex_);
- if (impl_->defaultLibraryDataPath_.empty())
+ if (impl_->installationPrefix_.empty())
{
impl_->findBinaryPath();
- impl_->defaultLibraryDataPath_ =
- Path::normalize(findDefaultLibraryDataPath(impl_->fullBinaryPath_));
+ impl_->installationPrefix_ =
+ Path::normalize(findInstallationPrefixPath(impl_->fullBinaryPath_,
+ &impl_->bSourceLayout_));
}
- return impl_->defaultLibraryDataPath_.c_str();
+ return InstallationPrefixInfo(
+ impl_->installationPrefix_.c_str(),
+ impl_->bSourceLayout_);
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
#include <vector>
-#include "../utility/common.h"
-#include "../utility/programcontext.h"
-#include "../utility/uniqueptr.h"
+#include <boost/shared_ptr.hpp>
+
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/programcontext.h"
namespace gmx
{
};
//! Shorthand for a smart pointer to ExecutableEnvironmentInterface.
-typedef gmx_unique_ptr<ExecutableEnvironmentInterface>::type
+typedef boost::shared_ptr<ExecutableEnvironmentInterface>
ExecutableEnvironmentPointer;
/*! \libinternal \brief
*/
virtual const char *fullBinaryPath() const;
/*! \brief
- * Returns the default path for \Gromacs data files.
+ * Returns the installation prefix (for finding \Gromacs data files).
*
* \throws std::bad_alloc if out of memory.
* \throws tMPI::system_error on thread synchronization errors.
* Returns a hardcoded path set during configuration time if there is
* an error in finding the library data files.
*/
- virtual const char *defaultLibraryDataPath() const;
+ virtual InstallationPrefixInfo installationPrefix() const;
/*! \brief
* Returns the full command line used to invoke the binary.
*
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/* This file is completely threadsafe - keep it that way! */
-#include "gromacs/commandline/pargs.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "pargs.h"
-#include <cctype>
-#include <cstdio>
#include <cstdlib>
#include <cstring>
-#ifdef HAVE_UNISTD_H
-#include <unistd.h>
-#endif
-
-#include "thread_mpi/threads.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/network.h"
+#include <algorithm>
+#include <list>
#include "gromacs/commandline/cmdlinehelpcontext.h"
#include "gromacs/commandline/cmdlinehelpwriter.h"
-#include "gromacs/commandline/shellcompletions.h"
+#include "gromacs/commandline/cmdlineparser.h"
#include "gromacs/fileio/timecontrol.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/filenameoptionmanager.h"
#include "gromacs/options/options.h"
+#include "gromacs/options/timeunitmanager.h"
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/path.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
/* The source code in this file should be thread-safe.
Please keep it that way. */
-static void usage(const char *type, const char *arg)
-{
- GMX_ASSERT(arg != NULL, "NULL command-line argument should not occur");
- gmx_fatal(FARGS, "Expected %s argument for option %s\n", type, arg);
-}
-
-/* Scan an int for argument argv[*i] from argument at argv[*i + 1].
- * eg: -p 32. argv[*i] is only used for error reporting.
- * If there is no value, or the conversion is not successful, the
- * routine exits with an error, otherwise it returns the value found.
- * *i is incremented once.
- */
-static int iscan(int argc, char *argv[], int *i)
-{
- const char *const arg = argv[*i];
- if (argc <= (*i)+1)
- {
- usage("an integer", arg);
- }
- const char *const value = argv[++(*i)];
- char *endptr;
- int var = std::strtol(value, &endptr, 10);
- if (*value == '\0' || *endptr != '\0')
- {
- usage("an integer", arg);
- }
- return var;
-}
-
-/* Same as above, but for large integer values */
-static gmx_int64_t istepscan(int argc, char *argv[], int *i)
-{
- const char *const arg = argv[*i];
- if (argc <= (*i)+1)
- {
- usage("an integer", arg);
- }
- const char *const value = argv[++(*i)];
- char *endptr;
- gmx_int64_t var = str_to_int64_t(value, &endptr);
- if (*value == '\0' || *endptr != '\0')
- {
- usage("an integer", arg);
- }
- return var;
-}
-
-/* Routine similar to the above, but working on doubles. */
-static double dscan(int argc, char *argv[], int *i)
-{
- const char *const arg = argv[*i];
- if (argc <= (*i)+1)
- {
- usage("a real", arg);
- }
- const char *const value = argv[++(*i)];
- char *endptr;
- double var = std::strtod(value, &endptr);
- if (*value == '\0' || *endptr != '\0')
- {
- usage("a real", arg);
- }
- return var;
-}
-
-/* Routine similar to the above, but working on strings. The pointer
- * returned is a pointer to the argv field.
- */
-static char *sscan(int argc, char *argv[], int *i)
-{
- if (argc > (*i)+1)
- {
- if ( (argv[(*i)+1][0] == '-') && (argc > (*i)+2) &&
- (argv[(*i)+2][0] != '-') )
- {
- fprintf(stderr, "Possible missing string argument for option %s\n\n",
- argv[*i]);
- }
- }
- else
- {
- usage("a string", argv[*i]);
- }
-
- return argv[++(*i)];
-}
-
-static gmx_bool is_hidden(t_pargs *pa)
-{
- return (strstr(pa->desc, "HIDDEN") != NULL);
-}
-
int nenum(const char *const enumc[])
{
int i;
return i;
}
-/* Read a number of arguments from the command line.
- * For etINT, etREAL and etCHAR an extra argument is read (when present)
- * for etBOOL the gmx_boolean option is changed to the negate value
- */
-static void get_pargs(int *argc, char *argv[], int nparg, t_pargs pa[])
-{
- int i, j, k, match;
- gmx_bool *bKeep;
- char buf[32];
- char *ptr;
-
- snew(bKeep, *argc+1);
- bKeep[0] = TRUE;
- bKeep[*argc] = TRUE;
-
- for (i = 1; (i < *argc); i++)
- {
- bKeep[i] = TRUE;
- for (j = 0; (j < nparg); j++)
- {
- if (pa[j].type == etBOOL)
- {
- sprintf(buf, "-no%s", pa[j].option+1);
- if (strcmp(pa[j].option, argv[i]) == 0)
- {
- *pa[j].u.b = TRUE;
- pa[j].bSet = TRUE;
- bKeep[i] = FALSE;
- }
- else if (strcmp(buf, argv[i]) == 0)
- {
- *pa[j].u.b = FALSE;
- pa[j].bSet = TRUE;
- bKeep[i] = FALSE;
- }
- }
- else if (strcmp(pa[j].option, argv[i]) == 0)
- {
- if (pa[j].bSet)
- {
- fprintf(stderr, "Setting option %s more than once!\n",
- pa[j].option);
- }
- pa[j].bSet = TRUE;
- bKeep[i] = FALSE;
- switch (pa[j].type)
- {
- case etINT:
- *pa[j].u.i = iscan(*argc, argv, &i);
- break;
- case etINT64:
- *pa[j].u.is = istepscan(*argc, argv, &i);
- break;
- case etTIME:
- case etREAL:
- *pa[j].u.r = dscan(*argc, argv, &i);
- break;
- case etSTR:
- *(pa[j].u.c) = sscan(*argc, argv, &i);
- break;
- case etENUM:
- match = -1;
- ptr = sscan(*argc, argv, &i);
- for (k = 1; (pa[j].u.c[k] != NULL); k++)
- {
- /* only check ptr against beginning of
- pa[j].u.c[k] */
- if (gmx_strncasecmp(ptr, pa[j].u.c[k], strlen(ptr)) == 0)
- {
- if ( ( match == -1 ) ||
- ( strlen(pa[j].u.c[k]) <
- strlen(pa[j].u.c[match]) ) )
- {
- match = k;
- }
- }
- }
- if (match != -1)
- {
- pa[j].u.c[0] = pa[j].u.c[match];
- }
- else
- {
- gmx_fatal(FARGS, "Invalid argument %s for option %s",
- ptr, pa[j].option);
- }
- break;
- case etRVEC:
- (*pa[j].u.rv)[0] = dscan(*argc, argv, &i);
- if ( (i+1 == *argc) ||
- ( (argv[i+1][0] == '-') &&
- !isdigit(argv[i+1][1]) ) )
- {
- (*pa[j].u.rv)[1] =
- (*pa[j].u.rv)[2] =
- (*pa[j].u.rv)[0];
- }
- else
- {
- bKeep[i] = FALSE;
- (*pa[j].u.rv)[1] = dscan(*argc, argv, &i);
- if ( (i+1 == *argc) ||
- ( (argv[i+1][0] == '-') &&
- !isdigit(argv[i+1][1]) ) )
- {
- gmx_fatal(FARGS,
- "%s: vector must have 1 or 3 real parameters",
- pa[j].option);
- }
- bKeep[i] = FALSE;
- (*pa[j].u.rv)[2] = dscan(*argc, argv, &i);
- }
- break;
- default:
- gmx_fatal(FARGS, "Invalid type %d in pargs", pa[j].type);
- }
- /* i may be incremented, so set it to not keep */
- bKeep[i] = FALSE;
- }
- }
- }
-
- /* Remove used entries */
- for (i = j = 0; (i <= *argc); i++)
- {
- if (bKeep[i])
- {
- argv[j++] = argv[i];
- }
- }
- (*argc) = j-1;
- sfree(bKeep);
-}
-
int opt2parg_int(const char *option, int nparg, t_pargs pa[])
{
int i;
* parse_common_args()
*/
-static void set_default_time_unit(const char *time_list[], gmx_bool bCanTime)
+namespace gmx
{
- int i = 0;
- const char *select = NULL;
-
- if (bCanTime)
- {
- select = getenv("GMXTIMEUNIT");
- if (select != NULL)
- {
- i = 1;
- while (time_list[i] && strcmp(time_list[i], select) != 0)
- {
- i++;
- }
- }
- }
- if (!bCanTime || select == NULL ||
- time_list[i] == NULL || strcmp(time_list[i], select) != 0)
- {
- /* Set it to the default: ps */
- i = 1;
- while (time_list[i] && strcmp(time_list[i], "ps") != 0)
- {
- i++;
- }
- }
- time_list[0] = time_list[i];
-}
-
-static void set_default_xvg_format(const char *xvg_list[])
+namespace
{
- int i;
- const char *select;
- select = getenv("GMX_VIEW_XVG");
- if (select == NULL)
- {
- /* The default is the first option */
- xvg_list[0] = xvg_list[1];
- }
- else
+/*! \brief
+ * Returns the index of the default xvg format.
+ *
+ * \ingroup module_commandline
+ */
+int getDefaultXvgFormat(gmx::ConstArrayRef<const char *> xvgFormats)
+{
+ const char *const select = getenv("GMX_VIEW_XVG");
+ if (select != NULL)
{
- i = 1;
- while (xvg_list[i] && strcmp(xvg_list[i], select) != 0)
+ ConstArrayRef<const char *>::const_iterator i =
+ std::find(xvgFormats.begin(), xvgFormats.end(), std::string(select));
+ if (i != xvgFormats.end())
{
- i++;
- }
- if (xvg_list[i] != NULL)
- {
- xvg_list[0] = xvg_list[i];
+ return i - xvgFormats.begin();
}
else
{
- xvg_list[0] = xvg_list[exvgNONE];
+ return exvgNONE - 1;
}
}
+ /* The default is the first option */
+ return 0;
}
-static int add_parg(int npargs, t_pargs *pa, t_pargs *pa_add)
-{
- memcpy(&(pa[npargs]), pa_add, sizeof(*pa_add));
-
- return npargs+1;
-}
-
-namespace gmx
-{
-
-namespace
-{
-
/*! \brief
- * Converts a t_filenm option into an Options option.
+ * Conversion helper between t_pargs/t_filenm and Options.
*
- * \param options Options object to add the new option to.
- * \param[in] fnm t_filenm option to convert.
+ * This class holds the necessary mapping between the old C structures and
+ * the new C++ options to allow copying values back after parsing for cases
+ * where the C++ options do not directly provide the type of value required for
+ * the C structures.
*
* \ingroup module_commandline
*/
-void filenmToOptions(Options *options, const t_filenm *fnm)
+class OptionsAdapter
+{
+ public:
+ /*! \brief
+ * Initializes the adapter to convert from a specified command line.
+ *
+ * The command line is required, because t_pargs wants to return
+ * strings by reference to the original command line.
+ * OptionsAdapter creates a copy of the `argv` array (but not the
+ * strings) to make this possible, even if the parser removes
+ * options it has recognized.
+ */
+ OptionsAdapter(int argc, const char *const argv[])
+ : argv_(argv, argv + argc)
+ {
+ }
+
+ /*! \brief
+ * Converts a t_filenm option into an Options option.
+ *
+ * \param options Options object to add the new option to.
+ * \param fnm t_filenm option to convert.
+ */
+ void filenmToOptions(Options *options, t_filenm *fnm);
+ /*! \brief
+ * Converts a t_pargs option into an Options option.
+ *
+ * \param options Options object to add the new option to.
+ * \param pa t_pargs option to convert.
+ */
+ void pargsToOptions(Options *options, t_pargs *pa);
+
+ /*! \brief
+ * Copies values back from options to t_pargs/t_filenm.
+ */
+ void copyValues(bool bReadNode);
+
+ private:
+ struct FileNameData
+ {
+ //! Creates a conversion helper for a given `t_filenm` struct.
+ explicit FileNameData(t_filenm *fnm) : fnm(fnm), optionInfo(NULL)
+ {
+ }
+
+ //! t_filenm structure to receive the final values.
+ t_filenm *fnm;
+ //! Option info object for the created FileNameOption.
+ FileNameOptionInfo *optionInfo;
+ //! Value storage for the created FileNameOption.
+ std::vector<std::string> values;
+ };
+ struct ProgramArgData
+ {
+ //! Creates a conversion helper for a given `t_pargs` struct.
+ explicit ProgramArgData(t_pargs *pa)
+ : pa(pa), optionInfo(NULL), enumIndex(0), boolValue(false)
+ {
+ }
+
+ //! t_pargs structure to receive the final values.
+ t_pargs *pa;
+ //! Option info object for the created option.
+ OptionInfo *optionInfo;
+ //! Value storage for a non-enum StringOption (unused for other types).
+ std::string stringValue;
+ //! Value storage for an enum option (unused for other types).
+ int enumIndex;
+ //! Value storage for a BooleanOption (unused for other types).
+ bool boolValue;
+ };
+
+ std::vector<const char *> argv_;
+ // These are lists instead of vectors to avoid relocating existing
+ // objects in case the container is reallocated (the Options object
+ // contains pointes to members of the objects, which would get
+ // invalidated).
+ std::list<FileNameData> fileNameOptions_;
+ std::list<ProgramArgData> programArgs_;
+
+ GMX_DISALLOW_COPY_AND_ASSIGN(OptionsAdapter);
+};
+
+void OptionsAdapter::filenmToOptions(Options *options, t_filenm *fnm)
{
+ if (fnm->opt == NULL)
+ {
+ // Existing code may use opt2fn() instead of ftp2fn() for
+ // options that use the default option name, so we need to
+ // keep the old behavior instead of fixing opt2fn().
+ // TODO: Check that this is not the case, remove this, and make
+ // opt2*() work even if fnm->opt is NULL for some options.
+ fnm->opt = ftp2defopt(fnm->ftp);
+ }
const bool bRead = ((fnm->flag & ffREAD) != 0);
const bool bWrite = ((fnm->flag & ffWRITE) != 0);
const bool bOptional = ((fnm->flag & ffOPT) != 0);
const bool bLibrary = ((fnm->flag & ffLIB) != 0);
const bool bMultiple = ((fnm->flag & ffMULT) != 0);
+ const bool bMissing = ((fnm->flag & ffALLOW_MISSING) != 0);
const char *const name = &fnm->opt[1];
const char * defName = fnm->fn;
+ int defType = -1;
if (defName == NULL)
{
defName = ftp2defnm(fnm->ftp);
}
- // Since we are not (yet) using this for actual parsing, we don't need to
- // set any storage.
- options->addOption(
- FileNameOption(name).defaultBasename(defName).legacyType(fnm->ftp)
- .readWriteFlags(bRead, bWrite).required(!bOptional)
- .libraryFile(bLibrary).multiValue(bMultiple)
- .description(ftp2desc(fnm->ftp)));
+ else if (Path::hasExtension(defName))
+ {
+ defType = fn2ftp(defName);
+ GMX_RELEASE_ASSERT(defType != efNR,
+ "File name option specifies an invalid extension");
+ }
+ fileNameOptions_.push_back(FileNameData(fnm));
+ FileNameData &data = fileNameOptions_.back();
+ data.optionInfo = options->addOption(
+ FileNameOption(name).storeVector(&data.values)
+ .defaultBasename(defName).defaultType(defType)
+ .legacyType(fnm->ftp).legacyOptionalBehavior()
+ .readWriteFlags(bRead, bWrite).required(!bOptional)
+ .libraryFile(bLibrary).multiValue(bMultiple)
+ .allowMissing(bMissing)
+ .description(ftp2desc(fnm->ftp)));
}
-/*! \brief
- * Converts a t_pargs option into an Options option.
- *
- * \param options Options object to add the new option to.
- * \param[in] pa t_pargs option to convert.
- *
- * \ingroup module_commandline
- */
-void pargsToOptions(Options *options, t_pargs *pa)
+void OptionsAdapter::pargsToOptions(Options *options, t_pargs *pa)
{
- const bool bHidden = is_hidden(pa);
+ const bool bHidden = startsWith(pa->desc, "HIDDEN");
const char *const name = &pa->option[1];
const char *const desc = (bHidden ? &pa->desc[6] : pa->desc);
- // Since we are not (yet) using this for actual parsing, we can take some
- // shortcuts and not set any storage where there is no direct
- // correspondence in the types.
+ programArgs_.push_back(ProgramArgData(pa));
+ ProgramArgData &data = programArgs_.back();
switch (pa->type)
{
case etINT:
- options->addOption(
- IntegerOption(name).store(pa->u.i)
- .description(desc).hidden(bHidden));
+ data.optionInfo = options->addOption(
+ IntegerOption(name).store(pa->u.i)
+ .description(desc).hidden(bHidden));
return;
case etINT64:
- options->addOption(
- Int64Option(name).store(pa->u.is)
- .description(desc).hidden(bHidden));
+ data.optionInfo = options->addOption(
+ Int64Option(name).store(pa->u.is)
+ .description(desc).hidden(bHidden));
return;
case etREAL:
- options->addOption(
- RealOption(name).store(pa->u.r)
- .description(desc).hidden(bHidden));
+ data.optionInfo = options->addOption(
+ RealOption(name).store(pa->u.r)
+ .description(desc).hidden(bHidden));
return;
case etTIME:
- options->addOption(
- RealOption(name).store(pa->u.r).timeValue()
- .description(desc).hidden(bHidden));
+ data.optionInfo = options->addOption(
+ RealOption(name).store(pa->u.r).timeValue()
+ .description(desc).hidden(bHidden));
return;
case etSTR:
{
const char *const defValue = (*pa->u.c != NULL ? *pa->u.c : "");
- options->addOption(
- StringOption(name).defaultValue(defValue)
- .description(desc).hidden(bHidden));
+ data.optionInfo = options->addOption(
+ StringOption(name).store(&data.stringValue)
+ .defaultValue(defValue)
+ .description(desc).hidden(bHidden));
return;
}
case etBOOL:
- options->addOption(
- BooleanOption(name).defaultValue(*pa->u.b)
- .description(desc).hidden(bHidden));
+ data.optionInfo = options->addOption(
+ BooleanOption(name).store(&data.boolValue)
+ .defaultValue(*pa->u.b)
+ .description(desc).hidden(bHidden));
return;
case etRVEC:
- options->addOption(
- RealOption(name).store(*pa->u.rv).vector()
- .description(desc).hidden(bHidden));
+ data.optionInfo = options->addOption(
+ RealOption(name).store(*pa->u.rv).vector()
+ .description(desc).hidden(bHidden));
return;
case etENUM:
- options->addOption(
- StringOption(name).defaultEnumIndex(nenum(pa->u.c) - 1)
- .enumValueFromNullTerminatedArray(pa->u.c + 1)
- .description(desc).hidden(bHidden));
+ {
+ const int defaultIndex = (pa->u.c[0] != NULL ? nenum(pa->u.c) - 1 : 0);
+ data.optionInfo = options->addOption(
+ StringOption(name).storeEnumIndex(&data.enumIndex)
+ .defaultEnumIndex(defaultIndex)
+ .enumValueFromNullTerminatedArray(pa->u.c + 1)
+ .description(desc).hidden(bHidden));
return;
+ }
}
GMX_THROW(NotImplementedError("Argument type not implemented"));
}
+void OptionsAdapter::copyValues(bool bReadNode)
+{
+ std::list<FileNameData>::const_iterator file;
+ for (file = fileNameOptions_.begin(); file != fileNameOptions_.end(); ++file)
+ {
+ if (!bReadNode && (file->fnm->flag & ffREAD))
+ {
+ continue;
+ }
+ if (file->optionInfo->isSet())
+ {
+ file->fnm->flag |= ffSET;
+ }
+ file->fnm->nfiles = file->values.size();
+ snew(file->fnm->fns, file->fnm->nfiles);
+ for (int i = 0; i < file->fnm->nfiles; ++i)
+ {
+ file->fnm->fns[i] = gmx_strdup(file->values[i].c_str());
+ }
+ }
+ std::list<ProgramArgData>::const_iterator arg;
+ for (arg = programArgs_.begin(); arg != programArgs_.end(); ++arg)
+ {
+ arg->pa->bSet = arg->optionInfo->isSet();
+ switch (arg->pa->type)
+ {
+ case etSTR:
+ {
+ if (arg->pa->bSet)
+ {
+ std::vector<const char *>::const_iterator pos =
+ std::find(argv_.begin(), argv_.end(), arg->stringValue);
+ GMX_RELEASE_ASSERT(pos != argv_.end(),
+ "String argument got a value not in argv");
+ *arg->pa->u.c = *pos;
+ }
+ break;
+ }
+ case etBOOL:
+ *arg->pa->u.b = arg->boolValue;
+ break;
+ case etENUM:
+ *arg->pa->u.c = arg->pa->u.c[arg->enumIndex + 1];
+ break;
+ default:
+ // For other types, there is nothing type-specific to do.
+ break;
+ }
+ }
+}
+
} // namespace
} // namespace gmx
output_env_t *oenv)
{
/* This array should match the order of the enum in oenv.h */
- const char *xvg_format[] = { NULL, "xmgrace", "xmgr", "none", NULL };
- /* This array should match the order of the enum in oenv.h */
- const char *time_units[] = {
- NULL, "fs", "ps", "ns", "us", "ms", "s",
- NULL
- };
- int nicelevel = 0, debug_level = 0;
- char *deffnm = NULL;
- real tbegin = 0, tend = 0, tdelta = 0;
- gmx_bool bView = FALSE;
-
- t_pargs *all_pa = NULL;
-
- t_pargs nice_pa = {
- "-nice", FALSE, etINT, {&nicelevel},
- "Set the nicelevel"
- };
- t_pargs deffnm_pa = {
- "-deffnm", FALSE, etSTR, {&deffnm},
- "Set the default filename for all file options"
- };
- t_pargs begin_pa = {
- "-b", FALSE, etTIME, {&tbegin},
- "First frame (%t) to read from trajectory"
- };
- t_pargs end_pa = {
- "-e", FALSE, etTIME, {&tend},
- "Last frame (%t) to read from trajectory"
- };
- t_pargs dt_pa = {
- "-dt", FALSE, etTIME, {&tdelta},
- "Only use frame when t MOD dt = first time (%t)"
- };
- t_pargs view_pa = {
- "-w", FALSE, etBOOL, {&bView},
- "View output [TT].xvg[tt], [TT].xpm[tt], [TT].eps[tt] and [TT].pdb[tt] files"
- };
- t_pargs xvg_pa = {
- "-xvg", FALSE, etENUM, {xvg_format},
- "xvg plot formatting"
- };
- t_pargs time_pa = {
- "-tu", FALSE, etENUM, {time_units},
- "Time unit"
- };
- /* Maximum number of extra arguments */
-#define EXTRA_PA 16
-
- t_pargs pca_pa[] = {
- { "-debug", FALSE, etINT, {&debug_level},
- "HIDDENWrite file with debug information, 1: short, 2: also x and f" },
- };
-#define NPCA_PA asize(pca_pa)
- gmx_bool bXvgr;
- int i, j, k, npall, max_pa;
+ const char *const xvg_formats[] = { "xmgrace", "xmgr", "none" };
// Handle the flags argument, which is a bit field
// The FF macro returns whether or not the bit is set
#define FF(arg) ((Flags & arg) == arg)
- /* Check for double arguments */
- for (i = 1; (i < *argc); i++)
- {
- if (argv[i] && (strlen(argv[i]) > 1) && (!std::isdigit(argv[i][1])))
- {
- for (j = i+1; (j < *argc); j++)
- {
- if ( (argv[i][0] == '-') && (argv[j][0] == '-') &&
- (strcmp(argv[i], argv[j]) == 0) )
- {
- if (FF(PCA_NOEXIT_ON_ARGS))
- {
- fprintf(stderr, "Double command line argument %s\n",
- argv[i]);
- }
- else
- {
- gmx_fatal(FARGS, "Double command line argument %s\n",
- argv[i]);
- }
- }
- }
- }
- }
- debug_gmx();
-
- /* Check ALL the flags ... */
- max_pa = NPCA_PA + EXTRA_PA + npargs+1;
- snew(all_pa, max_pa);
-
- for (i = npall = 0; (i < static_cast<int>(NPCA_PA)); i++)
- {
- npall = add_parg(npall, all_pa, &(pca_pa[i]));
- }
-
- if (FF(PCA_BE_NICE))
- {
- nicelevel = 19;
- }
- npall = add_parg(npall, all_pa, &nice_pa);
-
- if (FF(PCA_CAN_SET_DEFFNM))
- {
- npall = add_parg(npall, all_pa, &deffnm_pa);
- }
- if (FF(PCA_CAN_BEGIN))
- {
- npall = add_parg(npall, all_pa, &begin_pa);
- }
- if (FF(PCA_CAN_END))
- {
- npall = add_parg(npall, all_pa, &end_pa);
- }
- if (FF(PCA_CAN_DT))
- {
- npall = add_parg(npall, all_pa, &dt_pa);
- }
- if (FF(PCA_TIME_UNIT))
- {
- npall = add_parg(npall, all_pa, &time_pa);
- }
- if (FF(PCA_CAN_VIEW))
- {
- npall = add_parg(npall, all_pa, &view_pa);
- }
-
- bXvgr = FALSE;
- for (i = 0; (i < nfile); i++)
- {
- bXvgr = bXvgr || (fnm[i].ftp == efXVG);
- }
- if (bXvgr)
+ try
{
- npall = add_parg(npall, all_pa, &xvg_pa);
- }
+ double tbegin = 0.0, tend = 0.0, tdelta = 0.0;
+ bool bView = false;
+ int xvgFormat = 0;
+ gmx::TimeUnitManager timeUnitManager;
+ gmx::OptionsAdapter adapter(*argc, argv);
+ gmx::Options options(NULL, NULL);
+ gmx::FileNameOptionManager fileOptManager;
- /* Now append the program specific arguments */
- for (i = 0; (i < npargs); i++)
- {
- npall = add_parg(npall, all_pa, &(pa[i]));
- }
+ fileOptManager.disableInputOptionChecking(
+ FF(PCA_NOT_READ_NODE) || FF(PCA_DISABLE_INPUT_FILE_CHECKING));
+ options.addManager(&fileOptManager);
+ options.setDescription(gmx::constArrayRefFromArray<const char *>(desc, ndesc));
- /* set etENUM options to default */
- for (i = 0; (i < npall); i++)
- {
- if (all_pa[i].type == etENUM)
+ if (FF(PCA_CAN_SET_DEFFNM))
{
- all_pa[i].u.c[0] = all_pa[i].u.c[1];
+ fileOptManager.addDefaultFileNameOption(&options, "deffnm");
}
- }
- set_default_time_unit(time_units, FF(PCA_TIME_UNIT));
- set_default_xvg_format(xvg_format);
-
- /* Now parse all the command-line options */
- get_pargs(argc, argv, npall, all_pa);
-
- /* set program name, command line, and default values for output options */
- output_env_init(oenv, gmx::getProgramContext(), (time_unit_t)nenum(time_units), bView,
- (xvg_format_t)nenum(xvg_format), 0, debug_level);
-
- /* Parse the file args */
- parse_file_args(argc, argv, nfile, fnm, deffnm, !FF(PCA_NOT_READ_NODE));
-
- /* Open the debug file */
- if (debug_level > 0)
- {
- char buf[256];
-
- if (gmx_mpi_initialized())
+ if (FF(PCA_CAN_BEGIN))
{
- sprintf(buf, "%s%d.debug", output_env_get_short_program_name(*oenv),
- gmx_node_rank());
+ options.addOption(
+ gmx::DoubleOption("b").store(&tbegin).timeValue()
+ .description("First frame (%t) to read from trajectory"));
}
- else
+ if (FF(PCA_CAN_END))
{
- sprintf(buf, "%s.debug", output_env_get_short_program_name(*oenv));
+ options.addOption(
+ gmx::DoubleOption("e").store(&tend).timeValue()
+ .description("Last frame (%t) to read from trajectory"));
+ }
+ if (FF(PCA_CAN_DT))
+ {
+ options.addOption(
+ gmx::DoubleOption("dt").store(&tdelta).timeValue()
+ .description("Only use frame when t MOD dt = first time (%t)"));
+ }
+ if (FF(PCA_TIME_UNIT))
+ {
+ timeUnitManager.setTimeUnitFromEnvironment();
+ timeUnitManager.addTimeUnitOption(&options, "tu");
+ }
+ if (FF(PCA_CAN_VIEW))
+ {
+ options.addOption(
+ gmx::BooleanOption("w").store(&bView)
+ .description("View output [TT].xvg[tt], [TT].xpm[tt], "
+ "[TT].eps[tt] and [TT].pdb[tt] files"));
}
- init_debug(debug_level, buf);
- fprintf(stderr, "Opening debug file %s (src code file %s, line %d)\n",
- buf, __FILE__, __LINE__);
- }
+ bool bXvgr = false;
+ for (int i = 0; i < nfile; i++)
+ {
+ bXvgr = bXvgr || (fnm[i].ftp == efXVG);
+ }
+ xvgFormat = gmx::getDefaultXvgFormat(xvg_formats);
+ if (bXvgr)
+ {
+ options.addOption(
+ gmx::StringOption("xvg").enumValue(xvg_formats)
+ .storeEnumIndex(&xvgFormat)
+ .description("xvg plot formatting"));
+ }
- /* Now copy the results back... */
- for (i = 0, k = npall-npargs; (i < npargs); i++, k++)
- {
- memcpy(&(pa[i]), &(all_pa[k]), (size_t)sizeof(pa[i]));
- }
+ /* Now append the program specific arguments */
+ for (int i = 0; i < nfile; i++)
+ {
+ adapter.filenmToOptions(&options, &fnm[i]);
+ }
+ for (int i = 0; i < npargs; i++)
+ {
+ adapter.pargsToOptions(&options, &pa[i]);
+ }
- bool bExit = false;
- try
- {
const gmx::CommandLineHelpContext *context =
gmx::GlobalCommandLineHelpContext::get();
- bExit = (context != NULL);
- if (context != NULL && !(FF(PCA_QUIET)))
+ if (context != NULL)
{
- gmx::Options options(NULL, NULL);
- options.setDescription(gmx::constArrayRefFromArray(desc, ndesc));
- for (i = 0; i < nfile; i++)
- {
- gmx::filenmToOptions(&options, &fnm[i]);
- }
- for (i = 0; i < npall; i++)
- {
- gmx::pargsToOptions(&options, &all_pa[i]);
- }
+ GMX_RELEASE_ASSERT(gmx_node_rank() == 0,
+ "Help output should be handled higher up and "
+ "only get called only on the master rank");
gmx::CommandLineHelpWriter(options)
.setShowDescriptions(true)
- .setTimeUnitString(output_env_get_time_unit(*oenv))
+ .setTimeUnitString(timeUnitManager.timeUnitAsString())
.setKnownIssues(gmx::constArrayRefFromArray(bugs, nbugs))
.writeHelp(*context);
+ return FALSE;
}
- }
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
- /* Set the nice level */
-#if defined(HAVE_UNISTD_H) && !defined(__MINGW32__)
-#ifndef GMX_NO_NICE
- /* The some system, e.g. the catamount kernel on cray xt3 do not have nice(2). */
- if (nicelevel != 0 && !bExit)
- {
- static gmx_bool nice_set = FALSE; /* only set it once */
- static tMPI_Thread_mutex_t init_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
- tMPI_Thread_mutex_lock(&init_mutex);
- if (!nice_set)
- {
- if (nice(nicelevel) == -1)
- {
- /* Do nothing, but use the return value to avoid warnings. */
- }
- nice_set = TRUE;
- }
- tMPI_Thread_mutex_unlock(&init_mutex);
- }
-#endif
-#endif
+ /* Now parse all the command-line options */
+ gmx::CommandLineParser(&options).skipUnknown(FF(PCA_NOEXIT_ON_ARGS))
+ .parse(argc, argv);
+ options.finish();
- /* convert time options, must be done after printing! */
+ /* set program name, command line, and default values for output options */
+ output_env_init(oenv, gmx::getProgramContext(),
+ (time_unit_t)(timeUnitManager.timeUnit() + 1), bView,
+ (xvg_format_t)(xvgFormat + 1), 0);
- for (i = 0; i < npall; i++)
- {
- if (all_pa[i].type == etTIME && all_pa[i].bSet)
+ timeUnitManager.scaleTimeOptions(&options);
+
+ /* Extract Time info from arguments */
+ // TODO: Use OptionInfo objects instead of string constants
+ if (FF(PCA_CAN_BEGIN) && options.isSet("b"))
{
- *all_pa[i].u.r *= output_env_get_time_invfactor(*oenv);
+ setTimeValue(TBEGIN, tbegin);
}
- }
-
- /* Extract Time info from arguments */
- if (FF(PCA_CAN_BEGIN) && opt2parg_bSet("-b", npall, all_pa))
- {
- setTimeValue(TBEGIN, opt2parg_real("-b", npall, all_pa));
- }
-
- if (FF(PCA_CAN_END) && opt2parg_bSet("-e", npall, all_pa))
- {
- setTimeValue(TEND, opt2parg_real("-e", npall, all_pa));
- }
-
- if (FF(PCA_CAN_DT) && opt2parg_bSet("-dt", npall, all_pa))
- {
- setTimeValue(TDELTA, opt2parg_real("-dt", npall, all_pa));
- }
-
- /* clear memory */
- sfree(all_pa);
-
- if (!FF(PCA_NOEXIT_ON_ARGS))
- {
- if (*argc > 1)
+ if (FF(PCA_CAN_END) && options.isSet("e"))
+ {
+ setTimeValue(TEND, tend);
+ }
+ if (FF(PCA_CAN_DT) && options.isSet("dt"))
{
- gmx_cmd(argv[1]);
+ setTimeValue(TDELTA, tdelta);
}
+
+ adapter.copyValues(!FF(PCA_NOT_READ_NODE));
+
+ return TRUE;
}
- return !bExit;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
#undef FF
}
#ifndef GMX_COMMANDLINE_PARGS_H
#define GMX_COMMANDLINE_PARGS_H
-#include "../legacyheaders/types/simple.h"
-#include "../legacyheaders/oenv.h"
-#include "../fileio/filenm.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C"
#define PCA_CAN_SET_DEFFNM (1<<10)
/** Do not raise a fatal error when invalid options are encountered. */
#define PCA_NOEXIT_ON_ARGS (1<<11)
-/** Do not print help output (used for non-master nodes). */
-#define PCA_QUIET (1<<12)
-/** Default to low priority. */
-#define PCA_BE_NICE (1<<13)
/** Is this node not reading: for parallel all nodes but the master */
#define PCA_NOT_READ_NODE (1<<16)
+/** Don't do any special processing for ffREAD files */
+#define PCA_DISABLE_INPUT_FILE_CHECKING (1<<17)
/*! \brief
* Parse command-line arguments.
* by \p Flags.
*
* Recognized arguments are removed from the list.
+ *
+ * For full functionality, this function needs to be used within a function
+ * that is passed to gmx_run_cmain(). It should be called as the first thing in
+ * that function. Initialization code can be executed before it, but you need
+ * to be aware that if the program is executed with -h and MPI, the code before
+ * parse_common_args() only executes on the master node.
+ *
+ * If the return value is `FALSE`, the program should return immediately (this
+ * is necessary for -h and a few other cases).
+ *
+ * \see gmx_run_cmain().
*/
gmx_bool parse_common_args(int *argc, char *argv[], unsigned long Flags,
int nfile, t_filenm fnm[], int npargs, t_pargs *pa,
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_commandline
*/
-#include "gromacs/commandline/shellcompletions.h"
+#include "gmxpre.h"
+
+#include "shellcompletions.h"
#include <cstdio>
#include "gromacs/commandline/cmdlinehelpcontext.h"
#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/filenm.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/options/optionsvisitor.h"
-#include "gromacs/fileio/filenm.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/file.h"
#include <string>
#include <vector>
-#include "gromacs/utility/common.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
class Options;
//! \cond internal
-//! \addtogroup module_onlinehelp
+//! \addtogroup module_commandline
//! \{
//! Output format for ShellCompletionWriter.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_commandline
*/
-#include <gtest/gtest.h>
+#include "gmxpre.h"
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/commandline/cmdlinehelpwriter.h"
+
+#include <gtest/gtest.h>
#include "gromacs/commandline/cmdlinehelpcontext.h"
-#include "gromacs/commandline/cmdlinehelpwriter.h"
+#include "gromacs/math/vectypes.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/options/options.h"
using gmx::SelectionFileOption;
using gmx::SelectionOption;
- gmx::Options options(NULL, NULL);
+ gmx::Options options(NULL, NULL);
+ gmx::SelectionCollection selections;
+ gmx::SelectionOptionManager manager(&selections);
+ options.addManager(&manager);
options.addOption(SelectionFileOption("sf"));
options.addOption(SelectionOption("refsel").required()
.description("Reference selection option"));
options.addOption(SelectionOption("sel").required().valueCount(2)
.description("Selection option"));
- gmx::SelectionCollection selections;
- gmx::SelectionOptionManager manager(&selections);
- setManagerForSelectionOptions(&options, &manager);
options.finish();
manager.parseRequestedFromString(
"resname SOL;"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \ingroup module_commandline
*/
// For GMX_BINARY_SUFFIX
-#ifdef HAVE_CONFIG_H
+#include "gmxpre.h"
+
+#include "gromacs/commandline/cmdlinemodulemanager.h"
+
#include "config.h"
-#endif
#include <vector>
#include "gromacs/commandline/cmdlinehelpcontext.h"
#include "gromacs/commandline/cmdlinemodule.h"
-#include "gromacs/commandline/cmdlinemodulemanager.h"
#include "gromacs/commandline/cmdlineprogramcontext.h"
#include "gromacs/utility/file.h"
virtual const char *name() const { return name_; }
virtual const char *shortDescription() const { return descr_; }
+ MOCK_METHOD1(init, void(gmx::CommandLineModuleSettings *settings));
MOCK_METHOD2(run, int(int argc, char *argv[]));
MOCK_CONST_METHOD1(writeHelp, void(const gmx::CommandLineHelpContext &context));
}
private:
+ //! Disable nice() calls for tests.
+ void disableNice(gmx::CommandLineModuleSettings *settings)
+ {
+ settings->setDefaultNiceLevel(0);
+ }
//! Checks the context passed to writeHelp().
void checkHelpContext(const gmx::CommandLineHelpContext &context) const;
using ::testing::_;
using ::testing::Invoke;
using ::testing::WithArg;
+ ON_CALL(*this, init(_))
+ .WillByDefault(WithArg<0>(Invoke(this, &MockModule::disableNice)));
ON_CALL(*this, writeHelp(_))
.WillByDefault(WithArg<0>(Invoke(this, &MockModule::checkHelpContext)));
}
using ::testing::_;
using ::testing::Args;
using ::testing::ElementsAreArray;
+ EXPECT_CALL(mod1, init(_));
EXPECT_CALL(mod1, run(_, _))
.With(Args<1, 0>(ElementsAreArray(args.argv() + 1, args.argc() - 1)));
int rc = 0;
ASSERT_EQ(0, rc);
}
-TEST_F(CommandLineModuleManagerTest, RunsModuleHelpWithDashHWithSymLink)
-{
- const char *const cmdline[] = {
- "g_module", "-h"
- };
- CommandLine args(cmdline);
- initManager(args, "test");
- MockModule &mod1 = addModule("module", "First module");
- addModule("other", "Second module");
- using ::testing::_;
- EXPECT_CALL(mod1, writeHelp(_));
- mod1.setExpectedDisplayName("test module");
- int rc = 0;
- ASSERT_NO_THROW_GMX(rc = manager().run(args.argc(), args.argv()));
- ASSERT_EQ(0, rc);
-}
-
TEST_F(CommandLineModuleManagerTest, RunsModuleHelpWithDashHWithSingleModule)
{
const char *const cmdline[] = {
ASSERT_EQ(0, rc);
}
-TEST_F(CommandLineModuleManagerTest, RunsModuleBasedOnBinaryName)
-{
- const char *const cmdline[] = {
- "g_module", "-flag", "yes"
- };
- CommandLine args(cmdline);
- initManager(args, "test");
- MockModule &mod1 = addModule("module", "First module");
- addModule("other", "Second module");
- using ::testing::_;
- using ::testing::Args;
- using ::testing::ElementsAreArray;
- EXPECT_CALL(mod1, run(_, _))
- .With(Args<1, 0>(ElementsAreArray(args.argv(), args.argc())));
- int rc = 0;
- ASSERT_NO_THROW_GMX(rc = manager().run(args.argc(), args.argv()));
- ASSERT_EQ(0, rc);
-}
-
-TEST_F(CommandLineModuleManagerTest, RunsModuleBasedOnBinaryNameWithPathAndSuffix)
-{
- const char *const cmdline[] = {
- "/usr/local/gromacs/bin/g_module" GMX_BINARY_SUFFIX ".exe", "-flag", "yes"
- };
- CommandLine args(cmdline);
- initManager(args, "test");
- MockModule &mod1 = addModule("module", "First module");
- addModule("other", "Second module");
- using ::testing::_;
- using ::testing::Args;
- using ::testing::ElementsAreArray;
- EXPECT_CALL(mod1, run(_, _))
- .With(Args<1, 0>(ElementsAreArray(args.argv(), args.argc())));
- int rc = 0;
- ASSERT_NO_THROW_GMX(rc = manager().run(args.argc(), args.argv()));
- ASSERT_EQ(0, rc);
-}
-
TEST_F(CommandLineModuleManagerTest, HandlesConflictingBinaryAndModuleNames)
{
const char *const cmdline[] = {
using ::testing::_;
using ::testing::Args;
using ::testing::ElementsAreArray;
+ EXPECT_CALL(mod1, init(_));
EXPECT_CALL(mod1, run(_, _))
.With(Args<1, 0>(ElementsAreArray(args.argv() + 1, args.argc() - 1)));
int rc = 0;
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_commandline
*/
+#include "gmxpre.h"
+
+#include "gromacs/commandline/cmdlineparser.h"
+
#include <vector>
#include <gtest/gtest.h>
-#include "gromacs/commandline/cmdlineparser.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_commandline
*/
+#include "gmxpre.h"
+
+#include "gromacs/commandline/cmdlineprogramcontext.h"
+
+#include "config.h"
+
#include <string>
#include <vector>
+#include <boost/shared_ptr.hpp>
#include <gtest/gtest.h>
-#include "gromacs/commandline/cmdlineprogramcontext.h"
-#include "gromacs/fileio/path.h"
-#include "gromacs/utility/common.h"
-#include "gromacs/utility/uniqueptr.h"
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/path.h"
#include "testutils/cmdlinetest.h"
-#include "config.h"
-
using gmx::test::CommandLine;
using gmx::Path;
};
//! Shorthand for a smart pointer to TestExecutableEnvironment.
-typedef gmx::gmx_unique_ptr<TestExecutableEnvironment>::type
+typedef boost::shared_ptr<TestExecutableEnvironment>
TestExecutableEnvironmentPointer;
class CommandLineProgramContextTest : public ::testing::Test
void testBinaryPathSearch(const char *argv0)
{
ASSERT_TRUE(env_.get() != NULL);
- gmx::CommandLineProgramContext info(1, &argv0, move(env_));
+ gmx::CommandLineProgramContext info(1, &argv0, env_);
EXPECT_EQ(expectedExecutable_, info.fullBinaryPath());
}
void testBinaryPathSearch(const std::string &argv0)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* Currently, negative tests are not possible, because those trigger
* gmx_fatal() and terminate the whole test binary.
*
- * \todo
- * Add tests that exercise the machinery triggered by ffREAD to detect the
- * extension for certain types of files. Also some other paths in the file
- * name logic may not get tested by the current set.
- *
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_commandline
*/
-#include <gtest/gtest.h>
+#include "gmxpre.h"
#include "gromacs/commandline/pargs.h"
+
+#include <string>
+
+#include <gtest/gtest.h>
+
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/file.h"
+#include "gromacs/utility/path.h"
+#include "gromacs/utility/stringutil.h"
#include "testutils/cmdlinetest.h"
#include "testutils/testasserts.h"
+#include "testutils/testfilemanager.h"
namespace
{
class ParseCommonArgsTest : public ::testing::Test
{
public:
+ enum FileArgumentType
+ {
+ efFull,
+ efNoExtension,
+ efEmptyValue
+ };
+
ParseCommonArgsTest()
: oenv_(NULL), fileCount_(0)
{
int nfile() const { return fileCount_; }
- void parse(gmx::ConstArrayRef<const char *> cmdline,
- unsigned long flags,
- gmx::ArrayRef<t_filenm> fnm,
- gmx::ArrayRef<t_pargs> pa)
+ void parseFromArgs(unsigned long flags,
+ gmx::ArrayRef<t_filenm> fnm,
+ gmx::ArrayRef<t_pargs> pa)
{
- args_.initFromArray(cmdline);
fileCount_ = fnm.size();
bool bOk = parse_common_args(&args_.argc(), args_.argv(), flags,
fnm.size(), fnm.data(),
0, NULL, 0, NULL, &oenv_);
EXPECT_TRUE(bOk);
}
+ void parseFromArray(gmx::ConstArrayRef<const char *> cmdline,
+ unsigned long flags,
+ gmx::ArrayRef<t_filenm> fnm,
+ gmx::ArrayRef<t_pargs> pa)
+ {
+ args_.initFromArray(cmdline);
+ parseFromArgs(flags, fnm, pa);
+ }
+ std::string addFileArg(const char *name, const char *extension,
+ FileArgumentType type)
+ {
+ std::string filename(tempFiles_.getTemporaryFilePath(extension));
+ gmx::File::writeFileFromString(filename, "Dummy file");
+ if (name != NULL)
+ {
+ args_.append(name);
+ switch (type)
+ {
+ case efFull:
+ args_.append(filename);
+ break;
+ case efNoExtension:
+ args_.append(gmx::Path::stripExtension(filename));
+ break;
+ case efEmptyValue:
+ break;
+ }
+ }
+ return filename;
+ }
- CommandLine args_;
- output_env_t oenv_;
+ // This must be a member that persists until the end of the test,
+ // because string arguments are not duplicated in the output.
+ CommandLine args_;
private:
- size_t fileCount_;
+ output_env_t oenv_;
+ size_t fileCount_;
+ gmx::test::TestFileManager tempFiles_;
};
/********************************************************************
const char *const cmdline[] = {
"test", "-i1", "2", "-i2", "-3"
};
- parse(cmdline, 0, gmx::EmptyArrayRef(), pa);
+ parseFromArray(cmdline, 0, gmx::EmptyArrayRef(), pa);
EXPECT_EQ( 2, value1);
EXPECT_EQ(-3, value2);
EXPECT_EQ( 3, value3);
const char *const cmdline[] = {
"test", "-i1", "2", "-i2", "-3"
};
- parse(cmdline, 0, gmx::EmptyArrayRef(), pa);
+ parseFromArray(cmdline, 0, gmx::EmptyArrayRef(), pa);
EXPECT_EQ( 2, value1);
EXPECT_EQ(-3, value2);
EXPECT_EQ( 3, value3);
const char *const cmdline[] = {
"test", "-r1", "2", "-r2", "-.5"
};
- parse(cmdline, 0, gmx::EmptyArrayRef(), pa);
+ parseFromArray(cmdline, 0, gmx::EmptyArrayRef(), pa);
EXPECT_EQ( 2.0, value1);
EXPECT_EQ(-0.5, value2);
EXPECT_EQ( 2.5, value3);
const char *const cmdline[] = {
"test", "-s1", "", "-s2", "test"
};
- parse(cmdline, 0, gmx::EmptyArrayRef(), pa);
+ parseFromArray(cmdline, 0, gmx::EmptyArrayRef(), pa);
EXPECT_STREQ("", value1);
EXPECT_STREQ("test", value2);
EXPECT_STREQ("default", value3);
const char *const cmdline[] = {
"test", "-nob1", "-b2"
};
- parse(cmdline, 0, gmx::EmptyArrayRef(), pa);
+ parseFromArray(cmdline, 0, gmx::EmptyArrayRef(), pa);
EXPECT_FALSE(value1);
EXPECT_TRUE(value2);
EXPECT_TRUE(value3);
const char *const cmdline[] = {
"test", "-v1", "2", "1", "3", "-v2", "1"
};
- parse(cmdline, 0, gmx::EmptyArrayRef(), pa);
+ parseFromArray(cmdline, 0, gmx::EmptyArrayRef(), pa);
EXPECT_EQ(2.0, value1[XX]);
EXPECT_EQ(1.0, value1[YY]);
EXPECT_EQ(3.0, value1[ZZ]);
const char *const cmdline[] = {
"test", "-t1", "2", "-t2", "-.5"
};
- parse(cmdline, 0, gmx::EmptyArrayRef(), pa);
+ parseFromArray(cmdline, 0, gmx::EmptyArrayRef(), pa);
EXPECT_EQ( 2.0, value1);
EXPECT_EQ(-0.5, value2);
EXPECT_EQ( 2.5, value3);
const char *const cmdline[] = {
"test", "-t1", "2", "-t2", "-.5", "-tu", "ns"
};
- parse(cmdline, PCA_TIME_UNIT, gmx::EmptyArrayRef(), pa);
+ parseFromArray(cmdline, PCA_TIME_UNIT, gmx::EmptyArrayRef(), pa);
EXPECT_EQ( 2000.0, value1);
EXPECT_EQ(-500.0, value2);
EXPECT_EQ( 2.5, value3);
const char *const cmdline[] = {
"test", "-s1", "off", "-s2", "val"
};
- parse(cmdline, 0, gmx::EmptyArrayRef(), pa);
+ parseFromArray(cmdline, 0, gmx::EmptyArrayRef(), pa);
EXPECT_STREQ("off", value1[0]);
EXPECT_STREQ("value", value2[0]);
EXPECT_STREQ("default", value3[0]);
}
/********************************************************************
- * Tests for file name options
+ * Tests for file name options (output files, not dependent on file system)
*/
TEST_F(ParseCommonArgsTest, ParsesFileArgs)
{ efXVG, "-o1", "out1", ffOPTWR },
{ efXVG, "-o2", "out2", ffOPTWR },
{ efXVG, "-om", "outm", ffWRMULT },
- { efXVG, "-om2", "outm2", ffWRMULT },
+ { efXVG, "-om2", "outm2", ffWRMULT }
};
const char *const cmdline[] = {
"test", "-o1", "-o2", "test", "-om", "test1", "test2.xvg", "-om2"
};
- parse(cmdline, 0, fnm, gmx::EmptyArrayRef());
+ parseFromArray(cmdline, 0, fnm, gmx::EmptyArrayRef());
EXPECT_STREQ("out1.xvg", opt2fn_null("-o1", nfile(), fnm));
EXPECT_STREQ("test.xvg", opt2fn_null("-o2", nfile(), fnm));
char **files;
EXPECT_EQ(2, opt2fns(&files, "-om", nfile(), fnm));
- EXPECT_STREQ("test1.xvg", files[0]);
- EXPECT_STREQ("test2.xvg", files[1]);
+ EXPECT_TRUE(files != NULL);
+ if (files != NULL)
+ {
+ EXPECT_STREQ("test1.xvg", files[0]);
+ EXPECT_STREQ("test2.xvg", files[1]);
+ }
EXPECT_STREQ("outm2.xvg", opt2fn("-om2", nfile(), fnm));
done_filenms(nfile(), fnm);
}
{ efTRX, "-f2", NULL, ffOPTWR },
{ efTRX, "-f3", "trj3", ffWRITE },
{ efXVG, "-o", "out", ffWRITE },
- { efXVG, "-om", "outm", ffWRMULT },
+ { efXVG, "-om", "outm", ffWRMULT }
};
const char *const cmdline[] = {
"test"
};
- parse(cmdline, 0, fnm, gmx::EmptyArrayRef());
+ parseFromArray(cmdline, 0, fnm, gmx::EmptyArrayRef());
EXPECT_STREQ("topol.tpr", ftp2fn(efTPS, nfile(), fnm));
EXPECT_STREQ("traj.xtc", opt2fn("-f2", nfile(), fnm));
EXPECT_NULL(opt2fn_null("-f2", nfile(), fnm));
{ efTRX, "-f2", NULL, ffWRITE },
{ efTRX, "-f3", "trj3", ffWRITE },
{ efXVG, "-o", "out", ffWRITE },
- { efXVG, "-om", "outm", ffWRMULT },
+ { efXVG, "-om", "outm", ffWRMULT }
};
const char *const cmdline[] = {
"test", "-deffnm", "def", "-f2", "other", "-o"
};
- parse(cmdline, PCA_CAN_SET_DEFFNM, fnm, gmx::EmptyArrayRef());
+ parseFromArray(cmdline, PCA_CAN_SET_DEFFNM, fnm, gmx::EmptyArrayRef());
EXPECT_STREQ("def.tpr", ftp2fn(efTPS, nfile(), fnm));
EXPECT_STREQ("other.xtc", opt2fn("-f2", nfile(), fnm));
EXPECT_STREQ("def.xtc", opt2fn("-f3", nfile(), fnm));
done_filenms(nfile(), fnm);
}
+TEST_F(ParseCommonArgsTest, ParseFileArgsWithCustomDefaultExtension)
+{
+ t_filenm fnm[] = {
+ { efTRX, "-o1", "conf1.gro", ffWRITE },
+ { efTRX, "-o2", "conf2.pdb", ffWRITE },
+ { efTRX, "-o3", "conf3.gro", ffWRITE }
+ };
+ const char *const cmdline[] = {
+ "test", "-o2", "-o3", "test"
+ };
+ parseFromArray(cmdline, PCA_CAN_SET_DEFFNM, fnm, gmx::EmptyArrayRef());
+ EXPECT_STREQ("conf1.gro", opt2fn("-o1", nfile(), fnm));
+ EXPECT_STREQ("conf2.pdb", opt2fn("-o2", nfile(), fnm));
+ EXPECT_STREQ("test.gro", opt2fn("-o3", nfile(), fnm));
+ done_filenms(nfile(), fnm);
+}
+
+/********************************************************************
+ * Tests for file name options (input files, dependent on file system contents)
+ */
+
+TEST_F(ParseCommonArgsTest, HandlesNonExistentInputFiles)
+{
+ t_filenm fnm[] = {
+ { efTPS, "-s", NULL, ffREAD },
+ { efTRX, "-f", "trj", ffREAD },
+ { efTRX, "-f2", "trj2", ffREAD },
+ { efTRX, "-f3", "trj3", ffREAD },
+ { efTRX, "-f4", "trj4", ffREAD },
+ { efGRO, "-g", "cnf", ffREAD },
+ { efGRO, "-g2", "cnf2", ffREAD }
+ };
+ const char *const cmdline[] = {
+ "test", "-f2", "-f3", "other", "-f4", "trj.gro", "-g2", "foo"
+ };
+ parseFromArray(cmdline, PCA_DISABLE_INPUT_FILE_CHECKING, fnm, gmx::EmptyArrayRef());
+ EXPECT_STREQ("topol.tpr", ftp2fn(efTPS, nfile(), fnm));
+ EXPECT_STREQ("trj.xtc", opt2fn("-f", nfile(), fnm));
+ EXPECT_STREQ("trj2.xtc", opt2fn("-f2", nfile(), fnm));
+ EXPECT_STREQ("other.xtc", opt2fn("-f3", nfile(), fnm));
+ EXPECT_STREQ("trj.gro", opt2fn("-f4", nfile(), fnm));
+ EXPECT_STREQ("cnf.gro", opt2fn("-g", nfile(), fnm));
+ EXPECT_STREQ("foo.gro", opt2fn("-g2", nfile(), fnm));
+ done_filenms(nfile(), fnm);
+}
+
+TEST_F(ParseCommonArgsTest, HandlesNonExistentOptionalInputFiles)
+{
+ t_filenm fnm[] = {
+ { efTPS, "-s", NULL, ffOPTRD },
+ { efTRX, "-f", "trj", ffOPTRD }
+ };
+ const char *const cmdline[] = {
+ "test"
+ };
+ parseFromArray(cmdline, 0, fnm, gmx::EmptyArrayRef());
+ EXPECT_STREQ("topol.tpr", ftp2fn(efTPS, nfile(), fnm));
+ EXPECT_STREQ("trj.xtc", opt2fn("-f", nfile(), fnm));
+ done_filenms(nfile(), fnm);
+}
+
+TEST_F(ParseCommonArgsTest, AcceptsNonExistentInputFilesIfSpecified)
+{
+ t_filenm fnm[] = {
+ { efCPT, "-c", "file1", ffOPTRD | ffALLOW_MISSING },
+ { efCPT, "-c2", "file2", ffOPTRD | ffALLOW_MISSING },
+ { efCPT, "-c3", "file3", ffOPTRD | ffALLOW_MISSING },
+ { efCPT, "-c4", "file4", ffOPTRD | ffALLOW_MISSING },
+ { efTRX, "-f", "trj", ffOPTRD | ffALLOW_MISSING }
+ };
+ const char *const cmdline[] = {
+ "test", "-c2", "-c3", "nonexistent", "-c4", "nonexistent.cpt", "-f", "nonexistent"
+ };
+ parseFromArray(cmdline, 0, fnm, gmx::EmptyArrayRef());
+ EXPECT_STREQ("file1.cpt", opt2fn("-c", nfile(), fnm));
+ EXPECT_STREQ("file2.cpt", opt2fn("-c2", nfile(), fnm));
+ EXPECT_STREQ("nonexistent.cpt", opt2fn("-c3", nfile(), fnm));
+ EXPECT_STREQ("nonexistent.cpt", opt2fn("-c4", nfile(), fnm));
+ EXPECT_STREQ("nonexistent.xtc", opt2fn("-f", nfile(), fnm));
+ done_filenms(nfile(), fnm);
+}
+
+TEST_F(ParseCommonArgsTest, HandlesCompressedFiles)
+{
+ t_filenm fnm[] = {
+ { efTRX, "-f", NULL, ffREAD },
+ { efGRO, "-g", NULL, ffREAD }
+ };
+ args_.append("test");
+ std::string expectedF = addFileArg("-f", ".pdb.gz", efFull);
+ std::string expectedG = addFileArg("-g", ".gro.Z", efFull);
+ expectedF = gmx::Path::stripExtension(expectedF);
+ expectedG = gmx::Path::stripExtension(expectedG);
+ parseFromArgs(0, fnm, gmx::EmptyArrayRef());
+ EXPECT_EQ(expectedF, opt2fn("-f", nfile(), fnm));
+ EXPECT_EQ(expectedG, opt2fn("-g", nfile(), fnm));
+ done_filenms(nfile(), fnm);
+}
+
+TEST_F(ParseCommonArgsTest, AcceptsUnknownTrajectoryExtension)
+{
+ t_filenm fnm[] = {
+ { efTRX, "-f", NULL, ffREAD }
+ };
+ args_.append("test");
+ std::string expected = addFileArg("-f", ".foo", efFull);
+ parseFromArgs(0, fnm, gmx::EmptyArrayRef());
+ EXPECT_EQ(expected, opt2fn("-f", nfile(), fnm));
+ done_filenms(nfile(), fnm);
+}
+
+TEST_F(ParseCommonArgsTest, CompletesExtensionFromExistingFile)
+{
+ t_filenm fnm[] = {
+ { efTRX, "-f1", NULL, ffREAD },
+ { efTRX, "-f2", NULL, ffREAD },
+ { efTRX, "-f3", NULL, ffREAD },
+ { efTRX, "-f4", NULL, ffREAD }
+ };
+ args_.append("test");
+ std::string expected1 = addFileArg("-f1", "1.xtc", efNoExtension);
+ std::string expected2 = addFileArg("-f2", "2.gro", efNoExtension);
+ std::string expected3 = addFileArg("-f3", "3.tng", efNoExtension);
+ std::string expected4 = addFileArg("-f4", ".gro", efEmptyValue);
+ std::string def4 = gmx::Path::stripExtension(expected4);
+ fnm[3].fn = def4.c_str();
+ parseFromArgs(0, fnm, gmx::EmptyArrayRef());
+ EXPECT_EQ(expected1, opt2fn("-f1", nfile(), fnm));
+ EXPECT_EQ(expected2, opt2fn("-f2", nfile(), fnm));
+ EXPECT_EQ(expected3, opt2fn("-f3", nfile(), fnm));
+ EXPECT_EQ(expected4, opt2fn("-f4", nfile(), fnm));
+ done_filenms(nfile(), fnm);
+}
+
+TEST_F(ParseCommonArgsTest, CompletesExtensionFromExistingFileWithDefaultFileName)
+{
+ t_filenm fnm[] = {
+ { efTRX, "-f1", NULL, ffREAD },
+ { efSTO, "-f2", "foo", ffREAD },
+ { efTRX, "-f3", NULL, ffREAD },
+ { efSTX, "-f4", NULL, ffREAD }
+ };
+ args_.append("test");
+ std::string expected1 = addFileArg("-f1", "1.trr", efNoExtension);
+ std::string expected2 = addFileArg("-f2", ".pdb", efEmptyValue);
+ std::string expected3 = addFileArg("-f3", ".trr", efEmptyValue);
+ std::string expected4 = addFileArg(NULL, ".pdb", efEmptyValue);
+ std::string deffnm = gmx::Path::stripExtension(expected3);
+ args_.append("-deffnm");
+ args_.append(deffnm);
+ parseFromArgs(PCA_CAN_SET_DEFFNM, fnm, gmx::EmptyArrayRef());
+ EXPECT_EQ(expected1, opt2fn("-f1", nfile(), fnm));
+ EXPECT_EQ(expected2, opt2fn("-f2", nfile(), fnm));
+ EXPECT_EQ(expected3, opt2fn("-f3", nfile(), fnm));
+ EXPECT_EQ(expected4, opt2fn("-f4", nfile(), fnm));
+ done_filenms(nfile(), fnm);
+}
+
/********************************************************************
* Tests for general behavior
*/
+TEST_F(ParseCommonArgsTest, HandlesNonReadNode)
+{
+ t_filenm fnm[] = {
+ { efTPS, "-s", NULL, ffREAD },
+ { efTRX, "-f", NULL, ffREAD },
+ { efTRX, "-f2", NULL, ffREAD }
+ };
+ const char *const cmdline[] = {
+ "test", "-f", "-f2", "other"
+ };
+ parseFromArray(cmdline, PCA_NOT_READ_NODE, fnm, gmx::EmptyArrayRef());
+ EXPECT_NULL(fnm[0].fns);
+ EXPECT_NULL(fnm[1].fns);
+ EXPECT_NULL(fnm[2].fns);
+ done_filenms(nfile(), fnm);
+}
+
+TEST_F(ParseCommonArgsTest, HandlesNonReadNodeWithDefaultFileName)
+{
+ t_filenm fnm[] = {
+ { efTPS, "-s", NULL, ffREAD },
+ { efTRX, "-f", NULL, ffREAD },
+ { efTRX, "-f2", NULL, ffREAD }
+ };
+ const char *const cmdline[] = {
+ "test", "-deffnm", "def", "-f", "-f2", "other"
+ };
+ parseFromArray(cmdline, PCA_CAN_SET_DEFFNM | PCA_NOT_READ_NODE, fnm, gmx::EmptyArrayRef());
+ EXPECT_NULL(fnm[0].fns);
+ EXPECT_NULL(fnm[1].fns);
+ EXPECT_NULL(fnm[2].fns);
+ done_filenms(nfile(), fnm);
+}
+
TEST_F(ParseCommonArgsTest, CanKeepUnknownArgs)
{
int ivalue = 0;
"test", "foo", "-unk", "-o1", "-unk2", "-o2", "test",
"-i", "2", "-unk3", "-b", "-unk4"
};
- parse(cmdline, PCA_NOEXIT_ON_ARGS, fnm, pa);
+ parseFromArray(cmdline, PCA_NOEXIT_ON_ARGS, fnm, pa);
EXPECT_EQ(2, ivalue);
EXPECT_TRUE(bvalue);
EXPECT_STREQ("out1.xvg", opt2fn_null("-o1", nfile(), fnm));
Options to specify input and output files:
-f [<.xtc/.trr/...>] (path/to/long/trajectory/name.xtc) (Input)
- File name option with a long value: xtc trr cpt trj gro g96 pdb tng
+ File name option with a long value: xtc trr cpt gro g96 pdb tng
-f2 [<.xtc/.trr/...>] (path/to/long/trajectory.xtc) (Input)
- File name option with a long value: xtc trr cpt trj gro g96 pdb tng
+ File name option with a long value: xtc trr cpt gro g96 pdb tng
-lib [<.xtc/.trr/...>] (path/to/long/trajectory/name.xtc) (Input, Opt., Lib.)
- File name option with a long value and type: xtc trr cpt trj gro g96 pdb
- tng
+ File name option with a long value and type: xtc trr cpt gro g96 pdb tng
-longfileopt [<.dat>] (deffile.dat) (Input, Opt.)
File name option with a long name
-longfileopt2 [<.dat>] (path/to/long/file/name.dat) (Input, Opt., Lib.)
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
- Input file description: xtc trr cpt trj gro g96 pdb tng
+ Input file description: xtc trr cpt gro g96 pdb tng
-mult [<.xtc/.trr/...> [...]] (traj.xtc) (Input, Opt.)
- Multiple file description: xtc trr cpt trj gro g96 pdb tng
+ Multiple file description: xtc trr cpt gro g96 pdb tng
-lib [<.dat>] (libdata.dat) (Input, Opt., Lib.) Library file description
-io [<.dat>] (inout.dat) (In/Out, Opt.) Input/Output file description
-o <.xvg> (Output, Opt.) Output file description
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+file(GLOB GMXCORRFUNC_SOURCES *.c *.cpp)
+file(GLOB LMFIT_SOURCES ${CMAKE_SOURCE_DIR}/src/external/lmfit/*.c)
+
+set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${GMXCORRFUNC_SOURCES} ${LMFIT_SOURCES} PARENT_SCOPE)
+if (BUILD_TESTING)
+ add_subdirectory(tests)
+endif()
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+/*! \internal \file
+ * \brief
+ * Implements function to compute many autocorrelation functions
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_correlationfunctions
+ */
+#include "gmxpre.h"
+
+#include "autocorr.h"
#include <math.h>
#include <stdio.h>
#include <string.h>
-#include "macros.h"
-#include "typedefs.h"
-#include "physics.h"
+#include "gromacs/correlationfunctions/expfit.h"
+#include "gromacs/correlationfunctions/integrate.h"
+#include "gromacs/correlationfunctions/manyautocorrelation.h"
+#include "gromacs/correlationfunctions/polynomials.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
-#include "xvgr.h"
-#include "gromacs/fileio/futil.h"
-#include "gstat.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "correl.h"
+/*! \brief Shortcut macro to select modes. */
#define MODE(x) ((mode & (x)) == (x))
typedef struct {
real tbeginfit, tendfit;
} t_acf;
+/*! \brief Global variable set true if initialization routines are called. */
static gmx_bool bACFinit = FALSE;
+
+/*! \brief Data structure for storing command line variables. */
static t_acf acf;
enum {
enNorm, enCos, enSin
};
-int sffn2effn(const char **sffn)
-{
- int eFitFn, i;
-
- eFitFn = 0;
- for (i = 0; i < effnNR; i++)
- {
- if (sffn[i+1] && strcmp(sffn[0], sffn[i+1]) == 0)
- {
- eFitFn = i;
- }
- }
-
- return eFitFn;
-}
-
+/*! \brief Routine to compute ACF using FFT. */
static void low_do_four_core(int nfour, int nframes, real c1[], real cfour[],
- int nCos, gmx_bool bPadding)
+ int nCos)
{
int i = 0;
+ int fftcode;
real aver, *ans;
aver = 0.0;
default:
gmx_fatal(FARGS, "nCos = %d, %s %d", nCos, __FILE__, __LINE__);
}
- for (; (i < nfour); i++)
- {
- cfour[i] = 0.0;
- }
-
- if (bPadding)
- {
- aver /= nframes;
- /* printf("aver = %g\n",aver); */
- for (i = 0; (i < nframes); i++)
- {
- cfour[i] -= aver;
- }
- }
-
- snew(ans, 2*nfour);
- correl(cfour-1, cfour-1, nfour, ans-1);
- if (bPadding)
- {
- for (i = 0; (i < nfour); i++)
- {
- cfour[i] = ans[i]+sqr(aver);
- }
- }
- else
- {
- for (i = 0; (i < nfour); i++)
- {
- cfour[i] = ans[i];
- }
- }
-
- sfree(ans);
+ fftcode = many_auto_correl(1, nframes, nfour, &cfour);
}
+/*! \brief Routine to comput ACF without FFT. */
static void do_ac_core(int nframes, int nout,
real corr[], real c1[], int nrestart,
unsigned long mode)
{
int j, k, j3, jk3, m, n;
real ccc, cth;
- rvec xj, xk, rr;
+ rvec xj, xk;
if (nrestart < 1)
{
}
else if (MODE(eacP1) || MODE(eacP2) || MODE(eacP3))
{
+ unsigned int mmm;
+
for (m = 0; (m < DIM); m++)
{
xj[m] = c1[j3+m];
printf("j: %d, k: %d, xj:(%g,%g,%g), xk:(%g,%g,%g)\n",
j, k, xj[XX], xj[YY], xj[ZZ], xk[XX], xk[YY], xk[ZZ]);
}
-
- corr[k] += LegendreP(cth, mode); /* 1.5*cth*cth-0.5; */
+ mmm = 1;
+ if (MODE(eacP2))
+ {
+ mmm = 2;
+ }
+ else if (MODE(eacP3))
+ {
+ mmm = 3;
+ }
+ corr[k] += LegendreP(cth, mmm); /* 1.5*cth*cth-0.5; */
}
else if (MODE(eacRcross))
{
+ rvec xj, xk, rr;
for (m = 0; (m < DIM); m++)
{
xj[m] = c1[j3+m];
}
}
+/*! \brief Routine to normalize ACF, dividing by corr[0]. */
void normalize_acf(int nout, real corr[])
{
- int j;
- real c0;
+ int j;
+ double c0;
if (debug)
{
/* Normalisation makes that c[0] = 1.0 and that other points are scaled
* accordingly.
*/
- if (corr[0] == 0.0)
+ if (fabs(corr[0]) < 1e-5)
{
c0 = 1.0;
}
}
}
+/*! \brief Routine that averages ACFs. */
void average_acf(gmx_bool bVerbose, int n, int nitem, real **c1)
{
real c0;
}
}
+/*! \brief Normalize ACFs. */
void norm_and_scale_vectors(int nframes, real c1[], real scale)
{
int j, m;
}
}
-void dump_tmp(char *s, int n, real c[])
+/*! \brief Debugging */
+static void dump_tmp(char *s, int n, real c[])
{
FILE *fp;
int i;
gmx_ffclose(fp);
}
-real print_and_integrate(FILE *fp, int n, real dt, real c[], real *fit, int nskip)
-{
- real c0, sum;
- int j;
-
- /* Use trapezoidal rule for calculating integral */
- sum = 0.0;
- for (j = 0; (j < n); j++)
- {
- c0 = c[j];
- if (fp && (nskip == 0 || j % nskip == 0))
- {
- fprintf(fp, "%10.3f %10.5f\n", j*dt, c0);
- }
- if (j > 0)
- {
- sum += dt*(c0+c[j-1]);
- }
- }
- if (fp)
- {
- fprintf(fp, "&\n");
- if (fit)
- {
- for (j = 0; (j < n); j++)
- {
- if (nskip == 0 || j % nskip == 0)
- {
- fprintf(fp, "%10.3f %10.5f\n", j*dt, fit[j]);
- }
- }
- fprintf(fp, "&\n");
- }
- }
- return sum*0.5;
-}
-
-real evaluate_integral(int n, real x[], real y[], real dy[], real aver_start,
- real *stddev)
-{
- double sum, sum_var, w;
- double sum_tail = 0, sum2_tail = 0;
- int j, nsum_tail = 0;
-
- /* Use trapezoidal rule for calculating integral */
- if (n <= 0)
- {
- gmx_fatal(FARGS, "Evaluating integral: n = %d (file %s, line %d)",
- n, __FILE__, __LINE__);
- }
-
- sum = 0;
- sum_var = 0;
- for (j = 0; (j < n); j++)
- {
- w = 0;
- if (j > 0)
- {
- w += 0.5*(x[j] - x[j-1]);
- }
- if (j < n-1)
- {
- w += 0.5*(x[j+1] - x[j]);
- }
- sum += w*y[j];
- if (dy)
- {
- /* Assume all errors are uncorrelated */
- sum_var += sqr(w*dy[j]);
- }
-
- if ((aver_start > 0) && (x[j] >= aver_start))
- {
- sum_tail += sum;
- sum2_tail += sqrt(sum_var);
- nsum_tail += 1;
- }
- }
-
- if (nsum_tail > 0)
- {
- sum = sum_tail/nsum_tail;
- /* This is a worst case estimate, assuming all stddev's are correlated. */
- *stddev = sum2_tail/nsum_tail;
- }
- else
- {
- *stddev = sqrt(sum_var);
- }
-
- return sum;
-}
-
+/*! \brief High level ACF routine. */
void do_four_core(unsigned long mode, int nfour, int nf2, int nframes,
real c1[], real csum[], real ctmp[])
{
/********************************************
* N O R M A L
********************************************/
- low_do_four_core(nfour, nf2, c1, csum, enNorm, FALSE);
+ low_do_four_core(nfour, nf2, c1, csum, enNorm);
}
else if (MODE(eacCos))
{
}
/* Cosine term of AC function */
- low_do_four_core(nfour, nf2, ctmp, cfour, enCos, FALSE);
+ low_do_four_core(nfour, nf2, ctmp, cfour, enCos);
for (j = 0; (j < nf2); j++)
{
c1[j] = cfour[j];
}
/* Sine term of AC function */
- low_do_four_core(nfour, nf2, ctmp, cfour, enSin, FALSE);
+ low_do_four_core(nfour, nf2, ctmp, cfour, enSin);
for (j = 0; (j < nf2); j++)
{
c1[j] += cfour[j];
dump_tmp(buf, nf2, ctmp);
}
- low_do_four_core(nfour, nf2, ctmp, cfour, enNorm, FALSE);
+ low_do_four_core(nfour, nf2, ctmp, cfour, enNorm);
if (debug)
{
sprintf(buf, "c1off%d.xvg", m);
dump_tmp(buf, nf2, ctmp);
}
- low_do_four_core(nfour, nf2, ctmp, cfour, enNorm, FALSE);
+ low_do_four_core(nfour, nf2, ctmp, cfour, enNorm);
if (debug)
{
sprintf(buf, "c1ofout%d.xvg", m);
{
ctmp[j] = c1[DIM*j+m];
}
- low_do_four_core(nfour, nf2, ctmp, cfour, enNorm, FALSE);
+ low_do_four_core(nfour, nf2, ctmp, cfour, enNorm);
for (j = 0; (j < nf2); j++)
{
csum[j] += cfour[j];
}
}
-real fit_acf(int ncorr, int fitfn, const output_env_t oenv, gmx_bool bVerbose,
- real tbeginfit, real tendfit, real dt, real c1[], real *fit)
-{
- real fitparm[3];
- real tStart, tail_corr, sum, sumtot = 0, c_start, ct_estimate, *sig;
- int i, j, jmax, nf_int;
- gmx_bool bPrint;
-
- bPrint = bVerbose || bDebugMode();
-
- if (bPrint)
- {
- printf("COR:\n");
- }
-
- if (tendfit <= 0)
- {
- tendfit = ncorr*dt;
- }
- nf_int = min(ncorr, (int)(tendfit/dt));
- sum = print_and_integrate(debug, nf_int, dt, c1, NULL, 1);
-
- /* Estimate the correlation time for better fitting */
- ct_estimate = 0.5*c1[0];
- for (i = 1; (i < ncorr) && (c1[i] > 0); i++)
- {
- ct_estimate += c1[i];
- }
- ct_estimate *= dt/c1[0];
-
- if (bPrint)
- {
- printf("COR: Correlation time (plain integral from %6.3f to %6.3f ps) = %8.5f ps\n",
- 0.0, dt*nf_int, sum);
- printf("COR: Relaxation times are computed as fit to an exponential:\n");
- printf("COR: %s\n", longs_ffn[fitfn]);
- printf("COR: Fit to correlation function from %6.3f ps to %6.3f ps, results in a\n", tbeginfit, min(ncorr*dt, tendfit));
- }
-
- tStart = 0;
- if (bPrint)
- {
- printf("COR:%11s%11s%11s%11s%11s%11s%11s\n",
- "Fit from", "Integral", "Tail Value", "Sum (ps)", " a1 (ps)",
- (nfp_ffn[fitfn] >= 2) ? " a2 ()" : "",
- (nfp_ffn[fitfn] >= 3) ? " a3 (ps)" : "");
- }
-
- snew(sig, ncorr);
-
- if (tbeginfit > 0)
- {
- jmax = 3;
- }
- else
- {
- jmax = 1;
- }
- for (j = 0; ((j < jmax) && (tStart < tendfit) && (tStart < ncorr*dt)); j++)
- {
- /* Estimate the correlation time for better fitting */
- c_start = -1;
- ct_estimate = 0;
- for (i = 0; (i < ncorr) && (dt*i < tStart || c1[i] > 0); i++)
- {
- if (c_start < 0)
- {
- if (dt*i >= tStart)
- {
- c_start = c1[i];
- ct_estimate = 0.5*c1[i];
- }
- }
- else
- {
- ct_estimate += c1[i];
- }
- }
- if (c_start > 0)
- {
- ct_estimate *= dt/c_start;
- }
- else
- {
- /* The data is strange, so we need to choose somehting */
- ct_estimate = tendfit;
- }
- if (debug)
- {
- fprintf(debug, "tStart %g ct_estimate: %g\n", tStart, ct_estimate);
- }
-
- if (fitfn == effnEXP3)
- {
- fitparm[0] = 0.002*ncorr*dt;
- fitparm[1] = 0.95;
- fitparm[2] = 0.2*ncorr*dt;
- }
- else
- {
- /* Good initial guess, this increases the probability of convergence */
- fitparm[0] = ct_estimate;
- fitparm[1] = 1.0;
- fitparm[2] = 1.0;
- }
-
- /* Generate more or less appropriate sigma's */
- for (i = 0; i < ncorr; i++)
- {
- sig[i] = sqrt(ct_estimate+dt*i);
- }
-
- nf_int = min(ncorr, (int)((tStart+1e-4)/dt));
- sum = print_and_integrate(debug, nf_int, dt, c1, NULL, 1);
- tail_corr = do_lmfit(ncorr, c1, sig, dt, NULL, tStart, tendfit, oenv,
- bDebugMode(), fitfn, fitparm, 0);
- sumtot = sum+tail_corr;
- if (fit && ((jmax == 1) || (j == 1)))
- {
- for (i = 0; (i < ncorr); i++)
- {
- fit[i] = fit_function(fitfn, fitparm, i*dt);
- }
- }
- if (bPrint)
- {
- printf("COR:%11.4e%11.4e%11.4e%11.4e", tStart, sum, tail_corr, sumtot);
- for (i = 0; (i < nfp_ffn[fitfn]); i++)
- {
- printf(" %11.4e", fitparm[i]);
- }
- printf("\n");
- }
- tStart += tbeginfit;
- }
- sfree(sig);
-
- return sumtot;
-}
-
void low_do_autocorr(const char *fn, const output_env_t oenv, const char *title,
int nframes, int nitem, int nout, real **c1,
real dt, unsigned long mode, int nrestart,
}
if ((MODE(eacP3) || MODE(eacRcross)) && bFour)
{
- fprintf(stderr, "Can't combine mode %lu with FFT, turning off FFT\n", mode);
+ if (bVerbose)
+ {
+ fprintf(stderr, "Can't combine mode %lu with FFT, turning off FFT\n", mode);
+ }
bFour = FALSE;
}
if (MODE(eacNormal) && MODE(eacVector))
}
if (debug)
{
- gmx_ffclose(gp);
+ xvgrclose(gp);
}
if (nitem > 1)
{
}
if (fp)
{
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
sfree(fit);
}
+/*! \brief Legend for selecting Legendre polynomials. */
static const char *Leg[] = { NULL, "0", "1", "2", "3", NULL };
t_pargs *add_acf_pargs(int *npargs, t_pargs *pa)
{ "-endfit", FALSE, etREAL, {&acf.tendfit},
"Time where to end the exponential fit of the correlation function, -1 is until the end" },
};
-#define NPA asize(acfpa)
t_pargs *ppa;
- int i;
+ int i, npa;
- snew(ppa, *npargs+NPA);
+ npa = asize(acfpa);
+ snew(ppa, *npargs+npa);
for (i = 0; (i < *npargs); i++)
{
ppa[i] = pa[i];
}
- for (i = 0; (i < NPA); i++)
+ for (i = 0; (i < npa); i++)
{
ppa[*npargs+i] = acfpa[i];
}
- (*npargs) += NPA;
+ (*npargs) += npa;
acf.mode = 0;
acf.nrestart = 1;
return sffn2effn(s_ffn);
}
-
-void cross_corr(int n, real f[], real g[], real corr[])
-{
- int i, j;
-
- if (acf.bFour)
- {
- correl(f-1, g-1, n, corr-1);
- }
- else
- {
- for (i = 0; (i < n); i++)
- {
- for (j = i; (j < n); j++)
- {
- corr[j-i] += f[i]*g[j];
- }
- corr[i] /= (real)(n-i);
- }
- }
-}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal
+ * \defgroup module_correlationfunctions Correlation functions
+ * \ingroup group_analysismodules
+ * \brief
+ * Compute correlation functions and fit analytical functions to the result.
+ */
+/*! \libinternal
+ * \file
+ * \brief
+ * Declares routine for computing autocorrelation functions
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \inlibraryapi
+ * \ingroup module_correlationfunctions
+ */
+#ifndef GMX_AUTOCORR_H
+#define GMX_AUTOCORR_H
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/utility/real.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*! \brief Normal correlation f(t)*f(t+dt) */
+#define eacNormal (1<<0)
+/*! \brief Cosine correlation cos(f(t)-f(t+dt)) */
+#define eacCos (1<<1)
+/*! \brief Vector correlation f(t).f(t+dt) */
+#define eacVector (1<<2)
+/*! \brief Norm of cross product |f(t) (x) f(t+dt)| */
+#define eacRcross (1<<3 | eacVector)
+/*! \brief Vector with Legendre polynomial of order 0 (same as vector) */
+#define eacP0 (1<<4 | eacVector)
+/*! \brief Vector with Legendre polynomial of order P_1(f(t).f(t+dt)) */
+#define eacP1 (1<<5 | eacVector)
+/*! \brief Vector with Legendre polynomial of order P_2(f(t).f(t+dt)) */
+#define eacP2 (1<<6 | eacVector)
+/*! \brief Vector with Legendre polynomial of order P_3(f(t).f(t+dt)) */
+#define eacP3 (1<<7 | eacVector)
+/*! \brief Vector with Legendre polynomial of order P_4(f(t).f(t+dt)) */
+#define eacP4 (1<<8 | eacVector)
+/*! \brief Binary identy correlation (f(t) == f(t+dt)) */
+#define eacIden (1<<9) //Not supported for multiple cores
+
+/*! \brief
+ * Add commandline arguments related to autocorrelations to the existing array.
+ * *npargs must be initialised to the number of elements in pa,
+ * it will be incremented appropriately.
+ *
+ * \param npargs The number of arguments before and after (is changed in this function)
+ * \param[in] pa The initial argument list
+ * \return the new array
+ */
+t_pargs *add_acf_pargs(int *npargs, t_pargs *pa);
+
+/*! \brief
+ * Returns the number of points to output from a correlation function.
+ * Works only AFTER do_auto_corr has been called!
+ * \return the output length for the correlation function
+ */
+int get_acfnout(void);
+
+/*! \brief
+ * Returns the fitting function selected.
+ * Works only AFTER do_auto_corr has been called!
+ * \return the fit function type.
+ */
+int get_acffitfn(void);
+
+/*! \brief
+ * Calls low_do_autocorr (see below). add_acf_pargs has to be called before this
+ * can be used.
+ * \param[in] fn File name for xvg output (may this be NULL)?
+ * \param[in] oenv The output environment information
+ * \param[in] title is the title in the output file
+ * \param[in] nframes is the number of frames in the time series
+ * \param[in] nitem is the number of items
+ * \param[inout] c1 is an array of dimension [ 0 .. nitem-1 ] [ 0 .. nframes-1 ]
+ * on output, this array is filled with the correlation function
+ * to reduce storage
+ * \param[in] dt is the time between frames
+ * \param[in] mode Different types of ACF can be done, see above
+ * \param[in] bAver If set, all ndih C(t) functions are averaged into a single
+ * C(t)
+ */
+void do_autocorr(const char *fn, const output_env_t oenv,
+ const char *title,
+ int nframes, int nitem, real **c1,
+ real dt, unsigned long mode, gmx_bool bAver);
+
+/*! \brief
+ * Low level computation of autocorrelation functions
+ *
+ * do_autocorr calculates autocorrelation functions for many things.
+ * It takes a 2 d array containing nitem arrays of length nframes
+ * for each item the ACF is calculated.
+ *
+ * A number of "modes" exist for computation of the ACF controlled
+ * by variable mode, with the following meaning.
+ *
+ * Mode | Function
+ * -----------|------------
+ * eacNormal | C(t) = < X (tau) * X (tau+t) >
+ * eacCos | C(t) = < cos (X(tau) - X(tau+t)) >
+ * eacIden | C(t) = < (X(tau) == X(tau+t)) > (not fully supported yet)
+ * eacVector | C(t) = < X(tau) * X(tau+t)
+ * eacP1 | C(t) = < cos (X(tau) * X(tau+t) >
+ * eacP2 | C(t) = 1/2 * < 3 cos (X(tau) * X(tau+t) - 1 >
+ * eacRcross | C(t) = < ( X(tau) * X(tau+t) )^2 >
+ *
+ * For modes eacVector, eacP1, eacP2 and eacRcross the input should be
+ * 3 x nframes long, where each triplet is taken as a 3D vector
+ *
+ * For mode eacCos inputdata must be in radians, not degrees!
+ *
+ * Other parameters are:
+ *
+ * \param[in] fn is output filename (.xvg) where the correlation function(s) are printed
+ * \param[in] oenv controls output file properties
+ * \param[in] title is the title in the output file
+ * \param[in] nframes is the number of frames in the time series
+ * \param[in] nitem is the number of items
+ * \param[in] nout
+ * \param[inout] c1 is an array of dimension [ 0 .. nitem-1 ] [ 0 .. nframes-1 ]
+ * on output, this array is filled with the correlation function
+ * to reduce storage
+ * \param[in] dt is the time between frames
+ * \param[in] mode Different types of ACF can be done, see above
+ * \param[in] nrestart is the number of steps between restarts for direct ACFs
+ * (i.e. without FFT) When set to 1 all points are used as
+ * time origin for averaging
+ * \param[in] bAver If set, all ndih C(t) functions are averaged into a single
+ * C(t)
+ * \param[in] bNormalize If set, all ACFs will be normalized to start at 0
+ * \param[in] bVerbose If set output to console will be generated
+ * \param[in] tbeginfit Time to start fitting to the ACF
+ * \param[in] tendfit Time to end fitting to the ACF
+ * \param[in] nfitparm Number of fitting parameters in a multi-exponential fit
+ */
+void low_do_autocorr(const char *fn, const output_env_t oenv,
+ const char *title, int nframes, int nitem,
+ int nout, real **c1, real dt, unsigned long mode,
+ int nrestart, gmx_bool bAver, gmx_bool bNormalize,
+ gmx_bool bVerbose, real tbeginfit, real tendfit,
+ int nfitparm);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal
+ * \file
+ * \brief
+ * Implements routine for computing a cross correlation between two data sets
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_correlationfunctions
+ */
+#include "gmxpre.h"
+
+#include "crosscorr.h"
+
+#include "gromacs/fft/fft.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/smalloc.h"
+
+/*! \brief
+ * return the size witch the array should be after zero padding
+ *
+ * \param[in] n Factor to multiply by 2
+ * \return zeroPaddingSize
+ */
+static int zeroPaddingSize(int n)
+{
+ return 2*n;
+}
+
+/*! \brief
+ * Compute complex conjugate. Output in the first input variable.
+ *
+ * \param[in] in1 first complex number
+ * \param[in] in2 second complex number
+ */
+static void complexConjugatMult(double in1[], double in2[])
+{
+ double res[2];
+ res[0] = in1[0] * in2[0] + in1[1] * in2[1];
+ res[1] = in1[0] * -in2[1] + in1[1] * in2[0];
+ in1[0] = res[0];
+ in1[1] = res[1];
+}
+
+/*! \brief
+ * Compute one cross correlation corr = f x g using FFT.
+ *
+ * \param[in] n number of data point
+ * \param[in] f first function
+ * \param[in] g second function
+ * \param[out] corr output correlation
+ * \param[in] fft FFT data structure
+ */
+static void cross_corr_low(int n, real f[], real g[], real corr[], gmx_fft_t fft)
+{
+ int i;
+ const int size = zeroPaddingSize(n);
+ double ** in1, ** in2;
+ snew(in1, size);
+ snew(in2, size);
+
+ for (i = 0; i < size; i++)
+ {
+ snew(in1[i], 2);
+ snew(in2[i], 2);
+ }
+
+ for (i = 0; i < n; i++)
+ {
+ in1[i][0] = (double)f[i];
+ in1[i][1] = 0;
+ in2[i][0] = (double)g[i];
+ in2[i][1] = 0;
+ }
+ for (; i < size; i++)
+ {
+ in1[i][0] = 0;
+ in1[i][1] = 0;
+ in2[i][0] = 0;
+ in2[i][1] = 0;
+ }
+
+
+ gmx_fft_1d(fft, GMX_FFT_FORWARD, in1, in1);
+ gmx_fft_1d(fft, GMX_FFT_FORWARD, in2, in2);
+
+ for (i = 0; i < size; i++)
+ {
+ complexConjugatMult(in1[i], in2[i]);
+ in1[i][0] /= size;
+ }
+ gmx_fft_1d(fft, GMX_FFT_BACKWARD, in1, in1);
+
+ for (i = 0; i < n; i++)
+ {
+ corr[i] = (real)(in1[i][0]);
+ }
+
+ for (i = 0; i < size; i++)
+ {
+ sfree(in1[i]);
+ sfree(in2[i]);
+ }
+
+ sfree(in1);
+ sfree(in2);
+
+}
+
+void cross_corr(int n, real f[], real g[], real corr[])
+{
+ gmx_fft_t fft;
+ gmx_fft_init_1d(&fft, zeroPaddingSize(n), GMX_FFT_FLAG_CONSERVATIVE);
+ cross_corr_low( n, f, g, corr, fft);
+ gmx_fft_destroy(fft);
+ gmx_fft_cleanup();
+}
+
+void many_cross_corr(int nFunc, int * nData, real ** f, real ** g, real ** corr)
+{
+#pragma omp parallel
+ //gmx_fft_t is not thread safe, so structure are allocated per thread.
+ {
+ int i;
+
+#pragma omp for
+ for (i = 0; i < nFunc; i++)
+ {
+ gmx_fft_t fft;
+ gmx_fft_init_1d(&fft, zeroPaddingSize(nData[i]), GMX_FFT_FLAG_CONSERVATIVE);
+ cross_corr_low( nData[i], f[i], g[i], corr[i], fft);
+ gmx_fft_destroy(fft);
+ }
+ }
+ gmx_fft_cleanup();
+
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal
+ * \file
+ * \brief
+ * Declares routine for computing a cross correlation between two data sets
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \inlibraryapi
+ * \ingroup module_correlationfunctions
+ */
+#ifndef GMX_CROSSCORR_H
+#define GMX_CROSSCORR_H
+
+#include "gromacs/utility/real.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*! \brief
+ * fft cross correlation algorithm.
+ * Computes corr = f (.) g
+ *
+ * \param[in] n number of data point
+ * \param[in] f First function
+ * \param[in] g Second function
+ * \param[out] corr The cross correlation
+ */
+void cross_corr(int n, real f[], real g[], real corr[]);
+
+/*! \brief
+ * fft cross correlation algorithm.
+ *
+ * Computes corr[n] = f[n][i] (.) g[n][i], that is for nFunc
+ * pairs of arrays n the cross correlation is computed in parallel
+ * using OpenMP.
+ *
+ * \param[in] nFunc nuber of function to crosscorrelate
+ * \param[in] nData number of data point in eatch function
+ * \param[in] f 2D array of first function to crosscorrelate
+ * \param[in] g 2D array of second function to crosscorrelate
+ * \param[out] corr 2D array of the cross correlations
+ */
+void many_cross_corr(int nFunc, int * nData, real ** f, real ** g, real ** corr);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal
+ * \file
+ * \brief
+ * Implements routine for fitting a data set to a curve
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_correlationfunctions
+ */
+#include "gmxpre.h"
+
+#include "expfit.h"
+
+#include <math.h>
+#include <string.h>
+
+#include "external/lmfit/lmcurve.h"
+
+#include "gromacs/correlationfunctions/integrate.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/real.h"
+#include "gromacs/utility/smalloc.h"
+
+/*! \brief Number of parameters for each fitting function */
+static const int nfp_ffn[effnNR] = { 0, 1, 2, 3, 2, 5, 7, 9, 4, 3, 6};
+
+const char *s_ffn[effnNR+2] = {
+ NULL, "none", "exp", "aexp", "exp_exp", "vac",
+ "exp5", "exp7", "exp9", "erffit", "effnPRES", NULL, NULL
+};
+/* We don't allow errest as a choice on the command line */
+
+/*! \brief Long description for each fitting function type */
+static const char *longs_ffn[effnNR] = {
+ "no fit",
+ "y = exp(-x/a1)",
+ "y = a2 exp(-x/a1)",
+ "y = a2 exp(-x/a1) + (1-a2) exp(-x/a3)",
+ "y = exp(-v) (cosh(wv) + 1/w sinh(wv)), v = x/(2 a1), w = sqrt(1 - a2)",
+ "y = a1 exp(-x/a2) + a3 exp(-x/a4) + a5",
+ "y = a1 exp(-x/a2) + a3 exp(-x/a4) + a5 exp(-x/a6) + a7",
+ "y = a1 exp(-x/a2) + a3 exp(-x/a4) + a5 exp(-x/a6) + a7 exp(-x/a8) + a9",
+ "y = 1/2*(a1+a2) - 1/2*(a1-a2)*erf( (x-a3) /a4^2)",
+ "y = a2 *2*a1*((exp(-x/a1)-1)*(a1/x)+1)+(1-a2)*2*a3*((exp(-x/a3)-1)*(a3/x)+1)",
+ "y = (1-a1) * exp(-(x/a3)^a4)*cos(x*a2) + a1*exp(-(x/a5)^a6)"
+};
+
+int effnNparams(int effn)
+{
+ if ((0 <= effn) && (effn < effnNR))
+ {
+ return nfp_ffn[effn];
+ }
+ else
+ {
+ return -1;
+ }
+}
+
+const char *effnDescription(int effn)
+{
+ if ((0 <= effn) && (effn < effnNR))
+ {
+ return longs_ffn[effn];
+ }
+ else
+ {
+ return NULL;
+ }
+}
+
+int sffn2effn(const char **sffn)
+{
+ int eFitFn, i;
+
+ eFitFn = 0;
+ for (i = 0; i < effnNR; i++)
+ {
+ if (sffn[i+1] && strcmp(sffn[0], sffn[i+1]) == 0)
+ {
+ eFitFn = i;
+ }
+ }
+
+ return eFitFn;
+}
+
+/*! \brief Compute exponential function A exp(-x/tau) */
+static double myexp(double x, double A, double tau)
+{
+ if ((A == 0) || (tau == 0))
+ {
+ return 0;
+ }
+ return A*exp(-x/tau);
+}
+
+/*! \brief Compute y=(a0+a1)/2-(a0-a1)/2*erf((x-a2)/a3^2) */
+static double lmc_erffit (double x, const double *a)
+{
+ double erfarg;
+
+ erfarg = (x-a[2])/(a[3]*a[3]);
+ return (a[0]+a[1])/2-(a[0]-a[1])*gmx_erf(erfarg);
+}
+
+/*! \brief Compute y = exp(-x/a0) */
+static double lmc_exp_one_parm(double x, const double *a)
+{
+ return exp(-x/a[0]);
+}
+
+/*! \brief Compute y = a1 exp(-x/a0) */
+static double lmc_exp_two_parm(double x, const double *a)
+{
+ return a[1]*exp(-x/a[0]);
+}
+
+/*! \brief Compute y = a1 exp(-x/a0) + (1-a1) exp(-x/a2) */
+static double lmc_exp_3_parm(double x, const double *a)
+{
+ double e1, e2;
+
+ e1 = exp(-x/a[0]);
+ e2 = exp(-x/a[2]);
+ return a[1]*e1 + (1-a[1])*e2;
+}
+
+/*! \brief Compute y = a0 exp(-x/a1) + a2 exp(-x/a3) + a4 */
+static double lmc_exp_5_parm(double x, const double *a)
+{
+ double e1, e2;
+
+ e1 = exp(-x/a[1]);
+ e2 = exp(-x/a[3]);
+ return a[0]*e1 + a[2]*e2 + a[4];
+}
+
+/*! \brief Compute y = a0 exp(-x/a1) + a2 exp(-x/a3) + a4 exp(-x/a5) + a6 */
+static double lmc_exp_7_parm(double x, const double *a)
+{
+ double e1, e2, e3;
+
+ e1 = exp(-x/a[1]);
+ e2 = exp(-x/a[3]);
+ e3 = exp(-x/a[5]);
+ return a[0]*e1 + a[2]*e2 + a[4]*e3 + a[6];
+}
+
+/*! \brief Compute y = a0 exp(-x/a1) + a2 exp(-x/a3) + a4 exp(-x/a5) + a6 exp(-x/a7) + a8 */
+static double lmc_exp_9_parm(double x, const double *a)
+{
+ double e1, e2, e3, e4;
+
+ e1 = exp(-x/a[1]);
+ e2 = exp(-x/a[3]);
+ e3 = exp(-x/a[5]);
+ e4 = exp(-x/a[7]);
+ return a[0]*e1 + a[2]*e2 + a[4]*e3 + a[6]*e4 + a[8];
+}
+
+/*! \brief Compute y = (1-a1) * exp(-(x/a3)^a4)*cos(x*a2) + a1*exp(-(x/a5)^a6) */
+static double effnPRES_fun(double x, const double *a)
+{
+ double term1, term2, term3;
+
+ if (a[0] != 0)
+ {
+ term3 = a[0] * exp(-pow((x/a[4]), a[5]));
+ }
+ else
+ {
+ term3 = 0;
+ }
+
+ term1 = 1-a[0];
+ if (term1 != 0)
+ {
+ term2 = exp(-pow((x/a[2]), a[3])) * cos(x*a[1]);
+ }
+ else
+ {
+ term2 = 0;
+ }
+
+ return term1*term2 + term3;
+}
+
+/*! \brief Compute vac function */
+static double lmc_vac_2_parm(double x, const double *a)
+{
+ /* Fit to function
+ *
+ * y = 1/2 (1 - 1/w) exp(-(1+w)v) + 1/2 (1 + 1/w) exp(-(1-w)v)
+ *
+ * = exp(-v) (cosh(wv) + 1/w sinh(wv))
+ *
+ * v = x/(2 a1)
+ * w = sqrt(1 - a2)
+ *
+ * For tranverse current autocorrelation functions:
+ * a1 = tau
+ * a2 = 4 tau (eta/rho) k^2
+ *
+ */
+
+ double y, v, det, omega, omega2, em, ec, es;
+
+ v = x/(2*a[0]);
+ det = 1 - a[1];
+ em = exp(-v);
+ if (det != 0)
+ {
+ omega2 = fabs(det);
+ omega = sqrt(omega2);
+ if (det > 0)
+ {
+ ec = em*0.5*(exp(omega*v)+exp(-omega*v));
+ es = em*0.5*(exp(omega*v)-exp(-omega*v))/omega;
+ }
+ else
+ {
+ ec = em*cos(omega*v);
+ es = em*sin(omega*v)/omega;
+ }
+ y = ec + es;
+ }
+ else
+ {
+ y = (1+v)*em;
+ }
+ return y;
+}
+
+/*! \brief Compute error estimate */
+static double lmc_errest_3_parm(double x, const double *a)
+{
+ /*
+ e1 = (exp(-x/a1) - 1)
+ e2 = (exp(-x/a3) - 1)
+ v1= 2*a1 * (e1*a1/x + 1)
+ v2 = 2*a3 * (e2*a3/x + 1)
+ fun = a2*v1 + (1 - a2) * v2
+ */
+ double e1, e2, v1, v2;
+
+ if (a[0] != 0)
+ {
+ e1 = gmx_expm1(-x/a[0]);
+ }
+ else
+ {
+ e1 = 0;
+ }
+ if (a[2] != 0)
+ {
+ e2 = gmx_expm1(-x/a[2]);
+ }
+ else
+ {
+ e2 = 0;
+ }
+
+ if (x > 0)
+ {
+ v1 = 2*a[0]*(e1*a[0]/x + 1);
+ v2 = 2*a[2]*(e2*a[2]/x + 1);
+ return a[1]*v1 + (1-a[1])*v2;
+ }
+ else
+ {
+ return 0;
+ }
+}
+
+/*! \brief function type for passing to fitting routine */
+typedef double (*t_lmcurve)(double x, const double *a);
+
+/*! \brief array of fitting functions corresponding to the pre-defined types */
+t_lmcurve lmcurves[effnNR] = {
+ lmc_exp_one_parm, lmc_exp_one_parm, lmc_exp_two_parm,
+ lmc_exp_3_parm, lmc_vac_2_parm,
+ lmc_exp_5_parm, lmc_exp_7_parm,
+ lmc_exp_9_parm, lmc_erffit, lmc_errest_3_parm, effnPRES_fun
+};
+
+double fit_function(int eFitFn, double *parm, double x)
+{
+ // TODO: check that eFitFn is within bounds
+ return lmcurves[eFitFn](x, parm);
+}
+
+/*! \brief lmfit_exp supports up to 3 parameter fitting of exponential functions */
+static gmx_bool lmfit_exp(int nfit, double x[], double y[],
+ real ftol, int maxiter,
+ double parm[], gmx_bool bVerbose,
+ int eFitFn)
+{
+ double chisq, ochisq;
+ gmx_bool bCont;
+ int i, j;
+ lm_control_struct *control;
+ lm_status_struct *status;
+
+ if ((eFitFn < 0) || (eFitFn >= effnNR))
+ {
+ gmx_fatal(FARGS, "fitfn = %d, should be in 0..%d (%s,%d)",
+ effnNR-1, eFitFn, __FILE__, __LINE__);
+ }
+
+ snew(control, 1);
+ control->ftol = ftol;
+ control->xtol = ftol;
+ control->gtol = ftol;
+ control->epsilon = 0.1;
+ control->stepbound = 100;
+ control->patience = maxiter;
+ control->scale_diag = 1;
+ control->msgfile = stdout;
+ control->verbosity = (bVerbose ? 1 : 0);
+ control->n_maxpri = nfp_ffn[eFitFn];
+ control->m_maxpri = 0;
+ snew(status, 1);
+ /* Initial params */
+ chisq = 1e12;
+ j = 0;
+ if (bVerbose)
+ {
+ fprintf(stderr, "%4s %10s Parameters\n",
+ "Step", "chi^2");
+ }
+ do
+ {
+ ochisq = chisq;
+
+ lmcurve(nfp_ffn[eFitFn], parm, nfit, x, y,
+ lmcurves[eFitFn], control, status);
+ chisq = sqr(status->fnorm);
+ if (bVerbose)
+ {
+ int mmm;
+ fprintf(stderr, "%4d %10.5e", j, chisq);
+ for (mmm = 0; (mmm < nfp_ffn[eFitFn]); mmm++)
+ {
+ fprintf(stderr, " %10.5e", parm[mmm]);
+ }
+ fprintf(stderr, "\n");
+ }
+ j++;
+ bCont = ((fabs(ochisq - chisq) > fabs(ftol*chisq)) ||
+ ((ochisq == chisq)));
+ }
+ while (bCont && (j < maxiter));
+ if (bVerbose)
+ {
+ fprintf(stderr, "\n");
+ }
+
+ sfree(control);
+ sfree(status);
+
+ return TRUE;
+}
+
+/*! \brief See description in header file. */
+real do_lmfit(int ndata, real c1[], real sig[], real dt, real x0[],
+ real begintimefit, real endtimefit, const output_env_t oenv,
+ gmx_bool bVerbose, int eFitFn, double fitparms[], int fix)
+{
+ FILE *fp;
+ char buf[32];
+
+ int i, j, nparm, nfitpnts;
+ double integral, ttt;
+ double *parm, *dparm;
+ double *x, *y, *dy;
+#ifdef GMX_DOUBLE
+ real ftol = 1e-16;
+#else
+ real ftol = 1e-8;
+#endif
+ int maxiter = 50;
+
+ if (0 != fix)
+ {
+ fprintf(stderr, "Using fixed parameters in curve fitting is not working anymore\n");
+ }
+ nparm = nfp_ffn[eFitFn];
+ if (debug)
+ {
+ fprintf(debug, "There are %d points to fit %d vars!\n", ndata, nparm);
+ fprintf(debug, "Fit to function %d from %g through %g, dt=%g\n",
+ eFitFn, begintimefit, endtimefit, dt);
+ }
+
+ snew(x, ndata);
+ snew(y, ndata);
+ snew(dy, ndata);
+
+ j = 0;
+ for (i = 0; i < ndata; i++)
+ {
+ ttt = x0 ? x0[i] : dt*i;
+ if (ttt >= begintimefit && ttt <= endtimefit)
+ {
+ x[j] = ttt;
+ y[j] = c1[i];
+
+ /* mrqmin does not like sig to be zero */
+ if (sig[i] < 1.0e-7)
+ {
+ dy[j] = 1.0e-7;
+ }
+ else
+ {
+ dy[j] = sig[i];
+ }
+ if (debug)
+ {
+ fprintf(debug, "j= %d, i= %d, x= %g, y= %g, dy= %g\n",
+ j, i, x[j], y[j], dy[j]);
+ }
+ j++;
+ }
+ }
+ nfitpnts = j;
+ integral = 0;
+ if (nfitpnts < nparm)
+ {
+ fprintf(stderr, "Not enough data points for fitting!\n");
+ }
+ else
+ {
+ snew(parm, nparm);
+ snew(dparm, nparm);
+ if (fitparms)
+ {
+ for (i = 0; (i < nparm); i++)
+ {
+ parm[i] = fitparms[i];
+ }
+ }
+
+ if (!lmfit_exp(nfitpnts, x, y, ftol, maxiter, parm, bVerbose, eFitFn))
+ {
+ fprintf(stderr, "Fit failed!\n");
+ }
+ else if (nparm <= 3)
+ {
+ /* Compute the integral from begintimefit */
+ if (nparm == 3)
+ {
+ integral = (parm[0]*myexp(begintimefit, parm[1], parm[0]) +
+ parm[2]*myexp(begintimefit, 1-parm[1], parm[2]));
+ }
+ else if (nparm == 2)
+ {
+ integral = parm[0]*myexp(begintimefit, parm[1], parm[0]);
+ }
+ else if (nparm == 1)
+ {
+ integral = parm[0]*myexp(begintimefit, 1, parm[0]);
+ }
+ else
+ {
+ gmx_fatal(FARGS, "nparm = %d in file %s, line %d",
+ nparm, __FILE__, __LINE__);
+ }
+
+ /* Generate THE output */
+ if (bVerbose)
+ {
+ fprintf(stderr, "FIT: # points used in fit is: %d\n", nfitpnts);
+ fprintf(stderr, "FIT: %21s%21s%21s\n",
+ "parm0 ", "parm1 (ps) ", "parm2 (ps) ");
+ fprintf(stderr, "FIT: ------------------------------------------------------------\n");
+ fprintf(stderr, "FIT: %8.3g +/- %8.3g%9.4g +/- %8.3g%8.3g +/- %8.3g\n",
+ parm[0], dparm[0], parm[1], dparm[1], parm[2], dparm[2]);
+ fprintf(stderr, "FIT: Integral (calc with fitted function) from %g ps to inf. is: %g\n",
+ begintimefit, integral);
+
+ sprintf(buf, "test%d.xvg", nfitpnts);
+ fp = xvgropen(buf, "C(t) + Fit to C(t)", "Time (ps)", "C(t)", oenv);
+ fprintf(fp, "# parm0 = %g, parm1 = %g, parm2 = %g\n",
+ parm[0], parm[1], parm[2]);
+ for (j = 0; (j < nfitpnts); j++)
+ {
+ ttt = x0 ? x0[j] : dt*j;
+ fprintf(fp, "%10.5e %10.5e %10.5e\n",
+ ttt, c1[j],
+ lmcurves[eFitFn](ttt, parm));
+ }
+ xvgrclose(fp);
+ }
+ }
+ if (fitparms)
+ {
+ for (i = 0; (i < nparm); i++)
+ {
+ fitparms[i] = parm[i];
+ }
+ }
+ sfree(parm);
+ sfree(dparm);
+ }
+
+ sfree(x);
+ sfree(y);
+ sfree(dy);
+
+ return integral;
+}
+
+/*! See description in header file. */
+real fit_acf(int ncorr, int fitfn, const output_env_t oenv, gmx_bool bVerbose,
+ real tbeginfit, real tendfit, real dt, real c1[], real *fit)
+{
+ double fitparm[3];
+ double tStart, tail_corr, sum, sumtot = 0, c_start, ct_estimate;
+ real *sig;
+ int i, j, jmax, nf_int;
+ gmx_bool bPrint;
+
+ bPrint = bVerbose || bDebugMode();
+
+ if (bPrint)
+ {
+ printf("COR:\n");
+ }
+
+ if (tendfit <= 0)
+ {
+ tendfit = ncorr*dt;
+ }
+ nf_int = min(ncorr, (int)(tendfit/dt));
+ sum = print_and_integrate(debug, nf_int, dt, c1, NULL, 1);
+
+ /* Estimate the correlation time for better fitting */
+ ct_estimate = 0.5*c1[0];
+ for (i = 1; (i < ncorr) && (c1[i] > 0); i++)
+ {
+ ct_estimate += c1[i];
+ }
+ ct_estimate *= dt/c1[0];
+
+ if (bPrint)
+ {
+ printf("COR: Correlation time (plain integral from %6.3f to %6.3f ps) = %8.5f ps\n",
+ 0.0, dt*nf_int, sum);
+ printf("COR: Relaxation times are computed as fit to an exponential:\n");
+ printf("COR: %s\n", longs_ffn[fitfn]);
+ printf("COR: Fit to correlation function from %6.3f ps to %6.3f ps, results in a\n", tbeginfit, min(ncorr*dt, tendfit));
+ }
+
+ tStart = 0;
+ if (bPrint)
+ {
+ printf("COR:%11s%11s%11s%11s%11s%11s%11s\n",
+ "Fit from", "Integral", "Tail Value", "Sum (ps)", " a1 (ps)",
+ (nfp_ffn[fitfn] >= 2) ? " a2 ()" : "",
+ (nfp_ffn[fitfn] >= 3) ? " a3 (ps)" : "");
+ }
+
+ snew(sig, ncorr);
+
+ if (tbeginfit > 0)
+ {
+ jmax = 3;
+ }
+ else
+ {
+ jmax = 1;
+ }
+ for (j = 0; ((j < jmax) && (tStart < tendfit) && (tStart < ncorr*dt)); j++)
+ {
+ /* Estimate the correlation time for better fitting */
+ c_start = -1;
+ ct_estimate = 0;
+ for (i = 0; (i < ncorr) && (dt*i < tStart || c1[i] > 0); i++)
+ {
+ if (c_start < 0)
+ {
+ if (dt*i >= tStart)
+ {
+ c_start = c1[i];
+ ct_estimate = 0.5*c1[i];
+ }
+ }
+ else
+ {
+ ct_estimate += c1[i];
+ }
+ }
+ if (c_start > 0)
+ {
+ ct_estimate *= dt/c_start;
+ }
+ else
+ {
+ /* The data is strange, so we need to choose somehting */
+ ct_estimate = tendfit;
+ }
+ if (debug)
+ {
+ fprintf(debug, "tStart %g ct_estimate: %g\n", tStart, ct_estimate);
+ }
+
+ if (fitfn == effnEXP3)
+ {
+ fitparm[0] = 0.002*ncorr*dt;
+ fitparm[1] = 0.95;
+ fitparm[2] = 0.2*ncorr*dt;
+ }
+ else
+ {
+ /* Good initial guess, this increases the probability of convergence */
+ fitparm[0] = ct_estimate;
+ fitparm[1] = 1.0;
+ fitparm[2] = 1.0;
+ }
+
+ /* Generate more or less appropriate sigma's */
+ for (i = 0; i < ncorr; i++)
+ {
+ sig[i] = sqrt(ct_estimate+dt*i);
+ }
+
+ nf_int = min(ncorr, (int)((tStart+1e-4)/dt));
+ sum = print_and_integrate(debug, nf_int, dt, c1, NULL, 1);
+ tail_corr = do_lmfit(ncorr, c1, sig, dt, NULL, tStart, tendfit, oenv,
+ bDebugMode(), fitfn, fitparm, 0);
+ sumtot = sum+tail_corr;
+ if (fit && ((jmax == 1) || (j == 1)))
+ {
+ double mfp[3];
+ for (i = 0; (i < 3); i++)
+ {
+ mfp[i] = fitparm[i];
+ }
+ for (i = 0; (i < ncorr); i++)
+ {
+ fit[i] = lmcurves[fitfn](i*dt, mfp);
+ }
+ }
+ if (bPrint)
+ {
+ printf("COR:%11.4e%11.4e%11.4e%11.4e", tStart, sum, tail_corr, sumtot);
+ for (i = 0; (i < nfp_ffn[fitfn]); i++)
+ {
+ printf(" %11.4e", fitparm[i]);
+ }
+ printf("\n");
+ }
+ tStart += tbeginfit;
+ }
+ sfree(sig);
+
+ return sumtot;
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal
+ * \file
+ * \brief
+ * Declares routine for fitting a data set to a curve
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \inlibraryapi
+ * \ingroup module_correlationfunctions
+ */
+#ifndef GMX_EXPFIT_H
+#define GMX_EXPFIT_H
+
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/utility/real.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*! \brief
+ * Enum to select fitting functions
+ */
+enum {
+ effnNONE, effnEXP1, effnEXP2, effnEXP3, effnVAC,
+ effnEXP5, effnEXP7, effnEXP9, effnERF, effnERREST, effnPRES, effnNR
+};
+
+/*! \brief
+ * Short name of each function type.
+ * This is exported for now in order to use when
+ * calling parse_common_args.
+ */
+extern const char *s_ffn[effnNR+2];
+
+/*! \brief
+ * Returns description corresponding to the enum above, or NULL if out of range
+ * \param[in] effn Index
+ * \return Description or NULL
+ */
+const char *effnDescription(int effn);
+
+/*! \brief
+ * Returns number of function parameters associated with a fitting function.
+ * \param[in] effn Index
+ * \return number or -1 if index out of range
+ */
+int effnNparams(int effn);
+
+/*! \brief
+ * Returns corresponding to the selected enum option in sffn
+ * \param[in] sffn Two dimensional string array coming from parse_common_args
+ * \return the ffn enum
+ */
+int sffn2effn(const char **sffn);
+
+/*! \brief
+ * Returns the value of fit function eFitFn at x
+ * \param[in] eFitFn the index to the fitting function (0 .. effnNR)
+ * \param[in] parm Array of parameters, the length of which depends on eFitFn
+ * \param[in] x The value of x
+ * \return the value of the fit
+ */
+double fit_function(int eFitFn, double *parm, double x);
+
+/*! \brief
+ * Use Levenberg-Marquardt method to fit to a nfitparm parameter exponential
+ * or to a transverse current autocorrelation function.
+ *
+ * If x == NULL, the timestep dt will be used to create a time axis.
+ * \param[in] ndata Number of data points
+ * \param[in] c1 The data points
+ * \param[in] sig The standard deviation in the points
+ * \param[in] dt The time step
+ * \param[in] x The X-axis (may be NULL, see above)
+ * \param[in] begintimefit Starting time for fitting
+ * \param[in] endtimefit Ending time for fitting
+ * \param[in] oenv Output formatting information
+ * \param[in] bVerbose Should the routine write to console?
+ * \param[in] eFitFn Fitting function (0 .. effnNR)
+ * \param[out] fitparms[]
+ * \param[in] fix Constrains fit parameter i at it's starting value, when the i'th bit
+ * of fix is set.
+ * \return integral.
+ */
+real do_lmfit(int ndata, real c1[], real sig[], real dt, real *x,
+ real begintimefit, real endtimefit, const output_env_t oenv,
+ gmx_bool bVerbose, int eFitFn, double fitparms[], int fix);
+
+/*! \brief
+ * Fit an autocorrelation function to a pre-defined functional form
+ *
+ * \todo check parameters
+ * \param[in] ncorr
+ * \param[in] fitfn Fitting function (0 .. effnNR)
+ * \param[in] oenv Output formatting information
+ * \param[in] bVerbose Should the routine write to console?
+ * \param[in] tbeginfit Starting time for fitting
+ * \param[in] tendfit Ending time for fitting
+ * \param[in] dt The time step
+ * \param[in] c1 The data points
+ * \param[out] fit The fitting parameters
+ * \return the integral over the autocorrelation function?
+ */
+real fit_acf(int ncorr, int fitfn, const output_env_t oenv, gmx_bool bVerbose,
+ real tbeginfit, real tendfit, real dt, real c1[], real *fit);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \brief
+ * Implement routines for integrating a data set
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ */
+#include "gmxpre.h"
+
+#include "integrate.h"
+
+#include <math.h>
+#include <stdio.h>
+
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+
+/*! \brief Integrate a function and printe the integral value. */
+real print_and_integrate(FILE *fp, int n, real dt, const real c[],
+ const real *fit, int nskip)
+{
+ real c0, sum;
+ int j;
+
+ /* Use trapezoidal rule for calculating integral */
+ sum = 0.0;
+ for (j = 0; (j < n); j++)
+ {
+ c0 = c[j];
+ if (fp && (nskip == 0 || j % nskip == 0))
+ {
+ fprintf(fp, "%10.3f %10.5f\n", j*dt, c0);
+ }
+ if (j > 0)
+ {
+ sum += dt*(c0+c[j-1]);
+ }
+ }
+ if (fp)
+ {
+ fprintf(fp, "&\n");
+ if (fit)
+ {
+ for (j = 0; (j < n); j++)
+ {
+ if (nskip == 0 || j % nskip == 0)
+ {
+ fprintf(fp, "%10.3f %10.5f\n", j*dt, fit[j]);
+ }
+ }
+ fprintf(fp, "&\n");
+ }
+ }
+ return sum*0.5;
+}
+
+/*! \brief Compute and return the integral of a function. */
+real evaluate_integral(int n, const real x[], const real y[],
+ const real dy[], real aver_start,
+ real *stddev)
+{
+ double sum, sum_var, w;
+ double sum_tail = 0, sum2_tail = 0;
+ int j, nsum_tail = 0;
+
+ /* Use trapezoidal rule for calculating integral */
+ if (n <= 0)
+ {
+ gmx_fatal(FARGS, "Evaluating integral: n = %d (file %s, line %d)",
+ n, __FILE__, __LINE__);
+ }
+
+ sum = 0;
+ sum_var = 0;
+ for (j = 0; (j < n); j++)
+ {
+ w = 0;
+ if (j > 0)
+ {
+ w += 0.5*(x[j] - x[j-1]);
+ }
+ if (j < n-1)
+ {
+ w += 0.5*(x[j+1] - x[j]);
+ }
+ sum += w*y[j];
+ if (dy)
+ {
+ /* Assume all errors are uncorrelated */
+ sum_var += sqr(w*dy[j]);
+ }
+
+ if ((aver_start > 0) && (x[j] >= aver_start))
+ {
+ sum_tail += sum;
+ sum2_tail += sqrt(sum_var);
+ nsum_tail += 1;
+ }
+ }
+
+ if (nsum_tail > 0)
+ {
+ sum = sum_tail/nsum_tail;
+ /* This is a worst case estimate, assuming all stddev's are correlated. */
+ *stddev = sum2_tail/nsum_tail;
+ }
+ else
+ {
+ *stddev = sqrt(sum_var);
+ }
+
+ return sum;
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal
+ * \file
+ * \brief
+ * Declares routines for integrating a data set
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \inlibraryapi
+ * \ingroup module_correlationfunctions
+ */
+#ifndef GMX_INTEGRATE_H
+#define GMX_INTEGRATE_H
+
+#include <stdio.h>
+
+#include "gromacs/utility/real.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*! \brief
+ * Integrate the equispaced data in c[] from 0 to n using trapezium rule.
+ * If fit != NULL the fit is written as well.
+ * \param[in] fp File pointer to write to (maybe NULL)
+ * \param[in] n Number of data points
+ * \param[in] dt The time step between data points
+ * \param[in] c The data set
+ * \param[in] fit Fit to the function that is printed too if not a NULL pointer is passed.
+ * \param[in] nskip Determines whether all elements are written to the output file
+ * (written when i % nskip == 0)
+ * \return The integral
+ */
+real print_and_integrate(FILE *fp, int n, real dt, const real c[], const real *fit, int nskip);
+
+/*! \brief
+ * Integrate data in y using the trapezium rule, and, if given, use dy as weighting
+ *
+ * \param[in] n The number of data points
+ * \param[in] x The x coordinate
+ * \param[in] y The y data (function values)
+ * \param[in] dy The uncertainties (can be NULL)
+ * \param[in] aver_start should be set to a value where the function has
+ * converged to 0.
+ * \param[out] stddev The standard deviation in the integral
+ * \return the integral
+ */
+real evaluate_integral(int n, const real x[], const real y[], const real dy[], real aver_start,
+ real *stddev);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements function to compute many autocorrelation functions
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_correlationfunctions
+ */
+#include "gmxpre.h"
+
+#include "manyautocorrelation.h"
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "gromacs/fft/fft.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
+
+int many_auto_correl(int nfunc, int ndata, int nfft, real **c)
+{
+ #pragma omp parallel
+ {
+ typedef real complex[2];
+ int i, t, j, fftcode;
+ gmx_fft_t fft1;
+ complex *in, *out;
+ int i0, i1;
+ int nthreads, thread_id;
+
+ nthreads = gmx_omp_get_max_threads();
+ thread_id = gmx_omp_get_thread_num();
+ if ((0 == thread_id))
+ {
+ // fprintf(stderr, "There are %d threads for correlation functions\n", nthreads);
+ }
+ i0 = thread_id*nfunc/nthreads;
+ i1 = min(nfunc, (thread_id+1)*nfunc/nthreads);
+
+ fftcode = gmx_fft_init_1d(&fft1, nfft, GMX_FFT_FLAG_CONSERVATIVE);
+ /* Allocate temporary arrays */
+ snew(in, nfft);
+ snew(out, nfft);
+ for (i = i0; (i < i1); i++)
+ {
+ for (j = 0; j < ndata; j++)
+ {
+ in[j][0] = c[i][j];
+ in[j][1] = 0;
+ }
+ for (; (j < nfft); j++)
+ {
+ in[j][0] = in[j][1] = 0;
+ }
+
+ fftcode = gmx_fft_1d(fft1, GMX_FFT_BACKWARD, (void *)in, (void *)out);
+ for (j = 0; j < nfft; j++)
+ {
+ in[j][0] = (out[j][0]*out[j][0] + out[j][1]*out[j][1])/nfft;
+ in[j][1] = 0;
+ }
+ for (; (j < nfft); j++)
+ {
+ in[j][0] = in[j][1] = 0;
+ }
+
+ fftcode = gmx_fft_1d(fft1, GMX_FFT_FORWARD, (void *)in, (void *)out);
+ for (j = 0; (j < nfft); j++)
+ {
+ c[i][j] = out[j][0]/ndata;
+ }
+ }
+ /* Free the memory */
+ gmx_fft_destroy(fft1);
+ sfree(in);
+ sfree(out);
+ }
+ // gmx_fft_cleanup();
+ return 0;
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal
+ * \file
+ * \brief
+ * Declares routine for computing many correlation functions using OpenMP
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \inlibraryapi
+ * \ingroup module_correlationfunctions
+ */
+#ifndef GMX_MANYAUTOCORRELATION_H
+#define GMX_MANYAUTOCORRELATION_H
+
+#include "gromacs/fft/fft.h"
+#include "gromacs/utility/real.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*! \brief
+ * Perform many autocorrelation calculations.
+ *
+ * This routine performs many autocorrelation function calculations using FFTs.
+ * The GROMACS FFT library wrapper is employed. On return the c[] arrays contain
+ * a symmetric function that is useful for further FFT:ing, for instance in order to
+ * compute spectra.
+ *
+ * The functions uses OpenMP parallellization.
+ *
+ * \param[in] nfunc Number of data functions to autocorrelate
+ * \param[in] ndata Number of valid data points in the data
+ * \param[in] nfft Length of the data arrays, this should at least be 50% larger than ndata. The c arrays will filled with zero beyond ndata before computing the correlation.
+ * \param[inout] c Data array of size nfunc x nfft, will also be used for output
+ * \return fft error code, or zero if everything went fine (see fft/fft.h)
+ */
+int many_auto_correl(int nfunc, int ndata, int nfft, real **c);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+/*! \internal \file
+ * \brief
+ * Implements help function to compute Legendre polynomials
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \author Anders Gärdenäs <anders.gardenas@gmail.com>
+ * \ingroup module_correlationfunctions
+ */
+#include "gmxpre.h"
+
+#include "polynomials.h"
-#include <stdio.h>
-#include <math.h>
-#include "typedefs.h"
-#include "gmx_fatal.h"
-#include "gstat.h"
+#include "gromacs/utility/fatalerror.h"
-real LegendreP(real x, unsigned long m)
+real LegendreP(real x, unsigned int m)
{
real polynomial = 0, x2, x3;
switch (m)
{
- case eacP0:
+ case 0:
polynomial = 1.0;
break;
- case eacP1:
+ case 1:
polynomial = x;
break;
- case eacP2:
+ case 2:
x2 = x*x;
polynomial = 1.5*x2 - 0.5;
break;
- case eacP3:
+ case 3:
+ x2 = x*x;
+ polynomial = (5*x2*x - 3*x )* 0.5;
+ break;
+ case 4:
x2 = x*x;
polynomial = (35*x2*x2 - 30*x2 + 3)/8;
break;
- case eacP4:
+ case 5:
x2 = x*x;
x3 = x2*x;
polynomial = (63*x3*x2 - 70*x3 + 15*x)/8;
break;
default:
- gmx_fatal(FARGS, "Legendre polynomials of order %d are not supported, %s %d",
- m, __FILE__, __LINE__);
+ gmx_fatal(FARGS, "Legendre polynomials of order %u are not supported", m);
}
return (polynomial);
}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal
+ * \file
+ * \brief
+ * Declares routine for computing a Legendre polynomial
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \inlibraryapi
+ * \ingroup module_correlationfunctions
+ */
+#ifndef GMX_POLYNOMIALS_H
+#define GMX_POLYNOMIALS_H
+
+#include "gromacs/utility/real.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*! \brief
+ * Return Legendre polynomial value Pm(x)
+ * http://en.wikipedia.org/wiki/Legendre_polynomials
+ * \param[in] x The value
+ * \param[in] m The order of the polynomial (0-4 are supported)
+ * \return Pm(x)
+ */
+real LegendreP(real x, unsigned int m);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+gmx_add_unit_test(CorrelationsTest correlations-test
+ autocorr.cpp
+ correlationdataset.cpp
+ expfit.cpp)
+
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements test of autocorrelation function routines
+ *
+ * \author Anders Gärdenäs <anders.gardenas@gmail.com>
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_correlationfunctions
+ */
+#include "gmxpre.h"
+
+#include "gromacs/correlationfunctions/autocorr.h"
+
+#include <cmath>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/correlationfunctions/expfit.h"
+#include "gromacs/fft/fft.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/uniqueptr.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+#include "testutils/testfilemanager.h"
+
+#include "correlationdataset.h"
+
+namespace gmx
+{
+namespace
+{
+
+//! Definition of pointer to class containing test data.
+typedef gmx_unique_ptr<CorrelationDataSet>::type CorrelationDataSetPointer;
+
+class AutocorrTest : public ::testing::Test
+{
+ protected:
+
+ static int nrFrames_;
+ static CorrelationDataSetPointer data_;
+ // Need raw pointer for passing this to C routines
+ static t_pargs * tempArgs_;
+
+ test::TestReferenceData refData_;
+ test::TestReferenceChecker checker_;
+
+ // Use erefdataCreateMissing for creating new files
+ AutocorrTest( )
+ : checker_(refData_.rootChecker())
+ {
+#ifdef GMX_DOUBLE
+ checker_.setDefaultTolerance(test::relativeToleranceAsFloatingPoint(1, 1e-6));
+#else
+ checker_.setDefaultTolerance(test::relativeToleranceAsFloatingPoint(1, 1e-3));
+#endif
+ }
+
+ // Static initiation, only run once every test.
+ static void SetUpTestCase()
+ {
+ int n = 0;
+ std::string fileName = "testCOS3.xvg";
+ data_ = CorrelationDataSetPointer(new CorrelationDataSet(fileName));
+ nrFrames_ = data_->getNrLines();
+ tempArgs_ = add_acf_pargs(&n, NULL);
+ }
+
+ static void TearDownTestCase()
+ {
+
+ sfree(tempArgs_);
+ tempArgs_ = NULL;
+ gmx_fft_cleanup();
+ }
+
+ void test(unsigned long mode)
+ {
+ bool bAverage = false;
+ bool bNormalize = true;
+ bool bVerbose = false;
+ int nrRestart = 1;
+ int dim = getDim(mode);
+ std::vector<real> result;
+
+ for (int i = 0; i < nrFrames_; i++)
+ {
+ for (int m = 0; m < dim; m++)
+ {
+ result.push_back(data_->getValue(m, i));
+ }
+ }
+ real *ptr = static_cast<real*>(&(result[0]));
+ low_do_autocorr(0, 0, 0, nrFrames_, 1,
+ get_acfnout(), &ptr, data_->getDt(), mode,
+ nrRestart, bAverage, bNormalize,
+ bVerbose, data_->getStartTime(), data_->getEndTime(),
+ effnNONE);
+
+ double testResult = 0;
+ for (int i = 0; i < nrFrames_; i++)
+ {
+ testResult += result[i];
+ }
+ checker_.checkSequenceArray(nrFrames_, ptr,
+ "AutocorrelationFunction");
+ checker_.checkReal(testResult, "Integral");
+ }
+
+ int getDim(unsigned long type)
+ {
+ switch (type)
+ {
+ case eacNormal:
+ return 1;
+ case eacVector:
+ return 3;
+ case eacCos:
+ return 1;
+ case eacRcross:
+ return 3;
+ case eacP0:
+ return 3;
+ case eacP1:
+ return 3;
+ case eacP2:
+ return 3;
+ case eacP3:
+ return 3;
+ case eacP4:
+ return 3;
+ case eacIden:
+ return 1;
+ default:
+ GMX_RELEASE_ASSERT(false, "Invalid auto correlation option");
+ return -1;
+ }
+
+ }
+
+};
+
+int AutocorrTest::nrFrames_;
+CorrelationDataSetPointer AutocorrTest::data_;
+t_pargs * AutocorrTest::tempArgs_;
+
+TEST_F (AutocorrTest, EacNormal)
+{
+ test(eacNormal);
+}
+
+TEST_F (AutocorrTest, EacCos)
+{
+ test(eacCos);
+}
+
+TEST_F (AutocorrTest, EacVector)
+{
+ test(eacVector);
+}
+
+TEST_F (AutocorrTest, EacRcross)
+{
+ test(eacRcross);
+}
+
+TEST_F (AutocorrTest, EacP0)
+{
+ test(eacP0);
+}
+
+TEST_F (AutocorrTest, EacP1)
+{
+ test(eacP1);
+}
+
+TEST_F (AutocorrTest, EacP2)
+{
+ test(eacP2);
+}
+
+TEST_F (AutocorrTest, EacP3)
+{
+ test(eacP3);
+}
+
+TEST_F (AutocorrTest, EacP4)
+{
+ test(eacP4);
+}
+
+
+}
+
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements helper class for autocorrelation tests
+ *
+ * \author Anders Gärdenäs <anders.gardenas@gmail.com>
+ * \ingroup module_correlationfunctions
+ */
+#include "gmxpre.h"
+
+#include "correlationdataset.h"
+
+#include <cmath>
+
+#include <sstream>
+
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "testutils/testfilemanager.h"
+
+CorrelationDataSet::CorrelationDataSet(const std::string &fileName)
+{
+ std::string fileNm = gmx::test::TestFileManager::getInputFilePath(fileName.c_str());
+ nrLines_ = read_xvg(fileNm.c_str(), &tempValues_, &nrColumns_);
+
+ dt_ = tempValues_[0][1] - tempValues_[0][0];
+ startTime_ = tempValues_[0][0];
+ endTime_ = tempValues_[0][nrLines_-1];
+}
+
+CorrelationDataSet::~CorrelationDataSet()
+{
+ // Allocated in read_xvg, destroyed here.
+ for (int i = 0; i < nrColumns_; i++)
+ {
+ sfree(tempValues_[i]);
+ tempValues_[i] = NULL;
+ }
+ sfree(tempValues_);
+ tempValues_ = NULL;
+}
+
+real CorrelationDataSet::getValue(int set, int time) const
+{
+ if (set+1 < nrColumns_)
+ {
+ return tempValues_[set+1][time];
+ }
+ else
+ {
+ return 0;
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Declares helper class for autocorrelation tests
+ *
+ * \author Anders Gärdenäs <anders.gardenas@gmail.com>
+ * \ingroup module_correlationfunctions
+ */
+#ifndef GMX_CORRELATIONDATASET_H
+#define GMX_CORRELATIONDATASET_H
+
+#include <string>
+#include <vector>
+
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/real.h"
+
+class CorrelationDataSet
+{
+ double ** tempValues_;
+
+ int nrLines_;
+ int nrColumns_;
+ double startTime_;
+ double endTime_;
+ double dt_;
+
+ public:
+
+ /*! \brief
+ * Constructor
+ * \param[in] fileName containing function to test. *.xvg
+ */
+ explicit CorrelationDataSet(const std::string &fileName);
+
+ /*! \brief
+ * Return a value at an index
+ * \param[in] set the set number
+ * \param[in] t the time index of the value
+ */
+ real getValue(int set, int t) const;
+
+ /*! \brief
+ * Return the nummber of columns
+ */
+ int getNrColumns() const { return nrColumns_; }
+
+ /*! \brief
+ * Return the nummber of Lines
+ */
+ int getNrLines() const { return nrLines_; }
+
+ /*! \brief
+ * Return the time witch the function starts at
+ */
+ real getStartTime() const { return startTime_; }
+
+ /*! \brief
+ * Return the time the function ends at
+ */
+ real getEndTime() const { return endTime_; }
+
+ /*! \brief
+ * return delta time
+ */
+ real getDt() const { return dt_; }
+
+ /*! \brief
+ * Destructor
+ */
+ ~CorrelationDataSet();
+
+ private:
+ //! This class should not be copyable or assignable
+ GMX_DISALLOW_COPY_AND_ASSIGN(CorrelationDataSet);
+};
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements test of exponential fitting routines
+ *
+ * \author Anders Gärdenäs <anders.gardenas@gmail.com>
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_correlationfunctions
+ */
+#include "gmxpre.h"
+
+#include "gromacs/correlationfunctions/expfit.h"
+
+#include <cmath>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+#include "testutils/testfilemanager.h"
+
+//! Number of data files for testing.
+#define expTestNrTypes 3
+
+namespace gmx
+{
+
+namespace
+{
+
+class ExpfitTest : public ::testing::Test
+{
+
+ protected:
+ static int nrLines_;
+ static std::vector<real> values_[expTestNrTypes];
+ static int nrColumns_;
+ static std::vector<real> standardDev_;
+ static real startTime_;
+ static real endTime_;
+ static real timeDeriv_;
+ test::TestReferenceData refData_;
+ test::TestReferenceChecker checker_;
+ ExpfitTest( )
+ : checker_(refData_.rootChecker())
+ {
+ }
+
+ // Static initiation, only run once every test.
+ static void SetUpTestCase()
+ {
+ double ** tempValues;
+ std::string fileName[expTestNrTypes];
+ fileName[0] = test::TestFileManager::getInputFilePath("testINVEXP.xvg");
+ fileName[1] = test::TestFileManager::getInputFilePath("testPRES.xvg");
+ fileName[2] = test::TestFileManager::getInputFilePath("testEXP.xvg");
+ for (int i = 0; i < expTestNrTypes; i++)
+ {
+ const char * name = fileName[i].c_str();
+ // TODO: this assumes all files have the same length.
+ nrLines_ = read_xvg(name, &tempValues, &nrColumns_);
+
+ // Generating standard deviation
+ if (i == 0)
+ {
+ double fac = 1.0/nrLines_;
+ for (int j = 0; j < nrLines_; j++)
+ {
+ standardDev_.push_back(fac);
+ }
+ timeDeriv_ = tempValues[0][1] - tempValues[0][0];
+ startTime_ = tempValues[0][0];
+ endTime_ = tempValues[0][nrLines_-1];
+ }
+
+ for (int j = 0; j < nrLines_; j++)
+ {
+ values_[i].push_back((real)tempValues[1][j]);
+ }
+
+ // Free memory that was allocated in read_xvg
+ for (int i = 0; i < nrColumns_; i++)
+ {
+ sfree(tempValues[i]);
+ tempValues[i] = NULL;
+ }
+ sfree(tempValues);
+ tempValues = NULL;
+ }
+ }
+
+ static void TearDownTestCase()
+ {
+ }
+
+ void test(int type, double result[], double tolerance, int testType)
+ {
+ int nfitparm = effnNparams(type);
+
+ do_lmfit(nrLines_, &values_[testType][0], &standardDev_[0], timeDeriv_,
+ NULL, startTime_, endTime_, NULL, false, type, result, 0);
+
+ checker_.setDefaultTolerance(test::relativeToleranceAsFloatingPoint(1, tolerance));
+ checker_.checkSequenceArray(nfitparm, result, "result");
+ }
+};
+
+
+//static var
+int ExpfitTest::nrLines_;
+//cppcheck-suppress arrayIndexOutOfBounds fixed in 1.68-dev
+std::vector<real> ExpfitTest::values_[expTestNrTypes];
+int ExpfitTest::nrColumns_;
+std::vector<real> ExpfitTest::standardDev_;
+real ExpfitTest::startTime_;
+real ExpfitTest::endTime_;
+real ExpfitTest::timeDeriv_;
+
+TEST_F (ExpfitTest, EffnEXP1) {
+ double param[] = {25};
+ test(effnEXP1, param, 1e-6, 0);
+}
+
+TEST_F (ExpfitTest, EffnEXP2) {
+ double param[] = {35, 0.5};
+ test(effnEXP2, param, 1e-6, 0);
+}
+
+TEST_F (ExpfitTest, EffnEXP3) {
+ double param[] = {45, 0.5, 5};
+ test(effnEXP3, param, 1e-4, 0);
+}
+
+TEST_F (ExpfitTest, EffnEXP5) {
+ double param[] = {0.5, 5, 0.5, 50, 0.002};
+ test(effnEXP5, param, 1e-4, 0);
+}
+
+TEST_F (ExpfitTest, EffnEXP7) {
+ double param[] = {0.5, 5, -0.02, 0.5, 0.5, 50, -0.002};
+ test(effnEXP7, param, 1e-4, 0);
+}
+
+TEST_F (ExpfitTest, EffnEXP9) {
+ double param[] = {2, 1200, -1, 300, 0.7, 70, 0.5, 6, -0.5};
+ test(effnEXP9, param, 4e-2, 0);
+}
+
+TEST_F (ExpfitTest, EffnERF) {
+ double param[] = {0.5, 0.5, 0.5, 1};
+ test(effnERF, param, 1e-2, 0);
+}
+
+TEST_F (ExpfitTest, EffnERREST) {
+ double param[] = {0.5, 0.7, 0.3};
+ test(effnERREST, param, 1e-4, 2);
+}
+
+TEST_F (ExpfitTest, EffnVAC) {
+ double param[] = {0.5, 0.05};
+ test(effnVAC, param, 1e-4, 0);
+}
+
+TEST_F (ExpfitTest, DISABLED_EffnPRES) {
+ //TODO: This test is prodocues NaNs and INFs. Fix and then reactivate.
+ double param[] = {0, 10, 4, 1, 0.5, 1};
+ test(effnPRES, param, 1e-4, 1);
+}
+
+}
+
+}
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="AutocorrelationFunction">
+ <Int Name="Length">501</Int>
+ <Real>1</Real>
+ <Real>0.99659538</Real>
+ <Real>0.99595559</Real>
+ <Real>0.9944247</Real>
+ <Real>0.99254024</Real>
+ <Real>0.99074072</Real>
+ <Real>0.98782086</Real>
+ <Real>0.98476714</Real>
+ <Real>0.98145622</Real>
+ <Real>0.97775453</Real>
+ <Real>0.97388524</Real>
+ <Real>0.96959651</Real>
+ <Real>0.96521682</Real>
+ <Real>0.96071005</Real>
+ <Real>0.95656222</Real>
+ <Real>0.95218587</Real>
+ <Real>0.94799894</Real>
+ <Real>0.94426513</Real>
+ <Real>0.94049501</Real>
+ <Real>0.93681264</Real>
+ <Real>0.93319356</Real>
+ <Real>0.93034834</Real>
+ <Real>0.92801505</Real>
+ <Real>0.92570525</Real>
+ <Real>0.92359954</Real>
+ <Real>0.92197412</Real>
+ <Real>0.92073542</Real>
+ <Real>0.92040521</Real>
+ <Real>0.91959125</Real>
+ <Real>0.91971552</Real>
+ <Real>0.91937882</Real>
+ <Real>0.92004192</Real>
+ <Real>0.92134565</Real>
+ <Real>0.92249507</Real>
+ <Real>0.92415452</Real>
+ <Real>0.92598462</Real>
+ <Real>0.92835307</Real>
+ <Real>0.93056071</Real>
+ <Real>0.93232888</Real>
+ <Real>0.93553138</Real>
+ <Real>0.93841678</Real>
+ <Real>0.94149232</Real>
+ <Real>0.9445464</Real>
+ <Real>0.94751155</Real>
+ <Real>0.95099658</Real>
+ <Real>0.95437491</Real>
+ <Real>0.95766789</Real>
+ <Real>0.96085715</Real>
+ <Real>0.96405703</Real>
+ <Real>0.96722084</Real>
+ <Real>0.97044915</Real>
+ <Real>0.97360796</Real>
+ <Real>0.97608888</Real>
+ <Real>0.97839665</Real>
+ <Real>0.98092067</Real>
+ <Real>0.98309362</Real>
+ <Real>0.9850989</Real>
+ <Real>0.98661345</Real>
+ <Real>0.98806572</Real>
+ <Real>0.98921531</Real>
+ <Real>0.989797</Real>
+ <Real>0.99024576</Real>
+ <Real>0.99059737</Real>
+ <Real>0.99045819</Real>
+ <Real>0.99015921</Real>
+ <Real>0.98907006</Real>
+ <Real>0.98829621</Real>
+ <Real>0.98710001</Real>
+ <Real>0.98538107</Real>
+ <Real>0.98345906</Real>
+ <Real>0.98124063</Real>
+ <Real>0.97880316</Real>
+ <Real>0.97668463</Real>
+ <Real>0.97459376</Real>
+ <Real>0.97177458</Real>
+ <Real>0.9690451</Real>
+ <Real>0.96629435</Real>
+ <Real>0.96378684</Real>
+ <Real>0.96081358</Real>
+ <Real>0.95825708</Real>
+ <Real>0.95578271</Real>
+ <Real>0.95307195</Real>
+ <Real>0.95074266</Real>
+ <Real>0.94830912</Real>
+ <Real>0.94601887</Real>
+ <Real>0.94421709</Real>
+ <Real>0.94242907</Real>
+ <Real>0.94094354</Real>
+ <Real>0.93951678</Real>
+ <Real>0.93832368</Real>
+ <Real>0.93808126</Real>
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--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+file(GLOB DOMDEC_SOURCES *.cpp)
+set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${DOMDEC_SOURCES} PARENT_SCOPE)
+
+if (BUILD_TESTING)
+# add_subdirectory(tests)
+endif()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2005,2006,2007,2008,2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <stdio.h>
-#include <time.h>
+#include "domdec.h"
+
+#include "config.h"
+
+#include <assert.h>
+#include <limits.h>
#include <math.h>
-#include <string.h>
+#include <stdio.h>
#include <stdlib.h>
-#include <assert.h>
+#include <string.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "gmx_fatal_collective.h"
-#include "vec.h"
-#include "domdec.h"
-#include "domdec_network.h"
-#include "nrnb.h"
-#include "pbc.h"
-#include "chargegroup.h"
-#include "constr.h"
-#include "mdatoms.h"
-#include "names.h"
-#include "force.h"
-#include "pme.h"
-#include "mdrun.h"
-#include "nsgrid.h"
-#include "shellfc.h"
-#include "mtop_util.h"
-#include "gmx_ga2la.h"
-#include "macros.h"
-#include "nbnxn_search.h"
-#include "bondf.h"
-#include "gmx_omp_nthreads.h"
-#include "gpu_utils.h"
-
-#include "gromacs/fileio/futil.h"
+#include <algorithm>
+
+#include "gromacs/domdec/domdec_network.h"
+#include "gromacs/ewald/pme.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/pdbio.h"
+#include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/nsgrid.h"
+#include "gromacs/legacyheaders/shellfc.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/constr.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/legacyheaders/types/hw_info.h"
+#include "gromacs/legacyheaders/types/ifunc.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
+#include "gromacs/legacyheaders/types/nrnb.h"
+#include "gromacs/legacyheaders/types/ns.h"
+#include "gromacs/legacyheaders/types/nsgrid.h"
+#include "gromacs/legacyheaders/types/shellfc.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/state.h"
+#include "gromacs/listed-forces/manage-threading.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/pulling/pull_rotation.h"
+#include "gromacs/swap/swapcoords.h"
#include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
-#include "gromacs/swap/swapcoords.h"
#include "gromacs/utility/qsort_threadsafe.h"
-#include "gromacs/pulling/pull.h"
-#include "gromacs/pulling/pull_rotation.h"
-#include "gromacs/imd/imd.h"
+#include "gromacs/utility/real.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "domdec_constraints.h"
+#include "domdec_internal.h"
+#include "domdec_vsite.h"
#define DDRANK(dd, rank) (rank)
#define DDMASTERRANK(dd) (dd->masterrank)
rvec *buf, *sbuf;
ivec vis;
int is;
- gmx_bool bPBC, bScrew;
+ gmx_bool bShiftForcesNeedPbc, bScrew;
comm = dd->comm;
buf = comm->vbuf.v;
- n = 0;
nzone = comm->zones.n/2;
nat_tot = dd->nat_tot;
for (d = dd->ndim-1; d >= 0; d--)
{
- bPBC = (dd->ci[dd->dim[d]] == 0);
- bScrew = (bPBC && dd->bScrewPBC && dd->dim[d] == XX);
+ /* Only forces in domains near the PBC boundaries need to
+ consider PBC in the treatment of fshift */
+ bShiftForcesNeedPbc = (dd->ci[dd->dim[d]] == 0);
+ bScrew = (bShiftForcesNeedPbc && dd->bScrewPBC && dd->dim[d] == XX);
if (fshift == NULL && !bScrew)
{
- bPBC = FALSE;
+ bShiftForcesNeedPbc = FALSE;
}
/* Determine which shift vector we need */
clear_ivec(vis);
index = ind->index;
/* Add the received forces */
n = 0;
- if (!bPBC)
+ if (!bShiftForcesNeedPbc)
{
for (i = 0; i < ind->nsend[nzone]; i++)
{
}
else if (!bScrew)
{
+ /* fshift should always be defined if this function is
+ * called when bShiftForcesNeedPbc is true */
+ assert(NULL != fshift);
for (i = 0; i < ind->nsend[nzone]; i++)
{
at0 = cgindex[index[i]];
buf = &comm->vbuf.v[0][0];
- n = 0;
nzone = comm->zones.n/2;
nat_tot = dd->nat_tot;
for (d = dd->ndim-1; d >= 0; d--)
static void dd_move_cellx(gmx_domdec_t *dd, gmx_ddbox_t *ddbox,
rvec cell_ns_x0, rvec cell_ns_x1)
{
- int d, d1, dim, dim1, pos, buf_size, i, j, k, p, npulse, npulse_min;
+ int d, d1, dim, pos, buf_size, i, j, p, npulse, npulse_min;
gmx_ddzone_t *zp;
gmx_ddzone_t buf_s[DDZONECOMM_MAXZONE];
gmx_ddzone_t buf_r[DDZONECOMM_MAXZONE];
if (bPBC)
{
/* Take the minimum to avoid double communication */
- npulse_min = min(npulse, dd->nc[dim]-1-npulse);
+ npulse_min = std::min(npulse, dd->nc[dim]-1-npulse);
}
else
{
{
for (d1 = d; d1 < dd->ndim-1; d1++)
{
- extr_s[d1][0] = max(extr_s[d1][0], extr_r[d1][0]);
- extr_s[d1][1] = min(extr_s[d1][1], extr_r[d1][1]);
- extr_s[d1][2] = min(extr_s[d1][2], extr_r[d1][2]);
+ extr_s[d1][0] = std::max(extr_s[d1][0], extr_r[d1][0]);
+ extr_s[d1][1] = std::min(extr_s[d1][1], extr_r[d1][1]);
+ extr_s[d1][2] = std::min(extr_s[d1][2], extr_r[d1][2]);
}
}
}
{
if (bUse)
{
- buf_e[i].min0 = min(buf_e[i].min0, buf_r[i].min0);
- buf_e[i].max1 = max(buf_e[i].max1, buf_r[i].max1);
- buf_e[i].min1 = min(buf_e[i].min1, buf_r[i].min1);
+ buf_e[i].min0 = std::min(buf_e[i].min0, buf_r[i].min0);
+ buf_e[i].max1 = std::max(buf_e[i].max1, buf_r[i].max1);
+ buf_e[i].min1 = std::min(buf_e[i].min1, buf_r[i].min1);
}
if (dd->ndim == 3 && d == 0 && i == buf_size - 1)
}
if (bUse && dh[d1] >= 0)
{
- buf_e[i].mch0 = max(buf_e[i].mch0, buf_r[i].mch0-dh[d1]);
- buf_e[i].mch1 = max(buf_e[i].mch1, buf_r[i].mch1-dh[d1]);
+ buf_e[i].mch0 = std::max(buf_e[i].mch0, buf_r[i].mch0-dh[d1]);
+ buf_e[i].mch1 = std::max(buf_e[i].mch1, buf_r[i].mch1-dh[d1]);
}
}
/* Copy the received buffer to the send buffer,
for (d1 = d; d1 < dd->ndim-1; d1++)
{
- extr_s[d1][1] = min(extr_s[d1][1], buf_e[pos].min0);
- extr_s[d1][0] = max(extr_s[d1][0], buf_e[pos].max1);
- extr_s[d1][2] = min(extr_s[d1][2], buf_e[pos].min1);
+ extr_s[d1][1] = std::min(extr_s[d1][1], buf_e[pos].min0);
+ extr_s[d1][0] = std::max(extr_s[d1][0], buf_e[pos].max1);
+ extr_s[d1][2] = std::min(extr_s[d1][2], buf_e[pos].min1);
pos++;
}
{
print_ddzone(debug, 1, i, 0, &comm->zone_d1[i]);
}
- cell_ns_x0[dim] = min(cell_ns_x0[dim], comm->zone_d1[i].min0);
- cell_ns_x1[dim] = max(cell_ns_x1[dim], comm->zone_d1[i].max1);
+ cell_ns_x0[dim] = std::min(cell_ns_x0[dim], comm->zone_d1[i].min0);
+ cell_ns_x1[dim] = std::max(cell_ns_x1[dim], comm->zone_d1[i].max1);
}
}
if (dd->ndim >= 3)
{
print_ddzone(debug, 2, i, j, &comm->zone_d2[i][j]);
}
- cell_ns_x0[dim] = min(cell_ns_x0[dim], comm->zone_d2[i][j].min0);
- cell_ns_x1[dim] = max(cell_ns_x1[dim], comm->zone_d2[i][j].max1);
+ cell_ns_x0[dim] = std::min(cell_ns_x0[dim], comm->zone_d2[i][j].min0);
+ cell_ns_x1[dim] = std::max(cell_ns_x1[dim], comm->zone_d2[i][j].max1);
}
}
}
void dd_collect_vec(gmx_domdec_t *dd,
t_state *state_local, rvec *lv, rvec *v)
{
- gmx_domdec_master_t *ma;
- int n, i, c, a, nalloc = 0;
- rvec *buf = NULL;
-
dd_collect_cg(dd, state_local);
if (dd->nnodes <= GMX_DD_NNODES_SENDRECV)
{
gmx_domdec_master_t *ma;
int *scounts = NULL, *disps = NULL;
- int n, i, c, a, nalloc = 0;
+ int n, i, c, a;
rvec *buf = NULL;
if (DDMASTER(dd))
snew(grid_r, 2*dd->nnodes);
}
- dd_gather(dd, 2*sizeof(rvec), grid_s[0], DDMASTER(dd) ? grid_r[0] : NULL);
+ dd_gather(dd, 2*sizeof(rvec), grid_s, DDMASTER(dd) ? grid_r : NULL);
if (DDMASTER(dd))
{
gmx_fio_fclose(out);
}
-real dd_cutoff_mbody(gmx_domdec_t *dd)
+real dd_cutoff_multibody(const gmx_domdec_t *dd)
{
gmx_domdec_comm_t *comm;
int di;
r = comm->cellsize_min[dd->dim[0]];
for (di = 1; di < dd->ndim; di++)
{
- r = min(r, comm->cellsize_min[dd->dim[di]]);
+ r = std::min(r, comm->cellsize_min[dd->dim[di]]);
}
if (comm->bBondComm)
{
- r = max(r, comm->cutoff_mbody);
+ r = std::max(r, comm->cutoff_mbody);
}
else
{
- r = min(r, comm->cutoff);
+ r = std::min(r, comm->cutoff);
}
}
}
return r;
}
-real dd_cutoff_twobody(gmx_domdec_t *dd)
+real dd_cutoff_twobody(const gmx_domdec_t *dd)
{
real r_mb;
- r_mb = dd_cutoff_mbody(dd);
+ r_mb = dd_cutoff_multibody(dd);
- return max(dd->comm->cutoff, r_mb);
+ return std::max(dd->comm->cutoff, r_mb);
}
static int gmx_ddcoord2pmeindex(t_commrec *cr, int x, int y, int z)
{
gmx_domdec_t *dd;
- ivec coords, coords_pme, nc;
+ ivec coords;
int slab;
dd = cr->dd;
{
gmx_domdec_t *dd;
gmx_domdec_comm_t *comm;
- ivec coord, coord_pme;
int i;
int pmenode = -1;
if (comm->bCartesianPP_PME)
{
#ifdef GMX_MPI
+ ivec coord, coord_pme;
MPI_Cart_coords(cr->mpi_comm_mysim, sim_nodeid, DIM, coord);
if (coord[comm->cartpmedim] < dd->nc[comm->cartpmedim])
{
}
}
-gmx_bool gmx_pmeonlynode(t_commrec *cr, int sim_nodeid)
-{
- gmx_bool bPMEOnlyNode;
-
- if (DOMAINDECOMP(cr))
- {
- bPMEOnlyNode = (dd_simnode2pmenode(cr, sim_nodeid) == -1);
- }
- else
- {
- bPMEOnlyNode = FALSE;
- }
-
- return bPMEOnlyNode;
-}
-
void get_pme_ddnodes(t_commrec *cr, int pmenodeid,
int *nmy_ddnodes, int **my_ddnodes, int *node_peer)
{
static gmx_bool receive_vir_ener(t_commrec *cr)
{
gmx_domdec_comm_t *comm;
- int pmenode, coords[DIM], rank;
+ int pmenode;
gmx_bool bReceive;
bReceive = TRUE;
{
pmenode = dd_simnode2pmenode(cr, cr->sim_nodeid);
#ifdef GMX_MPI
+ ivec coords;
MPI_Cart_coords(cr->mpi_comm_mysim, cr->sim_nodeid, DIM, coords);
coords[comm->cartpmedim]++;
if (coords[comm->cartpmedim] < cr->dd->nc[comm->cartpmedim])
{
+ int rank;
MPI_Cart_rank(cr->mpi_comm_mysim, coords, &rank);
if (dd_simnode2pmenode(cr, rank) == pmenode)
{
{
int nzone, zone, zone1, cg0, cg1, cg1_p1, cg, cg_gl, a, a_gl;
int *zone2cg, *zone_ncg1, *index_gl, *gatindex;
- gmx_ga2la_t *ga2la;
- char *bLocalCG;
gmx_bool bCGs;
- bLocalCG = dd->comm->bLocalCG;
-
if (dd->nat_tot > dd->gatindex_nalloc)
{
dd->gatindex_nalloc = over_alloc_dd(dd->nat_tot);
static int check_bLocalCG(gmx_domdec_t *dd, int ncg_sys, const char *bLocalCG,
const char *where)
{
- int ncg, i, ngl, nerr;
+ int i, ngl, nerr;
nerr = 0;
if (bLocalCG == NULL)
/* The cut-off might have changed, e.g. by PME load balacning,
* from the value used to set comm->cellsize_min, so check it.
*/
- cellsize_min = max(cellsize_min, comm->cutoff/comm->cd[dim_ind].np_dlb);
+ cellsize_min = std::max(cellsize_min, comm->cutoff/comm->cd[dim_ind].np_dlb);
if (comm->bPMELoadBalDLBLimits)
{
/* Check for the cut-off limit set by the PME load balancing */
- cellsize_min = max(cellsize_min, comm->PMELoadBal_max_cutoff/comm->cd[dim_ind].np_dlb);
+ cellsize_min = std::max(cellsize_min, comm->PMELoadBal_max_cutoff/comm->cd[dim_ind].np_dlb);
}
}
{
if (comm->bPMELoadBalDLBLimits)
{
- cutoff = max(cutoff, comm->PMELoadBal_max_cutoff);
+ cutoff = std::max(cutoff, comm->PMELoadBal_max_cutoff);
}
- grid_jump_limit = max(grid_jump_limit,
- cutoff/comm->cd[dim_ind].np);
+ grid_jump_limit = std::max(grid_jump_limit,
+ cutoff/comm->cd[dim_ind].np);
}
return grid_jump_limit;
{
slab = pmeindex % ddpme->nslab;
}
- ddpme->pp_min[slab] = min(ddpme->pp_min[slab], xyz[dimind]);
- ddpme->pp_max[slab] = max(ddpme->pp_max[slab], xyz[dimind]);
+ ddpme->pp_min[slab] = std::min(ddpme->pp_min[slab], xyz[dimind]);
+ ddpme->pp_max[slab] = std::max(ddpme->pp_max[slab], xyz[dimind]);
}
}
{
npulse[d]++;
}
- cellsize_min[d] = min(cellsize_min[d], cellsize);
+ cellsize_min[d] = std::min(cellsize_min[d], cellsize);
}
if (setmode == setcellsizeslbLOCAL)
{
gmx_bool bUniform, gmx_int64_t step)
{
gmx_domdec_comm_t *comm;
- int ncd, d1, i, j, pos;
+ int ncd, d1, i, pos;
real *cell_size;
real load_aver, load_i, imbalance, change, change_max, sc;
real cellsize_limit_f, dist_min_f, dist_min_f_hard, space;
imbalance = (load_i - load_aver)/(load_aver > 0 ? load_aver : 1);
/* Determine the change of the cell size using underrelaxation */
change = -relax*imbalance;
- change_max = max(change_max, max(change, -change));
+ change_max = std::max(change_max, std::max(change, -change));
}
/* Limit the amount of scaling.
* We need to use the same rescaling for all cells in one row,
gmx_ddbox_t *ddbox)
{
gmx_domdec_comm_t *comm;
- int d1, dim1, pos;
+ int d1, pos;
comm = dd->comm;
{
gmx_domdec_master_t *ma;
int **tmp_ind = NULL, *tmp_nalloc = NULL;
- int i, icg, j, k, k0, k1, d, npbcdim;
+ int i, icg, j, k, k0, k1, d;
matrix tcm;
- rvec box_size, cg_cm;
+ rvec cg_cm;
ivec ind;
real nrcg, inv_ncg, pos_d;
atom_id *cgindex;
- gmx_bool bUnbounded, bScrew;
+ gmx_bool bScrew;
ma = dd->ma;
}
dd_scatterv(dd,
- DDMASTER(dd) ? ma->ibuf : NULL,
- DDMASTER(dd) ? ma->ibuf+dd->nnodes : NULL,
- DDMASTER(dd) ? ma->cg : NULL,
+ bMaster ? ma->ibuf : NULL,
+ bMaster ? ma->ibuf+dd->nnodes : NULL,
+ bMaster ? ma->cg : NULL,
dd->ncg_home*sizeof(int), dd->index_gl);
/* Determine the home charge group sizes */
int *move)
{
int npbcdim;
- int c, i, cg, k, k0, k1, d, dim, dim2, dir, d2, d3, d4, cell_d;
- int mc, cdd, nrcg, ncg_recv, nat_recv, nvs, nvr, nvec, vec;
+ int cg, k, k0, k1, d, dim, d2;
+ int mc, nrcg;
int flag;
gmx_bool bScrew;
ivec dev;
int *move;
int npbcdim;
int ncg[DIM*2], nat[DIM*2];
- int c, i, cg, k, k0, k1, d, dim, dim2, dir, d2, d3, d4, cell_d;
- int mc, cdd, nrcg, ncg_recv, nat_recv, nvs, nvr, nvec, vec;
+ int c, i, cg, k, d, dim, dim2, dir, d2, d3;
+ int mc, cdd, nrcg, ncg_recv, nvs, nvr, nvec, vec;
int sbuf[2], rbuf[2];
int home_pos_cg, home_pos_at, buf_pos;
int flag;
gmx_bool bV = FALSE, bSDX = FALSE, bCGP = FALSE;
- gmx_bool bScrew;
- ivec dev;
- real inv_ncg, pos_d;
+ real pos_d;
matrix tcm;
- rvec *cg_cm = NULL, cell_x0, cell_x1, limitd, limit0, limit1, cm_new;
+ rvec *cg_cm = NULL, cell_x0, cell_x1, limitd, limit0, limit1;
atom_id *cgindex;
cginfo_mb_t *cginfo_mb;
gmx_domdec_comm_t *comm;
{
dim = dd->dim[d];
ncg_recv = 0;
- nat_recv = 0;
nvr = 0;
for (dir = 0; dir < (dd->nc[dim] == 2 ? 1 : 2); dir++)
{
comm->cgcm_state[cdd], nvs,
comm->vbuf.v+nvr, i);
ncg_recv += rbuf[0];
- nat_recv += rbuf[1];
nvr += i;
}
gmx_domdec_comm_t *comm;
gmx_domdec_load_t *load;
gmx_domdec_root_t *root = NULL;
- int d, dim, cid, i, pos;
+ int d, dim, i, pos;
float cell_frac = 0, sbuf[DD_NLOAD_MAX];
gmx_bool bSepPME;
for (i = 0; i < dd->nc[dim]; i++)
{
load->sum += load->load[pos++];
- load->max = max(load->max, load->load[pos]);
+ load->max = std::max(load->max, load->load[pos]);
pos++;
if (dd->bGridJump)
{
/* This direction could not be load balanced properly,
* therefore we need to use the maximum iso the average load.
*/
- load->sum_m = max(load->sum_m, load->load[pos]);
+ load->sum_m = std::max(load->sum_m, load->load[pos]);
}
else
{
load->sum_m += load->load[pos];
}
pos++;
- load->cvol_min = min(load->cvol_min, load->load[pos]);
+ load->cvol_min = std::min(load->cvol_min, load->load[pos]);
pos++;
if (d < dd->ndim-1)
{
}
if (bSepPME)
{
- load->mdf = max(load->mdf, load->load[pos]);
+ load->mdf = std::max(load->mdf, load->load[pos]);
pos++;
- load->pme = max(load->pme, load->load[pos]);
+ load->pme = std::max(load->pme, load->load[pos]);
pos++;
}
}
void setup_dd_grid(FILE *fplog, gmx_domdec_t *dd)
{
- gmx_bool bZYX;
int d, dim, i, j, m;
ivec tmp, s;
int nzone, nzonep;
static void make_pp_communicator(FILE *fplog, t_commrec *cr, int gmx_unused reorder)
{
gmx_domdec_t *dd;
+ dd = cr->dd;
+
+#ifdef GMX_MPI
gmx_domdec_comm_t *comm;
- int i, rank, *buf;
+ int rank, *buf;
ivec periods;
-#ifdef GMX_MPI
MPI_Comm comm_cart;
-#endif
- dd = cr->dd;
comm = dd->comm;
-#ifdef GMX_MPI
if (comm->bCartesianPP)
{
/* Set up cartesian communication for the particle-particle part */
dd->nc[XX], dd->nc[YY], dd->nc[ZZ]);
}
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
periods[i] = TRUE;
}
/* Determine the master coordinates and rank.
* The DD master should be the same node as the master of this sim.
*/
- for (i = 0; i < dd->nnodes; i++)
+ for (int i = 0; i < dd->nnodes; i++)
{
if (comm->ddindex2simnodeid[i] == 0)
{
}
}
-static void receive_ddindex2simnodeid(t_commrec *cr)
+static void receive_ddindex2simnodeid(t_commrec gmx_unused *cr)
{
+#ifdef GMX_MPI
gmx_domdec_t *dd;
-
gmx_domdec_comm_t *comm;
- int *buf;
dd = cr->dd;
comm = dd->comm;
-#ifdef GMX_MPI
if (!comm->bCartesianPP_PME && comm->bCartesianPP)
{
+ int *buf;
snew(comm->ddindex2simnodeid, dd->nnodes);
snew(buf, dd->nnodes);
if (cr->duty & DUTY_PP)
{
buf[dd_index(dd->nc, dd->ci)] = cr->sim_nodeid;
}
-#ifdef GMX_MPI
/* Communicate the ddindex to simulation nodeid index */
MPI_Allreduce(buf, comm->ddindex2simnodeid, dd->nnodes, MPI_INT, MPI_SUM,
cr->mpi_comm_mysim);
-#endif
sfree(buf);
}
#endif
{
gmx_domdec_t *dd;
gmx_domdec_comm_t *comm;
- int i, rank;
+ int i;
gmx_bool bDiv[DIM];
- ivec periods;
#ifdef GMX_MPI
MPI_Comm comm_cart;
#endif
#ifdef GMX_MPI
if (comm->bCartesianPP_PME)
{
+ int rank;
+ ivec periods;
+
if (fplog)
{
fprintf(fplog, "Will use a Cartesian communicator for PP <-> PME: %d x %d x %d\n", comm->ntot[XX], comm->ntot[YY], comm->ntot[ZZ]);
}
MPI_Cart_create(cr->mpi_comm_mysim, DIM, comm->ntot, periods, reorder,
&comm_cart);
-
MPI_Comm_rank(comm_cart, &rank);
if (MASTERNODE(cr) && rank != 0)
{
for (i = 0; i < nc; i++)
{
dbl = 0;
- sscanf(size_string, "%lf%n", &dbl, &n);
+ sscanf(size_string, "%20lf%n", &dbl, &n);
if (dbl == 0)
{
gmx_fatal(FARGS, "Incorrect or not enough DD cell size entries for direction %s: '%s'", dir, size_string);
val = getenv(env_var);
if (val)
{
- if (sscanf(val, "%d", &nst) <= 0)
+ if (sscanf(val, "%20d", &nst) <= 0)
{
nst = 1;
}
{
d = dd->dim[di];
/* Check using the initial average cell size */
- r = min(r, ddbox->box_size[d]*ddbox->skew_fac[d]/dd->nc[d]);
+ r = std::min(r, ddbox->box_size[d]*ddbox->skew_fac[d]/dd->nc[d]);
}
return r;
const char *dlb_opt, gmx_bool bRecordLoad,
unsigned long Flags, t_inputrec *ir)
{
- gmx_domdec_t *dd;
int eDLB = -1;
char buf[STRLEN];
gmx_domdec_t *dd;
gmx_domdec_comm_t *comm;
int recload;
- int d, i, j;
real r_2b, r_mb, r_bonded = -1, r_bonded_limit = -1, limit, acs;
gmx_bool bC;
char buf[STRLEN];
+ const real tenPercentMargin = 1.1;
if (fplog)
{
* within nstlist steps. Since boundaries are allowed to displace by half
* a cell size, DD cells should be at least the size of the list buffer.
*/
- comm->cellsize_limit = max(comm->cellsize_limit,
- ir->rlistlong - max(ir->rvdw, ir->rcoulomb));
+ comm->cellsize_limit = std::max(comm->cellsize_limit,
+ ir->rlistlong - std::max(ir->rvdw, ir->rcoulomb));
if (comm->bInterCGBondeds)
{
}
else
{
- comm->cutoff = max(comm->cutoff, comm->cutoff_mbody);
+ comm->cutoff = std::max(comm->cutoff, comm->cutoff_mbody);
}
r_bonded_limit = comm->cutoff_mbody;
}
*/
if (Flags & MD_DDBONDCOMM)
{
- if (max(r_2b, r_mb) > comm->cutoff)
+ if (std::max(r_2b, r_mb) > comm->cutoff)
{
- r_bonded = max(r_2b, r_mb);
- r_bonded_limit = 1.1*r_bonded;
+ r_bonded = std::max(r_2b, r_mb);
+ r_bonded_limit = tenPercentMargin*r_bonded;
comm->bBondComm = TRUE;
}
else
{
r_bonded = r_mb;
- r_bonded_limit = min(1.1*r_bonded, comm->cutoff);
+ r_bonded_limit = std::min(tenPercentMargin*r_bonded, comm->cutoff);
}
/* We determine cutoff_mbody later */
}
/* No special bonded communication,
* simply increase the DD cut-off.
*/
- r_bonded_limit = 1.1*max(r_2b, r_mb);
+ r_bonded_limit = tenPercentMargin*std::max(r_2b, r_mb);
comm->cutoff_mbody = r_bonded_limit;
- comm->cutoff = max(comm->cutoff, comm->cutoff_mbody);
+ comm->cutoff = std::max(comm->cutoff, comm->cutoff_mbody);
}
}
if (fplog)
"Minimum cell size due to bonded interactions: %.3f nm\n",
r_bonded_limit);
}
- comm->cellsize_limit = max(comm->cellsize_limit, r_bonded_limit);
+ comm->cellsize_limit = std::max(comm->cellsize_limit, r_bonded_limit);
}
if (dd->bInterCGcons && rconstr <= 0)
"User supplied maximum distance required for P-LINCS: %.3f nm\n",
rconstr);
}
- comm->cellsize_limit = max(comm->cellsize_limit, rconstr);
+ comm->cellsize_limit = std::max(comm->cellsize_limit, rconstr);
comm->cgs_gl = gmx_mtop_global_cgs(mtop);
if (comm->eDLB != edlbNO)
{
/* Check if this does not limit the scaling */
- comm->cutoff_mbody = min(comm->cutoff_mbody, dlb_scale*acs);
+ comm->cutoff_mbody = std::min(comm->cutoff_mbody, dlb_scale*acs);
}
if (!comm->bBondComm)
{
/* Without bBondComm do not go beyond the n.b. cut-off */
- comm->cutoff_mbody = min(comm->cutoff_mbody, comm->cutoff);
+ comm->cutoff_mbody = std::min(comm->cutoff_mbody, comm->cutoff);
if (comm->cellsize_limit >= comm->cutoff)
{
/* We don't loose a lot of efficieny
}
}
/* Check if we did not end up below our original limit */
- comm->cutoff_mbody = max(comm->cutoff_mbody, r_bonded_limit);
+ comm->cutoff_mbody = std::max(comm->cutoff_mbody, r_bonded_limit);
if (comm->cutoff_mbody > comm->cellsize_limit)
{
cellsize_min = comm->cellsize_min[dd->dim[0]];
for (d = 1; d < dd->ndim; d++)
{
- cellsize_min = min(cellsize_min, comm->cellsize_min[dd->dim[d]]);
+ cellsize_min = std::min(cellsize_min, comm->cellsize_min[dd->dim[d]]);
}
if (cellsize_min < comm->cellsize_limit*1.05)
t_inputrec *ir, gmx_bool bBCheck, cginfo_mb_t *cginfo_mb)
{
gmx_domdec_comm_t *comm;
- gmx_bool bBondComm;
- int d;
dd_make_reverse_top(fplog, dd, mtop, vsite, ir, bBCheck);
limit = dd->comm->cellsize_min[XX];
for (d = 1; d < DIM; d++)
{
- limit = min(limit, dd->comm->cellsize_min[d]);
+ limit = std::min(limit, dd->comm->cellsize_min[d]);
}
}
{
fprintf(fplog, "%40s %-7s %6.3f nm\n",
"two-body bonded interactions", "(-rdd)",
- max(comm->cutoff, comm->cutoff_mbody));
+ std::max(comm->cutoff, comm->cutoff_mbody));
fprintf(fplog, "%40s %-7s %6.3f nm\n",
"multi-body bonded interactions", "(-rdd)",
- (comm->bBondComm || dd->bGridJump) ? comm->cutoff_mbody : min(comm->cutoff, limit));
+ (comm->bBondComm || dd->bGridJump) ? comm->cutoff_mbody : std::min(comm->cutoff, limit));
}
if (dd->vsite_comm)
{
/* Determine the maximum number of comm. pulses in one dimension */
- comm->cellsize_limit = max(comm->cellsize_limit, comm->cutoff_mbody);
+ comm->cellsize_limit = std::max(comm->cellsize_limit, comm->cutoff_mbody);
/* Determine the maximum required number of grid pulses */
if (comm->cellsize_limit >= comm->cutoff)
else
{
/* There is no cell size limit */
- npulse = max(dd->nc[XX]-1, max(dd->nc[YY]-1, dd->nc[ZZ]-1));
+ npulse = std::max(dd->nc[XX]-1, std::max(dd->nc[YY]-1, dd->nc[ZZ]-1));
}
if (!bNoCutOff && npulse > 1)
dim = dd->dim[d];
npulse_d = (int)(1 + dd->nc[dim]*comm->cutoff
/(ddbox->box_size[dim]*ddbox->skew_fac[dim]*dlb_scale));
- npulse_d_max = max(npulse_d_max, npulse_d);
+ npulse_d_max = std::max(npulse_d_max, npulse_d);
}
- npulse = min(npulse, npulse_d_max);
+ npulse = std::min(npulse, npulse_d_max);
}
/* This env var can override npulse */
comm->bVacDLBNoLimit = (ir->ePBC == epbcNONE);
for (d = 0; d < dd->ndim; d++)
{
- comm->cd[d].np_dlb = min(npulse, dd->nc[dd->dim[d]]-1);
+ comm->cd[d].np_dlb = std::min(npulse, dd->nc[dd->dim[d]]-1);
comm->cd[d].np_nalloc = comm->cd[d].np_dlb;
snew(comm->cd[d].ind, comm->cd[d].np_nalloc);
- comm->maxpulse = max(comm->maxpulse, comm->cd[d].np_dlb);
+ comm->maxpulse = std::max(comm->maxpulse, comm->cd[d].np_dlb);
if (comm->cd[d].np_dlb < dd->nc[dd->dim[d]]-1)
{
comm->bVacDLBNoLimit = FALSE;
/* cellsize_limit is set for LINCS in init_domain_decomposition */
if (!comm->bVacDLBNoLimit)
{
- comm->cellsize_limit = max(comm->cellsize_limit,
- comm->cutoff/comm->maxpulse);
+ comm->cellsize_limit = std::max(comm->cellsize_limit,
+ comm->cutoff/comm->maxpulse);
}
- comm->cellsize_limit = max(comm->cellsize_limit, comm->cutoff_mbody);
+ comm->cellsize_limit = std::max(comm->cellsize_limit, comm->cutoff_mbody);
/* Set the minimum cell size for each DD dimension */
for (d = 0; d < dd->ndim; d++)
{
}
if (comm->cutoff_mbody <= 0)
{
- comm->cutoff_mbody = min(comm->cutoff, comm->cellsize_limit);
+ comm->cutoff_mbody = std::min(comm->cutoff, comm->cellsize_limit);
}
if (comm->bDynLoadBal)
{
}
natoms_tot = comm->cgs_gl.index[comm->cgs_gl.nr];
- dd->ga2la = ga2la_init(natoms_tot, vol_frac*natoms_tot);
+ dd->ga2la = ga2la_init(natoms_tot, static_cast<int>(vol_frac*natoms_tot));
}
static gmx_bool test_dd_cutoff(t_commrec *cr,
c->c[1][1] = comm->cell_x0[dim1];
if (dd->bGridJump)
{
- c->c[1][1] = max(comm->cell_x0[dim1], comm->zone_d1[1].mch0);
+ c->c[1][1] = std::max(comm->cell_x0[dim1], comm->zone_d1[1].mch0);
if (bDistMB)
{
/* For the multi-body distance we need the maximum */
- c->bc[1] = max(comm->cell_x0[dim1], comm->zone_d1[1].p1_0);
+ c->bc[1] = std::max(comm->cell_x0[dim1], comm->zone_d1[1].p1_0);
}
}
/* Set the upper-right corner for rounding */
if (j >= 4)
{
c->c[2][j-4] =
- max(c->c[2][j-4],
- comm->zone_d2[zones->shift[i][dim0]][zones->shift[i][dim1]].mch0);
+ std::max(c->c[2][j-4],
+ comm->zone_d2[zones->shift[i][dim0]][zones->shift[i][dim1]].mch0);
}
}
}
{
for (j = 0; j < 2; j++)
{
- c->bc[2] = max(c->bc[2], comm->zone_d2[i][j].p1_0);
+ c->bc[2] = std::max(c->bc[2], comm->zone_d2[i][j].p1_0);
}
}
}
c->cr1[3] = comm->cell_x1[dim1];
if (dd->bGridJump)
{
- c->cr1[0] = max(comm->cell_x1[dim1], comm->zone_d1[1].mch1);
+ c->cr1[0] = std::max(comm->cell_x1[dim1], comm->zone_d1[1].mch1);
if (bDistMB)
{
/* For the multi-body distance we need the maximum */
- c->bcr1 = max(comm->cell_x1[dim1], comm->zone_d1[1].p1_1);
+ c->bcr1 = std::max(comm->cell_x1[dim1], comm->zone_d1[1].p1_1);
}
}
}
{
int dim_ind, dim, dim0, dim1, dim2, dimd, p, nat_tot;
int nzone, nzone_send, zone, zonei, cg0, cg1;
- int c, i, j, cg, cg_gl, nrcg;
+ int c, i, cg, cg_gl, nrcg;
int *zone_cg_range, pos_cg, *index_gl, *cgindex, *recv_i;
gmx_domdec_comm_t *comm;
gmx_domdec_zones_t *zones;
gmx_domdec_ind_t *ind;
cginfo_mb_t *cginfo_mb;
gmx_bool bBondComm, bDist2B, bDistMB, bDistBonded;
- real r_mb, r_comm2, r_scomm2, r_bcomm2, r_0, r_1, r2inc, inv_ncg;
+ real r_comm2, r_bcomm2;
dd_corners_t corners;
ivec tric_dist;
rvec *cg_cm, *normal, *v_d, *v_0 = NULL, *v_1 = NULL, *recv_vr;
for (dim_ind = 0; dim_ind < dd->ndim; dim_ind++)
{
- dim = dd->dim[dim_ind];
-
/* Check if we need to use triclinic distances */
tric_dist[dim_ind] = 0;
for (i = 0; i <= dim_ind; i++)
/* The rvec buffer is also required for atom buffers
* of size nrecv in dd_move_x and dd_move_f.
*/
- i = max(cd->ind[0].nrecv[nzone+1], ind->nrecv[nzone+1]);
+ i = std::max(cd->ind[0].nrecv[nzone+1], ind->nrecv[nzone+1]);
vec_rvec_check_alloc(&comm->vbuf2, i);
}
}
gmx_domdec_comm_t *comm;
gmx_domdec_zones_t *zones;
gmx_bool bDistMB;
- int z, zi, zj0, zj1, d, dim;
+ int z, zi, d, dim;
real rcs, rcmbs;
int i, j;
- real size_j, add_tric;
real vol;
comm = dd->comm;
* With multiple pulses this will lead
* to a larger zone then strictly necessary.
*/
- zones->size[z].x1[dim] = max(zones->size[z].x1[dim],
- zones->size[zi].x1[dim]+rcmbs);
+ zones->size[z].x1[dim] = std::max(zones->size[z].x1[dim],
+ zones->size[zi].x1[dim]+rcmbs);
}
}
}
{
if (zones->shift[z][dim] > 0)
{
- zones->size[z].x1[dim] = max(zones->size[z].x1[dim],
- zones->size[zi].x1[dim]+rcs);
+ zones->size[z].x1[dim] = std::max(zones->size[z].x1[dim],
+ zones->size[zi].x1[dim]+rcs);
}
}
}
{
for (i = 0; i < DIM; i++)
{
- corner_min[i] = min(corner_min[i], corner[i]);
- corner_max[i] = max(corner_max[i], corner[i]);
+ corner_min[i] = std::min(corner_min[i], corner[i]);
+ corner_max[i] = std::max(corner_max[i], corner[i]);
}
}
}
{
gmx_domdec_sort_t *sort;
gmx_cgsort_t *cgsort, *sort_i;
- int ncg_new, nsort2, nsort_new, i, *a, moved, *ibuf;
- int sort_last, sort_skip;
+ int ncg_new, nsort2, nsort_new, i, *a, moved;
sort = dd->comm->sort;
int ncg_home_old)
{
gmx_domdec_sort_t *sort;
- gmx_cgsort_t *cgsort, *sort_i;
+ gmx_cgsort_t *cgsort;
int *cgindex;
int ncg_new, i, *ibuf, cgsize;
rvec *vbuf;
t_block *cgs_gl;
gmx_int64_t step_pcoupl;
rvec cell_ns_x0, cell_ns_x1;
- int i, j, n, ncgindex_set, ncg_home_old = -1, ncg_moved, nat_f_novirsum;
+ int i, n, ncgindex_set, ncg_home_old = -1, ncg_moved, nat_f_novirsum;
gmx_bool bBoxChanged, bNStGlobalComm, bDoDLB, bCheckDLB, bTurnOnDLB, bLogLoad;
gmx_bool bRedist, bSortCG, bResortAll;
ivec ncells_old = {0, 0, 0}, ncells_new = {0, 0, 0}, np;
* so the extra communication cost is negligible.
*/
const int nddp_chk_dlb = 100;
-
bCheckDLB = (comm->n_load_collect == 0 ||
comm->n_load_have % nddp_chk_dlb == nddp_chk_dlb - 1);
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \defgroup module_domdec Spatial domain decomposition (for parallelization over MPI)
+ * \ingroup group_mdrun
+ *
+ * \brief Manages the decomposition of the simulation volume over MPI
+ * ranks to try to distribute work evenly with minimal communication
+ * overheads.
+ *
+ * \todo Get domdec stuff out of legacyheaders/types/commrec.h
+ *
+ * \author Berk Hess <hess@kth.se>
+ *
+ */
-#ifndef _domdec_h
-#define _domdec_h
+/*! \libinternal \file
+ *
+ * \brief This file declares functions for mdrun to call to manage the
+ * details of its domain decomposition.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \inlibraryapi
+ * \ingroup module_domdec
+ */
-#include "typedefs.h"
-#include "vsite.h"
-#include "genborn.h"
+#ifndef GMX_DOMDEC_DOMDEC_H
+#define GMX_DOMDEC_DOMDEC_H
+
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/constr.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/legacyheaders/types/hw_info.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
+#include "gromacs/legacyheaders/types/nrnb.h"
+#include "gromacs/legacyheaders/types/shellfc.h"
+#include "gromacs/legacyheaders/types/state.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#endif
-int ddglatnr(gmx_domdec_t *dd, int i);
-/* Returns the global topology atom number belonging to local atom index i.
- * This function is intended for writing ascii output
+/*! \brief Returns the global topology atom number belonging to local atom index i.
+ *
+ * This function is intended for writing ASCII output
* and returns atom numbers starting at 1.
* When dd=NULL returns i+1.
*/
+int ddglatnr(gmx_domdec_t *dd, int i);
+/*! \brief Return a block struct for the charge groups of the whole system */
t_block *dd_charge_groups_global(gmx_domdec_t *dd);
-/* Return a block struct for the charge groups of the whole system */
-
-gmx_bool dd_filled_nsgrid_home(gmx_domdec_t *dd);
-/* Is the ns grid already filled with the home particles? */
-void dd_store_state(gmx_domdec_t *dd, t_state *state);
-/* Store the global cg indices of the home cgs in state,
- * so it can be reset, even after a new DD partitioning.
+/*! \brief Store the global cg indices of the home cgs in state,
+ *
+ * This means it can be reset, even after a new DD partitioning.
*/
+void dd_store_state(gmx_domdec_t *dd, t_state *state);
+/*! \brief Returns a pointer to the gmx_domdec_zones_t struct */
gmx_domdec_zones_t *domdec_zones(gmx_domdec_t *dd);
+/*! \brief Sets the j-charge-group range for i-charge-group \p icg */
void dd_get_ns_ranges(gmx_domdec_t *dd, int icg,
int *jcg0, int *jcg1, ivec shift0, ivec shift1);
+/*! \brief Returns the atom range in the local state for atoms involved in virtual sites */
int dd_natoms_vsite(gmx_domdec_t *dd);
+/*! \brief Sets the atom range for atom in the local state for atoms received in constraints communication */
void dd_get_constraint_range(gmx_domdec_t *dd,
int *at_start, int *at_end);
-real dd_cutoff_mbody(gmx_domdec_t *dd);
-
-real dd_cutoff_twobody(gmx_domdec_t *dd);
-
+/*! \brief Get the number of PME nodes along x and y, can be called with dd=NULL */
void get_pme_nnodes(const gmx_domdec_t *dd,
int *npmenodes_x, int *npmenodes_y);
-/* Get the number of PME nodes along x and y, can be called with dd=NULL */
-
-gmx_bool gmx_pmeonlynode(t_commrec *cr, int nodeid);
-/* Return if nodeid in cr->mpi_comm_mysim is a PME-only node */
+/*! \brief Returns the set of DD nodes that communicate with pme node cr->nodeid */
void get_pme_ddnodes(t_commrec *cr, int pmenodeid,
int *nmy_ddnodes, int **my_ddnodes, int *node_peer);
-/* Returns the set of DD nodes that communicate with pme node cr->nodeid */
+/*! \brief Returns the maximum shift for coordinate communication in PME, dim x */
int dd_pme_maxshift_x(gmx_domdec_t *dd);
-/* Returns the maximum shift for coordinate communication in PME, dim x */
+/*! \brief Returns the maximum shift for coordinate communication in PME, dim y */
int dd_pme_maxshift_y(gmx_domdec_t *dd);
-/* Returns the maximum shift for coordinate communication in PME, dim y */
+/*! \brief Generates the MPI communicators for domain decomposition */
void make_dd_communicators(FILE *fplog, t_commrec *cr, int dd_node_order);
+/*! \brief Initialized the domain decomposition, chooses the DD grid and PME ranks */
gmx_domdec_t *
init_domain_decomposition(FILE *fplog,
t_commrec *cr,
gmx_ddbox_t *ddbox,
int *npme_x, int *npme_y);
+/*! \brief Initialize data structures for bonded interactions */
void dd_init_bondeds(FILE *fplog,
gmx_domdec_t *dd, gmx_mtop_t *mtop,
gmx_vsite_t *vsite,
t_inputrec *ir, gmx_bool bBCheck, cginfo_mb_t *cginfo_mb);
-/* Initialize data structures for bonded interactions */
+/*! \brief Returns if we need to do pbc for calculating bonded interactions */
gmx_bool dd_bonded_molpbc(gmx_domdec_t *dd, int ePBC);
-/* Returns if we need to do pbc for calculating bonded interactions */
+/*! \brief Set DD grid dimensions and limits
+ *
+ * Should be called after calling dd_init_bondeds.
+ */
void set_dd_parameters(FILE *fplog, gmx_domdec_t *dd, real dlb_scale,
t_inputrec *ir,
gmx_ddbox_t *ddbox);
-/* Set DD grid dimensions and limits,
- * should be called after calling dd_init_bondeds.
- */
-gmx_bool change_dd_cutoff(t_commrec *cr, t_state *state, t_inputrec *ir,
- real cutoff_req );
-/* Change the DD non-bonded communication cut-off.
+/*! \brief Change the DD non-bonded communication cut-off.
+ *
* This could fail when trying to increase the cut-off,
* then FALSE will be returned and the cut-off is not modified.
*/
+gmx_bool change_dd_cutoff(t_commrec *cr, t_state *state, t_inputrec *ir,
+ real cutoff_req );
-void change_dd_dlb_cutoff_limit(t_commrec *cr);
-/* Domain boundary changes due to the DD dynamic load balancing can limit
+/*! \brief Limit DLB to preserve the option of returning to the current cut-off.
+ *
+ * Domain boundary changes due to the DD dynamic load balancing can limit
* the cut-off distance that can be set in change_dd_cutoff. This function
* limits the DLB such that using the currently set cut-off should still be
* possible after subsequently setting a shorter cut-off with change_dd_cutoff.
*/
+void change_dd_dlb_cutoff_limit(t_commrec *cr);
+/*! \brief Return if the DLB lock is set */
gmx_bool dd_dlb_is_locked(const gmx_domdec_t *dd);
-/* Return if the DLB lock is set */
+/*! \brief Set a lock such that with DLB=auto DLB can (not) get turned on */
void dd_dlb_set_lock(gmx_domdec_t *dd, gmx_bool bValue);
-/* Set a lock such that with DLB=auto DLB can (not) get turned on */
-void dd_setup_dlb_resource_sharing(t_commrec *cr,
- const gmx_hw_info_t *hwinfo,
- const gmx_hw_opt_t *hw_opt);
-/* When domains (PP MPI ranks) share a GPU, the individual GPU wait times
+/*! \brief Set up communication for averaging GPU wait times over ranks
+ *
+ * When domains (PP MPI ranks) share a GPU, the individual GPU wait times
* are meaningless, as it depends on the order in which tasks on the same
* GPU finish. Therefore there wait times need to be averaged over the ranks
* sharing the same GPU. This function sets up the communication for that.
*/
+void dd_setup_dlb_resource_sharing(t_commrec *cr,
+ const gmx_hw_info_t *hwinfo,
+ const gmx_hw_opt_t *hw_opt);
+/*! \brief Sets up the DD communication setup */
void setup_dd_grid(FILE *fplog, gmx_domdec_t *dd);
+/*! \brief Collects local rvec arrays \p lv to \p v on the master rank */
void dd_collect_vec(gmx_domdec_t *dd,
t_state *state_local, rvec *lv, rvec *v);
+/*! \brief Collects the local state \p state_local to \p state on the master rank */
void dd_collect_state(gmx_domdec_t *dd,
t_state *state_local, t_state *state);
+/*! \brief Cycle counter indices used internally in the domain decomposition */
enum {
ddCyclStep, ddCyclPPduringPME, ddCyclF, ddCyclWaitGPU, ddCyclPME, ddCyclNr
};
+/*! \brief Add the wallcycle count to the DD counter */
void dd_cycles_add(gmx_domdec_t *dd, float cycles, int ddCycl);
-/* Add the wallcycle count to the DD counter */
+/*! \brief Start the force flop count */
void dd_force_flop_start(gmx_domdec_t *dd, t_nrnb *nrnb);
-/* Start the force flop count */
+/*! \brief Stop the force flop count */
void dd_force_flop_stop(gmx_domdec_t *dd, t_nrnb *nrnb);
-/* Stop the force flop count */
-float dd_pme_f_ratio(gmx_domdec_t *dd);
-/* Return the PME/PP force load ratio, or -1 if nothing was measured.
+/*! \brief Return the PME/PP force load ratio, or -1 if nothing was measured.
+ *
* Should only be called on the DD master node.
*/
+float dd_pme_f_ratio(gmx_domdec_t *dd);
+/*! \brief Communicate the coordinates to the neighboring cells and do pbc. */
void dd_move_x(gmx_domdec_t *dd, matrix box, rvec x[]);
-/* Communicate the coordinates to the neighboring cells and do pbc. */
-void dd_move_f(gmx_domdec_t *dd, rvec f[], rvec *fshift);
-/* Sum the forces over the neighboring cells.
+/*! \brief Sum the forces over the neighboring cells.
+ *
* When fshift!=NULL the shift forces are updated to obtain
* the correct virial from the single sum including f.
*/
+void dd_move_f(gmx_domdec_t *dd, rvec f[], rvec *fshift);
+/*! \brief Communicate a real for each atom to the neighboring cells. */
void dd_atom_spread_real(gmx_domdec_t *dd, real v[]);
-/* Communicate a real for each atom to the neighboring cells. */
+/*! \brief Sum the contributions to a real for each atom over the neighboring cells. */
void dd_atom_sum_real(gmx_domdec_t *dd, real v[]);
-/* Sum the contributions to a real for each atom over the neighboring cells. */
+/*! \brief Partition the system over the nodes.
+ *
+ * step is only used for printing error messages.
+ * If bMasterState==TRUE then state_global from the master node is used,
+ * else state_local is redistributed between the nodes.
+ * When f!=NULL, *f will be reallocated to the size of state_local.
+ */
void dd_partition_system(FILE *fplog,
gmx_int64_t step,
t_commrec *cr,
t_nrnb *nrnb,
gmx_wallcycle_t wcycle,
gmx_bool bVerbose);
-/* Partition the system over the nodes.
- * step is only used for printing error messages.
- * If bMasterState==TRUE then state_global from the master node is used,
- * else state_local is redistributed between the nodes.
- * When f!=NULL, *f will be reallocated to the size of state_local.
- */
+/*! \brief Reset all the statistics and counters for total run counting */
void reset_dd_statistics_counters(gmx_domdec_t *dd);
-/* Reset all the statistics and counters for total run counting */
+/*! \brief Print statistics for domain decomposition communication */
void print_dd_statistics(t_commrec *cr, t_inputrec *ir, FILE *fplog);
/* In domdec_con.c */
+/*! \brief Communicates the virtual site forces, reduces the shift forces when \p fshift != NULL */
void dd_move_f_vsites(gmx_domdec_t *dd, rvec *f, rvec *fshift);
+/*! \brief Clears the forces for virtual sites */
void dd_clear_f_vsites(gmx_domdec_t *dd, rvec *f);
+/*! \brief Move x0 and also x1 if x1!=NULL. bX1IsCoord tells if to do PBC on x1 */
void dd_move_x_constraints(gmx_domdec_t *dd, matrix box,
rvec *x0, rvec *x1, gmx_bool bX1IsCoord);
-/* Move x0 and also x1 if x1!=NULL. bX1IsCoord tells if to do PBC on x1 */
+/*! \brief Communicates the coordinates involved in virtual sites */
void dd_move_x_vsites(gmx_domdec_t *dd, matrix box, rvec *x);
+/*! \brief Returns the local atom count array for all constraints
+ *
+ * The local atom count for a constraint, possible values 2/1/0, is needed
+ * to avoid not/double-counting contributions linked to the Lagrange
+ * multiplier, such as the virial and free-energy derivatives.
+ */
int *dd_constraints_nlocalatoms(gmx_domdec_t *dd);
-void dd_clear_local_constraint_indices(gmx_domdec_t *dd);
-
-void dd_clear_local_vsite_indices(gmx_domdec_t *dd);
-
-int dd_make_local_vsites(gmx_domdec_t *dd, int at_start, t_ilist *lil);
-
-int dd_make_local_constraints(gmx_domdec_t *dd, int at_start,
- const gmx_mtop_t *mtop,
- const int *cginfo,
- gmx_constr_t constr, int nrec,
- t_ilist *il_local);
-
-void init_domdec_constraints(gmx_domdec_t *dd,
- gmx_mtop_t *mtop);
-
-void init_domdec_vsites(gmx_domdec_t *dd, int n_intercg_vsite);
-
-
/* In domdec_top.c */
+/*! \brief Print error output when interactions are missing */
void dd_print_missing_interactions(FILE *fplog, t_commrec *cr,
int local_count, gmx_mtop_t *top_global, t_state *state_local);
+/*! \brief Generate and store the reverse topology */
void dd_make_reverse_top(FILE *fplog,
gmx_domdec_t *dd, gmx_mtop_t *mtop,
gmx_vsite_t *vsite,
t_inputrec *ir, gmx_bool bBCheck);
+/*! \brief Store the local charge group index in \p lcgs */
void dd_make_local_cgs(gmx_domdec_t *dd, t_block *lcgs);
+/*! \brief Generate the local topology and virtual site data */
void dd_make_local_top(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
int npbcdim, matrix box,
rvec cellsize_min, ivec npulse,
gmx_vsite_t *vsite,
gmx_mtop_t *top, gmx_localtop_t *ltop);
+/*! \brief Sort ltop->ilist when we are doing free energy. */
void dd_sort_local_top(gmx_domdec_t *dd, t_mdatoms *mdatoms,
gmx_localtop_t *ltop);
-/* Sort ltop->ilist when we are doing free energy. */
+/*! \brief Construct local topology */
gmx_localtop_t *dd_init_local_top(gmx_mtop_t *top_global);
+/*! \brief Construct local state */
void dd_init_local_state(gmx_domdec_t *dd,
t_state *state_global, t_state *local_state);
+/*! \brief Generate a list of links between charge groups that are linked by bonded interactions */
t_blocka *make_charge_group_links(gmx_mtop_t *mtop, gmx_domdec_t *dd,
cginfo_mb_t *cginfo_mb);
+/*! \brief Calculate the maximum distance involved in 2-body and multi-body bonded interactions */
void dd_bonded_cg_distance(FILE *fplog, gmx_mtop_t *mtop,
t_inputrec *ir, rvec *x, matrix box,
gmx_bool bBCheck,
real *r_2b, real *r_mb);
+/*! \brief Dump a pdb file with the current DD home + communicated atoms.
+ *
+ * When natoms=-1, dump all known atoms.
+ */
void write_dd_pdb(const char *fn, gmx_int64_t step, const char *title,
gmx_mtop_t *mtop,
t_commrec *cr,
int natoms, rvec x[], matrix box);
-/* Dump a pdb file with the current DD home + communicated atoms.
- * When natoms=-1, dump all known atoms.
- */
/* In domdec_setup.c */
+/*! \brief Returns the volume fraction of the system that is communicated */
real comm_box_frac(ivec dd_nc, real cutoff, gmx_ddbox_t *ddbox);
-/* Returns the volume fraction of the system that is communicated */
+/*! \brief Determines the optimal DD cell setup dd->nc and possibly npmenodes
+ * for the system.
+ *
+ * On the master node returns the actual cellsize limit used.
+ */
real dd_choose_grid(FILE *fplog,
t_commrec *cr, gmx_domdec_t *dd, t_inputrec *ir,
gmx_mtop_t *mtop, matrix box, gmx_ddbox_t *ddbox,
gmx_bool bDynLoadBal, real dlb_scale,
real cellsize_limit, real cutoff_dd,
gmx_bool bInterCGBondeds);
-/* Determines the optimal DD cell setup dd->nc and possibly npmenodes
- * for the system.
- * On the master node returns the actual cellsize limit used.
- */
/* In domdec_box.c */
+/*! \brief Set the box and PBC data in \p ddbox */
void set_ddbox(gmx_domdec_t *dd, gmx_bool bMasterState, t_commrec *cr_sum,
t_inputrec *ir, matrix box,
gmx_bool bCalcUnboundedSize, t_block *cgs, rvec *x,
gmx_ddbox_t *ddbox);
+/*! \brief Set the box and PBC data in \p ddbox */
void set_ddbox_cr(t_commrec *cr, ivec *dd_nc,
t_inputrec *ir, matrix box, t_block *cgs, rvec *x,
gmx_ddbox_t *ddbox);
}
#endif
-#endif /* _domdec_h */
+#endif
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+/*! \internal \file
+ *
+ * \brief This file defines functions used by the domdec module
+ * for (bounding) box and pbc information generation.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_domdec
+ */
-#include "typedefs.h"
-#include "vec.h"
-#include "pbc.h"
-#include "types/commrec.h"
-#include "domdec.h"
-#include "domdec_network.h"
-#include "nsgrid.h"
-#include "network.h"
+#include "gmxpre.h"
-#include "gmx_fatal.h"
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/domdec_network.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nsgrid.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/fatalerror.h"
+/*! \brief Calculates the average and standard deviation in 3D of n charge groups */
static void calc_cgcm_av_stddev(t_block *cgs, int n, rvec *x, rvec av, rvec stddev,
t_commrec *cr_sum)
{
}
}
+/*! \brief Determines if dimensions require triclinic treatment and stores this info in ddbox */
static void set_tric_dir(ivec *dd_nc, gmx_ddbox_t *ddbox, matrix box)
{
int npbcdim, d, i, j;
}
}
+/*! \brief This function calculates and bounding box and pbc infor and populates ddbox */
static void low_set_ddbox(t_inputrec *ir, ivec *dd_nc, matrix box,
gmx_bool bCalcUnboundedSize, int ncg, t_block *cgs, rvec *x,
t_commrec *cr_sum,
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2006,2007,2008,2009,2010,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ *
+ * \brief This file implements functions for domdec to use
+ * while managing inter-atomic constraints.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_domdec
+ */
+
+#include "gmxpre.h"
+
+#include "domdec_constraints.h"
+
+#include <assert.h>
+
+#include <algorithm>
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/gmx_hash.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "domdec_specatomcomm.h"
+
+/*! \brief Struct used during constraint setup with domain decomposition */
+typedef struct gmx_domdec_constraints {
+ //! @cond Doxygen_Suppress
+ int *molb_con_offset; /**< Offset in the constraint array for each molblock */
+ int *molb_ncon_mol; /**< The number of constraints per molecule for each molblock */
+
+ int ncon; /**< The fully local and conneced constraints */
+ /* The global constraint number, only required for clearing gc_req */
+ int *con_gl; /**< Global constraint indices for local constraints */
+ int *con_nlocat; /**< Number of local atoms (2/1/0) for each constraint */
+ int con_nalloc; /**< Allocation size for \p con_gl and \p con_nlocat */
+
+ char *gc_req; /**< Boolean that tells if a global constraint index has been requested; note: size global #constraints */
+ gmx_hash_t ga2la; /**< Global to local communicated constraint atom only index */
+
+ /* Multi-threading stuff */
+ int nthread; /**< Number of threads used for DD constraint setup */
+ t_ilist *ils; /**< Constraint ilist working arrays, size \p nthread */
+ //! @endcond
+} gmx_domdec_constraints_t;
+
+void dd_move_x_constraints(gmx_domdec_t *dd, matrix box,
+ rvec *x0, rvec *x1, gmx_bool bX1IsCoord)
+{
+ if (dd->constraint_comm)
+ {
+ dd_move_x_specat(dd, dd->constraint_comm, box, x0, x1, bX1IsCoord);
+ }
+}
+
+int *dd_constraints_nlocalatoms(gmx_domdec_t *dd)
+{
+ if (dd->constraints)
+ {
+ return dd->constraints->con_nlocat;
+ }
+ else
+ {
+ return NULL;
+ }
+}
+
+void dd_clear_local_constraint_indices(gmx_domdec_t *dd)
+{
+ gmx_domdec_constraints_t *dc;
+ int i;
+
+ dc = dd->constraints;
+
+ for (i = 0; i < dc->ncon; i++)
+ {
+ dc->gc_req[dc->con_gl[i]] = 0;
+ }
+
+ if (dd->constraint_comm)
+ {
+ gmx_hash_clear_and_optimize(dc->ga2la);
+ }
+}
+
+void dd_clear_local_vsite_indices(gmx_domdec_t *dd)
+{
+ if (dd->vsite_comm)
+ {
+ gmx_hash_clear_and_optimize(dd->ga2la_vsite);
+ }
+}
+
+/*! \brief Walks over the constraints out from the local atoms into the non-local atoms and adds them to a list */
+static void walk_out(int con, int con_offset, int a, int offset, int nrec,
+ int ncon1, const t_iatom *ia1, const t_iatom *ia2,
+ const t_blocka *at2con,
+ const gmx_ga2la_t ga2la, gmx_bool bHomeConnect,
+ gmx_domdec_constraints_t *dc,
+ gmx_domdec_specat_comm_t *dcc,
+ t_ilist *il_local,
+ ind_req_t *ireq)
+{
+ int a1_gl, a2_gl, a_loc, i, coni, b;
+ const t_iatom *iap;
+
+ if (dc->gc_req[con_offset+con] == 0)
+ {
+ /* Add this non-home constraint to the list */
+ if (dc->ncon+1 > dc->con_nalloc)
+ {
+ dc->con_nalloc = over_alloc_large(dc->ncon+1);
+ srenew(dc->con_gl, dc->con_nalloc);
+ srenew(dc->con_nlocat, dc->con_nalloc);
+ }
+ dc->con_gl[dc->ncon] = con_offset + con;
+ dc->con_nlocat[dc->ncon] = (bHomeConnect ? 1 : 0);
+ dc->gc_req[con_offset+con] = 1;
+ if (il_local->nr + 3 > il_local->nalloc)
+ {
+ il_local->nalloc = over_alloc_dd(il_local->nr+3);
+ srenew(il_local->iatoms, il_local->nalloc);
+ }
+ iap = constr_iatomptr(ncon1, ia1, ia2, con);
+ il_local->iatoms[il_local->nr++] = iap[0];
+ a1_gl = offset + iap[1];
+ a2_gl = offset + iap[2];
+ /* The following indexing code can probably be optizimed */
+ if (ga2la_get_home(ga2la, a1_gl, &a_loc))
+ {
+ il_local->iatoms[il_local->nr++] = a_loc;
+ }
+ else
+ {
+ /* We set this index later */
+ il_local->iatoms[il_local->nr++] = -a1_gl - 1;
+ }
+ if (ga2la_get_home(ga2la, a2_gl, &a_loc))
+ {
+ il_local->iatoms[il_local->nr++] = a_loc;
+ }
+ else
+ {
+ /* We set this index later */
+ il_local->iatoms[il_local->nr++] = -a2_gl - 1;
+ }
+ dc->ncon++;
+ }
+ /* Check to not ask for the same atom more than once */
+ if (gmx_hash_get_minone(dc->ga2la, offset+a) == -1)
+ {
+ assert(dcc);
+ /* Add this non-home atom to the list */
+ if (ireq->n+1 > ireq->nalloc)
+ {
+ ireq->nalloc = over_alloc_large(ireq->n+1);
+ srenew(ireq->ind, ireq->nalloc);
+ }
+ ireq->ind[ireq->n++] = offset + a;
+ /* Temporarily mark with -2, we get the index later */
+ gmx_hash_set(dc->ga2la, offset+a, -2);
+ }
+
+ if (nrec > 0)
+ {
+ for (i = at2con->index[a]; i < at2con->index[a+1]; i++)
+ {
+ coni = at2con->a[i];
+ if (coni != con)
+ {
+ /* Walk further */
+ iap = constr_iatomptr(ncon1, ia1, ia2, coni);
+ if (a == iap[1])
+ {
+ b = iap[2];
+ }
+ else
+ {
+ b = iap[1];
+ }
+ if (!ga2la_get_home(ga2la, offset+b, &a_loc))
+ {
+ walk_out(coni, con_offset, b, offset, nrec-1,
+ ncon1, ia1, ia2, at2con,
+ ga2la, FALSE, dc, dcc, il_local, ireq);
+ }
+ }
+ }
+ }
+}
+
+/*! \brief Looks up SETTLE constraints for a range of charge-groups */
+static void atoms_to_settles(gmx_domdec_t *dd,
+ const gmx_mtop_t *mtop,
+ const int *cginfo,
+ const int **at2settle_mt,
+ int cg_start, int cg_end,
+ t_ilist *ils_local,
+ ind_req_t *ireq)
+{
+ gmx_ga2la_t ga2la;
+ gmx_mtop_atomlookup_t alook;
+ int settle;
+ int nral, sa;
+ int cg, a, a_gl, a_glsa, a_gls[3], a_locs[3];
+ int mb, molnr, a_mol, offset;
+ const gmx_molblock_t *molb;
+ const t_iatom *ia1;
+ gmx_bool a_home[3];
+ int nlocal;
+ gmx_bool bAssign;
+
+ ga2la = dd->ga2la;
+
+ alook = gmx_mtop_atomlookup_settle_init(mtop);
+
+ nral = NRAL(F_SETTLE);
+
+ for (cg = cg_start; cg < cg_end; cg++)
+ {
+ if (GET_CGINFO_SETTLE(cginfo[cg]))
+ {
+ for (a = dd->cgindex[cg]; a < dd->cgindex[cg+1]; a++)
+ {
+ a_gl = dd->gatindex[a];
+
+ gmx_mtop_atomnr_to_molblock_ind(alook, a_gl, &mb, &molnr, &a_mol);
+ molb = &mtop->molblock[mb];
+
+ settle = at2settle_mt[molb->type][a_mol];
+
+ if (settle >= 0)
+ {
+ offset = a_gl - a_mol;
+
+ ia1 = mtop->moltype[molb->type].ilist[F_SETTLE].iatoms;
+
+ bAssign = FALSE;
+ nlocal = 0;
+ for (sa = 0; sa < nral; sa++)
+ {
+ a_glsa = offset + ia1[settle*(1+nral)+1+sa];
+ a_gls[sa] = a_glsa;
+ a_home[sa] = ga2la_get_home(ga2la, a_glsa, &a_locs[sa]);
+ if (a_home[sa])
+ {
+ if (nlocal == 0 && a_gl == a_glsa)
+ {
+ bAssign = TRUE;
+ }
+ nlocal++;
+ }
+ }
+
+ if (bAssign)
+ {
+ if (ils_local->nr+1+nral > ils_local->nalloc)
+ {
+ ils_local->nalloc = over_alloc_dd(ils_local->nr+1+nral);
+ srenew(ils_local->iatoms, ils_local->nalloc);
+ }
+
+ ils_local->iatoms[ils_local->nr++] = ia1[settle*4];
+
+ for (sa = 0; sa < nral; sa++)
+ {
+ if (ga2la_get_home(ga2la, a_gls[sa], &a_locs[sa]))
+ {
+ ils_local->iatoms[ils_local->nr++] = a_locs[sa];
+ }
+ else
+ {
+ ils_local->iatoms[ils_local->nr++] = -a_gls[sa] - 1;
+ /* Add this non-home atom to the list */
+ if (ireq->n+1 > ireq->nalloc)
+ {
+ ireq->nalloc = over_alloc_large(ireq->n+1);
+ srenew(ireq->ind, ireq->nalloc);
+ }
+ ireq->ind[ireq->n++] = a_gls[sa];
+ /* A check on double atom requests is
+ * not required for settle.
+ */
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ gmx_mtop_atomlookup_destroy(alook);
+}
+
+/*! \brief Looks up constraint for the local atoms */
+static void atoms_to_constraints(gmx_domdec_t *dd,
+ const gmx_mtop_t *mtop,
+ const int *cginfo,
+ const t_blocka *at2con_mt, int nrec,
+ t_ilist *ilc_local,
+ ind_req_t *ireq)
+{
+ const t_blocka *at2con;
+ gmx_ga2la_t ga2la;
+ gmx_mtop_atomlookup_t alook;
+ int ncon1;
+ gmx_molblock_t *molb;
+ t_iatom *ia1, *ia2, *iap;
+ int nhome, cg, a, a_gl, a_mol, a_loc, b_lo, offset, mb, molnr, b_mol, i, con, con_offset;
+ gmx_domdec_constraints_t *dc;
+ gmx_domdec_specat_comm_t *dcc;
+
+ dc = dd->constraints;
+ dcc = dd->constraint_comm;
+
+ ga2la = dd->ga2la;
+
+ alook = gmx_mtop_atomlookup_init(mtop);
+
+ nhome = 0;
+ for (cg = 0; cg < dd->ncg_home; cg++)
+ {
+ if (GET_CGINFO_CONSTR(cginfo[cg]))
+ {
+ for (a = dd->cgindex[cg]; a < dd->cgindex[cg+1]; a++)
+ {
+ a_gl = dd->gatindex[a];
+
+ gmx_mtop_atomnr_to_molblock_ind(alook, a_gl, &mb, &molnr, &a_mol);
+ molb = &mtop->molblock[mb];
+
+ ncon1 = mtop->moltype[molb->type].ilist[F_CONSTR].nr/NRAL(F_SETTLE);
+
+ ia1 = mtop->moltype[molb->type].ilist[F_CONSTR].iatoms;
+ ia2 = mtop->moltype[molb->type].ilist[F_CONSTRNC].iatoms;
+
+ /* Calculate the global constraint number offset for the molecule.
+ * This is only required for the global index to make sure
+ * that we use each constraint only once.
+ */
+ con_offset =
+ dc->molb_con_offset[mb] + molnr*dc->molb_ncon_mol[mb];
+
+ /* The global atom number offset for this molecule */
+ offset = a_gl - a_mol;
+ at2con = &at2con_mt[molb->type];
+ for (i = at2con->index[a_mol]; i < at2con->index[a_mol+1]; i++)
+ {
+ con = at2con->a[i];
+ iap = constr_iatomptr(ncon1, ia1, ia2, con);
+ if (a_mol == iap[1])
+ {
+ b_mol = iap[2];
+ }
+ else
+ {
+ b_mol = iap[1];
+ }
+ if (ga2la_get_home(ga2la, offset+b_mol, &a_loc))
+ {
+ /* Add this fully home constraint at the first atom */
+ if (a_mol < b_mol)
+ {
+ if (dc->ncon+1 > dc->con_nalloc)
+ {
+ dc->con_nalloc = over_alloc_large(dc->ncon+1);
+ srenew(dc->con_gl, dc->con_nalloc);
+ srenew(dc->con_nlocat, dc->con_nalloc);
+ }
+ dc->con_gl[dc->ncon] = con_offset + con;
+ dc->con_nlocat[dc->ncon] = 2;
+ if (ilc_local->nr + 3 > ilc_local->nalloc)
+ {
+ ilc_local->nalloc = over_alloc_dd(ilc_local->nr + 3);
+ srenew(ilc_local->iatoms, ilc_local->nalloc);
+ }
+ b_lo = a_loc;
+ ilc_local->iatoms[ilc_local->nr++] = iap[0];
+ ilc_local->iatoms[ilc_local->nr++] = (a_gl == iap[1] ? a : b_lo);
+ ilc_local->iatoms[ilc_local->nr++] = (a_gl == iap[1] ? b_lo : a );
+ dc->ncon++;
+ nhome++;
+ }
+ }
+ else
+ {
+ /* We need the nrec constraints coupled to this constraint,
+ * so we need to walk out of the home cell by nrec+1 atoms,
+ * since already atom bg is not locally present.
+ * Therefore we call walk_out with nrec recursions to go
+ * after this first call.
+ */
+ walk_out(con, con_offset, b_mol, offset, nrec,
+ ncon1, ia1, ia2, at2con,
+ dd->ga2la, TRUE, dc, dcc, ilc_local, ireq);
+ }
+ }
+ }
+ }
+ }
+
+ gmx_mtop_atomlookup_destroy(alook);
+
+ if (debug)
+ {
+ fprintf(debug,
+ "Constraints: home %3d border %3d atoms: %3d\n",
+ nhome, dc->ncon-nhome,
+ dd->constraint_comm ? ireq->n : 0);
+ }
+}
+
+int dd_make_local_constraints(gmx_domdec_t *dd, int at_start,
+ const gmx_mtop_t *mtop,
+ const int *cginfo,
+ gmx_constr_t constr, int nrec,
+ t_ilist *il_local)
+{
+ gmx_domdec_constraints_t *dc;
+ t_ilist *ilc_local, *ils_local;
+ ind_req_t *ireq;
+ const t_blocka *at2con_mt;
+ const int **at2settle_mt;
+ gmx_hash_t ga2la_specat;
+ int at_end, i, j;
+ t_iatom *iap;
+
+ // This code should not be called unless this condition is true,
+ // because that's the only time init_domdec_constraints is
+ // called...
+ GMX_RELEASE_ASSERT(dd->bInterCGcons || dd->bInterCGsettles, "dd_make_local_constraints called when there are no local constraints");
+ // ... and init_domdec_constraints always sets
+ // dd->constraint_comm...
+ GMX_RELEASE_ASSERT(dd->constraint_comm, "Invalid use of dd_make_local_constraints before construction of constraint_comm");
+ // ... which static analysis needs to be reassured about, because
+ // otherwise, when dd->bInterCGsettles is
+ // true. dd->constraint_comm is unilaterally dereferenced before
+ // the call to atoms_to_settles.
+
+ dc = dd->constraints;
+
+ ilc_local = &il_local[F_CONSTR];
+ ils_local = &il_local[F_SETTLE];
+
+ dc->ncon = 0;
+ ilc_local->nr = 0;
+ if (dd->constraint_comm)
+ {
+ at2con_mt = atom2constraints_moltype(constr);
+ ireq = &dd->constraint_comm->ireq[0];
+ ireq->n = 0;
+ }
+ else
+ {
+ // Currently unreachable
+ at2con_mt = NULL;
+ ireq = NULL;
+ }
+
+ if (dd->bInterCGsettles)
+ {
+ at2settle_mt = atom2settle_moltype(constr);
+ ils_local->nr = 0;
+ }
+ else
+ {
+ /* Settle works inside charge groups, we assigned them already */
+ at2settle_mt = NULL;
+ }
+
+ if (at2settle_mt == NULL)
+ {
+ atoms_to_constraints(dd, mtop, cginfo, at2con_mt, nrec,
+ ilc_local, ireq);
+ }
+ else
+ {
+ int t0_set;
+ int thread;
+
+ /* Do the constraints, if present, on the first thread.
+ * Do the settles on all other threads.
+ */
+ t0_set = ((at2con_mt != NULL && dc->nthread > 1) ? 1 : 0);
+
+#pragma omp parallel for num_threads(dc->nthread) schedule(static)
+ for (thread = 0; thread < dc->nthread; thread++)
+ {
+ if (at2con_mt && thread == 0)
+ {
+ atoms_to_constraints(dd, mtop, cginfo, at2con_mt, nrec,
+ ilc_local, ireq);
+ }
+
+ if (thread >= t0_set)
+ {
+ int cg0, cg1;
+ t_ilist *ilst;
+ ind_req_t *ireqt;
+
+ /* Distribute the settle check+assignments over
+ * dc->nthread or dc->nthread-1 threads.
+ */
+ cg0 = (dd->ncg_home*(thread-t0_set ))/(dc->nthread-t0_set);
+ cg1 = (dd->ncg_home*(thread-t0_set+1))/(dc->nthread-t0_set);
+
+ if (thread == t0_set)
+ {
+ ilst = ils_local;
+ }
+ else
+ {
+ ilst = &dc->ils[thread];
+ }
+ ilst->nr = 0;
+
+ ireqt = &dd->constraint_comm->ireq[thread];
+ if (thread > 0)
+ {
+ ireqt->n = 0;
+ }
+
+ atoms_to_settles(dd, mtop, cginfo, at2settle_mt,
+ cg0, cg1,
+ ilst, ireqt);
+ }
+ }
+
+ /* Combine the generate settles and requested indices */
+ for (thread = 1; thread < dc->nthread; thread++)
+ {
+ t_ilist *ilst;
+ ind_req_t *ireqt;
+ int ia;
+
+ if (thread > t0_set)
+ {
+ ilst = &dc->ils[thread];
+ if (ils_local->nr + ilst->nr > ils_local->nalloc)
+ {
+ ils_local->nalloc = over_alloc_large(ils_local->nr + ilst->nr);
+ srenew(ils_local->iatoms, ils_local->nalloc);
+ }
+ for (ia = 0; ia < ilst->nr; ia++)
+ {
+ ils_local->iatoms[ils_local->nr+ia] = ilst->iatoms[ia];
+ }
+ ils_local->nr += ilst->nr;
+ }
+
+ ireqt = &dd->constraint_comm->ireq[thread];
+ if (ireq->n+ireqt->n > ireq->nalloc)
+ {
+ ireq->nalloc = over_alloc_large(ireq->n+ireqt->n);
+ srenew(ireq->ind, ireq->nalloc);
+ }
+ for (ia = 0; ia < ireqt->n; ia++)
+ {
+ ireq->ind[ireq->n+ia] = ireqt->ind[ia];
+ }
+ ireq->n += ireqt->n;
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "Settles: total %3d\n", ils_local->nr/4);
+ }
+ }
+
+ if (dd->constraint_comm)
+ {
+ int nral1;
+
+ at_end =
+ setup_specat_communication(dd, ireq, dd->constraint_comm,
+ dd->constraints->ga2la,
+ at_start, 2,
+ "constraint", " or lincs-order");
+
+ /* Fill in the missing indices */
+ ga2la_specat = dd->constraints->ga2la;
+
+ nral1 = 1 + NRAL(F_CONSTR);
+ for (i = 0; i < ilc_local->nr; i += nral1)
+ {
+ iap = ilc_local->iatoms + i;
+ for (j = 1; j < nral1; j++)
+ {
+ if (iap[j] < 0)
+ {
+ iap[j] = gmx_hash_get_minone(ga2la_specat, -iap[j]-1);
+ }
+ }
+ }
+
+ nral1 = 1 + NRAL(F_SETTLE);
+ for (i = 0; i < ils_local->nr; i += nral1)
+ {
+ iap = ils_local->iatoms + i;
+ for (j = 1; j < nral1; j++)
+ {
+ if (iap[j] < 0)
+ {
+ iap[j] = gmx_hash_get_minone(ga2la_specat, -iap[j]-1);
+ }
+ }
+ }
+ }
+ else
+ {
+ // Currently unreachable
+ at_end = at_start;
+ }
+
+ return at_end;
+}
+
+void init_domdec_constraints(gmx_domdec_t *dd,
+ gmx_mtop_t *mtop)
+{
+ gmx_domdec_constraints_t *dc;
+ gmx_molblock_t *molb;
+ int mb, ncon, c;
+
+ if (debug)
+ {
+ fprintf(debug, "Begin init_domdec_constraints\n");
+ }
+
+ snew(dd->constraints, 1);
+ dc = dd->constraints;
+
+ snew(dc->molb_con_offset, mtop->nmolblock);
+ snew(dc->molb_ncon_mol, mtop->nmolblock);
+
+ ncon = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molb = &mtop->molblock[mb];
+ dc->molb_con_offset[mb] = ncon;
+ dc->molb_ncon_mol[mb] =
+ mtop->moltype[molb->type].ilist[F_CONSTR].nr/3 +
+ mtop->moltype[molb->type].ilist[F_CONSTRNC].nr/3;
+ ncon += molb->nmol*dc->molb_ncon_mol[mb];
+ }
+
+ if (ncon > 0)
+ {
+ snew(dc->gc_req, ncon);
+ for (c = 0; c < ncon; c++)
+ {
+ dc->gc_req[c] = 0;
+ }
+ }
+
+ /* Use a hash table for the global to local index.
+ * The number of keys is a rough estimate, it will be optimized later.
+ */
+ dc->ga2la = gmx_hash_init(std::min(mtop->natoms/20,
+ mtop->natoms/(2*dd->nnodes)));
+
+ dc->nthread = gmx_omp_nthreads_get(emntDomdec);
+ snew(dc->ils, dc->nthread);
+
+ dd->constraint_comm = specat_comm_init(dc->nthread);
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2005,2006,2007,2008,2009,2010,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief This file declares functions for domdec to use
+ * while managing inter-atomic constraints.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_domdec
+ */
+
+#ifndef GMX_DOMDEC_DOMDEC_CONSTRAINTS_H
+#define GMX_DOMDEC_DOMDEC_CONSTRAINTS_H
+
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/constr.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/topology.h"
+
+/*! \brief Clears the local indices for the constraint communication setup */
+void dd_clear_local_constraint_indices(gmx_domdec_t *dd);
+
+/*! \brief Sets up communication and atom indices for all local+connected constraints */
+int dd_make_local_constraints(gmx_domdec_t *dd, int at_start,
+ const gmx_mtop_t *mtop,
+ const int *cginfo,
+ gmx_constr_t constr, int nrec,
+ t_ilist *il_local);
+
+/*! \brief Initializes the data structures for constraint communication */
+void init_domdec_constraints(gmx_domdec_t *dd,
+ gmx_mtop_t *mtop);
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 1991-2003 David van der Spoel, Erik Lindahl, University of Groningen.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-#ifndef _minvert_h
-#define _minvert_h
-
-#include "typedefs.h"
-
-/* A bunch of routines that works on matrices that run from 1 thru n
- * although they are allocated from 0 thru n
+/*! \internal \file
+ *
+ * \brief Declares implementation functions and types for the domain
+ * decomposition module.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_domdec
*/
+#ifndef GMX_DOMDEC_DOMDEC_INTERNAL_H
+#define GMX_DOMDEC_DOMDEC_INTERNAL_H
-extern void mat_mult(int n, real **A, real **B, real **C);
-
-extern real **mk_mat(int n);
-
-extern real **mk_mat2(int nrow, int ncol);
-
-extern void cp_mat(int n, real **src, real **dest);
+#include "gromacs/legacyheaders/types/commrec.h"
-extern void print_mat(FILE *fp, char *title, int n, real **a, int *indx);
-/* index may be NULL */
+/*! \brief Returns the DD cut-off distance for multi-body interactions */
+real dd_cutoff_multibody(const gmx_domdec_t *dd);
-extern void invert_mat(int n, real **A, real **Ainv);
+/*! \brief Returns the DD cut-off distance for two-body interactions */
+real dd_cutoff_twobody(const gmx_domdec_t *dd);
#endif
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+/*! \internal \file
+ *
+ * \brief This file defines functions for (mostly) the domdec module
+ * to use MPI functionality
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_domdec
+ */
+
+#include "gmxpre.h"
-#include <string.h>
-#include "types/commrec.h"
#include "domdec_network.h"
+#include "config.h"
+
+#include <string.h>
+
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/utility/gmxmpi.h"
+/*! \brief Returns the MPI rank of the domain decomposition master rank */
#define DDMASTERRANK(dd) (dd->masterrank)
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _domdec_network_h
-#define _domdec_network_h
-
-#include "typedefs.h"
+/*! \libinternal \file
+ *
+ * \brief This file declares functions for (mostly) the domdec module
+ * to use MPI functionality
+ *
+ * \todo Wrap the raw dd_bcast in md.cpp into a higher-level function
+ * in the domdec module, then this file can be module-internal.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \inlibraryapi
+ * \ingroup module_domdec
+ */
+#ifndef GMX_DOMDEC_DOMDEC_NETWORK_H
+#define GMX_DOMDEC_DOMDEC_NETWORK_H
-#ifdef __cplusplus
-extern "C" {
-#endif
+#include "gromacs/legacyheaders/typedefs.h"
+/* \brief */
enum {
dddirForward, dddirBackward
};
-/* Move integers in the comm. region one cell along the domain decomposition
- * in the dimension indexed by ddimind
- * forward (direction=dddirFoward) or backward (direction=dddirBackward).
+/*! \brief Move integers in the communication region one cell along
+ * the domain decomposition
+ *
+ * Moves in the dimension indexed by ddimind, either forward
+ * (direction=dddirFoward) or backward (direction=dddirBackward).
*/
void
dd_sendrecv_int(const gmx_domdec_t *dd,
int *buf_s, int n_s,
int *buf_r, int n_r);
-/* Move reals in the comm. region one cell along the domain decomposition
- * in the dimension indexed by ddimind
- * forward (direction=dddirFoward) or backward (direction=dddirBackward).
+/*! \brief Move reals in the comm. region one cell along the domain decomposition
+ *
+ * Moves in the dimension indexed by ddimind, either forward
+ * (direction=dddirFoward) or backward (direction=dddirBackward).
*/
void
dd_sendrecv_real(const gmx_domdec_t *dd,
real *buf_s, int n_s,
real *buf_r, int n_r);
-/* Move revc's in the comm. region one cell along the domain decomposition
- * in dimension indexed by ddimind
- * forward (direction=dddirFoward) or backward (direction=dddirBackward).
+/*! \brief Move revc's in the comm. region one cell along the domain decomposition
+ *
+ * Moves in dimension indexed by ddimind, either forward
+ * (direction=dddirFoward) or backward (direction=dddirBackward).
*/
void
dd_sendrecv_rvec(const gmx_domdec_t *dd,
rvec *buf_r, int n_r);
-/* Move revc's in the comm. region one cell along the domain decomposition
- * in dimension indexed by ddimind
- * simultaneously in the forward and backward directions.
+/*! \brief Move revc's in the comm. region one cell along the domain decomposition
+ *
+ * Moves in dimension indexed by ddimind, simultaneously in the forward
+ * and backward directions.
*/
void
dd_sendrecv2_rvec(const gmx_domdec_t *dd,
* The DD master node is the master for these operations.
*/
+/*! \brief Broadcasts \p nbytes from \p data on \p DDMASTERRANK to all PP ranks */
void
dd_bcast(gmx_domdec_t *dd, int nbytes, void *data);
-/* Copies src to dest on the master node and then broadcasts */
+/*! \brief Copies \p nbytes from \p src to \p dest on \p DDMASTERRANK
+ * and then broadcasts to \p dest on all PP ranks */
void
dd_bcastc(gmx_domdec_t *dd, int nbytes, void *src, void *dest);
+/*! \brief Scatters \p nbytes from \p src on \p DDMASTERRANK to all PP ranks, received in \p dest */
void
dd_scatter(gmx_domdec_t *dd, int nbytes, void *src, void *dest);
+/*! \brief Gathers \p nbytes from \p src on all PP ranks, received in \p dest on \p DDMASTERRANK */
void
dd_gather(gmx_domdec_t *dd, int nbytes, void *src, void *dest);
-/* If rcount==0, rbuf is allowed to be NULL */
+/*! \brief Scatters \p scounts bytes from \p src on \p DDMASTERRANK to all PP ranks, receiving \p rcount bytes in \p dest.
+ *
+ * See man MPI_Scatterv for details of how to construct scounts and disps.
+ * If rcount==0, rbuf is allowed to be NULL */
void
dd_scatterv(gmx_domdec_t *dd,
int *scounts, int *disps, void *sbuf,
int rcount, void *rbuf);
-/* If scount==0, sbuf is allowed to be NULL */
+/*! \brief Gathers \p rcount bytes from \p src on all PP ranks, received in \p scounts bytes in \p dest on \p DDMASTERRANK.
+ *
+ * See man MPI_Gatherv for details of how to construct scounts and disps.
+ *
+ * If scount==0, sbuf is allowed to be NULL */
void
dd_gatherv(gmx_domdec_t *dd,
int scount, void *sbuf,
int *rcounts, int *disps, void *rbuf);
-#ifdef __cplusplus
-}
#endif
-
-#endif /* _domdec_network_h */
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+/*! \internal \file
+ *
+ * \brief This file defines functions used by the domdec module
+ * in its initial setup phase.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_domdec
+ */
+
+#include "gmxpre.h"
-#include <stdio.h>
#include <assert.h>
-#include "domdec.h"
-#include "types/commrec.h"
-#include "network.h"
-#include "perf_est.h"
-#include "physics.h"
+#include <stdio.h>
+
+#include <cmath>
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/perf_est.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "names.h"
-/* Margin for setting up the DD grid */
+/*! \brief Margin for setting up the DD grid */
#define DD_GRID_MARGIN_PRES_SCALE 1.05
+/*! \brief Factorize \p n.
+ *
+ * \param[in] n Value to factorize
+ * \param[out] fac Pointer to array of factors (to be allocated in this function)
+ * \param[out] mfac Pointer to array of the number of times each factor repeats in the factorization (to be allocated in this function)
+ * \return The number of unique factors
+ */
static int factorize(int n, int **fac, int **mfac)
{
int d, ndiv;
return ndiv;
}
+/*! \brief Find largest divisor of \p n smaller than \p n*/
static gmx_bool largest_divisor(int n)
{
int ndiv, *div, *mdiv, ldiv;
return ldiv;
}
+/*! \brief Compute largest common divisor of \p n1 and \b n2 */
static int lcd(int n1, int n2)
{
int d, i;
return d;
}
-static gmx_bool fits_pme_ratio(int nnodes, int npme, float ratio)
+/*! \brief Returns TRUE when there are enough PME ranks for the ratio */
+static gmx_bool fits_pme_ratio(int nrank_tot, int nrank_pme, float ratio)
{
- return ((double)npme/(double)nnodes > 0.95*ratio);
+ return ((double)nrank_pme/(double)nrank_tot > 0.95*ratio);
}
-static gmx_bool fits_pp_pme_perf(int nnodes, int npme, float ratio)
+/*! \brief Returns TRUE when npme out of ntot ranks doing PME is expected to give reasonable performance */
+static gmx_bool fits_pp_pme_perf(int ntot, int npme, float ratio)
{
int ndiv, *div, *mdiv, ldiv;
int npp_root3, npme_root2;
- ndiv = factorize(nnodes-npme, &div, &mdiv);
+ ndiv = factorize(ntot - npme, &div, &mdiv);
ldiv = div[ndiv-1];
sfree(div);
sfree(mdiv);
- npp_root3 = (int)(pow(nnodes-npme, 1.0/3.0) + 0.5);
- npme_root2 = (int)(sqrt(npme) + 0.5);
+ npp_root3 = static_cast<int>(std::pow(ntot - npme, 1.0/3.0) + 0.5);
+ npme_root2 = static_cast<int>(std::sqrt(static_cast<double>(npme)) + 0.5);
/* The check below gives a reasonable division:
- * factor 5 allowed at 5 or more PP nodes,
- * factor 7 allowed at 49 or more PP nodes.
+ * factor 5 allowed at 5 or more PP ranks,
+ * factor 7 allowed at 49 or more PP ranks.
*/
if (ldiv > 3 + npp_root3)
{
return FALSE;
}
- /* Check if the number of PP and PME nodes have a reasonable sized
+ /* Check if the number of PP and PME ranks have a reasonable sized
* denominator in common, such that we can use 2D PME decomposition
* when required (which requires nx_pp == nx_pme).
* The factor of 2 allows for a maximum ratio of 2^2=4
* between nx_pme and ny_pme.
*/
- if (lcd(nnodes-npme, npme)*2 < npme_root2)
+ if (lcd(ntot - npme, npme)*2 < npme_root2)
{
return FALSE;
}
/* Does this division gives a reasonable PME load? */
- return fits_pme_ratio(nnodes, npme, ratio);
+ return fits_pme_ratio(ntot, npme, ratio);
}
+/*! \brief Make a guess for the number of PME ranks to use. */
static int guess_npme(FILE *fplog, gmx_mtop_t *mtop, t_inputrec *ir, matrix box,
- int nnodes)
+ int nrank_tot)
{
float ratio;
- int npme, nkx, nky;
- t_inputrec ir_try;
+ int npme;
ratio = pme_load_estimate(mtop, ir, box);
fprintf(fplog, "Guess for relative PME load: %.2f\n", ratio);
}
- /* We assume the optimal node ratio is close to the load ratio.
+ /* We assume the optimal rank ratio is close to the load ratio.
* The communication load is neglected,
* but (hopefully) this will balance out between PP and PME.
*/
- if (!fits_pme_ratio(nnodes, nnodes/2, ratio))
+ if (!fits_pme_ratio(nrank_tot, nrank_tot/2, ratio))
{
- /* We would need more than nnodes/2 PME only nodes,
+ /* We would need more than nrank_tot/2 PME only nodes,
* which is not possible. Since the PME load is very high,
- * we will not loose much performance when all nodes do PME.
+ * we will not loose much performance when all ranks do PME.
*/
return 0;
}
- /* First try to find npme as a factor of nnodes up to nnodes/3.
+ /* First try to find npme as a factor of nrank_tot up to nrank_tot/3.
* We start with a minimum PME node fraction of 1/16
* and avoid ratios which lead to large prime factors in nnodes-npme.
*/
- npme = (nnodes + 15)/16;
- while (npme <= nnodes/3)
+ npme = (nrank_tot + 15)/16;
+ while (npme <= nrank_tot/3)
{
- if (nnodes % npme == 0)
+ if (nrank_tot % npme == 0)
{
/* Note that fits_perf might change the PME grid,
* in the current implementation it does not.
*/
- if (fits_pp_pme_perf(nnodes, npme, ratio))
+ if (fits_pp_pme_perf(nrank_tot, npme, ratio))
{
break;
}
}
npme++;
}
- if (npme > nnodes/3)
+ if (npme > nrank_tot/3)
{
/* Try any possible number for npme */
npme = 1;
- while (npme <= nnodes/2)
+ while (npme <= nrank_tot/2)
{
/* Note that fits_perf may change the PME grid */
- if (fits_pp_pme_perf(nnodes, npme, ratio))
+ if (fits_pp_pme_perf(nrank_tot, npme, ratio))
{
break;
}
npme++;
}
}
- if (npme > nnodes/2)
+ if (npme > nrank_tot/2)
{
gmx_fatal(FARGS, "Could not find an appropriate number of separate PME ranks. i.e. >= %5f*#ranks (%d) and <= #ranks/2 (%d) and reasonable performance wise (grid_x=%d, grid_y=%d).\n"
"Use the -npme option of mdrun or change the number of ranks or the PME grid dimensions, see the manual for details.",
- ratio, (int)(0.95*ratio*nnodes+0.5), nnodes/2, ir->nkx, ir->nky);
+ ratio, (int)(0.95*ratio*nrank_tot + 0.5), nrank_tot/2, ir->nkx, ir->nky);
/* Keep the compiler happy */
npme = 0;
}
fprintf(fplog,
"Will use %d particle-particle and %d PME only ranks\n"
"This is a guess, check the performance at the end of the log file\n",
- nnodes-npme, npme);
+ nrank_tot - npme, npme);
}
fprintf(stderr, "\n"
"Will use %d particle-particle and %d PME only ranks\n"
"This is a guess, check the performance at the end of the log file\n",
- nnodes-npme, npme);
+ nrank_tot - npme, npme);
}
return npme;
}
+/*! \brief Return \p n divided by \p f rounded up to the next integer. */
static int div_up(int n, int f)
{
return (n + f - 1)/f;
real comm_box_frac(ivec dd_nc, real cutoff, gmx_ddbox_t *ddbox)
{
- int i, j, k, npp;
- rvec bt, nw;
+ int i, j, k;
+ rvec nw;
real comm_vol;
for (i = 0; i < DIM; i++)
{
- bt[i] = ddbox->box_size[i]*ddbox->skew_fac[i];
- nw[i] = dd_nc[i]*cutoff/bt[i];
+ real bt = ddbox->box_size[i]*ddbox->skew_fac[i];
+ nw[i] = dd_nc[i]*cutoff/bt;
}
- npp = 1;
comm_vol = 0;
for (i = 0; i < DIM; i++)
{
if (dd_nc[i] > 1)
{
- npp *= dd_nc[i];
comm_vol += nw[i];
for (j = i+1; j < DIM; j++)
{
return comm_vol;
}
+/*! \brief Return whether the DD inhomogeneous in the z direction */
static gmx_bool inhomogeneous_z(const t_inputrec *ir)
{
return ((EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD) &&
ir->ePBC == epbcXYZ && ir->ewald_geometry == eewg3DC);
}
-/* Avoid integer overflows */
+/*! \brief Estimate cost of PME FFT communication
+ *
+ * This only takes the communication into account and not imbalance
+ * in the calculation. But the imbalance in communication and calculation
+ * are similar and therefore these formulas also prefer load balance
+ * in the FFT and pme_solve calculation.
+ */
static float comm_pme_cost_vol(int npme, int a, int b, int c)
{
+ /* We use a float here, since an integer might overflow */
float comm_vol;
comm_vol = npme - 1;
comm_vol *= div_up(a, npme);
comm_vol *= div_up(b, npme);
comm_vol *= c;
+
return comm_vol;
}
+/*! \brief Estimate cost of communication for a possible domain decomposition. */
static float comm_cost_est(real limit, real cutoff,
matrix box, gmx_ddbox_t *ddbox,
int natoms, t_inputrec *ir,
int npme_tot, ivec nc)
{
ivec npme = {1, 1, 1};
- int i, j, k, nk, overlap;
+ int i, j, nk, overlap;
rvec bt;
float comm_vol, comm_vol_xf, comm_pme, cost_pbcdx;
/* This is the cost of a pbc_dx call relative to the cost
}
}
- /* PME FFT communication volume.
- * This only takes the communication into account and not imbalance
- * in the calculation. But the imbalance in communication and calculation
- * are similar and therefore these formulas also prefer load balance
- * in the FFT and pme_solve calculation.
- */
comm_pme += comm_pme_cost_vol(npme[YY], ir->nky, ir->nkz, ir->nkx);
comm_pme += comm_pme_cost_vol(npme[XX], ir->nkx, ir->nky, ir->nkz);
return 3*natoms*(comm_vol + cost_pbcdx) + comm_pme;
}
+/*! \brief Assign penalty factors to possible domain decompositions, based on the estimated communication costs. */
static void assign_factors(gmx_domdec_t *dd,
real limit, real cutoff,
matrix box, gmx_ddbox_t *ddbox,
float pbcdxr, int npme,
int ndiv, int *div, int *mdiv, ivec ir_try, ivec opt)
{
- int x, y, z, i;
+ int x, y, i;
float ce;
if (ndiv == 0)
}
}
+/*! \brief Determine the optimal distribution of DD cells for the simulation system and number of MPI ranks */
static real optimize_ncells(FILE *fplog,
int nnodes_tot, int npme_only,
gmx_bool bDynLoadBal, real dlb_scale,
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2006,2007,2008,2009,2010,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ *
+ * \brief This file implements functions for domdec to use
+ * while managing inter-atomic constraints.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_domdec
+ */
+
+#include "gmxpre.h"
+
+#include "domdec_specatomcomm.h"
+
+#include <assert.h>
+
+#include <algorithm>
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/domdec_network.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/gmx_hash.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
+
+void dd_move_f_specat(gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac,
+ rvec *f, rvec *fshift)
+{
+ gmx_specatsend_t *spas;
+ rvec *vbuf;
+ int n, n0, n1, d, dim, dir, i;
+ ivec vis;
+ int is;
+ gmx_bool bPBC, bScrew;
+
+ n = spac->at_end;
+ for (d = dd->ndim-1; d >= 0; d--)
+ {
+ dim = dd->dim[d];
+ if (dd->nc[dim] > 2)
+ {
+ /* Pulse the grid forward and backward */
+ spas = spac->spas[d];
+ n0 = spas[0].nrecv;
+ n1 = spas[1].nrecv;
+ n -= n1 + n0;
+ vbuf = spac->vbuf;
+ /* Send and receive the coordinates */
+ dd_sendrecv2_rvec(dd, d,
+ f+n+n1, n0, vbuf, spas[0].nsend,
+ f+n, n1, vbuf+spas[0].nsend, spas[1].nsend);
+ for (dir = 0; dir < 2; dir++)
+ {
+ bPBC = ((dir == 0 && dd->ci[dim] == 0) ||
+ (dir == 1 && dd->ci[dim] == dd->nc[dim]-1));
+ bScrew = (bPBC && dd->bScrewPBC && dim == XX);
+
+ spas = &spac->spas[d][dir];
+ /* Sum the buffer into the required forces */
+ if (!bPBC || (!bScrew && fshift == NULL))
+ {
+ for (i = 0; i < spas->nsend; i++)
+ {
+ rvec_inc(f[spas->a[i]], *vbuf);
+ vbuf++;
+ }
+ }
+ else
+ {
+ clear_ivec(vis);
+ vis[dim] = (dir == 0 ? 1 : -1);
+ is = IVEC2IS(vis);
+ if (!bScrew)
+ {
+ /* Sum and add to shift forces */
+ for (i = 0; i < spas->nsend; i++)
+ {
+ rvec_inc(f[spas->a[i]], *vbuf);
+ rvec_inc(fshift[is], *vbuf);
+ vbuf++;
+ }
+ }
+ else
+ {
+ /* Rotate the forces */
+ for (i = 0; i < spas->nsend; i++)
+ {
+ f[spas->a[i]][XX] += (*vbuf)[XX];
+ f[spas->a[i]][YY] -= (*vbuf)[YY];
+ f[spas->a[i]][ZZ] -= (*vbuf)[ZZ];
+ if (fshift)
+ {
+ rvec_inc(fshift[is], *vbuf);
+ }
+ vbuf++;
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ /* Two cells, so we only need to communicate one way */
+ spas = &spac->spas[d][0];
+ n -= spas->nrecv;
+ /* Send and receive the coordinates */
+ dd_sendrecv_rvec(dd, d, dddirForward,
+ f+n, spas->nrecv, spac->vbuf, spas->nsend);
+ /* Sum the buffer into the required forces */
+ if (dd->bScrewPBC && dim == XX &&
+ (dd->ci[dim] == 0 ||
+ dd->ci[dim] == dd->nc[dim]-1))
+ {
+ for (i = 0; i < spas->nsend; i++)
+ {
+ /* Rotate the force */
+ f[spas->a[i]][XX] += spac->vbuf[i][XX];
+ f[spas->a[i]][YY] -= spac->vbuf[i][YY];
+ f[spas->a[i]][ZZ] -= spac->vbuf[i][ZZ];
+ }
+ }
+ else
+ {
+ for (i = 0; i < spas->nsend; i++)
+ {
+ rvec_inc(f[spas->a[i]], spac->vbuf[i]);
+ }
+ }
+ }
+ }
+}
+
+void dd_move_x_specat(gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac,
+ matrix box,
+ rvec *x0,
+ rvec *x1, gmx_bool bX1IsCoord)
+{
+ gmx_specatsend_t *spas;
+ rvec *x, *vbuf, *rbuf;
+ int nvec, v, n, nn, ns0, ns1, nr0, nr1, nr, d, dim, dir, i;
+ gmx_bool bPBC, bScrew = FALSE;
+ rvec shift = {0, 0, 0};
+
+ nvec = 1;
+ if (x1 != NULL)
+ {
+ nvec++;
+ }
+
+ n = spac->at_start;
+ for (d = 0; d < dd->ndim; d++)
+ {
+ dim = dd->dim[d];
+ if (dd->nc[dim] > 2)
+ {
+ /* Pulse the grid forward and backward */
+ vbuf = spac->vbuf;
+ for (dir = 0; dir < 2; dir++)
+ {
+ if (dir == 0 && dd->ci[dim] == 0)
+ {
+ bPBC = TRUE;
+ bScrew = (dd->bScrewPBC && dim == XX);
+ copy_rvec(box[dim], shift);
+ }
+ else if (dir == 1 && dd->ci[dim] == dd->nc[dim]-1)
+ {
+ bPBC = TRUE;
+ bScrew = (dd->bScrewPBC && dim == XX);
+ for (i = 0; i < DIM; i++)
+ {
+ shift[i] = -box[dim][i];
+ }
+ }
+ else
+ {
+ bPBC = FALSE;
+ bScrew = FALSE;
+ }
+ spas = &spac->spas[d][dir];
+ for (v = 0; v < nvec; v++)
+ {
+ x = (v == 0 ? x0 : x1);
+ /* Copy the required coordinates to the send buffer */
+ if (!bPBC || (v == 1 && !bX1IsCoord))
+ {
+ /* Only copy */
+ for (i = 0; i < spas->nsend; i++)
+ {
+ copy_rvec(x[spas->a[i]], *vbuf);
+ vbuf++;
+ }
+ }
+ else if (!bScrew)
+ {
+ /* Shift coordinates */
+ for (i = 0; i < spas->nsend; i++)
+ {
+ rvec_add(x[spas->a[i]], shift, *vbuf);
+ vbuf++;
+ }
+ }
+ else
+ {
+ /* Shift and rotate coordinates */
+ for (i = 0; i < spas->nsend; i++)
+ {
+ (*vbuf)[XX] = x[spas->a[i]][XX] + shift[XX];
+ (*vbuf)[YY] = box[YY][YY] - x[spas->a[i]][YY] + shift[YY];
+ (*vbuf)[ZZ] = box[ZZ][ZZ] - x[spas->a[i]][ZZ] + shift[ZZ];
+ vbuf++;
+ }
+ }
+ }
+ }
+ /* Send and receive the coordinates */
+ spas = spac->spas[d];
+ ns0 = spas[0].nsend;
+ nr0 = spas[0].nrecv;
+ ns1 = spas[1].nsend;
+ nr1 = spas[1].nrecv;
+ if (nvec == 1)
+ {
+ dd_sendrecv2_rvec(dd, d,
+ spac->vbuf+ns0, ns1, x0+n, nr1,
+ spac->vbuf, ns0, x0+n+nr1, nr0);
+ }
+ else
+ {
+ /* Communicate both vectors in one buffer */
+ rbuf = spac->vbuf2;
+ dd_sendrecv2_rvec(dd, d,
+ spac->vbuf+2*ns0, 2*ns1, rbuf, 2*nr1,
+ spac->vbuf, 2*ns0, rbuf+2*nr1, 2*nr0);
+ /* Split the buffer into the two vectors */
+ nn = n;
+ for (dir = 1; dir >= 0; dir--)
+ {
+ nr = spas[dir].nrecv;
+ for (v = 0; v < 2; v++)
+ {
+ x = (v == 0 ? x0 : x1);
+ for (i = 0; i < nr; i++)
+ {
+ copy_rvec(*rbuf, x[nn+i]);
+ rbuf++;
+ }
+ }
+ nn += nr;
+ }
+ }
+ n += nr0 + nr1;
+ }
+ else
+ {
+ spas = &spac->spas[d][0];
+ /* Copy the required coordinates to the send buffer */
+ vbuf = spac->vbuf;
+ for (v = 0; v < nvec; v++)
+ {
+ x = (v == 0 ? x0 : x1);
+ if (dd->bScrewPBC && dim == XX &&
+ (dd->ci[XX] == 0 || dd->ci[XX] == dd->nc[XX]-1))
+ {
+ /* Here we only perform the rotation, the rest of the pbc
+ * is handled in the constraint or viste routines.
+ */
+ for (i = 0; i < spas->nsend; i++)
+ {
+ (*vbuf)[XX] = x[spas->a[i]][XX];
+ (*vbuf)[YY] = box[YY][YY] - x[spas->a[i]][YY];
+ (*vbuf)[ZZ] = box[ZZ][ZZ] - x[spas->a[i]][ZZ];
+ vbuf++;
+ }
+ }
+ else
+ {
+ for (i = 0; i < spas->nsend; i++)
+ {
+ copy_rvec(x[spas->a[i]], *vbuf);
+ vbuf++;
+ }
+ }
+ }
+ /* Send and receive the coordinates */
+ if (nvec == 1)
+ {
+ dd_sendrecv_rvec(dd, d, dddirBackward,
+ spac->vbuf, spas->nsend, x0+n, spas->nrecv);
+ }
+ else
+ {
+ /* Communicate both vectors in one buffer */
+ rbuf = spac->vbuf2;
+ dd_sendrecv_rvec(dd, d, dddirBackward,
+ spac->vbuf, 2*spas->nsend, rbuf, 2*spas->nrecv);
+ /* Split the buffer into the two vectors */
+ nr = spas[0].nrecv;
+ for (v = 0; v < 2; v++)
+ {
+ x = (v == 0 ? x0 : x1);
+ for (i = 0; i < nr; i++)
+ {
+ copy_rvec(*rbuf, x[n+i]);
+ rbuf++;
+ }
+ }
+ }
+ n += spas->nrecv;
+ }
+ }
+}
+
+int setup_specat_communication(gmx_domdec_t *dd,
+ ind_req_t *ireq,
+ gmx_domdec_specat_comm_t *spac,
+ gmx_hash_t ga2la_specat,
+ int at_start,
+ int vbuf_fac,
+ const char *specat_type,
+ const char *add_err)
+{
+ int nsend[2], nlast, nsend_zero[2] = {0, 0}, *nsend_ptr;
+ int d, dim, ndir, dir, nr, ns, i, nrecv_local, n0, start, indr, ind, buf[2];
+ int nat_tot_specat, nat_tot_prev, nalloc_old;
+ gmx_bool bPBC;
+ gmx_specatsend_t *spas;
+
+ if (debug)
+ {
+ fprintf(debug, "Begin setup_specat_communication for %s\n", specat_type);
+ }
+
+ /* nsend[0]: the number of atoms requested by this node only,
+ * we communicate this for more efficients checks
+ * nsend[1]: the total number of requested atoms
+ */
+ nsend[0] = ireq->n;
+ nsend[1] = nsend[0];
+ nlast = nsend[1];
+ for (d = dd->ndim-1; d >= 0; d--)
+ {
+ /* Pulse the grid forward and backward */
+ dim = dd->dim[d];
+ bPBC = (dim < dd->npbcdim);
+ if (dd->nc[dim] == 2)
+ {
+ /* Only 2 cells, so we only need to communicate once */
+ ndir = 1;
+ }
+ else
+ {
+ ndir = 2;
+ }
+ for (dir = 0; dir < ndir; dir++)
+ {
+ if (!bPBC &&
+ dd->nc[dim] > 2 &&
+ ((dir == 0 && dd->ci[dim] == dd->nc[dim] - 1) ||
+ (dir == 1 && dd->ci[dim] == 0)))
+ {
+ /* No pbc: the fist/last cell should not request atoms */
+ nsend_ptr = nsend_zero;
+ }
+ else
+ {
+ nsend_ptr = nsend;
+ }
+ /* Communicate the number of indices */
+ dd_sendrecv_int(dd, d, dir == 0 ? dddirForward : dddirBackward,
+ nsend_ptr, 2, spac->nreq[d][dir], 2);
+ nr = spac->nreq[d][dir][1];
+ if (nlast+nr > ireq->nalloc)
+ {
+ ireq->nalloc = over_alloc_dd(nlast+nr);
+ srenew(ireq->ind, ireq->nalloc);
+ }
+ /* Communicate the indices */
+ dd_sendrecv_int(dd, d, dir == 0 ? dddirForward : dddirBackward,
+ ireq->ind, nsend_ptr[1], ireq->ind+nlast, nr);
+ nlast += nr;
+ }
+ nsend[1] = nlast;
+ }
+ if (debug)
+ {
+ fprintf(debug, "Communicated the counts\n");
+ }
+
+ /* Search for the requested atoms and communicate the indices we have */
+ nat_tot_specat = at_start;
+ nrecv_local = 0;
+ for (d = 0; d < dd->ndim; d++)
+ {
+ /* Pulse the grid forward and backward */
+ if (dd->dim[d] >= dd->npbcdim || dd->nc[dd->dim[d]] > 2)
+ {
+ ndir = 2;
+ }
+ else
+ {
+ ndir = 1;
+ }
+ nat_tot_prev = nat_tot_specat;
+ for (dir = ndir-1; dir >= 0; dir--)
+ {
+ if (nat_tot_specat > spac->bSendAtom_nalloc)
+ {
+ nalloc_old = spac->bSendAtom_nalloc;
+ spac->bSendAtom_nalloc = over_alloc_dd(nat_tot_specat);
+ srenew(spac->bSendAtom, spac->bSendAtom_nalloc);
+ for (i = nalloc_old; i < spac->bSendAtom_nalloc; i++)
+ {
+ spac->bSendAtom[i] = FALSE;
+ }
+ }
+ spas = &spac->spas[d][dir];
+ n0 = spac->nreq[d][dir][0];
+ nr = spac->nreq[d][dir][1];
+ if (debug)
+ {
+ fprintf(debug, "dim=%d, dir=%d, searching for %d atoms\n",
+ d, dir, nr);
+ }
+ start = nlast - nr;
+ spas->nsend = 0;
+ nsend[0] = 0;
+ for (i = 0; i < nr; i++)
+ {
+ indr = ireq->ind[start+i];
+ ind = -1;
+ /* Check if this is a home atom and if so ind will be set */
+ if (!ga2la_get_home(dd->ga2la, indr, &ind))
+ {
+ /* Search in the communicated atoms */
+ ind = gmx_hash_get_minone(ga2la_specat, indr);
+ }
+ if (ind >= 0)
+ {
+ if (i < n0 || !spac->bSendAtom[ind])
+ {
+ if (spas->nsend+1 > spas->a_nalloc)
+ {
+ spas->a_nalloc = over_alloc_large(spas->nsend+1);
+ srenew(spas->a, spas->a_nalloc);
+ }
+ /* Store the local index so we know which coordinates
+ * to send out later.
+ */
+ spas->a[spas->nsend] = ind;
+ spac->bSendAtom[ind] = TRUE;
+ if (spas->nsend+1 > spac->ibuf_nalloc)
+ {
+ spac->ibuf_nalloc = over_alloc_large(spas->nsend+1);
+ srenew(spac->ibuf, spac->ibuf_nalloc);
+ }
+ /* Store the global index so we can send it now */
+ spac->ibuf[spas->nsend] = indr;
+ if (i < n0)
+ {
+ nsend[0]++;
+ }
+ spas->nsend++;
+ }
+ }
+ }
+ nlast = start;
+ /* Clear the local flags */
+ for (i = 0; i < spas->nsend; i++)
+ {
+ spac->bSendAtom[spas->a[i]] = FALSE;
+ }
+ /* Send and receive the number of indices to communicate */
+ nsend[1] = spas->nsend;
+ dd_sendrecv_int(dd, d, dir == 0 ? dddirBackward : dddirForward,
+ nsend, 2, buf, 2);
+ if (debug)
+ {
+ fprintf(debug, "Send to rank %d, %d (%d) indices, "
+ "receive from rank %d, %d (%d) indices\n",
+ dd->neighbor[d][1-dir], nsend[1], nsend[0],
+ dd->neighbor[d][dir], buf[1], buf[0]);
+ if (gmx_debug_at)
+ {
+ for (i = 0; i < spas->nsend; i++)
+ {
+ fprintf(debug, " %d", spac->ibuf[i]+1);
+ }
+ fprintf(debug, "\n");
+ }
+ }
+ nrecv_local += buf[0];
+ spas->nrecv = buf[1];
+ if (nat_tot_specat + spas->nrecv > dd->gatindex_nalloc)
+ {
+ dd->gatindex_nalloc =
+ over_alloc_dd(nat_tot_specat + spas->nrecv);
+ srenew(dd->gatindex, dd->gatindex_nalloc);
+ }
+ /* Send and receive the indices */
+ dd_sendrecv_int(dd, d, dir == 0 ? dddirBackward : dddirForward,
+ spac->ibuf, spas->nsend,
+ dd->gatindex+nat_tot_specat, spas->nrecv);
+ nat_tot_specat += spas->nrecv;
+ }
+
+ /* Allocate the x/f communication buffers */
+ ns = spac->spas[d][0].nsend;
+ nr = spac->spas[d][0].nrecv;
+ if (ndir == 2)
+ {
+ ns += spac->spas[d][1].nsend;
+ nr += spac->spas[d][1].nrecv;
+ }
+ if (vbuf_fac*ns > spac->vbuf_nalloc)
+ {
+ spac->vbuf_nalloc = over_alloc_dd(vbuf_fac*ns);
+ srenew(spac->vbuf, spac->vbuf_nalloc);
+ }
+ if (vbuf_fac == 2 && vbuf_fac*nr > spac->vbuf2_nalloc)
+ {
+ spac->vbuf2_nalloc = over_alloc_dd(vbuf_fac*nr);
+ srenew(spac->vbuf2, spac->vbuf2_nalloc);
+ }
+
+ /* Make a global to local index for the communication atoms */
+ for (i = nat_tot_prev; i < nat_tot_specat; i++)
+ {
+ gmx_hash_change_or_set(ga2la_specat, dd->gatindex[i], i);
+ }
+ }
+
+ /* Check that in the end we got the number of atoms we asked for */
+ if (nrecv_local != ireq->n)
+ {
+ if (debug)
+ {
+ fprintf(debug, "Requested %d, received %d (tot recv %d)\n",
+ ireq->n, nrecv_local, nat_tot_specat-at_start);
+ if (gmx_debug_at)
+ {
+ for (i = 0; i < ireq->n; i++)
+ {
+ ind = gmx_hash_get_minone(ga2la_specat, ireq->ind[i]);
+ fprintf(debug, " %s%d",
+ (ind >= 0) ? "" : "!",
+ ireq->ind[i]+1);
+ }
+ fprintf(debug, "\n");
+ }
+ }
+ fprintf(stderr, "\nDD cell %d %d %d: Neighboring cells do not have atoms:",
+ dd->ci[XX], dd->ci[YY], dd->ci[ZZ]);
+ for (i = 0; i < ireq->n; i++)
+ {
+ if (gmx_hash_get_minone(ga2la_specat, ireq->ind[i]) < 0)
+ {
+ fprintf(stderr, " %d", ireq->ind[i]+1);
+ }
+ }
+ fprintf(stderr, "\n");
+ gmx_fatal(FARGS, "DD cell %d %d %d could only obtain %d of the %d atoms that are connected via %ss from the neighboring cells. This probably means your %s lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells%s%s.",
+ dd->ci[XX], dd->ci[YY], dd->ci[ZZ],
+ nrecv_local, ireq->n, specat_type,
+ specat_type, add_err,
+ dd->bGridJump ? " or use the -rcon option of mdrun" : "");
+ }
+
+ spac->at_start = at_start;
+ spac->at_end = nat_tot_specat;
+
+ if (debug)
+ {
+ fprintf(debug, "Done setup_specat_communication\n");
+ }
+
+ return nat_tot_specat;
+}
+
+gmx_domdec_specat_comm_t *specat_comm_init(int nthread)
+{
+ gmx_domdec_specat_comm_t *spac;
+
+ snew(spac, 1);
+ spac->nthread = nthread;
+ snew(spac->ireq, spac->nthread);
+
+ return spac;
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2005,2006,2007,2008,2009,2010,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief This file declares functions for domdec to use
+ * while managing communication of atoms required for special purposes
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_domdec
+ */
+
+#ifndef GMX_DOMDEC_DOMDEC_SPECATOMCOMM_H
+#define GMX_DOMDEC_DOMDEC_SPECATOMCOMM_H
+
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+
+typedef struct {
+ int nsend;
+ int *a;
+ int a_nalloc;
+ int nrecv;
+} gmx_specatsend_t;
+
+typedef struct {
+ int *ind;
+ int nalloc;
+ int n;
+} ind_req_t;
+
+/*! \internal \brief Struct with setup and buffers for special atom communication */
+typedef struct gmx_domdec_specat_comm {
+ /* The number of indices to receive during the setup */
+ int nreq[DIM][2][2]; /**< The nr. of atoms requested, per DIM, direction and direct/indirect */
+ /* The atoms to send */
+ gmx_specatsend_t spas[DIM][2]; /**< The communication setup per DIM, direction */
+ gmx_bool *bSendAtom; /**< Work buffer that tells if spec.atoms should be sent */
+ int bSendAtom_nalloc; /**< Allocation size of \p bSendAtom */
+ /* Send buffers */
+ int *ibuf; /**< Integer send buffer */
+ int ibuf_nalloc; /**< Allocation size of \p ibuf */
+ rvec *vbuf; /**< rvec send buffer */
+ int vbuf_nalloc; /**< Allocation size of \p vbuf */
+ rvec *vbuf2; /**< rvec send buffer */
+ int vbuf2_nalloc; /**< Allocation size of \p vbuf2 */
+ /* The range in the local buffer(s) for received atoms */
+ int at_start; /**< Start index of received atoms */
+ int at_end; /**< End index of received atoms */
+
+ /* The atom indices we need from the surrounding cells.
+ * We can gather the indices over nthread threads.
+ */
+ int nthread; /**< Number of threads used for spec.atom communication */
+ ind_req_t *ireq; /**< Index request buffer per thread, allocation size \p nthread */
+} gmx_domdec_specat_comm_t;
+
+/*! \brief Communicates the force for special atoms, the shift forces are reduced with \p fshift != NULL */
+void dd_move_f_specat(gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac,
+ rvec *f, rvec *fshift);
+
+/*! \brief Communicates the coordinates for special atoms
+ *
+ * \param[in] dd Domain decomposition struct
+ * \param[in] spac Special atom communication struct
+ * \param[in] box Box, used for pbc
+ * \param[in,out] x0 Vector to communicate
+ * \param[in,out] x1 Vector to communicate, when != NULL
+ * \param[in] bX1IsCoord Tells is \p x1 is a coordinate vector (needs pbc)
+ */
+void dd_move_x_specat(gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac,
+ matrix box,
+ rvec *x0,
+ rvec *x1, gmx_bool bX1IsCoord);
+
+/*! \brief Sets up the communication for special atoms
+ *
+ * \param[in] dd Domain decomposition struct
+ * \param[in] ireq List of requested atom indices
+ * \param[in,out] spac Special atom communication struct
+ * \param[out] ga2la_specat Global to local special atom index
+ * \param[in] at_start Index in local state where to start storing communicated atoms
+ * \param[in] vbuf_fac Buffer factor, 1 or 2 for communicating 1 or 2 vectors
+ * \param[in] specat_type Name of the special atom, used for error message
+ * \param[in] add_err Text to add at the end of error message when atoms can't be found
+ */
+int setup_specat_communication(gmx_domdec_t *dd,
+ ind_req_t *ireq,
+ gmx_domdec_specat_comm_t *spac,
+ gmx_hash_t ga2la_specat,
+ int at_start,
+ int vbuf_fac,
+ const char *specat_type,
+ const char *add_err);
+
+/*! \brief Initialize a special communication struct */
+gmx_domdec_specat_comm_t *specat_comm_init(int nthread);
+
+#endif
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+/*! \internal \file
+ *
+ * \brief This file defines functions used by the domdec module
+ * while managing the construction, use and error checking for
+ * topologies local to a DD rank.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_domdec
+ */
+
+#include "gmxpre.h"
#include <string.h>
-#include "typedefs.h"
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/domdec_network.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topsort.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
-#include "types/commrec.h"
-#include "domdec.h"
-#include "domdec_network.h"
-#include "names.h"
-#include "network.h"
-#include "vec.h"
-#include "pbc.h"
-#include "chargegroup.h"
-#include "gromacs/gmxlib/topsort.h"
-#include "mtop_util.h"
-#include "mshift.h"
-#include "vsite.h"
-#include "gmx_ga2la.h"
-#include "force.h"
-#include "gmx_omp_nthreads.h"
-
-#include "gmx_fatal.h"
-
-/* for dd_init_local_state */
+
+#include "domdec_constraints.h"
+#include "domdec_internal.h"
+#include "domdec_vsite.h"
+
+/*! \brief The number of integer item in the local state, used for broadcasting of the state */
#define NITEM_DD_INIT_LOCAL_STATE 5
typedef struct {
int *index; /* Index for each atom into il */
int *il; /* ftype|type|a0|...|an|ftype|... */
-} gmx_reverse_ilist_t;
+} reverse_ilist_t;
typedef struct {
int a_start;
int a_end;
int natoms_mol;
int type;
-} gmx_molblock_ind_t;
+} molblock_ind_t;
+/*! \brief Struct for thread local work data for local topology generation */
+typedef struct {
+ t_idef idef; /**< Partial local topology */
+ int **vsite_pbc; /**< vsite PBC structure */
+ int *vsite_pbc_nalloc; /**< Allocation sizes for vsite_pbc */
+ int nbonded; /**< The number of bondeds in this struct */
+ t_blocka excl; /**< List of exclusions */
+ int excl_count; /**< The total exclusion count for \p excl */
+} thread_work_t;
+
+/*! \brief Struct for the reverse topology: links bonded interactions to atomsx */
typedef struct gmx_reverse_top {
- gmx_bool bExclRequired; /* Do we require all exclusions to be assigned? */
- gmx_bool bConstr; /* Are there constraints in this revserse top? */
- gmx_bool bSettle; /* Are there settles in this revserse top? */
- gmx_bool bBCheck; /* All bonded interactions have to be assigned? */
- gmx_bool bMultiCGmols; /* Are the multi charge-group molecules? */
- gmx_reverse_ilist_t *ril_mt; /* Reverse ilist for all moltypes */
- int ril_mt_tot_size;
- int ilsort; /* The sorting state of bondeds for free energy */
- gmx_molblock_ind_t *mbi;
- int nmolblock;
+ //! @cond Doxygen_Suppress
+ gmx_bool bExclRequired; /**< Do we require all exclusions to be assigned? */
+ gmx_bool bConstr; /**< Are there constraints in this revserse top? */
+ gmx_bool bSettle; /**< Are there settles in this revserse top? */
+ gmx_bool bBCheck; /**< All bonded interactions have to be assigned? */
+ gmx_bool bMultiCGmols; /**< Are the multi charge-group molecules? */
+ reverse_ilist_t *ril_mt; /**< Reverse ilist for all moltypes */
+ int ril_mt_tot_size; /**< The size of ril_mt[?].index summed over all entries */
+ int ilsort; /**< The sorting state of bondeds for free energy */
+ molblock_ind_t *mbi; /**< molblock to global atom index for quick lookup of molblocks on atom index */
+ int nmolblock; /**< The number of molblocks, size of \p mbi */
/* Work data structures for multi-threading */
- int nthread;
- t_idef *idef_thread;
- int ***vsite_pbc;
- int **vsite_pbc_nalloc;
- int *nbonded_thread;
- t_blocka *excl_thread;
- int *excl_count_thread;
+ int nthread; /**< The number of threads to be used */
+ thread_work_t *th_work; /**< Thread work array for local topology generation */
/* Pointers only used for an error message */
- gmx_mtop_t *err_top_global;
- gmx_localtop_t *err_top_local;
+ gmx_mtop_t *err_top_global; /**< Pointer to the global top, only used for error reporting */
+ gmx_localtop_t *err_top_local; /**< Pointer to the local top, only used for error reporting */
+ //! @endcond
} gmx_reverse_top_t;
+/*! \brief Returns the number of atom entries for il in gmx_reverse_top_t */
static int nral_rt(int ftype)
{
- /* Returns the number of atom entries for il in gmx_reverse_top_t */
int nral;
nral = NRAL(ftype);
return nral;
}
-/* This function tells which interactions need to be assigned exactly once */
+/*! \brief Return whether interactions of type \p ftype need to be assigned exactly once */
static gmx_bool dd_check_ftype(int ftype, gmx_bool bBCheck,
gmx_bool bConstr, gmx_bool bSettle)
{
(bSettle && ftype == F_SETTLE));
}
+/*! \brief Print a header on error messages */
static void print_error_header(FILE *fplog, char *moltypename, int nprint)
{
fprintf(fplog, "\nMolecule type '%s'\n", moltypename);
nprint);
}
+/*! \brief Help print error output when interactions are missing */
static void print_missing_interactions_mb(FILE *fplog, t_commrec *cr,
gmx_reverse_top_t *rt,
char *moltypename,
- gmx_reverse_ilist_t *ril,
+ reverse_ilist_t *ril,
int a_start, int a_end,
int nat_mol, int nmol,
t_idef *idef)
{
int nril_mol, *assigned, *gatindex;
- int ftype, ftype_j, nral, i, j_mol, j, k, a0, a0_mol, mol, a, a_gl;
+ int ftype, ftype_j, nral, i, j_mol, j, a0, a0_mol, mol, a;
int nprint;
t_ilist *il;
t_iatom *ia;
sfree(assigned);
}
+/*! \brief Help print error output when interactions are missing */
static void print_missing_interactions_atoms(FILE *fplog, t_commrec *cr,
gmx_mtop_t *mtop, t_idef *idef)
{
if (DDMASTER(dd))
{
- fprintf(fplog, "\nA list of missing interactions:\n");
+ if (fplog)
+ {
+ fprintf(fplog, "\nA list of missing interactions:\n");
+ }
fprintf(stderr, "\nA list of missing interactions:\n");
rest_global = dd->nbonded_global;
rest_local = local_count;
|| (dd->reverse_top->bConstr && ftype == F_CONSTR)
|| (dd->reverse_top->bSettle && ftype == F_SETTLE))
{
- nral = NRAL(ftype);
n = gmx_mtop_ftype_count(err_top_global, ftype);
if (ftype == F_CONSTR)
{
{
sprintf(buf, "%20s of %6d missing %6d",
interaction_function[ftype].longname, n, -ndiff);
- fprintf(fplog, "%s\n", buf);
+ if (fplog)
+ {
+ fprintf(fplog, "%s\n", buf);
+ }
fprintf(stderr, "%s\n", buf);
}
rest_global -= n;
{
sprintf(buf, "%20s of %6d missing %6d", "exclusions",
rest_global, -ndiff);
- fprintf(fplog, "%s\n", buf);
+ if (fplog)
+ {
+ fprintf(fplog, "%s\n", buf);
+ }
fprintf(stderr, "%s\n", buf);
}
}
}
else
{
- gmx_fatal(FARGS, "%d of the %d bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (%g nm) or the two-body cut-off distance (%g nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck", -ndiff_tot, cr->dd->nbonded_global, dd_cutoff_mbody(cr->dd), dd_cutoff_twobody(cr->dd));
+ gmx_fatal(FARGS, "%d of the %d bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (%g nm) or the two-body cut-off distance (%g nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck", -ndiff_tot, cr->dd->nbonded_global, dd_cutoff_multibody(cr->dd), dd_cutoff_twobody(cr->dd));
}
}
}
+/*! \brief Return global topology molecule information for global atom index \p i_gl */
static void global_atomnr_to_moltype_ind(gmx_reverse_top_t *rt, int i_gl,
int *mb, int *mt, int *mol, int *i_mol)
{
- int molb;
-
-
- gmx_molblock_ind_t *mbi = rt->mbi;
- int start = 0;
- int end = rt->nmolblock; /* exclusive */
- int mid;
+ molblock_ind_t *mbi = rt->mbi;
+ int start = 0;
+ int end = rt->nmolblock; /* exclusive */
+ int mid;
/* binary search for molblock_ind */
while (TRUE)
*i_mol = (i_gl - mbi->a_start) - (*mol)*mbi->natoms_mol;
}
-static int count_excls(t_block *cgs, t_blocka *excls, int *n_intercg_excl)
+/*! \brief Count the exclusions for all atoms in \p cgs */
+static int count_excls(const t_block *cgs, const t_blocka *excls,
+ int *n_intercg_excl)
{
- int n, n_inter, cg, at0, at1, at, excl, atj;
+ int n, cg, at0, at1, at, excl, atj;
n = 0;
*n_intercg_excl = 0;
return n;
}
+/*! \brief Run the reverse ilist generation and store it when \p bAssign = TRUE */
static int low_make_reverse_ilist(t_ilist *il_mt, t_atom *atom,
int **vsite_pbc,
int *count,
bVSite = (interaction_function[ftype].flags & IF_VSITE);
nral = NRAL(ftype);
il = &il_mt[ftype];
- ia = il->iatoms;
for (i = 0; i < il->nr; i += 1+nral)
{
ia = il->iatoms + i;
return nint;
}
+/*! \brief Make the reverse ilist: a list of bonded interactions linked to atoms */
static int make_reverse_ilist(gmx_moltype_t *molt,
int **vsite_pbc,
gmx_bool bConstr, gmx_bool bSettle,
gmx_bool bBCheck,
gmx_bool bLinkToAllAtoms,
- gmx_reverse_ilist_t *ril_mt)
+ reverse_ilist_t *ril_mt)
{
int nat_mt, *count, i, nint_mt;
return nint_mt;
}
-static void destroy_reverse_ilist(gmx_reverse_ilist_t *ril)
+/*! \brief Destroys a reverse_ilist_t struct */
+static void destroy_reverse_ilist(reverse_ilist_t *ril)
{
sfree(ril->index);
sfree(ril->il);
}
+/*! \brief Generate the reverse topology */
static gmx_reverse_top_t *make_reverse_top(gmx_mtop_t *mtop, gmx_bool bFE,
int ***vsite_pbc_molt,
gmx_bool bConstr, gmx_bool bSettle,
}
rt->nthread = gmx_omp_nthreads_get(emntDomdec);
- snew(rt->idef_thread, rt->nthread);
+ snew(rt->th_work, rt->nthread);
if (vsite_pbc_molt != NULL)
{
- snew(rt->vsite_pbc, rt->nthread);
- snew(rt->vsite_pbc_nalloc, rt->nthread);
for (thread = 0; thread < rt->nthread; thread++)
{
- snew(rt->vsite_pbc[thread], F_VSITEN-F_VSITE2+1);
- snew(rt->vsite_pbc_nalloc[thread], F_VSITEN-F_VSITE2+1);
+ snew(rt->th_work[thread].vsite_pbc, F_VSITEN-F_VSITE2+1);
+ snew(rt->th_work[thread].vsite_pbc_nalloc, F_VSITEN-F_VSITE2+1);
}
}
- snew(rt->nbonded_thread, rt->nthread);
- snew(rt->excl_thread, rt->nthread);
- snew(rt->excl_count_thread, rt->nthread);
return rt;
}
gmx_vsite_t *vsite,
t_inputrec *ir, gmx_bool bBCheck)
{
- int mb, n_recursive_vsite, nexcl, nexcl_icg, a;
+ int mb, nexcl, nexcl_icg;
gmx_molblock_t *molb;
gmx_moltype_t *molt;
}
}
+/*! \brief Store a vsite interaction at the end of \p il
+ *
+ * This routine is very similar to add_ifunc, but vsites interactions
+ * have more work to do than other kinds of interactions, and the
+ * complex way nral (and thus vector contents) depends on ftype
+ * confuses static analysis tools unless we fuse the vsite
+ * atom-indexing organization code with the ifunc-adding code, so that
+ * they can see that nral is the same value. */
+static gmx_inline void
+add_ifunc_for_vsites(t_iatom *tiatoms, gmx_ga2la_t ga2la,
+ int nral, gmx_bool bHomeA,
+ int a, int a_gl, int a_mol,
+ const t_iatom *iatoms,
+ t_ilist *il)
+{
+ t_iatom *liatoms;
+
+ if (il->nr+1+nral > il->nalloc)
+ {
+ il->nalloc = over_alloc_large(il->nr+1+nral);
+ srenew(il->iatoms, il->nalloc);
+ }
+ liatoms = il->iatoms + il->nr;
+ il->nr += 1 + nral;
+
+ /* Copy the type */
+ tiatoms[0] = iatoms[0];
+
+ if (bHomeA)
+ {
+ /* We know the local index of the first atom */
+ tiatoms[1] = a;
+ }
+ else
+ {
+ /* Convert later in make_local_vsites */
+ tiatoms[1] = -a_gl - 1;
+ }
+
+ for (int k = 2; k < 1+nral; k++)
+ {
+ int ak_gl = a_gl + iatoms[k] - a_mol;
+ if (!ga2la_get_home(ga2la, ak_gl, &tiatoms[k]))
+ {
+ /* Copy the global index, convert later in make_local_vsites */
+ tiatoms[k] = -(ak_gl + 1);
+ }
+ // Note that ga2la_get_home always sets the third parameter if
+ // it returns TRUE
+ }
+ for (int k = 0; k < 1+nral; k++)
+ {
+ liatoms[k] = tiatoms[k];
+ }
+}
+
+/*! \brief Store a bonded interaction at the end of \p il */
static gmx_inline void add_ifunc(int nral, t_iatom *tiatoms, t_ilist *il)
{
t_iatom *liatoms;
il->nr += 1 + nral;
}
+/*! \brief Store a position restraint in idef and iatoms, complex because the parameters are different for each entry */
static void add_posres(int mol, int a_mol, const gmx_molblock_t *molb,
t_iatom *iatoms, const t_iparams *ip_in,
t_idef *idef)
iatoms[0] = n;
}
+/*! \brief Store a flat-bottomed position restraint in idef and iatoms, complex because the parameters are different for each entry */
static void add_fbposres(int mol, int a_mol, const gmx_molblock_t *molb,
t_iatom *iatoms, const t_iparams *ip_in,
t_idef *idef)
iatoms[0] = n;
}
+/*! \brief Store a virtual site interaction, complex because of PBC and recursion */
static void add_vsite(gmx_ga2la_t ga2la, int *index, int *rtil,
int ftype, int nral,
gmx_bool bHomeA, int a, int a_gl, int a_mol,
t_iatom *iatoms,
t_idef *idef, int **vsite_pbc, int *vsite_pbc_nalloc)
{
- int k, ak_gl, vsi, pbc_a_mol;
- t_iatom tiatoms[1+MAXATOMLIST], *iatoms_r;
+ int k, vsi, pbc_a_mol;
+ t_iatom tiatoms[1+MAXATOMLIST];
int j, ftype_r, nral_r;
- /* Copy the type */
- tiatoms[0] = iatoms[0];
-
- if (bHomeA)
- {
- /* We know the local index of the first atom */
- tiatoms[1] = a;
- }
- else
- {
- /* Convert later in make_local_vsites */
- tiatoms[1] = -a_gl - 1;
- }
-
- for (k = 2; k < 1+nral; k++)
- {
- ak_gl = a_gl + iatoms[k] - a_mol;
- if (!ga2la_get_home(ga2la, ak_gl, &tiatoms[k]))
- {
- /* Copy the global index, convert later in make_local_vsites */
- tiatoms[k] = -(ak_gl + 1);
- }
- }
-
/* Add this interaction to the local topology */
- add_ifunc(nral, tiatoms, &idef->il[ftype]);
+ add_ifunc_for_vsites(tiatoms, ga2la, nral, bHomeA, a, a_gl, a_mol, iatoms, &idef->il[ftype]);
+
if (vsite_pbc)
{
vsi = idef->il[ftype].nr/(1+nral) - 1;
}
}
+/*! \brief Update the local atom to local charge group index */
static void make_la2lc(gmx_domdec_t *dd)
{
int *cgindex, *la2lc, cg, a;
}
}
+/*! \brief Returns the squared distance between charge groups \p i and \p j */
static real dd_dist2(t_pbc *pbc_null, rvec *cg_cm, const int *la2lc, int i, int j)
{
rvec dx;
return norm2(dx);
}
-/* Append the nsrc t_blocka block structures in src to *dest */
-static void combine_blocka(t_blocka *dest, const t_blocka *src, int nsrc)
+/*! \brief Append t_blocka block structures 1 to nsrc in src to *dest */
+static void combine_blocka(t_blocka *dest, const thread_work_t *src, int nsrc)
{
int ni, na, s, i;
- ni = src[nsrc-1].nr;
+ ni = src[nsrc-1].excl.nr;
na = 0;
for (s = 0; s < nsrc; s++)
{
- na += src[s].nra;
+ na += src[s].excl.nra;
}
if (ni + 1 > dest->nalloc_index)
{
dest->nalloc_a = over_alloc_large(dest->nra+na);
srenew(dest->a, dest->nalloc_a);
}
- for (s = 0; s < nsrc; s++)
+ for (s = 1; s < nsrc; s++)
{
- for (i = dest->nr+1; i < src[s].nr+1; i++)
+ for (i = dest->nr+1; i < src[s].excl.nr+1; i++)
{
- dest->index[i] = dest->nra + src[s].index[i];
+ dest->index[i] = dest->nra + src[s].excl.index[i];
}
- for (i = 0; i < src[s].nra; i++)
+ for (i = 0; i < src[s].excl.nra; i++)
{
- dest->a[dest->nra+i] = src[s].a[i];
+ dest->a[dest->nra+i] = src[s].excl.a[i];
}
- dest->nr = src[s].nr;
- dest->nra += src[s].nra;
+ dest->nr = src[s].excl.nr;
+ dest->nra += src[s].excl.nra;
}
}
-/* Append the nsrc t_idef structures in src to *dest,
+/*! \brief Append t_idef structures 1 to nsrc in src to *dest,
* virtual sites need special attention, as pbc info differs per vsite.
*/
-static void combine_idef(t_idef *dest, const t_idef *src, int nsrc,
- gmx_vsite_t *vsite, int ***vsite_pbc_t)
+static void combine_idef(t_idef *dest, const thread_work_t *src, int nsrc,
+ gmx_vsite_t *vsite)
{
- int ftype, n, s, i;
- t_ilist *ild;
- const t_ilist *ils;
- gmx_bool vpbc;
- int nral1 = 0, ftv = 0;
+ int ftype;
for (ftype = 0; ftype < F_NRE; ftype++)
{
+ int n, s;
+
n = 0;
- for (s = 0; s < nsrc; s++)
+ for (s = 1; s < nsrc; s++)
{
- n += src[s].il[ftype].nr;
+ n += src[s].idef.il[ftype].nr;
}
if (n > 0)
{
+ t_ilist *ild;
+
ild = &dest->il[ftype];
if (ild->nr + n > ild->nalloc)
srenew(ild->iatoms, ild->nalloc);
}
+ gmx_bool vpbc;
+ int nral1 = 0, ftv = 0;
+
vpbc = ((interaction_function[ftype].flags & IF_VSITE) &&
vsite->vsite_pbc_loc != NULL);
if (vpbc)
}
}
- for (s = 0; s < nsrc; s++)
+ for (s = 1; s < nsrc; s++)
{
- ils = &src[s].il[ftype];
+ const t_ilist *ils;
+ int i;
+
+ ils = &src[s].idef.il[ftype];
for (i = 0; i < ils->nr; i++)
{
ild->iatoms[ild->nr+i] = ils->iatoms[i];
for (i = 0; i < ils->nr; i += nral1)
{
vsite->vsite_pbc_loc[ftv][(ild->nr+i)/nral1] =
- vsite_pbc_t[s][ftv][i/nral1];
+ src[s].vsite_pbc[ftv][i/nral1];
}
}
/* Position restraints need an additional treatment */
if (dest->il[F_POSRES].nr > 0)
{
+ int n, s, i;
+
n = dest->il[F_POSRES].nr/2;
if (n > dest->iparams_posres_nalloc)
{
srenew(dest->iparams_posres, dest->iparams_posres_nalloc);
}
/* Set n to the number of original position restraints in dest */
- for (s = 0; s < nsrc; s++)
+ for (s = 1; s < nsrc; s++)
{
- n -= src[s].il[F_POSRES].nr/2;
+ n -= src[s].idef.il[F_POSRES].nr/2;
}
- for (s = 0; s < nsrc; s++)
+ for (s = 1; s < nsrc; s++)
{
- for (i = 0; i < src[s].il[F_POSRES].nr/2; i++)
+ for (i = 0; i < src[s].idef.il[F_POSRES].nr/2; i++)
{
/* Correct the index into iparams_posres */
dest->il[F_POSRES].iatoms[n*2] = n;
/* Copy the position restraint force parameters */
- dest->iparams_posres[n] = src[s].iparams_posres[i];
+ dest->iparams_posres[n] = src[s].idef.iparams_posres[i];
n++;
}
}
}
}
-/* This function looks up and assigns bonded interactions for zone iz.
+/*! \brief This function looks up and assigns bonded interactions for zone iz.
+ *
* With thread parallelizing each thread acts on a different atom range:
* at_start to at_end.
*/
return nbonded_local;
}
+/*! \brief Set the exclusion data for i-zone \p iz for the case of no exclusions */
static void set_no_exclusions_zone(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
int iz, t_blocka *lexcls)
{
}
}
+/*! \brief Set the exclusion data for i-zone \p iz */
static int make_exclusions_zone(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
const gmx_moltype_t *moltype,
gmx_bool bRCheck, real rc2,
int iz,
int cg_start, int cg_end)
{
- int nizone, n, count, jla0, jla1, jla;
+ int n, count, jla0, jla1, jla;
int cg, la0, la1, la, a_gl, mb, mt, mol, a_mol, j, aj_mol;
const t_blocka *excls;
gmx_ga2la_t ga2la;
- int a_loc;
int cell;
ga2la = dd->ga2la;
return count;
}
+/*! \brief Ensure we have enough space in \p ba for \p nindex_max indices */
static void check_alloc_index(t_blocka *ba, int nindex_max)
{
if (nindex_max+1 > ba->nalloc_index)
}
}
+/*! \brief Ensure that we have enough space for exclusion storate in \p lexcls */
static void check_exclusions_alloc(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
t_blocka *lexcls)
{
for (thread = 1; thread < dd->reverse_top->nthread; thread++)
{
- check_alloc_index(&dd->reverse_top->excl_thread[thread], nr);
+ check_alloc_index(&dd->reverse_top->th_work[thread].excl, nr);
}
}
+/*! \brief Set the total count indexes for the local exclusions, needed by several functions */
static void finish_local_exclusions(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
t_blocka *lexcls)
{
}
}
+/*! \brief Clear a t_idef struct */
static void clear_idef(t_idef *idef)
{
int ftype;
}
}
+/*! \brief Generate and store all required local bonded interactions in \p idef and local exclusions in \p lexcls */
static int make_local_bondeds_excls(gmx_domdec_t *dd,
gmx_domdec_zones_t *zones,
const gmx_mtop_t *mtop,
{
int cg0t, cg1t;
t_idef *idef_t;
- int ftype;
int **vsite_pbc;
int *vsite_pbc_nalloc;
t_blocka *excl_t;
}
else
{
- idef_t = &rt->idef_thread[thread];
+ idef_t = &rt->th_work[thread].idef;
clear_idef(idef_t);
}
}
else
{
- vsite_pbc = rt->vsite_pbc[thread];
- vsite_pbc_nalloc = rt->vsite_pbc_nalloc[thread];
+ vsite_pbc = rt->th_work[thread].vsite_pbc;
+ vsite_pbc_nalloc = rt->th_work[thread].vsite_pbc_nalloc;
}
}
else
vsite_pbc_nalloc = NULL;
}
- rt->nbonded_thread[thread] =
+ rt->th_work[thread].nbonded =
make_bondeds_zone(dd, zones,
mtop->molblock,
bRCheckMB, rcheck, bRCheck2B, rc2,
}
else
{
- excl_t = &rt->excl_thread[thread];
+ excl_t = &rt->th_work[thread].excl;
excl_t->nr = 0;
excl_t->nra = 0;
}
- rt->excl_count_thread[thread] =
+ rt->th_work[thread].excl_count =
make_exclusions_zone(dd, zones,
mtop->moltype, bRCheck2B, rc2,
la2lc, pbc_null, cg_cm, cginfo,
if (rt->nthread > 1)
{
- combine_idef(idef, rt->idef_thread+1, rt->nthread-1,
- vsite, rt->vsite_pbc+1);
+ combine_idef(idef, rt->th_work, rt->nthread, vsite);
}
for (thread = 0; thread < rt->nthread; thread++)
{
- nbonded_local += rt->nbonded_thread[thread];
+ nbonded_local += rt->th_work[thread].nbonded;
}
if (iz < nzone_excl)
{
if (rt->nthread > 1)
{
- combine_blocka(lexcls, rt->excl_thread+1, rt->nthread-1);
+ combine_blocka(lexcls, rt->th_work, rt->nthread);
}
for (thread = 0; thread < rt->nthread; thread++)
{
- *excl_count += rt->excl_count_thread[thread];
+ *excl_count += rt->th_work[thread].excl_count;
}
}
}
gmx_vsite_t *vsite,
gmx_mtop_t *mtop, gmx_localtop_t *ltop)
{
- gmx_bool bUniqueExcl, bRCheckMB, bRCheck2B, bRCheckExcl;
+ gmx_bool bRCheckMB, bRCheck2B;
real rc = -1;
ivec rcheck;
int d, nexcl;
bRCheckMB = FALSE;
bRCheck2B = FALSE;
- bRCheckExcl = FALSE;
if (dd->reverse_top->bMultiCGmols)
{
d, cellsize_min[d], d, rcheck[d], bRCheck2B);
}
}
- if (dd->reverse_top->bExclRequired)
- {
- bRCheckExcl = bRCheck2B;
- }
- else
- {
- /* If we don't have forces on exclusions,
- * we don't care about exclusions being assigned mulitple times.
- */
- bRCheckExcl = FALSE;
- }
if (bRCheckMB || bRCheck2B)
{
make_la2lc(dd);
state_local->flags = buf[0];
}
+/*! \brief Check if a link is stored in \p link between charge groups \p cg_gl and \p cg_gl_j and if not so, store a link */
static void check_link(t_blocka *link, int cg_gl, int cg_gl_j)
{
- int k, aj;
+ int k;
gmx_bool bFound;
bFound = FALSE;
for (k = link->index[cg_gl]; k < link->index[cg_gl+1]; k++)
{
+ GMX_RELEASE_ASSERT(link->a, "Inconsistent NULL pointer while making charge-group links");
if (link->a[k] == cg_gl_j)
{
bFound = TRUE;
}
if (!bFound)
{
+ GMX_RELEASE_ASSERT(link->a || link->index[cg_gl+1]+1 > link->nalloc_a,
+ "Inconsistent allocation of link");
/* Add this charge group link */
if (link->index[cg_gl+1]+1 > link->nalloc_a)
{
}
}
+/*! \brief Allocate and return an array of the charge group index for all atoms */
static int *make_at2cg(t_block *cgs)
{
int *at2cg, cg, a;
t_block *cgs;
t_blocka *excls;
int *a2c;
- gmx_reverse_ilist_t ril;
+ reverse_ilist_t ril;
t_blocka *link;
cginfo_mb_t *cgi_mb;
return link;
}
+/*! \brief Set the distance, function type and atom indices for the longest distance between molecules of molecule type \p molt for two-body and multi-body bonded interactions */
static void bonded_cg_distance_mol(gmx_moltype_t *molt, int *at2cg,
gmx_bool bBCheck, gmx_bool bExcl, rvec *cg_cm,
real *r_2b, int *ft2b, int *a2_1, int *a2_2,
*r_mb = sqrt(r2_mb);
}
+//! Compute charge group centers of mass for molecule \p molt
static void get_cgcm_mol(gmx_moltype_t *molt, gmx_ffparams_t *ffparams,
int ePBC, t_graph *graph, matrix box,
gmx_vsite_t *vsite,
calc_cgcm(NULL, 0, molt->cgs.nr, &molt->cgs, xs, cg_cm);
}
+//! Returns whether \p molt has a virtual site
static int have_vsite_molt(gmx_moltype_t *molt)
{
int i;
real *r_2b, real *r_mb)
{
gmx_bool bExclRequired;
- int mb, cg_offset, at_offset, *at2cg, mol;
+ int mb, at_offset, *at2cg, mol;
t_graph graph;
gmx_vsite_t *vsite;
gmx_molblock_t *molb;
*r_2b = 0;
*r_mb = 0;
- cg_offset = 0;
at_offset = 0;
for (mb = 0; mb < mtop->nmolblock; mb++)
{
molt = &mtop->moltype[molb->type];
if (molt->cgs.nr == 1 || molb->nmol == 0)
{
- cg_offset += molb->nmol*molt->cgs.nr;
at_offset += molb->nmol*molt->atoms.nr;
}
else
a_mb_2 = at_offset + amol_mb_2;
}
- cg_offset += molt->cgs.nr;
at_offset += molt->atoms.nr;
}
sfree(cg_cm);
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2006,2007,2008,2009,2010,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ *
+ * \brief This file implements functions for domdec to use
+ * while managing inter-atomic constraints.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_domdec
+ */
+
+#include "gmxpre.h"
+
+#include "domdec_vsite.h"
+
+#include <assert.h>
+
+#include <algorithm>
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/gmx_hash.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "domdec_specatomcomm.h"
+
+void dd_move_f_vsites(gmx_domdec_t *dd, rvec *f, rvec *fshift)
+{
+ if (dd->vsite_comm)
+ {
+ dd_move_f_specat(dd, dd->vsite_comm, f, fshift);
+ }
+}
+
+void dd_clear_f_vsites(gmx_domdec_t *dd, rvec *f)
+{
+ int i;
+
+ if (dd->vsite_comm)
+ {
+ for (i = dd->vsite_comm->at_start; i < dd->vsite_comm->at_end; i++)
+ {
+ clear_rvec(f[i]);
+ }
+ }
+}
+
+void dd_move_x_vsites(gmx_domdec_t *dd, matrix box, rvec *x)
+{
+ if (dd->vsite_comm)
+ {
+ dd_move_x_specat(dd, dd->vsite_comm, box, x, NULL, FALSE);
+ }
+}
+
+int dd_make_local_vsites(gmx_domdec_t *dd, int at_start, t_ilist *lil)
+{
+ gmx_domdec_specat_comm_t *spac;
+ ind_req_t *ireq;
+ gmx_hash_t ga2la_specat;
+ int ftype, nral, i, j, a;
+ t_ilist *lilf;
+ t_iatom *iatoms;
+ int at_end;
+
+ spac = dd->vsite_comm;
+ ireq = &spac->ireq[0];
+ ga2la_specat = dd->ga2la_vsite;
+
+ ireq->n = 0;
+ /* Loop over all the home vsites */
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (interaction_function[ftype].flags & IF_VSITE)
+ {
+ nral = NRAL(ftype);
+ lilf = &lil[ftype];
+ for (i = 0; i < lilf->nr; i += 1+nral)
+ {
+ iatoms = lilf->iatoms + i;
+ /* Check if we have the other atoms */
+ for (j = 1; j < 1+nral; j++)
+ {
+ if (iatoms[j] < 0)
+ {
+ /* This is not a home atom,
+ * we need to ask our neighbors.
+ */
+ a = -iatoms[j] - 1;
+ /* Check to not ask for the same atom more than once */
+ if (gmx_hash_get_minone(dd->ga2la_vsite, a) == -1)
+ {
+ /* Add this non-home atom to the list */
+ if (ireq->n+1 > ireq->nalloc)
+ {
+ ireq->nalloc = over_alloc_large(ireq->n+1);
+ srenew(ireq->ind, ireq->nalloc);
+ }
+ ireq->ind[ireq->n++] = a;
+ /* Temporarily mark with -2,
+ * we get the index later.
+ */
+ gmx_hash_set(ga2la_specat, a, -2);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ at_end = setup_specat_communication(dd, ireq, dd->vsite_comm, ga2la_specat,
+ at_start, 1, "vsite", "");
+
+ /* Fill in the missing indices */
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (interaction_function[ftype].flags & IF_VSITE)
+ {
+ nral = NRAL(ftype);
+ lilf = &lil[ftype];
+ for (i = 0; i < lilf->nr; i += 1+nral)
+ {
+ iatoms = lilf->iatoms + i;
+ for (j = 1; j < 1+nral; j++)
+ {
+ if (iatoms[j] < 0)
+ {
+ iatoms[j] = gmx_hash_get_minone(ga2la_specat, -iatoms[j]-1);
+ }
+ }
+ }
+ }
+ }
+
+ return at_end;
+}
+
+void init_domdec_vsites(gmx_domdec_t *dd, int n_intercg_vsite)
+{
+ if (debug)
+ {
+ fprintf(debug, "Begin init_domdec_vsites\n");
+ }
+
+ /* Use a hash table for the global to local index.
+ * The number of keys is a rough estimate, it will be optimized later.
+ */
+ dd->ga2la_vsite = gmx_hash_init(std::min(n_intercg_vsite/20,
+ n_intercg_vsite/(2*dd->nnodes)));
+
+ dd->vsite_comm = specat_comm_init(1);
+}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014, by the GROMACS development team, led by
+ * Copyright (c) 2005,2006,2007,2008,2009,2010,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/*! \file
- * \brief
- * Generated include file for configuration macros that affect installed
- * headers.
+/*! \internal \file
*
- * This include file will configured by CMake and installed with GROMACS
- * header files so that they can refer to a central location for \#defines that
- * will be available for builds of projects that depend on GROMACS.
+ * \brief This file declares functions for domdec to use
+ * while managing virtual sites.
*
- * gmx_header_config.h should be included instead of this file to allow usage
- * of relative install paths.
- *
- * \inlibraryapi
- * \ingroup module_utility
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_domdec
*/
-#ifdef __CYGWIN__
-#define GMX_CYGWIN
-#endif
+#ifndef GMX_DOMDEC_DOMDEC_VSITE_H
+#define GMX_DOMDEC_DOMDEC_VSITE_H
-#if defined( _WIN32 ) || defined( _WIN64 )
-#define GMX_NATIVE_WINDOWS
-#endif
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/topology.h"
+
+/*! \brief Clears the local indices for the virtual site communication setup */
+void dd_clear_local_vsite_indices(gmx_domdec_t *dd);
-/** Define if we have sufficient C++11 support */
-#cmakedefine GMX_CXX11
+/*! \brief Sets up communication and atom indices for all local vsites */
+int dd_make_local_vsites(gmx_domdec_t *dd, int at_start, t_ilist *lil);
+
+/*! \brief Initializes the data structures for virtual site communication */
+void init_domdec_vsites(gmx_domdec_t *dd, int n_intercg_vsite);
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "edsam.h"
#include <stdio.h>
#include <string.h>
#include <time.h>
-#include "typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "names.h"
#include "gromacs/fileio/confio.h"
-#include "txtdump.h"
-#include "vec.h"
-#include "nrnb.h"
-#include "mshift.h"
-#include "mdrun.h"
-#include "update.h"
-#include "physics.h"
-#include "mtop_util.h"
-#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/fileio/gmxfio.h"
-#include "xvgr.h"
-#include "gromacs/mdlib/groupcoord.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
#include "gromacs/linearalgebra/nrjac.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/groupcoord.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
-/* We use the same defines as in mvdata.c here */
+/* We use the same defines as in broadcaststructs.cpp here */
#define block_bc(cr, d) gmx_bcast( sizeof(d), &(d), (cr))
#define nblock_bc(cr, nr, d) gmx_bcast((nr)*sizeof((d)[0]), (d), (cr))
#define snew_bc(cr, d, nr) { if (!MASTER(cr)) {snew((d), (nr)); }}
{
srenew(names, count);
sprintf(buf, "Vfl_%d", count);
- names[count-1] = strdup(buf);
+ names[count-1] = gmx_strdup(buf);
actual = actual->next_edi;
count++;
}
init_edsamstate(ed, EDstate);
/* The master opens the ED output file */
+ /* TODO This file is never closed... */
if (Flags & MD_APPENDFILES)
{
ed->edo = gmx_fio_fopen(opt2fn("-eo", nfile, fnm), "a+");
sprintf(tmp, "%c %s", EDgroupchar, value);
add_to_string_aligned(LegendStr, tmp);
sprintf(tmp2, "%s (%s)", tmp, unit);
- (*setname)[*nsets] = strdup(tmp2);
+ (*setname)[*nsets] = gmx_strdup(tmp2);
(*nsets)++;
}
ed->bFirst = FALSE;
}
+
+void done_ed(gmx_edsam_t *ed)
+{
+ if (*ed)
+ {
+ /* ed->edo is opened sometimes with xvgropen, sometimes with
+ * gmx_fio_fopen, so we use the least common denominator for
+ * closing. */
+ gmx_fio_fclose((*ed)->edo);
+ }
+
+ /* TODO deallocate ed and set pointer to NULL */
+}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ESSENTIALDYNAMICS_EDSAM_H
#define GMX_ESSENTIALDYNAMICS_EDSAM_H
-#include "typedefs.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
void do_flood(t_commrec *cr, t_inputrec *ir, rvec x[], rvec force[], gmx_edsam_t ed,
matrix box, gmx_int64_t step, gmx_bool bNS);
+/*! \brief Clean up
+ *
+ * \param ed The essential dynamics data
+ */
+void done_ed(gmx_edsam_t *ed);
#ifdef __cplusplus
}
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+file(GLOB EWALD_SOURCES *.c)
+set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${EWALD_SOURCES} PARENT_SCOPE)
+
+if (BUILD_TESTING)
+# add_subdirectory(tests)
+endif()
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "ewald.h"
-#include <stdio.h>
#include <math.h>
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "physics.h"
-#include "coulomb.h"
-#include "macros.h"
+#include <stdio.h>
-#include "gromacs/fileio/futil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/smalloc.h"
-#define TOL 2e-5
-
-struct ewald_tab
+struct gmx_ewald_tab_t
{
int nx, ny, nz, kmax;
cvec **eir;
t_complex *tab_xy, *tab_qxyz;
};
+void init_ewald_tab(struct gmx_ewald_tab_t **et, const t_inputrec *ir, FILE *fp)
+{
+ int n;
+ snew(*et, 1);
+ if (fp)
+ {
+ fprintf(fp, "Will do ordinary reciprocal space Ewald sum.\n");
+ }
-/* TODO: fix thread-safety */
+ (*et)->nx = ir->nkx+1;
+ (*et)->ny = ir->nky+1;
+ (*et)->nz = ir->nkz+1;
+ (*et)->kmax = max((*et)->nx, max((*et)->ny, (*et)->nz));
+ (*et)->eir = NULL;
+ (*et)->tab_xy = NULL;
+ (*et)->tab_qxyz = NULL;
+}
/* the other routines are in complex.h */
static t_complex conjmul(t_complex a, t_complex b)
return c;
}
-
-
-
static void tabulate_eir(int natom, rvec x[], int kmax, cvec **eir, rvec lll)
{
int i, j, m;
}
}
-void init_ewald_tab(ewald_tab_t *et, const t_inputrec *ir, FILE *fp)
-{
- int n;
-
- snew(*et, 1);
- if (fp)
- {
- fprintf(fp, "Will do ordinary reciprocal space Ewald sum.\n");
- }
-
- (*et)->nx = ir->nkx+1;
- (*et)->ny = ir->nky+1;
- (*et)->nz = ir->nkz+1;
- (*et)->kmax = max((*et)->nx, max((*et)->ny, (*et)->nz));
- (*et)->eir = NULL;
- (*et)->tab_xy = NULL;
- (*et)->tab_qxyz = NULL;
-}
-
-
-
real do_ewald(t_inputrec *ir,
rvec x[], rvec f[],
real chargeA[], real chargeB[],
t_commrec *cr, int natoms,
matrix lrvir, real ewaldcoeff,
real lambda, real *dvdlambda,
- ewald_tab_t et)
+ struct gmx_ewald_tab_t *et)
{
real factor = -1.0/(4*ewaldcoeff*ewaldcoeff);
real scaleRecip = 4.0*M_PI/(box[XX]*box[YY]*box[ZZ])*ONE_4PI_EPS0/ir->epsilon_r; /* 1/(Vol*e0) */
return energy;
}
+
+real ewald_charge_correction(t_commrec *cr, t_forcerec *fr, real lambda,
+ matrix box,
+ real *dvdlambda, tensor vir)
+
+{
+ real vol, fac, qs2A, qs2B, vc, enercorr;
+ int d;
+
+ if (MASTER(cr))
+ {
+ /* Apply charge correction */
+ vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
+
+ fac = M_PI*ONE_4PI_EPS0/(fr->epsilon_r*2.0*vol*vol*sqr(fr->ewaldcoeff_q));
+
+ qs2A = fr->qsum[0]*fr->qsum[0];
+ qs2B = fr->qsum[1]*fr->qsum[1];
+
+ vc = (qs2A*(1 - lambda) + qs2B*lambda)*fac;
+
+ enercorr = -vol*vc;
+
+ *dvdlambda += -vol*(qs2B - qs2A)*fac;
+
+ for (d = 0; d < DIM; d++)
+ {
+ vir[d][d] += vc;
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "Total charge correction: Vcharge=%g\n", enercorr);
+ }
+ }
+ else
+ {
+ enercorr = 0;
+ }
+
+ return enercorr;
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GMX_EWALD_EWALD_H
+#define GMX_EWALD_EWALD_H
+
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* Forward declaration of type for managing Ewald tables */
+struct gmx_ewald_tab_t;
+
+/*! \brief Initialize the tables used in the Ewald long-ranged part */
+void
+init_ewald_tab(struct gmx_ewald_tab_t **et, const t_inputrec *ir,
+ FILE *fp);
+
+/*! \brief Do the long-ranged part of an Ewald calculation */
+real
+do_ewald(t_inputrec *ir,
+ rvec x[], rvec f[],
+ real chargeA[], real chargeB[],
+ rvec box,
+ t_commrec *cr, int natoms,
+ matrix lrvir, real ewaldcoeff,
+ real lambda, real *dvdlambda,
+ struct gmx_ewald_tab_t *et);
+
+/*! \brief Calculate the correction to the Ewald sum, due to a net system
+ * charge.
+ *
+ * Should only be called on one thread. */
+real
+ewald_charge_correction(t_commrec *cr, t_forcerec *fr, real lambda, matrix box,
+ real *dvdlambda, tensor vir);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <stdio.h>
-#include <math.h>
-#include "gromacs/math/utilities.h"
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "vec.h"
-#include "coulomb.h"
-#include "gromacs/utility/smalloc.h"
-#include "physics.h"
-#include "txtdump.h"
-#include "gromacs/fileio/futil.h"
-#include "names.h"
-#include "macros.h"
-
-real calc_ewaldcoeff_q(real rc, real dtol)
-{
- real x = 5, low, high;
- int n, i = 0;
-
-
- do
- {
- i++;
- x *= 2;
- }
- while (gmx_erfc(x*rc) > dtol);
-
- n = i+60; /* search tolerance is 2^-60 */
- low = 0;
- high = x;
- for (i = 0; i < n; i++)
- {
- x = (low+high)/2;
- if (gmx_erfc(x*rc) > dtol)
- {
- low = x;
- }
- else
- {
- high = x;
- }
- }
- return x;
-}
+#include "gmxpre.h"
-static real ewald_function_lj(real x, real rc)
-{
- real xrc, xrc2, xrc4, factor;
- xrc = x*rc;
- xrc2 = xrc*xrc;
- xrc4 = xrc2*xrc2;
-#ifdef GMX_DOUBLE
- factor = exp(-xrc2)*(1 + xrc2 + xrc4/2.0);
-#else
- factor = expf(-xrc2)*(1 + xrc2 + xrc4/2.0);
-#endif
+#include "long-range-correction.h"
- return factor;
-}
-
-real calc_ewaldcoeff_lj(real rc, real dtol)
-{
- real x = 5, low, high;
- int n, i = 0;
-
- do
- {
- i++;
- x *= 2.0;
- }
- while (ewald_function_lj(x, rc) > dtol);
+#include <math.h>
- n = i + 60; /* search tolerance is 2^-60 */
- low = 0;
- high = x;
- for (i = 0; i < n; ++i)
- {
- x = (low + high) / 2.0;
- if (ewald_function_lj(x, rc) > dtol)
- {
- low = x;
- }
- else
- {
- high = x;
- }
- }
- return x;
-}
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
/* There's nothing special to do here if just masses are perturbed,
* but if either charge or type is perturbed then the implementation
}
}
}
-
-real ewald_charge_correction(t_commrec *cr, t_forcerec *fr, real lambda,
- matrix box,
- real *dvdlambda, tensor vir)
-
-{
- real vol, fac, qs2A, qs2B, vc, enercorr;
- int d;
-
- if (MASTER(cr))
- {
- /* Apply charge correction */
- vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
-
- fac = M_PI*ONE_4PI_EPS0/(fr->epsilon_r*2.0*vol*vol*sqr(fr->ewaldcoeff_q));
-
- qs2A = fr->qsum[0]*fr->qsum[0];
- qs2B = fr->qsum[1]*fr->qsum[1];
-
- vc = (qs2A*(1 - lambda) + qs2B*lambda)*fac;
-
- enercorr = -vol*vc;
-
- *dvdlambda += -vol*(qs2B - qs2A)*fac;
-
- for (d = 0; d < DIM; d++)
- {
- vir[d][d] += vc;
- }
-
- if (debug)
- {
- fprintf(debug, "Total charge correction: Vcharge=%g\n", enercorr);
- }
- }
- else
- {
- enercorr = 0;
- }
-
- return enercorr;
-}
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _coulomb_h
-#define _coulomb_h
+#ifndef GMX_EWALD_LONG_RANGE_CORRECTION_H
+#define GMX_EWALD_LONG_RANGE_CORRECTION_H
-#include <stdio.h>
-#include "typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#endif
-/* Ewald related stuff */
-
-void
-init_ewald_tab(ewald_tab_t *et, const t_inputrec *ir,
- FILE *fp);
-/* initialize the ewald table (as found in the t_forcerec) */
-
-real
-calc_ewaldcoeff_q(real rc, real dtol);
-/* Determines the Ewald parameter, both for Ewald and PME */
-
-extern real calc_ewaldcoeff_lj(real rc, real dtol);
-/* Determines the Ewald parameters for LJ-PME */
-
-real
-do_ewald(t_inputrec *ir,
- rvec x[], rvec f[],
- real chargeA[], real chargeB[],
- rvec box,
- t_commrec *cr, int natoms,
- matrix lrvir, real ewaldcoeff,
- real lambda, real *dvdlambda,
- ewald_tab_t et);
-/* Do an Ewald calculation for the long range electrostatics. */
-
+/*! \brief Calculate long-range Ewald correction terms.
+ *
+ * For the group cutoff scheme (only), calculates the correction to
+ * the Ewald sums (electrostatic and/or LJ) due to pairs excluded from
+ * the long-ranged part.
+ *
+ * For both cutoff schemes, but only for Coulomb interactions,
+ * calculates correction for surface dipole terms. */
void
ewald_LRcorrection(int start, int end,
t_commrec *cr, int thread, t_forcerec *fr,
real *Vcorr_q, real *Vcorr_lj,
real lambda_q, real lambda_lj,
real *dvdlambda_q, real *dvdlambda_lj);
-/* Calculate the Long range correction to the Ewald sums,
- * electrostatic and/or LJ, due to excluded pairs and/or
- * surface dipole terms.
- */
-
-real
-ewald_charge_correction(t_commrec *cr, t_forcerec *fr, real lambda, matrix box,
- real *dvdlambda, tensor vir);
-/* Calculate the Long range correction to the Ewald sum,
- * due to a net system charge.
- * Should only be called on one thread.
- */
#ifdef __cplusplus
}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/* TODO This file is a temporary holding area for stuff local to the
+ * PME code, before it acquires some more normal ewald/file.c and
+ * ewald/file.h structure. In future clean up, get rid of this file,
+ * to build more normal. */
+
+#ifndef GMX_EWALD_PME_INTERNAL_H
+#define GMX_EWALD_PME_INTERNAL_H
+
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+int gmx_pme_reinit(gmx_pme_t * pmedata,
+ t_commrec * cr,
+ gmx_pme_t pme_src,
+ const t_inputrec * ir,
+ ivec grid_size);
+/* As gmx_pme_init, but takes most settings, except the grid, from pme_src */
+
+/* The following three routines are for PME/PP node splitting in pme_pp.c */
+
+/* Abstract type for PME <-> PP communication */
+typedef struct gmx_pme_pp *gmx_pme_pp_t;
+
+void gmx_pme_check_restrictions(int pme_order,
+ int nkx, int nky, int nkz,
+ int nnodes_major,
+ int nnodes_minor,
+ gmx_bool bUseThreads,
+ gmx_bool bFatal,
+ gmx_bool *bValidSettings);
+/* Check restrictions on pme_order and the PME grid nkx,nky,nkz.
+ * With bFatal=TRUE, a fatal error is generated on violation,
+ * bValidSettings=NULL can be passed.
+ * With bFatal=FALSE, *bValidSettings reports the validity of the settings.
+ * bUseThreads tells if any MPI rank doing PME uses more than 1 threads.
+ * If at calling you bUseThreads is unknown, pass TRUE for conservative
+ * checking.
+ */
+
+gmx_pme_pp_t gmx_pme_pp_init(t_commrec *cr);
+/* Initialize the PME-only side of the PME <-> PP communication */
+
+void gmx_pme_send_switchgrid(t_commrec *cr, ivec grid_size, real ewaldcoeff_q, real ewaldcoeff_lj);
+/* Tell our PME-only node to switch to a new grid size */
+
+/* Return values for gmx_pme_recv_q_x */
+enum {
+ pmerecvqxX, /* calculate PME mesh interactions for new x */
+ pmerecvqxFINISH, /* the simulation should finish, we should quit */
+ pmerecvqxSWITCHGRID, /* change the PME grid size */
+ pmerecvqxRESETCOUNTERS /* reset the cycle and flop counters */
+};
+
+int gmx_pme_recv_coeffs_coords(gmx_pme_pp_t pme_pp,
+ int *natoms,
+ real **chargeA, real **chargeB,
+ real **sqrt_c6A, real **sqrt_c6B,
+ real **sigmaA, real **sigmaB,
+ matrix box, rvec **x, rvec **f,
+ int *maxshift_x, int *maxshift_y,
+ gmx_bool *bFreeEnergy_q, gmx_bool *bFreeEnergy_lj,
+ real *lambda_q, real *lambda_lj,
+ gmx_bool *bEnerVir, int *pme_flags,
+ gmx_int64_t *step,
+ ivec grid_size, real *ewaldcoeff_q, real *ewaldcoeff_lj);
+;
+/* With return value:
+ * pmerecvqxX: all parameters set, chargeA and chargeB can be NULL
+ * pmerecvqxFINISH: no parameters set
+ * pmerecvqxSWITCHGRID: only grid_size and *ewaldcoeff are set
+ * pmerecvqxRESETCOUNTERS: *step is set
+ */
+
+void gmx_pme_send_force_vir_ener(gmx_pme_pp_t pme_pp,
+ rvec *f, matrix vir_q, real energy_q,
+ matrix vir_lj, real energy_lj,
+ real dvdlambda_q, real dvdlambda_lj,
+ float cycles);
+/* Send the PME mesh force, virial and energy to the PP-only nodes */
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
+#include "gmxpre.h"
+
+#include "pme-load-balancing.h"
+
+#include "config.h"
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/ewald/pme-internal.h"
+#include "gromacs/legacyheaders/calcgrid.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
-#include "types/commrec.h"
-#include "network.h"
-#include "calcgrid.h"
-#include "pme.h"
-#include "vec.h"
-#include "domdec.h"
-#include "nbnxn_cuda_data_mgmt.h"
-#include "force.h"
-#include "macros.h"
-#include "md_logging.h"
-#include "pme_loadbal.h"
/* Parameters and setting for one PP-PME setup */
typedef struct {
pme_lb->cur = pme_lb->start - 1;
}
-gmx_bool pme_load_balance(pme_load_balancing_t pme_lb,
- t_commrec *cr,
- FILE *fp_err,
- FILE *fp_log,
- t_inputrec *ir,
- t_state *state,
- double cycles,
- interaction_const_t *ic,
- nonbonded_verlet_t *nbv,
- gmx_pme_t *pmedata,
- gmx_int64_t step)
+gmx_bool pme_load_balance(pme_load_balancing_t pme_lb,
+ t_commrec *cr,
+ FILE *fp_err,
+ FILE *fp_log,
+ t_inputrec *ir,
+ t_state *state,
+ double cycles,
+ interaction_const_t *ic,
+ struct nonbonded_verlet_t *nbv,
+ gmx_pme_t *pmedata,
+ gmx_int64_t step)
{
gmx_bool OK;
pme_setup_t *set;
}
bUsesSimpleTables = uses_simple_tables(ir->cutoff_scheme, nbv, 0);
- if (pme_lb->cutoff_scheme == ecutsVERLET &&
- nbv->grp[0].kernel_type == nbnxnk8x8x8_CUDA)
- {
- nbnxn_cuda_pme_loadbal_update_param(nbv->cu_nbv, ic);
-
- /* With tMPI + GPUs some ranks may be sharing GPU(s) and therefore
- * also sharing texture references. To keep the code simple, we don't
- * treat texture references as shared resources, but this means that
- * the coulomb_tab texture ref will get updated by multiple threads.
- * Hence, to ensure that the non-bonded kernels don't start before all
- * texture binding operations are finished, we need to wait for all ranks
- * to arrive here before continuing.
- *
- * Note that we could omit this barrier if GPUs are not shared (or
- * texture objects are used), but as this is initialization code, there
- * is not point in complicating things.
- */
+ nbnxn_cuda_pme_loadbal_update_param(nbv, ic);
+
+ /* With tMPI + GPUs some ranks may be sharing GPU(s) and therefore
+ * also sharing texture references. To keep the code simple, we don't
+ * treat texture references as shared resources, but this means that
+ * the coulomb_tab texture ref will get updated by multiple threads.
+ * Hence, to ensure that the non-bonded kernels don't start before all
+ * texture binding operations are finished, we need to wait for all ranks
+ * to arrive here before continuing.
+ *
+ * Note that we could omit this barrier if GPUs are not shared (or
+ * texture objects are used), but as this is initialization code, there
+ * is not point in complicating things.
+ */
#ifdef GMX_THREAD_MPI
- if (PAR(cr))
- {
- gmx_barrier(cr);
- }
-#endif /* GMX_THREAD_MPI */
+ if (PAR(cr) && use_GPU(nbv))
+ {
+ gmx_barrier(cr);
}
+#endif /* GMX_THREAD_MPI */
/* Usually we won't need the simple tables with GPUs.
* But we do with hybrid acceleration and with free energy.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _pme_loadbal_h
-#define _pme_loadbal_h
+#ifndef GMX_EWALD_PME_LOAD_BALANCING_H
+#define GMX_EWALD_PME_LOAD_BALANCING_H
+
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/legacyheaders/types/state.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
typedef struct pme_load_balancing *pme_load_balancing_t;
* factors as well as DD load balancing.
* Returns TRUE the load balancing continues, FALSE is the balancing is done.
*/
-gmx_bool pme_load_balance(pme_load_balancing_t pme_lb,
- t_commrec *cr,
- FILE *fp_err,
- FILE *fp_log,
- t_inputrec *ir,
- t_state *state,
- double cycles,
- interaction_const_t *ic,
- nonbonded_verlet_t *nbv,
- gmx_pme_t *pmedata,
- gmx_int64_t step);
+gmx_bool pme_load_balance(pme_load_balancing_t pme_lb,
+ t_commrec *cr,
+ FILE *fp_err,
+ FILE *fp_log,
+ t_inputrec *ir,
+ t_state *state,
+ double cycles,
+ interaction_const_t *ic,
+ struct nonbonded_verlet_t *nbv,
+ gmx_pme_t *pmedata,
+ gmx_int64_t step);
/* Restart the PME load balancing discarding all timings gathered up till now */
void restart_pme_loadbal(pme_load_balancing_t pme_lb, int n);
t_commrec *cr, FILE *fplog,
gmx_bool bNonBondedOnGPU);
-#endif /* _pme_loadbal_h */
+#ifdef __cplusplus
+}
+#endif
+
+#endif
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "config.h"
+#include <math.h>
#include <stdio.h>
#include <string.h>
-#include <math.h>
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "pme.h"
-#include "network.h"
-#include "domdec.h"
-#include "sighandler.h"
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/ewald/pme-internal.h"
+#include "gromacs/ewald/pme.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/sighandler.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
enum {
eCommType_ChargeA, eCommType_ChargeB, eCommType_SQRTC6A, eCommType_SQRTC6B,
* /Erik 001109
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <stdio.h>
-#include <string.h>
-#include <math.h>
-#include <assert.h>
-#include "typedefs.h"
-#include "txtdump.h"
-#include "vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "coulomb.h"
-#include "gmx_fatal.h"
#include "pme.h"
-#include "network.h"
-#include "physics.h"
-#include "nrnb.h"
-#include "macros.h"
+#include "config.h"
+
+#include <assert.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "gromacs/ewald/pme-internal.h"
+#include "gromacs/fft/fft.h"
#include "gromacs/fft/parallel_3dfft.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/pdbio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/nrnb.h"
#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
+/* Include the SIMD macro file and then check for support */
+#include "gromacs/simd/simd.h"
+#include "gromacs/simd/simd_math.h"
#include "gromacs/timing/cyclecounter.h"
#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/real.h"
+#include "gromacs/utility/smalloc.h"
+
+#ifdef DEBUG_PME
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/futil.h"
+#endif
-/* Include the SIMD macro file and then check for support */
-#include "gromacs/simd/simd.h"
-#include "gromacs/simd/simd_math.h"
#ifdef GMX_SIMD_HAVE_REAL
/* Turn on arbitrary width SIMD intrinsics for PME solve */
# define PME_SIMD_SOLVE
int recv_size; /* Receive buffer width, used with OpenMP */
} pme_grid_comm_t;
+typedef real *splinevec[DIM];
+
typedef struct {
#ifdef GMX_MPI
MPI_Comm mpi_comm;
#define PME_SPREAD_SIMD4_ALIGNED
#define PME_ORDER 4
#endif
-#include "pme_simd4.h"
+#include "gromacs/ewald/pme-simd4.h" /* IWYU pragma: keep */
#else
DO_BSPLINE(4);
#endif
#ifdef PME_SIMD4_SPREAD_GATHER
#define PME_SPREAD_SIMD4_ALIGNED
#define PME_ORDER 5
-#include "pme_simd4.h"
+#include "gromacs/ewald/pme-simd4.h" /* IWYU pragma: keep */
#else
DO_BSPLINE(5);
#endif
static void realloc_work(pme_work_t *work, int nkx)
{
- int simd_width;
+ int simd_width, i;
if (nkx > work->nalloc)
{
snew_aligned(work->tmp2, work->nalloc+simd_width, simd_width*sizeof(real));
snew_aligned(work->eterm, work->nalloc+simd_width, simd_width*sizeof(real));
srenew(work->m2inv, work->nalloc);
+#ifndef NDEBUG
+ for (i = 0; i < work->nalloc+simd_width; i++)
+ {
+ work->denom[i] = 1; /* init to 1 to avoid 1/0 exceptions of simd padded elements */
+ }
+#endif
}
}
#define PME_GATHER_F_SIMD4_ALIGNED
#define PME_ORDER 4
#endif
-#include "pme_simd4.h"
+#include "gromacs/ewald/pme-simd4.h" /* IWYU pragma: keep */
#else
DO_FSPLINE(4);
#endif
#ifdef PME_SIMD4_SPREAD_GATHER
#define PME_GATHER_F_SIMD4_ALIGNED
#define PME_ORDER 5
-#include "pme_simd4.h"
+#include "gromacs/ewald/pme-simd4.h" /* IWYU pragma: keep */
#else
DO_FSPLINE(5);
#endif
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _pme_h
-#define _pme_h
+#ifndef GMX_EWALD_PME_H
+#define GMX_EWALD_PME_H
#include <stdio.h>
-#include "typedefs.h"
-#include "../math/gmxcomplex.h"
-#include "../timing/walltime_accounting.h"
-#include "../legacyheaders/network.h"
+
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/legacyheaders/types/nrnb.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#endif
-typedef real *splinevec[DIM];
-
enum {
GMX_SUM_GRID_FORWARD, GMX_SUM_GRID_BACKWARD
};
* Return value 0 indicates all well, non zero is an error code.
*/
-int gmx_pme_reinit(gmx_pme_t * pmedata,
- t_commrec * cr,
- gmx_pme_t pme_src,
- const t_inputrec * ir,
- ivec grid_size);
-/* As gmx_pme_init, but takes most settings, except the grid, from pme_src */
-
int gmx_pme_destroy(FILE *log, gmx_pme_t *pmedata);
/* Destroy the pme data structures resepectively.
* Return value 0 indicates all well, non zero is an error code.
* Currently does not work in parallel or with free energy.
*/
-/* The following three routines are for PME/PP node splitting in pme_pp.c */
-
-/* Abstract type for PME <-> PP communication */
-typedef struct gmx_pme_pp *gmx_pme_pp_t;
-
-void gmx_pme_check_restrictions(int pme_order,
- int nkx, int nky, int nkz,
- int nnodes_major,
- int nnodes_minor,
- gmx_bool bUseThreads,
- gmx_bool bFatal,
- gmx_bool *bValidSettings);
-/* Check restrictions on pme_order and the PME grid nkx,nky,nkz.
- * With bFatal=TRUE, a fatal error is generated on violation,
- * bValidSettings=NULL can be passed.
- * With bFatal=FALSE, *bValidSettings reports the validity of the settings.
- * bUseThreads tells if any MPI rank doing PME uses more than 1 threads.
- * If at calling you bUseThreads is unknown, pass TRUE for conservative
- * checking.
- */
-
-gmx_pme_pp_t gmx_pme_pp_init(t_commrec *cr);
-/* Initialize the PME-only side of the PME <-> PP communication */
-
void gmx_pme_send_parameters(t_commrec *cr,
const interaction_const_t *ic,
gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj,
void gmx_pme_send_finish(t_commrec *cr);
/* Tell our PME-only node to finish */
-void gmx_pme_send_switchgrid(t_commrec *cr, ivec grid_size, real ewaldcoeff_q, real ewaldcoeff_lj);
-/* Tell our PME-only node to switch to a new grid size */
-
void gmx_pme_send_resetcounters(t_commrec *cr, gmx_int64_t step);
/* Tell our PME-only node to reset all cycle and flop counters */
float *pme_cycles);
/* PP nodes receive the long range forces from the PME nodes */
-/* Return values for gmx_pme_recv_q_x */
-enum {
- pmerecvqxX, /* calculate PME mesh interactions for new x */
- pmerecvqxFINISH, /* the simulation should finish, we should quit */
- pmerecvqxSWITCHGRID, /* change the PME grid size */
- pmerecvqxRESETCOUNTERS /* reset the cycle and flop counters */
-};
-
-int gmx_pme_recv_coeffs_coords(gmx_pme_pp_t pme_pp,
- int *natoms,
- real **chargeA, real **chargeB,
- real **sqrt_c6A, real **sqrt_c6B,
- real **sigmaA, real **sigmaB,
- matrix box, rvec **x, rvec **f,
- int *maxshift_x, int *maxshift_y,
- gmx_bool *bFreeEnergy_q, gmx_bool *bFreeEnergy_lj,
- real *lambda_q, real *lambda_lj,
- gmx_bool *bEnerVir, int *pme_flags,
- gmx_int64_t *step,
- ivec grid_size, real *ewaldcoeff_q, real *ewaldcoeff_lj);
-;
-/* With return value:
- * pmerecvqxX: all parameters set, chargeA and chargeB can be NULL
- * pmerecvqxFINISH: no parameters set
- * pmerecvqxSWITCHGRID: only grid_size and *ewaldcoeff are set
- * pmerecvqxRESETCOUNTERS: *step is set
- */
-
-void gmx_pme_send_force_vir_ener(gmx_pme_pp_t pme_pp,
- rvec *f, matrix vir_q, real energy_q,
- matrix vir_lj, real energy_lj,
- real dvdlambda_q, real dvdlambda_lj,
- float cycles);
-/* Send the PME mesh force, virial and energy to the PP-only nodes */
-
#ifdef __cplusplus
}
#endif
# GLOB is used to get full paths
file(GLOB FFT_SOURCES
- fft.c fft5d.cpp parallel_3dfft.c)
+ fft.cpp fft5d.cpp parallel_3dfft.cpp)
if (GMX_FFT_FFTPACK)
- file(GLOB FFT_SPECIFIC_SOURCES fft_fftpack.c)
+ file(GLOB FFT_SPECIFIC_SOURCES fft_fftpack.cpp)
list(APPEND FFT_SPECIFIC_SOURCES
${CMAKE_SOURCE_DIR}/src/external/fftpack/fftpack.c)
endif()
file(GLOB FFT_SPECIFIC_SOURCES fft_fftw3.cpp)
endif()
if (GMX_FFT_MKL)
- file(GLOB FFT_SPECIFIC_SOURCES fft_mkl.c)
+ file(GLOB FFT_SPECIFIC_SOURCES fft_mkl.cpp)
endif()
set(LIBGROMACS_SOURCES
${LIBGROMACS_SOURCES} ${FFT_SOURCES} ${FFT_SPECIFIC_SOURCES} PARENT_SCOPE)
-set(FFT_PUBLIC_HEADERS
- fft.h)
-gmx_install_headers(fft ${FFT_PUBLIC_HEADERS})
+gmx_install_headers(fft.h)
if (BUILD_TESTING)
add_subdirectory(tests)
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "fft.h"
+
+#include "config.h"
+
+#include <errno.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include <errno.h>
-#include "types/simple.h"
-#include "gmx_fatal.h"
-#include "gromacs/fft/fft.h"
#include "gromacs/math/gmxcomplex.h"
-
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/real.h"
/* This file contains common fft utility functions, but not
* the actual transform implementations. Check the
#include <stdio.h>
-#include "../legacyheaders/types/simple.h"
-#include "../math/gmxcomplex.h"
+#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <algorithm>
+#include "fft5d.h"
+#include "config.h"
+
+#include <assert.h>
+#include <float.h>
+#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
+#include <algorithm>
+
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
+
#ifdef NOGMX
#define GMX_PARALLEL_ENV_INITIALIZED 1
#else
#endif
#endif
-#include "gromacs/utility/gmxmpi.h"
-
#ifdef GMX_OPENMP
/* TODO: Do we still need this? Are we still planning ot use fftw + OpenMP? */
#define FFT5D_THREADS
/* #define FFT5D_FFTW_THREADS (now set by cmake) */
#endif
-#include "fft5d.h"
-#include <float.h>
-#include <math.h>
-#include <assert.h>
-#include "gromacs/utility/smalloc.h"
-
#ifndef __FLT_EPSILON__
#define __FLT_EPSILON__ FLT_EPSILON
#define __DBL_EPSILON__ DBL_EPSILON
FILE* debug = 0;
#endif
-#include "gmx_fatal.h"
-
-
#ifdef GMX_FFT_FFTW3
#include "thread_mpi/mutex.h"
+
#include "gromacs/utility/exceptions.h"
/* none of the fftw3 calls, except execute(), are thread-safe, so
we need to serialize them with this mutex. */
s = 0;
/*lin: x,y,z*/
- if (plan->flags&FFT5D_DEBUG && thread == 0)
+ if ((plan->flags&FFT5D_DEBUG) && thread == 0)
{
print_localdata(lin, "%d %d: copy in lin\n", s, plan);
}
time_fft += MPI_Wtime()-time;
}
#endif
- if (plan->flags&FFT5D_DEBUG && thread == 0)
+ if ((plan->flags&FFT5D_DEBUG) && thread == 0)
{
print_localdata(lout, "%d %d: FFT %d\n", s, plan);
}
time_local += MPI_Wtime()-time;
}
#endif
- if (plan->flags&FFT5D_DEBUG && thread == 0)
+ if ((plan->flags&FFT5D_DEBUG) && thread == 0)
{
print_localdata(lin, "%d %d: tranposed %d\n", s+1, plan);
}
}
#endif
- if (plan->flags&FFT5D_DEBUG && thread == 0)
+ if ((plan->flags&FFT5D_DEBUG) && thread == 0)
{
print_localdata(lout, "%d %d: FFT %d\n", s, plan);
}
#ifndef FFT5D_H_
#define FFT5D_H_
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "config.h"
#ifdef NOGMX
/*#define GMX_MPI*/
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2003 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include <errno.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
-#include <errno.h>
-
-#include "gromacs/fft/fft.h"
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gmx_fatal.h"
#include "external/fftpack/fftpack.h"
+#include "gromacs/fft/fft.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/real.h"
+
/*! \internal
* \brief
* Contents of the FFTPACK fft datatype.
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2003 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <errno.h>
#include <stdlib.h>
#include <fftw3.h>
+#include "thread_mpi/mutex.h"
+
#include "gromacs/fft/fft.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
#ifdef GMX_DOUBLE
#define FFTWPREFIX(name) fftw_ ## name
#define FFTWPREFIX(name) fftwf_ ## name
#endif
-#include "thread_mpi/mutex.h"
-#include "gromacs/utility/exceptions.h"
-
/* none of the fftw3 calls, except execute(), are thread-safe, so
we need to serialize them with this mutex. */
static tMPI::mutex big_fftw_mutex;
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2003 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <errno.h>
#include <stdlib.h>
#include <mkl_service.h>
#include "gromacs/fft/fft.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/* For MKL version (<10.0), we should define MKL_LONG. */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "parallel_3dfft.h"
+
+#include <errno.h>
#include <stdlib.h>
#include <string.h>
-#include <errno.h>
#include "gromacs/fft/fft.h"
-#include "gromacs/fft/parallel_3dfft.h"
+#include "gromacs/fft/fft5d.h"
#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
-
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-
-#include "fft5d.h"
struct gmx_parallel_3dfft {
fft5d_plan p1, p2;
static void reorder_ivec_yzx(ivec v)
{
- real tmp;
+ int tmp;
tmp = v[0];
v[XX] = v[2];
#ifndef GMX_FFT_PARALLEL_3DFFT_H
#define GMX_FFT_PARALLEL_3DFFT_H
-#include "../legacyheaders/types/nrnb.h"
-#include "../legacyheaders/types/simple.h"
-#include "../math/gmxcomplex.h"
-#include "../utility/gmxmpi.h"
-#include "fft.h"
+#include "gromacs/fft/fft.h"
+#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
* \author Roland Schulz <roland@utk.edu>
* \ingroup module_fft
*/
+#include "gmxpre.h"
+
+#include "gromacs/fft/fft.h"
+
#include <vector>
#include <gtest/gtest.h>
-#include "gromacs/fft/fft.h"
#include "gromacs/fft/parallel_3dfft.h"
#include "gromacs/utility/stringutil.h"
// TODO: These tolerances are just something that has been observed
// to be sufficient to pass the tests. It would be nicer to
// actually argue about why they are sufficient (or what is).
-#ifdef GMX_DOUBLE
- checker_.setDefaultTolerance(gmx::test::relativeRealTolerance(10.0, 512));
-#else
- checker_.setDefaultTolerance(gmx::test::relativeRealTolerance(10.0, 64));
-#endif
+ checker_.setDefaultTolerance(
+ gmx::test::relativeToleranceAsPrecisionDependentUlp(10.0, 64, 512));
}
~BaseFFTTest()
{
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${FILEIO_SOURCES} PARENT_SCOPE)
-set(FILEIO_PUBLIC_HEADERS
+gmx_install_headers(
confio.h
enxio.h
filenm.h
- futil.h
gmxfio.h
matio.h
mdoutf.h
+ mtxio.h
pdbio.h
tpxio.h
trajectory_writing.h
trxio.h
xdr_datatype.h
xtcio.h
+ xvgr.h
)
-gmx_install_headers(fileio ${FILEIO_PUBLIC_HEADERS})
if (GMX_USE_TNG AND TNG_IO_DEFINITIONS)
set_property(SOURCE tngio.cpp
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "confio.h"
-#include <math.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
#include <errno.h>
-#include "macros.h"
+#include <math.h>
+#include <stdio.h>
+
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xdrf.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
-#include "confio.h"
-#include "vec.h"
-#include "symtab.h"
-#include "futil.h"
-#include "xdrf.h"
-#include "filenm.h"
-#include "pdbio.h"
-#include "tpxio.h"
-#include "trxio.h"
-#include "gmx_fatal.h"
-#include "copyrite.h"
-#include "pbc.h"
-#include "mtop_util.h"
-#include "gmxfio.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define CHAR_SHIFT 24
if (fr->title == NULL)
{
fgets2(line, STRLEN, fp);
- fr->title = strdup(line);
+ fr->title = gmx_strdup(line);
}
bEnd = FALSE;
while (!bEnd && fgets2(line, STRLEN, fp))
gmx_fio_fclose(in);
}
+static gmx_bool gmx_one_before_eof(FILE *fp)
+{
+ char data[4];
+ gmx_bool beof;
+
+ if ((beof = fread(data, 1, 1, fp)) == 1)
+ {
+ gmx_fseek(fp, -1, SEEK_CUR);
+ }
+ return !beof;
+}
+
gmx_bool gro_next_x_or_v(FILE *status, t_trxframe *fr)
{
t_atoms atoms;
double tt;
int ndec = 0, i;
- if (gmx_eof(status))
+ if (gmx_one_before_eof(status))
{
return FALSE;
}
gmx_fio_fclose(out);
break;
case efTPR:
- case efTPB:
- case efTPA:
gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
break;
default:
gmx_fio_fclose(out);
break;
case efTPR:
- case efTPB:
- case efTPA:
gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
break;
default:
case efESP:
*natoms = get_espresso_coordnum(infile);
break;
- case efTPA:
- case efTPB:
case efTPR:
{
t_tpxheader tpx;
read_espresso_conf(infile, atoms, x, v, box);
break;
case efTPR:
- case efTPB:
- case efTPA:
snew(mtop, 1);
i = read_tpx(infile, NULL, box, &natoms, x, v, NULL, mtop);
if (ePBC)
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_FILEIO_CONFIO_H
#define GMX_FILEIO_CONFIO_H
+#include <stdio.h>
-#include "../legacyheaders/typedefs.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/types/simple.h"
/* For reading coordinate files it is assumed that enough memory
* has been allocated beforehand.
extern "C" {
#endif
+struct gmx_mtop_t;
+struct t_atoms;
+
int read_g96_conf(FILE *fp, const char *infile, t_trxframe *fr, char *line);
/* read a Gromos96 coordinate or trajectory file, *
* returns the number of atoms *
int gro_first_x_or_v(FILE *status, t_trxframe *fr);
/* read first/next x and/or v frame from gro file */
-void write_hconf_indexed_p(FILE *out, const char *title, t_atoms *atoms,
+void write_hconf_indexed_p(FILE *out, const char *title, struct t_atoms *atoms,
int nx, const atom_id index[], int ndec,
rvec *x, rvec *v, matrix box);
-void write_hconf_p(FILE *out, const char *title, t_atoms *atoms, int ndec,
+void write_hconf_p(FILE *out, const char *title, struct t_atoms *atoms, int ndec,
rvec *x, rvec *v, matrix box);
/* Write a Gromos file with precision ndec: number of decimal places in x,
* v has one place more. */
void write_sto_conf_indexed(const char *outfile, const char *title,
- t_atoms *atoms,
+ struct t_atoms *atoms,
rvec x[], rvec *v, int ePBC, matrix box,
atom_id nindex, atom_id index[]);
/* like write_sto_conf, but indexed */
void write_sto_conf(const char *outfile, const char *title,
- t_atoms *atoms,
+ struct t_atoms *atoms,
rvec x[], rvec *v, int ePBC, matrix box);
/* write atoms, x, v (if .gro and not NULL) and box (if not NULL)
* to an STO (.gro or .pdb) file */
void write_sto_conf_mtop(const char *outfile, const char *title,
- gmx_mtop_t *mtop,
+ struct gmx_mtop_t *mtop,
rvec x[], rvec *v, int ePBC, matrix box);
/* As write_sto_conf, but uses a gmx_mtop_t struct */
/* read the number of atoms from an STX file */
void read_stx_conf(const char *infile, char *title,
- t_atoms *atoms,
+ struct t_atoms *atoms,
rvec x[], rvec *v, int *ePBC, matrix box);
/* Read atoms, x, v and box from an STX file.
* If ePBC!=NULL return the type of pbc in *ePBC or -1 if unknown.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "enxio.h"
+#include <stdlib.h>
#include <string.h>
-#include "futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/xdrf.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "gmxfio.h"
-#include "enxio.h"
-#include "vec.h"
-#include "xdrf.h"
-#include "macros.h"
/* The source code in this file should be thread-safe.
Please keep it that way. */
{
if (sb->fval_alloc)
{
- free(sb->fval);
+ sfree(sb->fval);
sb->fval_alloc = 0;
sb->fval = NULL;
}
if (sb->dval_alloc)
{
- free(sb->dval);
+ sfree(sb->dval);
sb->dval_alloc = 0;
sb->dval = NULL;
}
if (sb->ival_alloc)
{
- free(sb->ival);
+ sfree(sb->ival);
sb->ival_alloc = 0;
sb->ival = NULL;
}
if (sb->lval_alloc)
{
- free(sb->lval);
+ sfree(sb->lval);
sb->lval_alloc = 0;
sb->lval = NULL;
}
if (sb->cval_alloc)
{
- free(sb->cval);
+ sfree(sb->cval);
sb->cval_alloc = 0;
sb->cval = NULL;
}
{
if (sb->sval[i])
{
- free(sb->sval[i]);
+ sfree(sb->sval[i]);
}
}
- free(sb->sval);
+ sfree(sb->sval);
sb->sval_alloc = 0;
sb->sval = NULL;
}
{
enxsubblock_free(&(eb->sub[i]));
}
- free(eb->sub);
+ sfree(eb->sub);
eb->nsub_alloc = 0;
eb->sub = NULL;
}
{
enxblock_free(&(fr->block[b]));
}
- free(fr->block);
+ sfree(fr->block);
}
void add_blocks_enxframe(t_enxframe *fr, int n)
}
else
{
- nm->unit = strdup("kJ/mol");
+ nm->unit = gmx_strdup("kJ/mol");
}
}
}
int i, b;
gmx_bool bRead, bOK, bOK1, bSane;
real tmp1, tmp2, rdum;
- char buf[22];
/*int d_size;*/
bOK = TRUE;
{
fprintf(stderr, "\nWARNING: there may be something wrong with energy file %s\n",
gmx_fio_getname(ef->fio));
- fprintf(stderr, "Found: step=%s, nre=%d, nblock=%d, time=%g.\n"
+ fprintf(stderr, "Found: step=%"GMX_PRId64 ", nre=%d, nblock=%d, time=%g.\n"
"Trying to skip frame expect a crash though\n",
- gmx_step_str(fr->step, buf), fr->nre, fr->nblock, fr->t);
+ fr->step, fr->nre, fr->nblock, fr->t);
}
if (bRead && fr->nre > fr->e_alloc)
{
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_FILEIO_ENXIO_H
#define GMX_FILEIO_ENXIO_H
-#include "../legacyheaders/typedefs.h"
-#include "../legacyheaders/pbc.h"
-#include "gmxfio.h"
-#include "xdr_datatype.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/xdr_datatype.h"
+#include "gromacs/legacyheaders/types/energy.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/state.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct gmx_groups_t;
+
/**************************************************************
* These are the base datatypes + functions for reading and
* writing energy files (.edr). They are either called directly
/* Reads enx_frames, memory in fr is (re)allocated if necessary */
void get_enx_state(const char *fn, real t,
- gmx_groups_t *groups, t_inputrec *ir,
+ struct gmx_groups_t *groups, t_inputrec *ir,
t_state *state);
/*
* Reads state variables from enx file fn at time t.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "filenm.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "filenm.h"
#include <stdio.h>
-#include <stdlib.h>
#include <string.h>
-#include "futil.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/cstringutil.h"
-#include "types/simple.h"
-#include "types/commrec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* XDR should be available on all platforms now,
* but we keep the possibility of turning it off...
/* Use bitflag ... */
#define IS_SET(fn) ((fn.flag & ffSET) != 0)
#define IS_OPT(fn) ((fn.flag & ffOPT) != 0)
-#define IS_MULT(fn) ((fn.flag & ffMULT) != 0)
-#define UN_SET(fn) (fn.flag = (fn.flag & ~ffSET))
-#define DO_SET(fn) (fn.flag = (fn.flag | ffSET))
enum
{
#ifdef USE_XDR
efXTC, efTRR, efCPT,
#endif
- efTRJ, efGRO, efG96, efPDB, efTNG
+ efGRO, efG96, efPDB, efTNG
};
#define NTRXS asize(trxs)
#ifdef USE_XDR
efXTC, efTRR,
#endif
- efTRJ, efGRO, efG96, efPDB, efTNG
+ efGRO, efG96, efPDB, efTNG
};
#define NTROS asize(tros)
#ifdef USE_XDR
efTRR, efCPT,
#endif
- efTRJ, efTNG
+ efTNG
};
#define NTRNS asize(trns)
static const int stxs[] =
{
- efGRO, efG96, efPDB, efBRK, efENT, efESP,
+ efGRO, efG96, efPDB, efBRK, efENT, efESP
#ifdef USE_XDR
- efTPR,
+ , efTPR
#endif
- efTPB, efTPA
};
#define NSTXS asize(stxs)
-static const int tpxs[] =
-{
-#ifdef USE_XDR
- efTPR,
-#endif
- efTPB, efTPA
-};
-#define NTPXS asize(tpxs)
-
static const int tpss[] =
{
#ifdef USE_XDR
efTPR,
#endif
- efTPB, efTPA, efGRO, efG96, efPDB, efBRK, efENT
+ efGRO, efG96, efPDB, efBRK, efENT
};
#define NTPSS asize(tpss)
{ eftGEN, ".???", "traj", NULL,
"Full precision trajectory", NTRNS, trns },
{ eftXDR, ".trr", "traj", NULL, "Trajectory in portable xdr format" },
- { eftBIN, ".trj", "traj", NULL, "Trajectory file (architecture specific)" },
{ eftGEN, ".???", "traj_comp", NULL,
"Compressed trajectory (tng format or portable xdr format)", NTRCOMPRESSED, trcompressed},
{ eftXDR, ".xtc", "traj", NULL,
{ eftASC, ".ndx", "index", "-n", "Index file", },
{ eftASC, ".top", "topol", "-p", "Topology file"},
{ eftASC, ".itp", "topinc", NULL, "Include file for topology"},
- { eftGEN, ".???", "topol", "-s", "Run input file", NTPXS, tpxs },
{ eftGEN, ".???", "topol", "-s", "Structure+mass(db)", NTPSS, tpss },
{ eftXDR, ".tpr", "topol", "-s", "Portable xdr run input file"},
- { eftASC, ".tpa", "topol", "-s", "Ascii run input file"},
- { eftBIN, ".tpb", "topol", "-s", "Binary run input file"},
{ eftASC, ".tex", "doc", "-o", "LaTeX file"},
{ eftASC, ".rtp", "residue", NULL, "Residue Type file used by pdb2gmx" },
{ eftASC, ".atp", "atomtp", NULL, "Atomtype file used by pdb2gmx" },
return "sto";
case efSTX:
return "stx";
- case efTPX:
- return "tpx";
case efTPS:
return "tps";
default:
}
}
-static void check_opts(int nf, t_filenm fnm[])
+const char *ftp2defopt(int ftp)
{
- int i;
- const t_deffile *df;
-
- for (i = 0; (i < nf); i++)
+ if ((0 <= ftp) && (ftp < efNR))
{
- df = &(deffile[fnm[i].ftp]);
- if (fnm[i].opt == NULL)
- {
- if (df->defopt == NULL)
- {
- gmx_fatal(FARGS, "No default cmd-line option for %s (type %d)\n",
- deffile[fnm[i].ftp].ext, fnm[i].ftp);
- }
- else
- {
- fnm[i].opt = df->defopt;
- }
- }
+ return deffile[ftp].defopt;
+ }
+ else
+ {
+ return NULL;
}
}
return i;
}
-static void set_extension(char *buf, int ftp)
-{
- int len, extlen;
- const t_deffile *df;
-
- /* check if extension is already at end of filename */
- df = &(deffile[ftp]);
- len = strlen(buf);
- extlen = strlen(df->ext);
- if ((len <= extlen) || (gmx_strcasecmp(&(buf[len - extlen]), df->ext) != 0))
- {
- strcat(buf, df->ext);
- }
-}
-
-static void add_filenm(t_filenm *fnm, const char *filenm)
-{
- srenew(fnm->fns, fnm->nfiles+1);
- fnm->fns[fnm->nfiles] = strdup(filenm);
- fnm->nfiles++;
-}
-
-static void set_grpfnm(t_filenm *fnm, const char *name, const char *deffnm)
-{
- char buf[256], buf2[256];
- int i, type;
- gmx_bool bValidExt;
- int nopts;
- const int *ftps;
-
- nopts = deffile[fnm->ftp].ntps;
- ftps = deffile[fnm->ftp].tps;
- if ((nopts == 0) || (ftps == NULL))
- {
- gmx_fatal(FARGS, "nopts == 0 || ftps == NULL");
- }
-
- bValidExt = FALSE;
- if (name && deffnm == NULL)
- {
- strcpy(buf, name);
- /* First check whether we have a valid filename already */
- type = fn2ftp(name);
- if ((fnm->flag & ffREAD) && (fnm->ftp == efTRX))
- {
- /*if file exist don't add an extension for trajectory reading*/
- bValidExt = gmx_fexist(name);
- }
- for (i = 0; (i < nopts) && !bValidExt; i++)
- {
- if (type == ftps[i])
- {
- bValidExt = TRUE;
- }
- }
- }
- else if (deffnm != NULL)
- {
- strcpy(buf, deffnm);
- }
- else
- {
- /* No name given, set the default name */
- strcpy(buf, ftp2defnm(fnm->ftp));
- }
-
- if (!bValidExt && (fnm->flag & ffREAD))
- {
- /* for input-files only: search for filenames in the directory */
- for (i = 0; (i < nopts) && !bValidExt; i++)
- {
- type = ftps[i];
- strcpy(buf2, buf);
- set_extension(buf2, type);
- if (gmx_fexist(buf2))
- {
- bValidExt = TRUE;
- strcpy(buf, buf2);
- }
- }
- }
-
- if (!bValidExt)
- {
- /* Use the first extension type */
- set_extension(buf, ftps[0]);
- }
-
- add_filenm(fnm, buf);
-}
-
-static void set_filenm(t_filenm *fnm, const char *name, const char *deffnm,
- gmx_bool bReadNode)
-{
- /* Set the default filename, extension and option for those fields that
- * are not already set. An extension is added if not present, if fn = NULL
- * or empty, the default filename is given.
- */
- char buf[256];
- int i, len, extlen;
-
- if ((fnm->flag & ffREAD) && !bReadNode)
- {
- return;
- }
-
- if ((fnm->ftp < 0) || (fnm->ftp >= efNR))
- {
- gmx_fatal(FARGS, "file type out of range (%d)", fnm->ftp);
- }
-
- if (name)
- {
- strcpy(buf, name);
- }
- if ((fnm->flag & ffREAD) && name && gmx_fexist(name))
- {
- /* check if filename ends in .gz or .Z, if so remove that: */
- len = strlen(name);
- for (i = 0; i < NZEXT; i++)
- {
- extlen = strlen(z_ext[i]);
- if (len > extlen)
- {
- if (gmx_strcasecmp(name+len-extlen, z_ext[i]) == 0)
- {
- buf[len-extlen] = '\0';
- break;
- }
- }
- }
- }
-
- if (deffile[fnm->ftp].ntps)
- {
- set_grpfnm(fnm, name ? buf : NULL, deffnm);
- }
- else
- {
- if (name == NULL || deffnm != NULL)
- {
- if (deffnm != NULL)
- {
- strcpy(buf, deffnm);
- }
- else
- {
- strcpy(buf, ftp2defnm(fnm->ftp));
- }
- }
- set_extension(buf, fnm->ftp);
-
- add_filenm(fnm, buf);
- }
-}
-
-static void set_filenms(int nf, t_filenm fnm[], const char *deffnm, gmx_bool bReadNode)
-{
- int i;
-
- for (i = 0; (i < nf); i++)
- {
- if (!IS_SET(fnm[i]))
- {
- set_filenm(&(fnm[i]), fnm[i].fn, deffnm, bReadNode);
- }
- }
-}
-
-void parse_file_args(int *argc, char *argv[], int nf, t_filenm fnm[],
- const char *deffnm, gmx_bool bReadNode)
-{
- int i, j;
- gmx_bool *bRemove;
-
- check_opts(nf, fnm);
-
- for (i = 0; (i < nf); i++)
- {
- UN_SET(fnm[i]);
- }
-
- if (*argc > 1)
- {
- snew(bRemove, (*argc)+1);
- i = 1;
- do
- {
- for (j = 0; (j < nf); j++)
- {
- if (strcmp(argv[i], fnm[j].opt) == 0)
- {
- DO_SET(fnm[j]);
- bRemove[i] = TRUE;
- i++;
- /* check if we are out of arguments for this option */
- if ((i >= *argc) || (argv[i][0] == '-'))
- {
- set_filenm(&fnm[j], fnm[j].fn, deffnm, bReadNode);
- }
- /* sweep up all file arguments for this option */
- while ((i < *argc) && (argv[i][0] != '-'))
- {
- set_filenm(&fnm[j], argv[i], NULL, bReadNode);
- bRemove[i] = TRUE;
- i++;
- /* only repeat for 'multiple' file options: */
- if (!IS_MULT(fnm[j]))
- {
- break;
- }
- }
-
- break; /* jump out of 'j' loop */
- }
- }
- /* No file found corresponding to option argv[i] */
- if (j == nf)
- {
- i++;
- }
- }
- while (i < *argc);
-
- /* Remove used entries */
- for (i = j = 0; (i <= *argc); i++)
- {
- if (!bRemove[i])
- {
- argv[j++] = argv[i];
- }
- }
- (*argc) = j - 1;
- sfree(bRemove);
- }
-
- set_filenms(nf, fnm, deffnm, bReadNode);
-
-}
-
const char *opt2fn(const char *opt, int nfile, const t_filenm fnm[])
{
int i;
extpos = strrchr(buf, '.');
*extpos = '\0';
sprintf(newname, "%s%s.%s", buf, suffix, extpos + 1);
- free(fnm[i].fns[j]);
- fnm[i].fns[j] = strdup(newname);
+ sfree(fnm[i].fns[j]);
+ fnm[i].fns[j] = gmx_strdup(newname);
}
}
}
ret[i] = tfn[i]; /* just directly copy all non-string fields */
if (tfn[i].opt)
{
- ret[i].opt = strdup(tfn[i].opt);
+ ret[i].opt = gmx_strdup(tfn[i].opt);
}
else
{
if (tfn[i].fn)
{
- ret[i].fn = strdup(tfn[i].fn);
+ ret[i].fn = gmx_strdup(tfn[i].fn);
}
else
{
snew(ret[i].fns, tfn[i].nfiles);
for (j = 0; j < tfn[i].nfiles; j++)
{
- ret[i].fns[j] = strdup(tfn[i].fns[j]);
+ ret[i].fns[j] = gmx_strdup(tfn[i].fns[j]);
}
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_FILEIO_FILENM_H
#define GMX_FILEIO_FILENM_H
-#include "../legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
/* this enum should correspond to the array deffile in gmxlib/filenm.c */
enum {
efMDP,
- efTRX, efTRO, efTRN, efTRR, efTRJ, efCOMPRESSED, efXTC, efTNG,
+ efTRX, efTRO, efTRN, efTRR, efCOMPRESSED, efXTC, efTNG,
efEDR,
efSTX, efSTO, efGRO, efG96, efPDB, efBRK, efENT, efESP, efPQR,
efCPT,
efLOG, efXVG, efOUT,
efNDX,
efTOP, efITP,
- efTPX, efTPS, efTPR, efTPA, efTPB,
+ efTPS, efTPR,
efTEX, efRTP, efATP, efHDB,
efDAT, efDLG,
efMAP, efEPS, efMAT, efM2P,
#define ffOPT 1<<3
#define ffLIB 1<<4
#define ffMULT 1<<5
+#define ffALLOW_MISSING 1<<6
#define ffRW (ffREAD | ffWRITE)
#define ffOPTRD (ffREAD | ffOPT)
#define ffOPTWR (ffWRITE| ffOPT)
const char *ftp2defnm(int ftp);
/* Return default file name for file type */
+const char *ftp2defopt(int ftp);
+/* Return default option name for file type */
+
const char *ftp2ftype(int ftp);
/* Return Binary or ASCII depending on file type */
-void parse_file_args(int *argc, char *argv[], int nf, t_filenm fnm[],
- const char *deffnm, gmx_bool bReadNode);
-/* Parse command line for file names. When bKeep is set args are
- * not removed from argv. */
-
const char *opt2fn(const char *opt, int nfile, const t_filenm fnm[]);
/* Return the filename belonging to cmd-line option opt, or NULL when
* no such option. */
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef GMX_FILEIO_FUTIL_H
-#define GMX_FILEIO_FUTIL_H
-
-#include <stdio.h>
-#include "../legacyheaders/typedefs.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-/* Native windows uses backslash path separators.
- * Cygwin and everybody else in the world use slash.
- */
-#include "../utility/gmx_header_config.h"
-#ifdef GMX_NATIVE_WINDOWS
-#define DIR_SEPARATOR '\\'
-#else
-#define DIR_SEPARATOR '/'
-#endif
-
-/* Now get the maximum path size. */
-#ifdef PATH_MAX
-# define GMX_PATH_MAX PATH_MAX
-#elif defined MAX_PATH
-# define GMX_PATH_MAX MAX_PATH
-#else
-# define GMX_PATH_MAX 4096
-#endif
-
-typedef gmx_int64_t gmx_off_t;
-
-void no_buffers(void);
-/* Turn off buffering of files (which is default) for debugging purposes */
-
-gmx_bool gmx_fexist(const char *fname);
-/* Return TRUE when fname exists, FALSE otherwise */
-
-gmx_bool gmx_fexist_master(const char *fname, t_commrec *cr);
-/* Return TRUE when fname exists, FALSE otherwise, bcast from master to others */
-
-gmx_bool gmx_eof(FILE *fp);
-/* Return TRUE on end-of-file, FALSE otherwise */
-
-gmx_bool is_pipe(FILE *fp);
-/* Check whether the file (opened by gmx_ffopen) is a pipe */
-
-/* Make a backup of file if necessary.
- Return false if there was a problem.
- */
-gmx_bool make_backup(const char * file);
-
-FILE *gmx_ffopen(const char *file, const char *mode);
-/* Return a valid file pointer when successful, exits otherwise
- * If the file is in compressed format, open a pipe which uncompresses
- * the file! Therefore, files must be closed with gmx_ffclose (see below)
- */
-
-int gmx_ffclose(FILE *fp);
-/* Close files or pipes */
-
-
-void frewind(FILE *fp);
-/* Does not rewind pipes, but does so for normal files */
-
-#define rewind frewind
-
-
-int gmx_fseek(FILE *stream, gmx_off_t offset, int whence);
-/* OS-independent fseek. 64-bit when available */
-
-gmx_off_t gmx_ftell(FILE *stream);
-/* OS-independent fseek. 64-bit when available. */
-
-
-gmx_bool is_pipe(FILE *fp);
-
-char *gmxlibfn(const char *file);
-/* allocates and returns a string with the full file name for a library file */
-
-FILE *libopen(const char *file);
-/* Open a library file for reading. This looks in the current directory
- * first, and then in the library directory. If the file is not found,
- * it terminates with a fatal_error
- */
-
-/* Opaque data type to list directories */
-typedef struct gmx_directory *
- gmx_directory_t;
-
-/* Open a directory for reading. The first argument should be a pointer
- * to a declared gmx_directory_t variable. Returns 0 on success.
- */
-int
-gmx_directory_open(gmx_directory_t *p_gmxdir, const char *dirname);
-
-
-/* Given an initialized gmx_directory_t, if there are more files in
- * the directory this routine returns 0 and write the next name
- * into the USER-PROVIDED buffer name. The last argument is the max
- * number of characters that will be written. Just as strncpy, the
- * string will NOT be terminated it it is longer than maxlength_name.
- */
-int
-gmx_directory_nextfile(gmx_directory_t gmxdir, char *name, int maxlength_name);
-
-/* Release all data for a directory structure */
-int
-gmx_directory_close(gmx_directory_t gmxdir);
-
-
-char *low_gmxlibfn(const char *file, gmx_bool bAddCWD, gmx_bool bFatal);
-
-FILE *low_libopen(const char *file, gmx_bool bFatal);
-/* The same as the above, but does not terminate if (!bFatal) */
-
-/* Create unique name for temp file (wrapper around mkstemp).
- * Buf should be at least 7 bytes long
- */
-void gmx_tmpnam(char *buf);
-
-/* truncte the file to the specified length */
-int gmx_truncatefile(char *path, gmx_off_t length);
-
-/* rename/move the file (atomically, if the OS makes that available) oldname
- to newname */
-int gmx_file_rename(const char *oldname, const char *newname);
-
-/* copy the file (data only) oldname to newname. if copy_if_empty==FALSE,
- the file won't be copied if it's empty.*/
-int gmx_file_copy(const char *oldname, const char *newname, gmx_bool copy_if_empty);
-
-/* do an fsync() on an open file pointer.
- Only use this during checkpointing! */
-int gmx_fsync(FILE *fp);
-
-void gmx_chdir(const char *directory);
-void gmx_getcwd(char *buffer, size_t size);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* GMX_FILEIO_FUTIL_H */
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#ifdef GMX_INTERNAL_XDR
-#include <stdlib.h>
+#include "gmx_system_xdr.h"
+
#include <limits.h>
+#include <stdlib.h>
#include <string.h>
-#include "gmx_system_xdr.h"
-
/* NB - THIS FILE IS ONLY USED ON MICROSOFT WINDOWS, since that
* system doesn't provide any standard XDR system libraries. It will
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gmxfio.h"
+
+#include "config.h"
#include <errno.h>
#include <stdio.h>
#include <string.h>
+
#ifdef HAVE_IO_H
#include <io.h>
#endif
#include "thread_mpi/threads.h"
-#include "gmx_fatal.h"
-#include "macros.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio_int.h"
+#include "gromacs/fileio/md5.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "futil.h"
-#include "filenm.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gmxfio.h"
-#include "md5.h"
-
-#include "gmxfio_int.h"
+#include "gromacs/utility/snprintf.h"
/* This is the new improved and thread safe version of gmxfio. */
static const int ftpXDR[] =
{ efTPR, efTRR, efEDR, efXTC, efTNG, efMTX, efCPT };
static const int ftpASC[] =
-{ efTPA, efGRO, efPDB };
+{ efGRO, efPDB, efG96 };
static const int ftpBIN[] =
-{ efTPB, efTRJ, efTNG };
+{ efTNG };
#ifdef HAVE_XML
static const int ftpXML[] =
{ efXML};
#endif
-const char *itemstr[eitemNR] =
-{
- "[header]", "[inputrec]", "[box]", "[topology]", "[coordinates]",
- "[velocities]", "[forces]"
-};
-
const char *eioNames[eioNR] =
{
"REAL", "INT", "GMX_STE_T", "UCHAR", "NUCHAR", "USHORT", "RVEC", "NRVEC",
"IVEC", "STRING"
};
-
-
-/* Comment strings for TPA only */
-const char *comment_str[eitemNR] = {
- "; The header holds information on the number of atoms etc. and on whether\n"
- "; certain items are present in the file or not.\n"
- "; \n"
- "; WARNING\n"
- "; DO NOT EDIT THIS FILE BY HAND\n"
- "; The GROMACS preprocessor performs a lot of checks on your input that\n"
- "; you ignore when editing this. Your simulation may crash because of this\n",
- "; The inputrec holds the parameters for MD such as the number of steps,\n"
- "; the timestep and the cut-offs.\n",
- "; The simulation box in nm.\n",
- "; The topology section describes the topology of the molecules\n"
- "; i.e. bonds, angles and dihedrals etc. and also holds the force field\n"
- "; parameters.\n",
- "; The atomic coordinates in nm\n",
- "; The atomic velocities in nm/ps\n",
- "; The forces on the atoms in nm/ps^2\n"
-};
-
-
-
-
/******************************************************************
*
* Internal functions:
gmx_bool bRead, bReadWrite;
int xdrid;
- if (fn2ftp(fn) == efTPA)
+ /* sanitize the mode string */
+ if (strncmp(mode, "r+", 2) == 0)
+ {
+ strcpy(newmode, "r+");
+ }
+ else if (mode[0] == 'r')
+ {
+ strcpy(newmode, "r");
+ }
+ else if (strncmp(mode, "w+", 2) == 0)
+ {
+ strcpy(newmode, "w+");
+ }
+ else if (mode[0] == 'w')
{
- strcpy(newmode, mode);
+ strcpy(newmode, "w");
+ }
+ else if (strncmp(mode, "a+", 2) == 0)
+ {
+ strcpy(newmode, "a+");
+ }
+ else if (mode[0] == 'a')
+ {
+ strcpy(newmode, "a");
}
else
{
- /* sanitize the mode string */
- if (strncmp(mode, "r+", 2) == 0)
- {
- strcpy(newmode, "r+");
- }
- else if (mode[0] == 'r')
- {
- strcpy(newmode, "r");
- }
- else if (strncmp(mode, "w+", 2) == 0)
- {
- strcpy(newmode, "w+");
- }
- else if (mode[0] == 'w')
- {
- strcpy(newmode, "w");
- }
- else if (strncmp(mode, "a+", 2) == 0)
- {
- strcpy(newmode, "a+");
- }
- else if (mode[0] == 'a')
- {
- strcpy(newmode, "a");
- }
- else
- {
- gmx_fatal(FARGS, "DEATH HORROR in gmx_fio_open, mode is '%s'", mode);
- }
+ gmx_fatal(FARGS, "DEATH HORROR in gmx_fio_open, mode is '%s'", mode);
}
/* Check if it should be opened as a binary file */
if (fn)
{
fio->iFTP = fn2ftp(fn);
- fio->fn = strdup(fn);
+ fio->fn = gmx_strdup(fn);
fio->bStdio = FALSE;
/* If this file type is in the list of XDR files, open it like that */
gmx_fseek(fio->fp, 0, SEEK_END);
}
}
- else
- {
- /* Use stdin/stdout for I/O */
- fio->iFTP = efTPA;
- fio->fp = bRead ? stdin : stdout;
- fio->fn = strdup("STDIO");
- fio->bStdio = TRUE;
- }
fio->bRead = bRead;
fio->bReadWrite = bReadWrite;
fio->bDouble = (sizeof(real) == sizeof(double));
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_FILEIO_GMXFIO_H
#include <stdio.h>
-#include "../legacyheaders/typedefs.h"
-#include "futil.h"
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
typedef struct t_fileio t_fileio;
-extern const char *itemstr[eitemNR];
-extern const char *comment_str[eitemNR];
-
/* NOTE ABOUT THREAD SAFETY:
The functions are all thread-safe, provided that two threads don't
t_fileio *gmx_fio_open(const char *fn, const char *mode);
/* Open a new file for reading or writing.
* The file type will be deduced from the file name.
- * If fn is NULL, stdin / stdout will be used for Ascii I/O (TPA type)
- * mode may be "r", "w", or "a". You should append a "b" to the mode
- * if you are writing a binary file, but the routine will also
- * doublecheck it and try to do it if you forgot. This has no effect on
- * unix, but is important on windows.
*/
int gmx_fio_close(t_fileio *fp);
***************************************************/
void gmx_fio_rewind(t_fileio *fio);
-/* Rewind the tpa file in fio */
+/* Rewind the file in fio */
int gmx_fio_flush(t_fileio *fio);
/* Flush the fio, returns 0 on success */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+#include "config.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
+#include <assert.h>
#include <ctype.h>
#include <errno.h>
#include <stdio.h>
#include <string.h>
+
#ifdef HAVE_IO_H
#include <io.h>
#endif
-#include "gmx_fatal.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "futil.h"
-#include "filenm.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/gmxfio_int.h"
+#include "gromacs/fileio/md5.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/utility/cstringutil.h"
-#include "gmxfio.h"
-#include "md5.h"
-
-#include "gmxfio_int.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
/* This is the part that reads dummy and ascii files. */
int i, m, res = 0, *iptr, ix;
gmx_int64_t s;
double d, x;
+ char c;
real *ptr;
- unsigned char uc, *ucptr;
+ unsigned char *ucptr;
char *cptr;
#define NEXT_ITEM_BUF_LEN 128
char ni_buf[NEXT_ITEM_BUF_LEN];
}
break;
case eioUCHAR:
- res = sscanf(next_item(fp, ni_buf, NEXT_ITEM_BUF_LEN), "%c", &uc);
+ res = sscanf(next_item(fp, ni_buf, NEXT_ITEM_BUF_LEN), "%c", &c);
if (item)
{
- *((unsigned char *) item) = uc;
+ *((unsigned char *) item) = (unsigned char)c;
}
break;
case eioNUCHAR:
}
break;
case eioNRVEC:
+ assert(item);
for (i = 0; (i < nitem); i++)
{
ptr = ((rvec *) item)[i];
{
res = sscanf(next_item(fp, ni_buf, NEXT_ITEM_BUF_LEN), "%lf\n",
&x);
- if (item)
- {
- ptr[m] = x;
- }
+ ptr[m] = x;
}
}
break;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <errno.h>
#include <stdio.h>
#include <string.h>
+
#ifdef HAVE_IO_H
#include <io.h>
#endif
-#include "macros.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/gmxfio_int.h"
+#include "gromacs/fileio/md5.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "futil.h"
-#include "filenm.h"
-#include "gmxfio.h"
-#include "md5.h"
-
-#include "gmxfio_int.h"
/* This is the part that reads dummy and ascii files. */
#include "thread_mpi/lock.h"
-#include "xdrf.h"
+#include "gromacs/fileio/xdrf.h"
/* the reader/writer functions for t_iotype */
typedef gmx_bool read_func (t_fileio *fio, void *item, int nitem, int eio,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
-#include <stdio.h>
#include <errno.h>
+#include <stdio.h>
+
#ifdef HAVE_IO_H
#include <io.h>
#endif
-#include "macros.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/gmxfio_int.h"
+#include "gromacs/fileio/md5.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "futil.h"
-#include "filenm.h"
-#include "gmxfio.h"
-#include "md5.h"
-
-#include "gmxfio_int.h"
/*******************************************************************
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <errno.h>
#include <stdio.h>
#include <string.h>
+
#ifdef HAVE_IO_H
#include <io.h>
#endif
-#include "gmx_fatal.h"
-#include "macros.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/gmxfio_int.h"
+#include "gromacs/fileio/md5.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "futil.h"
-#include "filenm.h"
-#include "gmxfio.h"
-#include "md5.h"
-
-#include "gmxfio_int.h"
/* This is the part that reads xdr files. */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <limits.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
-#include "xdrf.h"
-#include "xdr_datatype.h"
-#include "futil.h"
+#include "gromacs/fileio/xdr_datatype.h"
+#include "gromacs/fileio/xdrf.h"
+#include "gromacs/utility/futil.h"
/* This is just for clarity - it can never be anything but 4! */
#define XDR_INT_SIZE 4
}
}
}
- return -1;
}
return -1;
}
}
- return -1;
}
}
}
}
- return -1;
}
/* Currently not used, just for completeness */
}
}
}
- return -1;
}
return -1;
}
}
- return -1;
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "matio.h"
-#include <stdio.h>
#include <ctype.h>
+#include <stdio.h>
#include <algorithm>
-#include "sysstuff.h"
-#include "futil.h"
-#include "gromacs/utility/cstringutil.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "matio.h"
-#include "gmxfio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/math/utilities.h"
-#include "copyrite.h"
-
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
#define round(a) (int)(a+0.5)
*m = NULL;
}
-void clear_matrix(int nx, int ny, real **m)
-{
- int x, y;
-
- for (x = 0; x < nx; x++)
- {
- for (y = 0; y < ny; y++)
- {
- m[x][y] = 0;
- }
- }
-}
-
gmx_bool matelmt_cmp(t_xpmelmt e1, t_xpmelmt e2)
{
return (e1.c1 == e2.c1) && (e1.c2 == e2.c2);
sscanf(line, "%s%s%lf%lf%lf", code, desc, &r, &g, &b);
m[i].code.c1 = code[0];
m[i].code.c2 = 0;
- m[i].desc = strdup(desc);
+ m[i].desc = gmx_strdup(desc);
m[i].rgb.r = r;
m[i].rgb.g = g;
m[i].rgb.b = b;
in = libopen(fn);
n = getcmap(in, fn, map);
- gmx_fio_fclose(in);
+ gmx_ffclose(in);
return n;
}
return fg;
}
-void skipstr(char *line)
+static void skipstr(char *line)
{
int i, c;
line[c-i] = '\0';
}
-char *line2string(char **line)
+static char *line2string(char **line)
{
int i;
return *line;
}
-void parsestring(char *line, const char *label, char *string)
+static void parsestring(char *line, const char *label, char *string)
{
if (strstr(line, label))
{
}
}
-void read_xpm_entry(FILE *in, t_matrix *mm)
+static void read_xpm_entry(FILE *in, t_matrix *mm)
{
t_mapping *map;
char *line_buf = NULL, *line = NULL, *str, buf[256] = {0};
line = strchr(line, '\"');
line++;
line2string(&line);
- map[m].desc = strdup(line);
+ map[m].desc = gmx_strdup(line);
m++;
}
}
sfree(line_buf);
}
-int read_xpm_matrix(const char *fnm, t_matrix **matrix)
+int read_xpm_matrix(const char *fnm, t_matrix **mat)
{
FILE *in;
char *line = NULL;
{
if (strstr(line, "/* XPM */"))
{
- srenew(*matrix, nmat+1);
- read_xpm_entry(in, &(*matrix)[nmat]);
+ srenew(*mat, nmat+1);
+ read_xpm_entry(in, &(*mat)[nmat]);
nmat++;
}
}
return nmat;
}
-real **matrix2real(t_matrix *matrix, real **mat)
+real **matrix2real(t_matrix *in, real **out)
{
t_mapping *map;
double tmp;
real *rmap;
int i, j, nmap;
- nmap = matrix->nmap;
- map = matrix->map;
+ nmap = in->nmap;
+ map = in->map;
snew(rmap, nmap);
for (i = 0; i < nmap; i++)
rmap[i] = tmp;
}
- if (mat == NULL)
+ if (out == NULL)
{
- snew(mat, matrix->nx);
- for (i = 0; i < matrix->nx; i++)
+ snew(out, in->nx);
+ for (i = 0; i < in->nx; i++)
{
- snew(mat[i], matrix->ny);
+ snew(out[i], in->ny);
}
}
- for (i = 0; i < matrix->nx; i++)
+ for (i = 0; i < in->nx; i++)
{
- for (j = 0; j < matrix->ny; j++)
+ for (j = 0; j < in->ny; j++)
{
- mat[i][j] = rmap[matrix->matrix[i][j]];
+ out[i][j] = rmap[in->matrix[i][j]];
}
}
sfree(rmap);
fprintf(stderr, "Converted a %dx%d matrix with %d levels to reals\n",
- matrix->nx, matrix->ny, nmap);
+ in->nx, in->ny, nmap);
- return mat;
+ return out;
}
-void write_xpm_header(FILE *out,
- const char *title, const char *legend,
- const char *label_x, const char *label_y,
- gmx_bool bDiscrete)
+static void write_xpm_header(FILE *out,
+ const char *title, const char *legend,
+ const char *label_x, const char *label_y,
+ gmx_bool bDiscrete)
{
fprintf(out, "/* XPM */\n");
try
nlevels-1);
}
-void write_xpm_map3(FILE *out, int n_x, int n_y, int *nlevels,
- real lo, real mid, real hi,
- t_rgb rlo, t_rgb rmid, t_rgb rhi)
+static void write_xpm_map3(FILE *out, int n_x, int n_y, int *nlevels,
+ real lo, real mid, real hi,
+ t_rgb rlo, t_rgb rmid, t_rgb rhi)
{
int i, nmid;
real r, g, b, clev_lo, clev_hi;
-void write_xpm_map_split(FILE *out, int n_x, int n_y,
- int *nlevel_top, real lo_top, real hi_top,
- t_rgb rlo_top, t_rgb rhi_top,
- gmx_bool bDiscreteColor,
- int *nlevel_bot, real lo_bot, real hi_bot,
- t_rgb rlo_bot, t_rgb rhi_bot)
+static void write_xpm_map_split(FILE *out, int n_x, int n_y,
+ int *nlevel_top, real lo_top, real hi_top,
+ t_rgb rlo_top, t_rgb rhi_top,
+ gmx_bool bDiscreteColor,
+ int *nlevel_bot, real lo_bot, real hi_bot,
+ t_rgb rlo_bot, t_rgb rhi_bot)
{
int ntot;
}
-void write_xpm_map(FILE *out, int n_x, int n_y, int *nlevels, real lo, real hi,
- t_rgb rlo, t_rgb rhi)
+static void write_xpm_map(FILE *out, int n_x, int n_y, int *nlevels,
+ real lo, real hi, t_rgb rlo, t_rgb rhi)
{
int i, nlo;
real invlevel, r, g, b;
}
}
-void write_xpm_axis(FILE *out, const char *axis, gmx_bool bSpatial, int n,
- real *label)
+static void write_xpm_axis(FILE *out, const char *axis, gmx_bool bSpatial,
+ int n, real *label)
{
int i;
}
}
-void write_xpm_data(FILE *out, int n_x, int n_y, real **matrix,
- real lo, real hi, int nlevels)
+static void write_xpm_data(FILE *out, int n_x, int n_y, real **mat,
+ real lo, real hi, int nlevels)
{
int i, j, c;
real invlevel;
fprintf(out, "\"");
for (i = 0; (i < n_x); i++)
{
- c = gmx_nint((matrix[i][j]-lo)*invlevel);
+ c = gmx_nint((mat[i][j]-lo)*invlevel);
if (c < 0)
{
c = 0;
}
}
-void write_xpm_data3(FILE *out, int n_x, int n_y, real **matrix,
- real lo, real mid, real hi, int nlevels)
+static void write_xpm_data3(FILE *out, int n_x, int n_y, real **mat,
+ real lo, real mid, real hi, int nlevels)
{
int i, j, c = 0, nmid;
real invlev_lo, invlev_hi;
fprintf(out, "\"");
for (i = 0; (i < n_x); i++)
{
- if (matrix[i][j] >= mid)
+ if (mat[i][j] >= mid)
{
- c = nmid+gmx_nint((matrix[i][j]-mid)*invlev_hi);
+ c = nmid+gmx_nint((mat[i][j]-mid)*invlev_hi);
}
- else if (matrix[i][j] >= lo)
+ else if (mat[i][j] >= lo)
{
- c = gmx_nint((matrix[i][j]-lo)*invlev_lo);
+ c = gmx_nint((mat[i][j]-lo)*invlev_lo);
}
else
{
}
}
-void write_xpm_data_split(FILE *out, int n_x, int n_y, real **matrix,
- real lo_top, real hi_top, int nlevel_top,
- real lo_bot, real hi_bot, int nlevel_bot)
+static void write_xpm_data_split(FILE *out, int n_x, int n_y, real **mat,
+ real lo_top, real hi_top, int nlevel_top,
+ real lo_bot, real hi_bot, int nlevel_bot)
{
int i, j, c;
real invlev_top, invlev_bot;
{
if (i < j)
{
- c = nlevel_bot+round((matrix[i][j]-lo_top)*invlev_top);
+ c = nlevel_bot+round((mat[i][j]-lo_top)*invlev_top);
if ((c < nlevel_bot) || (c >= nlevel_bot+nlevel_top))
{
- gmx_fatal(FARGS, "Range checking i = %d, j = %d, c = %d, bot = %d, top = %d matrix[i,j] = %f", i, j, c, nlevel_bot, nlevel_top, matrix[i][j]);
+ gmx_fatal(FARGS, "Range checking i = %d, j = %d, c = %d, bot = %d, top = %d matrix[i,j] = %f", i, j, c, nlevel_bot, nlevel_top, mat[i][j]);
}
}
else if (i > j)
{
- c = round((matrix[i][j]-lo_bot)*invlev_bot);
+ c = round((mat[i][j]-lo_bot)*invlev_bot);
if ((c < 0) || (c >= nlevel_bot+nlevel_bot))
{
- gmx_fatal(FARGS, "Range checking i = %d, j = %d, c = %d, bot = %d, top = %d matrix[i,j] = %f", i, j, c, nlevel_bot, nlevel_top, matrix[i][j]);
+ gmx_fatal(FARGS, "Range checking i = %d, j = %d, c = %d, bot = %d, top = %d matrix[i,j] = %f", i, j, c, nlevel_bot, nlevel_top, mat[i][j]);
}
}
else
const char *title, const char *legend,
const char *label_x, const char *label_y,
int n_x, int n_y, real axis_x[], real axis_y[],
- real *matrix[], real lo, real mid, real hi,
+ real *mat[], real lo, real mid, real hi,
t_rgb rlo, t_rgb rmid, t_rgb rhi, int *nlevels)
{
/* See write_xpm.
write_xpm_map3(out, n_x, n_y, nlevels, lo, mid, hi, rlo, rmid, rhi);
write_xpm_axis(out, "x", flags & MAT_SPATIAL_X, n_x, axis_x);
write_xpm_axis(out, "y", flags & MAT_SPATIAL_Y, n_y, axis_y);
- write_xpm_data3(out, n_x, n_y, matrix, lo, mid, hi, *nlevels);
+ write_xpm_data3(out, n_x, n_y, mat, lo, mid, hi, *nlevels);
}
void write_xpm_split(FILE *out, unsigned int flags,
const char *title, const char *legend,
const char *label_x, const char *label_y,
int n_x, int n_y, real axis_x[], real axis_y[],
- real *matrix[],
+ real *mat[],
real lo_top, real hi_top, int *nlevel_top,
t_rgb rlo_top, t_rgb rhi_top,
real lo_bot, real hi_bot, int *nlevel_bot,
bDiscreteColor, nlevel_bot, lo_bot, hi_bot, rlo_bot, rhi_bot);
write_xpm_axis(out, "x", flags & MAT_SPATIAL_X, n_x, axis_x);
write_xpm_axis(out, "y", flags & MAT_SPATIAL_Y, n_y, axis_y);
- write_xpm_data_split(out, n_x, n_y, matrix, lo_top, hi_top, *nlevel_top,
+ write_xpm_data_split(out, n_x, n_y, mat, lo_top, hi_top, *nlevel_top,
lo_bot, hi_bot, *nlevel_bot);
}
const char *title, const char *legend,
const char *label_x, const char *label_y,
int n_x, int n_y, real axis_x[], real axis_y[],
- real *matrix[], real lo, real hi,
+ real *mat[], real lo, real hi,
t_rgb rlo, t_rgb rhi, int *nlevels)
{
/* out xpm file
write_xpm_map(out, n_x, n_y, nlevels, lo, hi, rlo, rhi);
write_xpm_axis(out, "x", flags & MAT_SPATIAL_X, n_x, axis_x);
write_xpm_axis(out, "y", flags & MAT_SPATIAL_Y, n_y, axis_y);
- write_xpm_data(out, n_x, n_y, matrix, lo, hi, *nlevels);
+ write_xpm_data(out, n_x, n_y, mat, lo, hi, *nlevels);
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_FILEIO_MATIO_H
#define GMX_FILEIO_MATIO_H
-#include "../legacyheaders/typedefs.h"
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/types/rgb.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#endif
+typedef struct {
+ char c1; /* should all be non-zero (and printable and not '"') */
+ char c2; /*
+ * should all be zero (single char color names: smaller xpm's)
+ * or should all be non-zero (double char color names: more colors)
+ */
+} t_xpmelmt;
+
+typedef short t_matelmt;
+
+typedef struct {
+ t_xpmelmt code; /* see comment for t_xpmelmt */
+ const char *desc;
+ t_rgb rgb;
+} t_mapping;
+
+#define MAT_SPATIAL_X (1<<0)
+#define MAT_SPATIAL_Y (1<<1)
+/* Defines if x and y are spatial dimensions,
+ * when not, there are n axis ticks at the middle of the elements,
+ * when set, there are n+1 axis ticks at the edges of the elements.
+ */
+
+typedef struct {
+ unsigned int flags; /* The possible flags are defined above */
+ int nx, ny;
+ int y0;
+ char title[256];
+ char legend[256];
+ char label_x[256];
+ char label_y[256];
+ gmx_bool bDiscrete;
+ real *axis_x;
+ real *axis_y;
+ t_matelmt **matrix;
+ int nmap;
+ t_mapping *map;
+} t_matrix;
+/* title matrix title
+ * legend label for the continuous legend
+ * label_x label for the x-axis
+ * label_y label for the y-axis
+ * nx, ny size of the matrix
+ * axis_x[] the x-ticklabels
+ * axis_y[] the y-ticklables
+ * *matrix[] element x,y is matrix[x][y]
+ * nmap number of color levels for the output(?)
+ */
+
gmx_bool matelmt_cmp(t_xpmelmt e1, t_xpmelmt e2);
t_matelmt searchcmap(int n, t_mapping map[], t_xpmelmt c);
void writecmap(const char *fn, int n, t_mapping map[]);
/* print mapping table to fn */
-int read_xpm_matrix(const char *fnm, t_matrix **matrix);
+int read_xpm_matrix(const char *fnm, t_matrix **mat);
/* Reads a number of matrices from .xpm file fnm and returns this number */
-real **matrix2real(t_matrix *matrix, real **mat);
+real **matrix2real(t_matrix *in, real **out);
/* Converts an matrix in a t_matrix struct to a matrix of reals
* When mat==NULL memory will be allocated
* Returns NULL when something went wrong
const char *title, const char *legend,
const char *label_x, const char *label_y,
int n_x, int n_y, real axis_x[], real axis_y[],
- real *matrix[], real lo, real mid, real hi,
+ real *mat[], real lo, real mid, real hi,
t_rgb rlo, t_rgb rmid, t_rgb rhi, int *nlevels);
/* See write_xpm.
* Writes a colormap varying as rlo -> rmid -> rhi.
const char *title, const char *legend,
const char *label_x, const char *label_y,
int n_x, int n_y, real axis_x[], real axis_y[],
- real *matrix[],
+ real *mat[],
real lo_top, real hi_top, int *nlevel_top,
t_rgb rlo_top, t_rgb rhi_top,
real lo_bot, real hi_bot, int *nlevel_bot,
const char *title, const char *legend,
const char *label_x, const char *label_y,
int n_x, int n_y, real t_x[], real t_y[],
- real *matrix[], real lo, real hi,
+ real *mat[], real lo, real hi,
t_rgb rlo, t_rgb rhi, int *nlevels);
/* out xpm file
* flags flags, defined types/matrix.h
* n_x, n_y size of the matrix
* axis_x[] the x-ticklabels (n_x or n_x+1)
* axis_y[] the y-ticklables (n_y or n_y+1)
- * *matrix[] element x,y is matrix[x][y]
+ * *mat[] element x,y is mat[x][y]
* lo output lower than lo is set to lo
* hi output higher than hi is set to hi
* rlo rgb value for level lo
void done_matrix(int nx, real ***m);
-void clear_matrix(int nx, int ny, real **m);
-
#ifdef __cplusplus
}
#endif
* the use of GMX_INTEGER_BIG_ENDIAN, and the renaming of the
* functions md5_init, md5_append and md5_finish to have a gmx_ prefix
* (to avoid name clashes). */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#ifdef GMX_INTEGER_BIG_ENDIAN
#define ARCH_IS_BIG_ENDIAN 1
*/
#include "md5.h"
+
#include <string.h>
#undef BYTE_ORDER /* 1 = big-endian, -1 = little-endian, 0 = unknown */
#else
/* Define storage for little-endian or both types of CPUs. */
md5_word_t xbuf[16];
- /* cppcheck-suppress unassignedVariable */
const md5_word_t *X;
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
#include "mdoutf.h"
-#include "gromacs/legacyheaders/xvgr.h"
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/fileio/tngio.h"
+#include "gromacs/fileio/trajectory_writing.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/legacyheaders/mdrun.h"
#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/mvdata.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "trnio.h"
-#include "xtcio.h"
-#include "tngio.h"
-#include "trajectory_writing.h"
-#include "checkpoint.h"
-#include "copyrite.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/math/vec.h"
#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
struct gmx_mdoutf {
t_fileio *fp_trn;
{
if (bAppendFiles)
{
- of->fp_dhdl = gmx_fio_fopen(opt2fn("-field", nfile, fnm),
- filemode);
+ of->fp_field = gmx_fio_fopen(opt2fn("-field", nfile, fnm),
+ filemode);
}
else
{
}
if (of->fp_field != NULL)
{
+ /* This is opened sometimes with xvgropen, sometimes with
+ * gmx_fio_fopen, so we use the least common denominator for closing.
+ */
gmx_fio_fclose(of->fp_field);
}
#define GMX_FILEIO_MDOUTF_H
#include <stdio.h>
-#include "../legacyheaders/types/simple.h"
-#include "../legacyheaders/types/topology.h"
-#include "../legacyheaders/types/inputrec.h"
-#include "../legacyheaders/types/oenv.h"
-#include "../legacyheaders/network.h"
-#include "filenm.h"
-#include "enxio.h"
+
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/basedefinitions.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+struct gmx_mtop_t;
typedef struct gmx_mdoutf *gmx_mdoutf_t;
int mdrun_flags,
const t_commrec *cr,
const t_inputrec *ir,
- gmx_mtop_t *mtop,
+ struct gmx_mtop_t *mtop,
const output_env_t oenv,
gmx_wallcycle_t wcycle);
void mdoutf_write_to_trajectory_files(FILE *fplog, t_commrec *cr,
gmx_mdoutf_t of,
int mdof_flags,
- gmx_mtop_t *top_global,
+ struct gmx_mtop_t *top_global,
gmx_int64_t step, double t,
t_state *state_local, t_state *state_global,
rvec *f_local, rvec *f_global);
#define MDOF_CPT (1<<4)
#define MDOF_IMD (1<<5)
+#ifdef __cplusplus
+}
+#endif
#endif /* GMX_FILEIO_MDOUTF_H */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "mtxio.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "mtxio.h"
/* This module provides routines to read/write sparse or full storage
* matrices from/to files. It is normally used for the Hessian matrix
* in normal mode analysis.
*/
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/xdrf.h"
#include "gromacs/linearalgebra/sparsematrix.h"
-
+#include "gromacs/utility/baseversion.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
/* Just a number to identify our file type */
gmx_fio_do_int(fio, i);
/* Write generating Gromacs version */
- gmx_fio_write_string(fio, GromacsVersion());
+ gmx_fio_write_string(fio, gmx_version());
/* Write 1 for double, 0 for single precision */
if (sizeof(real) == sizeof(double))
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* in normal mode analysis.
*/
-#ifndef GMX_LINEARALGEBRA_MTXIO_H
-#define GMX_LINEARALGEBRA_MTXIO_H
+#ifndef GMX_FILEIO_MTXIO_H
+#define GMX_FILEIO_MTXIO_H
-#include "../legacyheaders/types/simple.h"
-
-#include "sparsematrix.h"
+#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "pdbio.h"
#include <ctype.h>
+#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/ifunc.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
-#include "vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "symtab.h"
-#include "pdbio.h"
-#include "vec.h"
-#include "copyrite.h"
-#include "futil.h"
-#include "atomprop.h"
-#include "physics.h"
-#include "pbc.h"
-#include "gmxfio.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
typedef struct {
int ai, aj;
int nlongname = 0;
int chainnum, lastchainnum;
int lastresind, lastchainresind;
- gmx_residuetype_t rt;
+ gmx_residuetype_t*rt;
const char *p_restype;
const char *p_lastrestype;
if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic)
{
- fprintf(out, "ANISOU%5u %-4.4s%4.4s%c%4d%c %7d%7d%7d%7d%7d%7d\n",
+ fprintf(out, "ANISOU%5d %-4.4s%4.4s%c%4d%c %7d%7d%7d%7d%7d%7d\n",
(i+1)%100000, nm, resnm, ch, resnr,
(resic == '\0') ? ' ' : resic,
atoms->pdbinfo[i].uij[0], atoms->pdbinfo[i].uij[1],
#ifndef GMX_FILEIO_PDBIO_H
#define GMX_FILEIO_PDBIO_H
-#include "../legacyheaders/sysstuff.h"
-#include "../legacyheaders/typedefs.h"
-#include "../legacyheaders/symtab.h"
-#include "../legacyheaders/atomprop.h"
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct gmx_atomprop;
+struct t_atoms;
+struct t_topology;
+
typedef struct gmx_conect_t *gmx_conect;
/* Enumerated type for pdb records. The other entries are ignored
* This function is fundamentally broken as far as thread-safety is concerned.
*/
-void write_pdbfile_indexed(FILE *out, const char *title, t_atoms *atoms,
+void write_pdbfile_indexed(FILE *out, const char *title, struct t_atoms *atoms,
rvec x[], int ePBC, matrix box, char chain,
int model_nr, atom_id nindex, const atom_id index[],
gmx_conect conect, gmx_bool bTerSepChains);
/* REALLY low level */
-void write_pdbfile(FILE *out, const char *title, t_atoms *atoms,
+void write_pdbfile(FILE *out, const char *title, struct t_atoms *atoms,
rvec x[], int ePBC, matrix box, char chain,
int model_nr, gmx_conect conect, gmx_bool bTerSepChains);
/* Low level pdb file writing routine.
* which may be useful for visualization purposes.
*/
-void get_pdb_atomnumber(t_atoms *atoms, gmx_atomprop_t aps);
+void get_pdb_atomnumber(struct t_atoms *atoms, struct gmx_atomprop *aps);
/* Routine to extract atomic numbers from the atom names */
int read_pdbfile(FILE *in, char *title, int *model_nr,
- t_atoms *atoms, rvec x[], int *ePBC, matrix box,
+ struct t_atoms *atoms, rvec x[], int *ePBC, matrix box,
gmx_bool bChange, gmx_conect conect);
/* Function returns number of atoms found.
* ePBC and gmx_conect structure may be NULL.
*/
void read_pdb_conf(const char *infile, char *title,
- t_atoms *atoms, rvec x[], int *ePBC, matrix box,
+ struct t_atoms *atoms, rvec x[], int *ePBC, matrix box,
gmx_bool bChange, gmx_conect conect);
/* Read a pdb file and extract ATOM and HETATM fields.
* Read a box from the CRYST1 line, return 0 box when no CRYST1 is found.
void gmx_conect_add(gmx_conect conect, int ai, int aj);
/* Add a connection between ai and aj (numbered from 0 to natom-1) */
-gmx_conect gmx_conect_generate(t_topology *top);
+gmx_conect gmx_conect_generate(struct t_topology *top);
/* Generate a conect structure from a topology */
gmx_conect gmx_conect_init(void);
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "strdb.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "strdb.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include "gmx_fatal.h"
-#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/cstringutil.h"
-
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
gmx_bool get_a_line(FILE *fp, char line[], int n)
{
#ifdef DEBUG
fprintf(stderr, "Have read: %s\n", buf);
#endif
- ptr[i] = strdup(buf);
+ ptr[i] = gmx_strdup(buf);
}
gmx_ffclose(in);
maxi += 50;
srenew(ptr, maxi);
}
- ptr[i] = strdup(buf);
+ ptr[i] = gmx_strdup(buf);
i++;
}
nstr = i;
#include <stdio.h>
-#include "../legacyheaders/types/simple.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
* \author Mark Abraham <mark.j.abraham@gmail.com>
* \ingroup module_fileio
*/
-#include <gtest/gtest.h>
-#include <string>
+#include "gmxpre.h"
-#include "gromacs/fileio/path.h"
#include "gromacs/fileio/tngio.h"
+
+#include <string>
+
+#include <gtest/gtest.h>
+
#include "gromacs/fileio/tngio_for_tools.h"
+#include "gromacs/utility/path.h"
#include "testutils/testfilemanager.h"
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "gromacs/fileio/timecontrol.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "timecontrol.h"
#include "thread_mpi/threads.h"
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/real.h"
/* The source code in this file should be thread-safe.
Please keep it that way. */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_FILEIO_TIMECONTROL_H
#define GMX_FILEIO_TIMECONTROL_H
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C"
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "tngio.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "tngio.h"
-#ifdef HAVE_UNISTD_H
-#include <unistd.h>
-#endif
+#include "config.h"
#ifdef GMX_USE_TNG
#include "tng/tng_io.h"
#endif
+#include "gromacs/fileio/gmxfio.h"
#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/physics.h"
+#include "gromacs/legacyheaders/types/ifunc.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
-#include "gromacs/utility/common.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/programcontext.h"
-#include "gmxfio.h"
+#include "gromacs/utility/sysinfo.h"
static const char *modeToVerb(char mode)
{
*/
if (mode == 'w')
{
-#ifndef GMX_FAHCORE
- /* only make backups for normal gromacs */
make_backup(filename);
-#endif
}
/* tng must not be pointing at already allocated memory.
// tng_last_program_name_set(*tng, programInfo);
// }
-#if defined(HAVE_UNISTD_H) && !defined(__MINGW32__)
char username[256];
- if (!getlogin_r(username, 256))
+ if (!gmx_getusername(username, 256))
{
if (mode == 'w')
{
// {
// tng_last_user_name_set(*tng, username);
// }
-#endif
}
#else
gmx_file("GROMACS was compiled without TNG support, cannot handle this file type");
#ifndef GMX_FILEIO_TNGIO_H
#define GMX_FILEIO_TNGIO_H
-#include "gromacs/legacyheaders/typedefs.h"
#include "tng/tng_io_fwd.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
+
#ifdef __cplusplus
extern "C" {
#endif
}
#endif
+struct gmx_mtop_t;
+
/*! \brief Open a TNG trajectory file
*
* \param filename Name of file to open
* \param tng Valid handle to a TNG trajectory
* \param mtop Pointer to a topology (can be NULL)
*/
-void gmx_tng_add_mtop(tng_trajectory_t tng,
- const gmx_mtop_t *mtop);
+void gmx_tng_add_mtop(tng_trajectory_t tng,
+ const struct gmx_mtop_t *mtop);
/*! \brief Do all TNG preparation for full-precision whole-system
* trajectory writing during MD simulations.
* \param mtop Global topology
* \param ir Input settings (for writing frequencies)
*/
-void gmx_tng_prepare_md_writing(tng_trajectory_t tng,
- const gmx_mtop_t *mtop,
- const t_inputrec *ir);
+void gmx_tng_prepare_md_writing(tng_trajectory_t tng,
+ const struct gmx_mtop_t *mtop,
+ const t_inputrec *ir);
/*! \brief Set the default compression precision for TNG writing
*
* \param mtop Global topology
* \param ir Input settings (for writing frequencies)
*/
-void gmx_tng_prepare_low_prec_writing(tng_trajectory_t tng,
- const gmx_mtop_t *mtop,
- const t_inputrec *ir);
+void gmx_tng_prepare_low_prec_writing(tng_trajectory_t tng,
+ const struct gmx_mtop_t *mtop,
+ const t_inputrec *ir);
/*! \brief Write a frame to a TNG file
*
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
#include "tngio_for_tools.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "config.h"
#include <math.h>
-#include "tngio.h"
-#include "trx.h"
-
#ifdef GMX_USE_TNG
#include "tng/tng_io.h"
#endif
-#include "gromacs/legacyheaders/types/atoms.h"
-#include "gromacs/legacyheaders/physics.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
-
-#include "gromacs/utility/common.h"
+#include "gromacs/fileio/tngio.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/math/units.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
void gmx_prepare_tng_writing(const char *filename,
size = sizeof(double);
break;
default:
- size = 0; /* Just to make the compiler happy. */
gmx_incons("Illegal datatype of box shape values!");
}
for (int i = 0; i < DIM; i++)
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
#ifndef GMX_FILEIO_TNGIO_FOR_TOOLS_H
#define GMX_FILEIO_TNGIO_FOR_TOOLS_H
-#include "gromacs/legacyheaders/typedefs.h"
+#include <stdio.h>
+
#include "tng/tng_io_fwd.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
#ifdef __cplusplus
extern "C" {
#endif
}
#endif
+struct gmx_mtop_t;
+struct t_trxframe;
+
/*! \brief Prepare to write TNG output from trajectory conversion tools */
void gmx_prepare_tng_writing(const char *filename,
char mode,
tng_trajectory_t *in,
tng_trajectory_t *out,
int nAtoms,
- const gmx_mtop_t *mtop,
+ const struct gmx_mtop_t *mtop,
const atom_id *index,
const char *indexGroupName);
* atoms.
*/
void gmx_write_tng_from_trxframe(tng_trajectory_t output,
- t_trxframe *frame,
+ struct t_trxframe *frame,
int natoms);
/*! \brief Creates a molecule containing only the indexed atoms and sets
/*! \brief Read the first/next TNG frame. */
gmx_bool gmx_read_next_tng_frame(tng_trajectory_t input,
- t_trxframe *fr,
+ struct t_trxframe *fr,
gmx_int64_t *requestedIds,
int numRequestedIds);
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
/* This file is completely threadsafe - keep it that way! */
+#include "tpxio.h"
+
+#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-#include "names.h"
-#include "symtab.h"
-#include "futil.h"
-#include "filenm.h"
-#include "gmxfio.h"
-#include "tpxio.h"
-#include "txtdump.h"
-#include "confio.h"
-#include "atomprop.h"
-#include "copyrite.h"
-#include "vec.h"
-#include "mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define TPX_TAG_RELEASE "release"
/* Needed for backward compatibility */
#define MAXNODES 256
-static void _do_section(t_fileio *fio, int key, gmx_bool bRead, const char *src,
- int line)
-{
- char buf[STRLEN];
- gmx_bool bDbg;
-
- if (gmx_fio_getftp(fio) == efTPA)
- {
- if (!bRead)
- {
- gmx_fio_write_string(fio, itemstr[key]);
- bDbg = gmx_fio_getdebug(fio);
- gmx_fio_setdebug(fio, FALSE);
- gmx_fio_write_string(fio, comment_str[key]);
- gmx_fio_setdebug(fio, bDbg);
- }
- else
- {
- if (gmx_fio_getdebug(fio))
- {
- fprintf(stderr, "Looking for section %s (%s, %d)",
- itemstr[key], src, line);
- }
-
- do
- {
- gmx_fio_do_string(fio, buf);
- }
- while ((gmx_strcasecmp(buf, itemstr[key]) != 0));
-
- if (gmx_strcasecmp(buf, itemstr[key]) != 0)
- {
- gmx_fatal(FARGS, "\nCould not find section heading %s", itemstr[key]);
- }
- else if (gmx_fio_getdebug(fio))
- {
- fprintf(stderr, " and found it\n");
- }
- }
- }
-}
-
-#define do_section(fio, key, bRead) _do_section(fio, key, bRead, __FILE__, __LINE__)
-
/**************************************************************
*
* Now the higer level routines that do io of the structures and arrays
for (i = 0; (i < nr); i++)
{
gmx_fio_do_string(fio, buf);
- symbuf->buf[i] = strdup(buf);
+ symbuf->buf[i] = gmx_strdup(buf);
}
}
else
gmx_fio_checktype(fio);
gmx_fio_setdebug(fio, bDebugMode());
- /* NEW! XDR tpb file */
+ /* XDR binary topology file */
precision = sizeof(real);
if (bRead)
{
gmx_fio_getname(fio), fver, tpx_version);
}
- do_section(fio, eitemHEADER, bRead);
gmx_fio_do_int(fio, tpx->natoms);
if (fver >= 28)
{
#define do_test(fio, b, p) if (bRead && (p != NULL) && !b) gmx_fatal(FARGS, "No %s in %s",#p, gmx_fio_getname(fio))
do_test(fio, tpx.bBox, state->box);
- do_section(fio, eitemBOX, bRead);
if (tpx.bBox)
{
gmx_fio_ndo_rvec(fio, state->box, DIM);
if (file_version < 26)
{
do_test(fio, tpx.bIr, ir);
- do_section(fio, eitemIR, bRead);
if (tpx.bIr)
{
if (ir)
}
do_test(fio, tpx.bTop, mtop);
- do_section(fio, eitemTOP, bRead);
if (tpx.bTop)
{
if (mtop)
}
}
do_test(fio, tpx.bX, state->x);
- do_section(fio, eitemX, bRead);
if (tpx.bX)
{
if (bRead)
}
do_test(fio, tpx.bV, state->v);
- do_section(fio, eitemV, bRead);
if (tpx.bV)
{
if (bRead)
}
do_test(fio, tpx.bF, f);
- do_section(fio, eitemF, bRead);
if (tpx.bF)
{
gmx_fio_ndo_rvec(fio, f, state->natoms);
if (file_version >= 26)
{
do_test(fio, tpx.bIr, ir);
- do_section(fio, eitemIR, bRead);
if (tpx.bIr)
{
if (file_version >= 53)
gmx_bool fn2bTPX(const char *file)
{
- switch (fn2ftp(file))
- {
- case efTPR:
- case efTPB:
- case efTPA:
- return TRUE;
- default:
- return FALSE;
- }
+ return (efTPR == fn2ftp(file));
}
static void done_gmx_groups_t(gmx_groups_t *g)
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* can also be used with the routines in gmxfio.h
*
**************************************************************/
-#include "../legacyheaders/typedefs.h"
-#include "gmxfio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/state.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct gmx_mtop_t;
+struct t_atoms;
+struct t_block;
+struct t_topology;
+
typedef struct
{
int bIr; /* Non zero if input_rec is present */
* These routines handle reading and writing of preprocessed
* topology files in any of the following formats:
* TPR : topology in XDR format, portable accross platforms
- * TPB : binary topology, not portable accross platforms
- * TPA : ascii topology (possibbly huge)
* TRR : trajectory in XDR format (non compressed)
- * TRJ : trajectory in binary format
*
* Files are written in the precision with which the source are compiled,
* but double and single precision can be read by either.
*/
void write_tpx_state(const char *fn,
- t_inputrec *ir, t_state *state, gmx_mtop_t *mtop);
+ t_inputrec *ir, t_state *state, struct gmx_mtop_t *mtop);
/* Write a file, and close it again.
- * If fn == NULL, an efTPA file will be written to stdout (which
- * will not be closed afterwards)
*/
void read_tpx_state(const char *fn,
t_inputrec *ir, t_state *state, rvec *f,
- gmx_mtop_t *mtop);
+ struct gmx_mtop_t *mtop);
int read_tpx(const char *fn,
t_inputrec *ir, matrix box, int *natoms,
- rvec *x, rvec *v, rvec *f, gmx_mtop_t *mtop);
+ rvec *x, rvec *v, rvec *f, struct gmx_mtop_t *mtop);
/* Read a file, and close it again.
- * If fn == NULL, an efTPA file will be read from stdin (which
- * will not be closed afterwards)
* When step, t or lambda are NULL they will not be stored.
* Returns ir->ePBC, if it could be read from the file.
*/
int read_tpx_top(const char *fn,
t_inputrec *ir, matrix box, int *natoms,
- rvec *x, rvec *v, rvec *f, t_topology *top);
+ rvec *x, rvec *v, rvec *f, struct t_topology *top);
/* As read_tpx, but for the old t_topology struct */
gmx_bool fn2bTPX(const char *file);
/* return if *file is one of the TPX file types */
-gmx_bool read_tps_conf(const char *infile, char *title, t_topology *top,
+gmx_bool read_tps_conf(const char *infile, char *title, struct t_topology *top,
int *ePBC, rvec **x, rvec **v, matrix box, gmx_bool bMass);
/* Read title, top.atoms, x, v (if not NULL) and box from an STX file,
* memory for atoms, x and v will be allocated.
* else if bMass=TRUE, read the masses into top.atoms from the mass database.
*/
-void tpx_make_chain_identifiers(t_atoms *atoms, t_block *mols);
+void tpx_make_chain_identifiers(struct t_atoms *atoms, struct t_block *mols);
#ifdef __cplusplus
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "vec.h"
-#include "sim_util.h"
-#include "mdrun.h"
-#include "confio.h"
#include "trajectory_writing.h"
-#include "mdoutf.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/mdoutf.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/smalloc.h"
void
do_md_trajectory_writing(FILE *fplog,
if (bCPT)
{
(*nchkpt)++;
- bCPT = FALSE;
}
debug_gmx();
if (bLastStep && step_rel == ir->nsteps &&
#define GMX_FILEIO_TRAJECTORY_WRITING_H
#include <stdio.h>
-#include "filenm.h"
-#include "mdoutf.h"
-#include "../legacyheaders/typedefs.h"
-#include "../legacyheaders/mdebin.h"
+
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/mdoutf.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/timing/wallcycle.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
/*! \brief Wrapper routine for writing trajectories during mdrun
*
);
+#ifdef __cplusplus
+}
+#endif
+
#endif /* GMX_FILEIO_TRAJECTORY_WRITING_H */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "trnio.h"
#include <string.h>
-#include "sysstuff.h"
+
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "txtdump.h"
-#include "names.h"
-#include "futil.h"
-#include "trnio.h"
-#include "gmxfio.h"
#define BUFSIZE 128
#define GROMACS_MAGIC 1993
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/**************************************************************
*
- * These routines handle trj (trajectory) I/O, they read and
- * write trj/trr files. The routines should be able to read single
+ * These routines handle trr (trajectory) I/O, they read and
+ * write trr files. The routines should be able to read single
* and double precision files without the user noting it.
* The files are backward compatible, therefore the header holds
* some unused variables.
*
**************************************************************/
-#include "../legacyheaders/typedefs.h"
-#include "gmxfio.h"
+#include "gromacs/fileio/gmxfio.h"
#ifdef __cplusplus
extern "C" {
} t_trnheader;
t_fileio *open_trn(const char *fn, const char *mode);
-/* Open a trj / trr file */
+/* Open a trr / trr file */
void close_trn(t_fileio *fio);
/* Close it */
#ifndef GMX_FILEIO_TRX_H
#define GMX_FILEIO_TRX_H
-#include "../legacyheaders/types/atoms.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_atoms;
+
typedef struct gmxvmdplugin t_gmxvmdplugin;
-typedef struct trxframe
+typedef struct t_trxframe
{
int flags; /* flags for read_first/next_frame */
int not_ok; /* integrity flags */
real lambda; /* free energy perturbation lambda */
int fep_state; /* which fep state are we in? */
gmx_bool bAtoms;
- t_atoms *atoms; /* atoms struct (natoms) */
+ struct t_atoms *atoms; /* atoms struct (natoms) */
gmx_bool bPrec;
real prec; /* precision of x, fraction of 1 nm */
gmx_bool bX;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
#include "trxio.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "config.h"
#include <assert.h>
#include <math.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#ifdef GMX_USE_PLUGINS
-#include "vmdio.h"
-#endif
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/timecontrol.h"
+#include "gromacs/fileio/tngio.h"
+#include "gromacs/fileio/tngio_for_tools.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/fileio/xdrf.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "pbc.h"
-#include "gmxfio.h"
-#include "trxio.h"
-#include "tpxio.h"
-#include "trnio.h"
-#include "tngio.h"
-#include "tngio_for_tools.h"
-#include "names.h"
-#include "vec.h"
-#include "futil.h"
-#include "xtcio.h"
-#include "pdbio.h"
-#include "confio.h"
-#include "checkpoint.h"
-#include "xdrf.h"
-#include "gromacs/fileio/timecontrol.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#ifdef GMX_USE_PLUGINS
+#include "gromacs/fileio/vmdio.h"
+#endif
/* defines for frame counter output */
#define SKIP1 10
switch (ftp)
{
- case efTRJ:
case efTRR:
case efTNG:
break;
switch (ftp)
{
- case efTRJ:
case efTRR:
case efTNG:
if (fr->bV)
case efXTC:
write_xtc(status->fio, nind, fr->step, fr->time, fr->box, xout, prec);
break;
- case efTRJ:
case efTRR:
fwrite_trn(status->fio, nframes_read(status),
fr->time, fr->step, fr->box, nind, xout, vout, fout);
switch (ftp)
{
- case efTRN:
- case efTRJ:
case efTRR:
case efTNG:
if (vout)
switch (gmx_fio_getftp(status->fio))
{
- case efTRJ:
case efTRR:
break;
default:
case efXTC:
write_xtc(status->fio, fr->natoms, fr->step, fr->time, fr->box, fr->x, prec);
break;
- case efTRJ:
case efTRR:
fwrite_trn(status->fio, fr->step, fr->time, fr->lambda, fr->box, fr->natoms,
fr->bX ? fr->x : NULL, fr->bV ? fr->v : NULL, fr->bF ? fr->f : NULL);
}
switch (ftp)
{
- case efTRJ:
case efTRR:
bRet = gmx_next_frame(status, fr);
break;
}
switch (ftp)
{
- case efTRJ:
case efTRR:
break;
case efCPT:
#ifndef GMX_FILEIO_TRXIO_H
#define GMX_FILEIO_TRXIO_H
-#include "../legacyheaders/typedefs.h"
-#include "filenm.h"
-#include "../legacyheaders/readinp.h"
-#include "pdbio.h"
-#include "../legacyheaders/oenv.h"
-#include "gmxfio.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/readinp.h"
#ifdef __cplusplus
extern "C" {
}
#endif
+struct gmx_mtop_t;
+struct t_atoms;
+struct t_topology;
+struct t_trxframe;
+
/* a dedicated status type contains fp, etc. */
typedef struct t_trxstatus t_trxstatus;
* 1/(nm) */
real ndec2prec(int ndec);
-void clear_trxframe(t_trxframe *fr, gmx_bool bFirst);
+void clear_trxframe(struct t_trxframe *fr, gmx_bool bFirst);
/* Set all content gmx_booleans to FALSE.
* When bFirst = TRUE, set natoms=-1, all pointers to NULL
* and all data to zero.
*/
-void set_trxframe_ePBC(t_trxframe *fr, int ePBC);
+void set_trxframe_ePBC(struct t_trxframe *fr, int ePBC);
/* Set the type of periodic boundary conditions, ePBC=-1 is not set */
int nframes_read(t_trxstatus *status);
/* Returns the number of frames read from the trajectory */
-int write_trxframe_indexed(t_trxstatus *status, t_trxframe *fr, int nind,
+int write_trxframe_indexed(t_trxstatus *status, struct t_trxframe *fr, int nind,
const atom_id *ind, gmx_conect gc);
/* Write an indexed frame to a TRX file, see write_trxframe. gc may be NULL */
-int write_trxframe(t_trxstatus *status, t_trxframe *fr, gmx_conect gc);
+int write_trxframe(t_trxstatus *status, struct t_trxframe *fr, gmx_conect gc);
/* Write a frame to a TRX file.
* Only entries for which the gmx_boolean is TRUE will be written,
* except for step, time, lambda and/or box, which may not be
* gc is important for pdb file writing only and may be NULL.
*/
-int write_trx(t_trxstatus *status, int nind, const atom_id *ind, t_atoms *atoms,
+int write_trx(t_trxstatus *status, int nind, const atom_id *ind, struct t_atoms *atoms,
int step, real time, matrix box, rvec x[], rvec *v,
gmx_conect gc);
/* Write an indexed frame to a TRX file.
* atoms can be NULL for file types which don't need atom names.
*/
-void trjtools_gmx_prepare_tng_writing(const char *filename,
- char filemode,
- t_trxstatus *in,
- t_trxstatus **out,
- const char *infile,
- const int natoms,
- const gmx_mtop_t *mtop,
- const atom_id *index,
- const char *index_group_name);
+void trjtools_gmx_prepare_tng_writing(const char *filename,
+ char filemode,
+ t_trxstatus *in,
+ t_trxstatus **out,
+ const char *infile,
+ const int natoms,
+ const struct gmx_mtop_t *mtop,
+ const atom_id *index,
+ const char *index_group_name);
/* Sets up *out for writing TNG. If *in != NULL and contains a TNG trajectory
* some data, e.g. molecule system, will be copied over from *in to *out.
* If *in == NULL a file name (infile) of a TNG file can be provided instead
* tng_trajectory_t are encapsulated, so client trajectory-writing
* code with a t_trxstatus can't just call the TNG writing
* function. */
-void write_tng_frame(t_trxstatus *status,
- t_trxframe *fr);
+void write_tng_frame(t_trxstatus *status,
+ struct t_trxframe *fr);
void close_trx(t_trxstatus *status);
-/* Close trj file as opened with read_first_x, read_frist_frame
+/* Close trajectory file as opened with read_first_x, read_frist_frame
* or open_trx. Identical to close_trj.
*/
#define FRAME_NOT_OK (HEADER_NOT_OK | DATA_NOT_OK)
int read_first_frame(const output_env_t oenv, t_trxstatus **status,
- const char *fn, t_trxframe *fr, int flags);
+ const char *fn, struct t_trxframe *fr, int flags);
/* Read the first frame which is in accordance with flags, which are
* defined further up in this file.
* Returns natoms when succeeded, 0 otherwise.
*/
gmx_bool read_next_frame(const output_env_t oenv, t_trxstatus *status,
- t_trxframe *fr);
+ struct t_trxframe *fr);
/* Reads the next frame which is in accordance with fr->flags.
* Returns TRUE when succeeded, FALSE otherwise.
*/
*/
void close_trj(t_trxstatus *status);
-/* Close trj file as opened with read_first_x, read_frist_frame
+/* Close trajectory file as opened with read_first_x, read_first_frame
* or open_trx. Identical to close_trx.
*/
void rewind_trj(t_trxstatus *status);
-/* Rewind trj file as opened with read_first_x */
+/* Rewind trajectory file as opened with read_first_x */
-t_topology *read_top(const char *fn, int *ePBC);
+struct t_topology *read_top(const char *fn, int *ePBC);
/* Extract a topology data structure from a topology file.
* If ePBC!=NULL *ePBC gives the pbc type.
*/
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "vmdio.h"
+
+#include "config.h"
/* Derived from PluginMgr.C and catdcd.c */
/* */
/*****************************************************************************/
-#include <stdlib.h>
+#include <assert.h>
#include <stdio.h>
+#include <stdlib.h>
#include <string.h>
-#include <assert.h>
-#include <config.h>
/*
* Plugin header files; get plugin source from www.ks.uiuc.edu/Research/vmd"
*/
#ifndef _WIN32_IE
#define _WIN32_IE 0x0500 /* SHGetFolderPath is available since WinXP/IE5 */
#endif
-#include <windows.h>
#include <shlobj.h>
+#include <windows.h>
#endif
-#include "gromacs/utility/smalloc.h"
-#include "futil.h"
-#include "vmdio.h"
-
-#include "types/simple.h"
-#include "vec.h"
-#include "gmxfio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
typedef int (*initfunc)(void);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-#ifndef GMX_FILEIO_VMDIO_H_
-#define GMX_FILEIO_VMDIO_H_
+#ifndef GMX_FILEIO_VMDIO_H
+#define GMX_FILEIO_VMDIO_H
#include "external/vmd_molfile/molfile_plugin.h"
-#include "trx.h"
+
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_trxframe;
+
struct gmxvmdplugin
{
molfile_plugin_t *api;
gmx_bool bV;
};
-int read_first_vmd_frame(const char *fn, struct trxframe *fr);
-gmx_bool read_next_vmd_frame(struct trxframe *fr);
+int read_first_vmd_frame(const char *fn, struct t_trxframe *fr);
+gmx_bool read_next_vmd_frame(struct t_trxframe *fr);
#ifdef __cplusplus
}
#endif
-#endif /* GMX_FILEIO_VMDIO_H_ */
+#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "writeps.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "writeps.h"
#include <stdio.h>
-#include "gmx_fatal.h"
-#include "gromacs/utility/smalloc.h"
-
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
const char *fontnm[efontNR] = {
"Times-Roman", "Times-Italic", "Times-Bold", "Times-BoldItalic",
#define GMX_FILEIO_WRITEPS_H
#include <stdio.h>
-#include "../legacyheaders/types/matrix.h"
-#include "../legacyheaders/types/simple.h"
+
+#include "gromacs/legacyheaders/types/rgb.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "typedefs.h"
-#include "xdrf.h"
-#include "gmx_fatal.h"
+#include "gromacs/fileio/xdrf.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
int xdr_real(XDR *xdrs, real *r)
imaj = (int)imaj64;
imin = (int)imin64;
ret = xdr_int(xdrs, &imaj);
- ret = xdr_int(xdrs, &imin);
+ ret |= xdr_int(xdrs, &imin);
*i = (((gmx_int64_t)imaj << 32) | ((gmx_int64_t)imin & two_p32_m1));
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_FILEIO_XDRF_H
#include <stdio.h>
-#include "../legacyheaders/typedefs.h"
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __PGI /*Portland group compiler*/
#define int64_t long long
#include "config.h"
#ifdef GMX_INTERNAL_XDR
-#include "gmx_system_xdr.h"
+#include "gromacs/fileio/gmx_system_xdr.h"
#else
#include <rpc/rpc.h>
#include <rpc/xdr.h>
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <string.h>
-#include "typedefs.h"
-#include "xdrf.h"
-#include "gmxfio.h"
#include "xtcio.h"
+
+#include <string.h>
+
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/xdrf.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "futil.h"
-#include "gmx_fatal.h"
#define XTC_MAGIC 1995
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_FILEIO_XTCIO_H
#define GMX_FILEIO_XTCIO_H
-#include "../legacyheaders/typedefs.h"
-#include "gmxfio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <string.h>
-#include <ctype.h>
-#include <time.h>
+#include "xvgr.h"
-#ifdef HAVE_SYS_TIME_H
-#include <sys/time.h>
-#endif
+#include <ctype.h>
+#include <string.h>
-#include "sysstuff.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/futil.h"
-#include "copyrite.h"
-#include "oenv.h"
-#include "gromacs/utility/smalloc.h"
-#include "xvgr.h"
-#include "viewit.h"
-#include "vec.h"
#include "gromacs/fileio/gmxfio.h"
-
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
-#include "gmx_fatal.h"
-#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/sysinfo.h"
gmx_bool output_env_get_print_xvgr_codes(const output_env_t oenv)
{
const output_env_t oenv)
{
char pukestr[100], buf[STRLEN];
- time_t t;
if (output_env_get_print_xvgr_codes(oenv))
{
- time(&t);
- gmx_ctime_r(&t, buf, STRLEN);
+ gmx_format_current_time(buf, STRLEN);
fprintf(fp, "# This file was created %s", buf);
try
{
gmx::BinaryInformationSettings settings;
settings.generatedByHeader(true);
settings.linePrefix("# ");
- gmx::printBinaryInformation(fp, gmx::getProgramContext(), settings);
+ gmx::printBinaryInformation(fp, output_env_get_program_context(oenv),
+ settings);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
- fprintf(fp, "# %s is part of G R O M A C S:\n#\n", ShortProgram());
+ fprintf(fp, "# %s is part of G R O M A C S:\n#\n",
+ output_env_get_program_display_name(oenv));
bromacs(pukestr, 99);
fprintf(fp, "# %s\n#\n", pukestr);
fprintf(fp, "@ title \"%s\"\n", xvgrstr(title, oenv, buf, STRLEN));
static int wordcount(char *ptr)
{
- int i, n, is[2];
+ int i, n = 0, is[2];
int cur = 0;
#define prev (1-cur)
- if (strlen(ptr) == 0)
- {
- return 0;
- }
- /* fprintf(stderr,"ptr='%s'\n",ptr); */
- n = 1;
- for (i = 0; (ptr[i] != '\0'); i++)
+ if (NULL != ptr)
{
- is[cur] = isspace(ptr[i]);
- if ((i > 0) && (is[cur] && !is[prev]))
+ for (i = 0; (ptr[i] != '\0'); i++)
{
- n++;
+ is[cur] = isspace(ptr[i]);
+ if ((0 == i) && !is[cur])
+ {
+ n++;
+ }
+ else if ((i > 0) && (!is[cur] && is[prev]))
+ {
+ n++;
+ }
+ cur = prev;
}
- cur = prev;
}
return n;
}
ptr1 = strchr(ptr0, '"');
if (ptr1 != NULL)
{
- str = strdup(ptr0);
+ str = gmx_strdup(ptr0);
str[ptr1-ptr0] = '\0';
}
else
{
- str = strdup("");
+ str = gmx_strdup("");
}
}
else
{
- str = strdup("");
+ str = gmx_strdup("");
}
return str;
*y = yy;
sfree(tmpbuf);
+ sfree(base);
+ sfree(fmt);
if (legend_nalloc > 0)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_FILEIO_XVGR_H
+#define GMX_FILEIO_XVGR_H
-#ifndef _xvgr_h
-#define _xvgr_h
+#include <stdio.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "viewit.h"
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
}
#endif
-#endif /* _xvgr_h */
+#endif
file(GLOB GMXANA_SOURCES *.c *.cpp)
-set(GMXANA_PUBLIC_HEADERS
+gmx_install_headers(
gstat.h
)
-gmx_install_headers(gmxana ${GMXANA_PUBLIC_HEADERS})
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${GMXANA_SOURCES} PARENT_SCOPE)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <stdio.h>
#include <string.h>
-#include "physics.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "txtdump.h"
-#include "bondf.h"
-#include "xvgr.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "gstat.h"
+
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/trxio.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
void print_one(const output_env_t oenv, const char *base, const char *name,
const char *title, const char *ylabel, int nf, real time[],
{
fprintf(fp, "%10g %10g\n", time[k], data[k]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
static int calc_RBbin(real phi, int gmx_unused multiplicity, real gmx_unused core_frac)
{
fprintf(fp, "%10.3f %10d\n", time[j], tr_f[j]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
/* Compute histogram from # transitions per dihedral */
fprintf(fp, "%10.3f %10d\n", ttime/i, tr_f[i]);
}
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
sfree(tr_f);
}
}
fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
/* and finally print out occupancies to a single file */
}
sfree(chi_prtrj);
- gmx_ffclose(fpall);
+ xvgrclose(fpall);
fprintf(stderr, "\n");
}
*S2 = tdc*tdc+tds*tds;
}
-static void calc_angles(t_pbc *pbc,
+static void calc_angles(struct t_pbc *pbc,
int n3, atom_id index[], real ang[], rvec x_s[])
{
int i, ix, t1, t2;
}
}
-static void calc_dihs(t_pbc *pbc,
+static void calc_dihs(struct t_pbc *pbc,
int n4, atom_id index[], real ang[], rvec x_s[])
{
int i, ix, t1, t2, t3;
real *dih[],
const output_env_t oenv)
{
- t_pbc *pbc;
- t_trxstatus *status;
- int i, angind, natoms, total, teller;
- int nangles, n_alloc;
- real t, fraction, pifac, aa, angle;
- real *angles[2];
- matrix box;
- rvec *x;
- int cur = 0;
+ struct t_pbc *pbc;
+ t_trxstatus *status;
+ int i, angind, natoms, total, teller;
+ int nangles, n_alloc;
+ real t, fraction, pifac, aa, angle;
+ real *angles[2];
+ matrix box;
+ rvec *x;
+ int cur = 0;
#define prev (1-cur)
snew(pbc, 1);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <stdio.h>
-#include "types/simple.h"
-#include "gmx_fatal.h"
+
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/real.h"
/*Make range-array (Permutation identity) for sorting */
void rangeArray(int *ar, int size)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _binsearch_h
#define _binsearch_h
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include "cmat.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "xvgr.h"
+
#include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
t_mat *init_mat(int n1, gmx_bool b1D)
{
{
fprintf(fp, "%10g %10d\n", i/fac, histo[i]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
sfree(histo);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _cmat_h
#define _cmat_h
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
typedef struct {
int i, j;
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
-
-#include "gromacs/fft/fft.h"
-#include "gromacs/utility/smalloc.h"
-#include "correl.h"
-
-#define SWAP(a, b) tempr = (a); (a) = (b); (b) = tempr
-
-void four1(real data[], int nn, int isign)
-{
- int n, mmax, m, j, istep, i;
- double wtemp, wr, wpr, wpi, wi, theta;
- real tempr, tempi;
-
- n = nn << 1;
- j = 1;
- for (i = 1; i < n; i += 2)
- {
- if (j > i)
- {
- SWAP(data[j], data[i]);
- SWAP(data[j+1], data[i+1]);
- }
- m = n >> 1;
- while (m >= 2 && j > m)
- {
- j -= m;
- m >>= 1;
- }
- j += m;
- }
- mmax = 2;
- while (n > mmax)
- {
- istep = 2*mmax;
- theta = 6.28318530717959/(isign*mmax);
- wtemp = sin(0.5*theta);
- wpr = -2.0*wtemp*wtemp;
- wpi = sin(theta);
- wr = 1.0;
- wi = 0.0;
- for (m = 1; m < mmax; m += 2)
- {
- for (i = m; i <= n; i += istep)
- {
- j = i+mmax;
- tempr = wr*data[j]-wi*data[j+1];
- tempi = wr*data[j+1]+wi*data[j];
- data[j] = data[i]-tempr;
- data[j+1] = data[i+1]-tempi;
- data[i] += tempr;
- data[i+1] += tempi;
- }
- wr = (wtemp = wr)*wpr-wi*wpi+wr;
- wi = wi*wpr+wtemp*wpi+wi;
- }
- mmax = istep;
- }
-}
-
-#undef SWAP
-
-static void realft(real data[], int n, int isign)
-{
- int i, i1, i2, i3, i4, n2p3;
- real c1 = 0.5, c2, h1r, h1i, h2r, h2i;
- double wr, wi, wpr, wpi, wtemp, theta;
-
- theta = 3.141592653589793/(double) n;
- if (isign == 1)
- {
- c2 = -0.5;
- four1(data, n, 1);
- }
- else
- {
- c2 = 0.5;
- theta = -theta;
- }
- wtemp = sin(0.5*theta);
- wpr = -2.0*wtemp*wtemp;
- wpi = sin(theta);
- wr = 1.0+wpr;
- wi = wpi;
- n2p3 = 2*n+3;
- for (i = 2; i <= n/2; i++)
- {
- i4 = 1+(i3 = n2p3-(i2 = 1+(i1 = i+i-1)));
- h1r = c1*(data[i1]+data[i3]);
- h1i = c1*(data[i2]-data[i4]);
- h2r = -c2*(data[i2]+data[i4]);
- h2i = c2*(data[i1]-data[i3]);
- data[i1] = h1r+wr*h2r-wi*h2i;
- data[i2] = h1i+wr*h2i+wi*h2r;
- data[i3] = h1r-wr*h2r+wi*h2i;
- data[i4] = -h1i+wr*h2i+wi*h2r;
- wr = (wtemp = wr)*wpr-wi*wpi+wr;
- wi = wi*wpr+wtemp*wpi+wi;
- }
- if (isign == 1)
- {
- data[1] = (h1r = data[1])+data[2];
- data[2] = h1r-data[2];
- }
- else
- {
- data[1] = c1*((h1r = data[1])+data[2]);
- data[2] = c1*(h1r-data[2]);
- four1(data, n, -1);
- }
-}
-
-static void twofft(real data1[], real data2[], real fft1[], real fft2[], int n)
-{
- int nn3, nn2, jj, j;
- real rep, rem, aip, aim;
-
- nn3 = 1+(nn2 = 2+n+n);
- for (j = 1, jj = 2; j <= n; j++, jj += 2)
- {
- fft1[jj-1] = data1[j];
- fft1[jj] = data2[j];
- }
- four1(fft1, n, 1);
- fft2[1] = fft1[2];
- fft1[2] = fft2[2] = 0.0;
- for (j = 3; j <= n+1; j += 2)
- {
- rep = 0.5*(fft1[j]+fft1[nn2-j]);
- rem = 0.5*(fft1[j]-fft1[nn2-j]);
- aip = 0.5*(fft1[j+1]+fft1[nn3-j]);
- aim = 0.5*(fft1[j+1]-fft1[nn3-j]);
- fft1[j] = rep;
- fft1[j+1] = aim;
- fft1[nn2-j] = rep;
- fft1[nn3-j] = -aim;
- fft2[j] = aip;
- fft2[j+1] = -rem;
- fft2[nn2-j] = aip;
- fft2[nn3-j] = rem;
- }
-}
-
-void correl(real data1[], real data2[], int n, real ans[])
-{
- int no2, i;
- real dum, *fft;
-
- snew(fft, 2*n+1);
- twofft(data1, data2, fft, ans, n);
- no2 = n/2;
- for (i = 2; i <= n+2; i += 2)
- {
- dum = ans[i-1];
- ans[i-1] = (fft[i-1]*dum+fft[i]*ans[i])/no2;
- ans[i] = (fft[i]*dum-fft[i-1]*ans[i])/no2;
- }
- ans[2] = ans[n+1];
- realft(ans, no2, -1);
- sfree(fft);
-}
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
/* dens_filter.c
* Routines for Filters and convolutions
*/
-#include <math.h>
-#include "typedefs.h"
#include "dens_filter.h"
+
+#include <math.h>
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
#include "gromacs/utility/smalloc.h"
-#include "vec.h"
#ifdef GMX_DOUBLE
#define EXP(x) (exp(x))
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2013, by the GROMACS development team, led by
+ * Copyright (c) 2011,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _dens_filter_h
#define _dens_filter_h
-#include "types/simple.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C"
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <stdlib.h>
#include <string.h>
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "gstat.h"
-#include "gmx_fatal.h"
-#include "index.h"
t_dlist *mk_dlist(FILE *log,
t_atoms *atoms, int *nlist,
gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bHChi,
- int maxchi, int r0, gmx_residuetype_t rt)
+ int maxchi, int r0, gmx_residuetype_t *rt)
{
int ires, i, j, k, ii;
t_dihatms atm, prev;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "symtab.h"
void replace_atom(t_topology *top, int inr, char *anm, char *resnm,
real q, real m, int type)
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
#include "eigio.h"
-#include "gromacs/fileio/trnio.h"
+
#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
void read_eigenvectors(const char *file, int *natoms, gmx_bool *bFit,
rvec **xref, gmx_bool *bDMR,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _eigio_h
#define _eigio_h
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
enum {
eWXR_NO, eWXR_YES, eWXR_NOFIT
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-#include <string.h>
-
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "xvgr.h"
-#include "gromacs/fileio/futil.h"
-#include "gstat.h"
-#include "vec.h"
-#include "index.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
-
-const int nfp_ffn[effnNR] = { 0, 1, 2, 3, 2, 5, 7, 9, 4, 3};
-
-const char *s_ffn[effnNR+2] = {
- NULL, "none", "exp", "aexp", "exp_exp", "vac",
- "exp5", "exp7", "exp9", "erffit", NULL, NULL
-};
-/* We don't allow errest as a choice on the command line */
-
-const char *longs_ffn[effnNR] = {
- "no fit",
- "y = exp(-x/a1)",
- "y = a2 exp(-x/a1)",
- "y = a2 exp(-x/a1) + (1-a2) exp(-x/a3)",
- "y = exp(-v) (cosh(wv) + 1/w sinh(wv)), v = x/(2 a1), w = sqrt(1 - a2)",
- "y = a1 exp(-x/a2) + a3 exp(-x/a4) + a5",
- "y = a1 exp(-x/a2) + a3 exp(-x/a4) + a5 exp(-x/a6) + a7",
- "y = a1 exp(-x/a2) + a3 exp(-x/a4) + a5 exp(-x/a6) + a7 exp(-x/a8) + a9",
- "y = 1/2*(a1+a2) - 1/2*(a1-a2)*erf( (x-a3) /a4^2)",
- "y = a2*ee(a1,x) + (1-a2)*ee(a2,x)"
-};
-
-extern gmx_bool mrqmin_new(real x[], real y[], real sig[], int ndata, real a[],
- int ia[], int ma, real **covar, real **alpha, real *chisq,
- void (*funcs)(real, real [], real *, real []),
- real *alamda);
-
-static real myexp(real x, real A, real tau)
-{
- if ((A == 0) || (tau == 0))
- {
- return 0;
- }
- return A*exp(-x/tau);
-}
-
-void erffit (real x, real a[], real *y, real dyda[])
-{
-/* Fuction
- * y=(a1+a2)/2-(a1-a2)/2*erf((x-a3)/a4^2)
- */
-
- real erfarg;
- real erfval;
- real erfarg2;
- real derf;
-
- erfarg = (x-a[3])/(a[4]*a[4]);
- erfarg2 = erfarg*erfarg;
- erfval = gmx_erf(erfarg)/2;
- derf = M_2_SQRTPI*(a[1]-a[2])/2*exp(-erfarg2)/(a[4]*a[4]);
- *y = (a[1]+a[2])/2-(a[1]-a[2])*erfval;
- dyda[1] = 1/2-erfval;
- dyda[2] = 1/2+erfval;
- dyda[3] = derf;
- dyda[4] = 2*derf*erfarg;
-}
-
-
-
-static void exp_one_parm(real x, real a[], real *y, real dyda[])
-{
- /* Fit to function
- *
- * y = exp(-x/a1)
- *
- */
-
- real e1;
-
- e1 = exp(-x/a[1]);
- *y = e1;
- dyda[1] = x*e1/sqr(a[1]);
-}
-
-static void exp_two_parm(real x, real a[], real *y, real dyda[])
-{
- /* Fit to function
- *
- * y = a2 exp(-x/a1)
- *
- */
-
- real e1;
-
- e1 = exp(-x/a[1]);
- *y = a[2]*e1;
- dyda[1] = x*a[2]*e1/sqr(a[1]);
- dyda[2] = e1;
-}
-
-static void exp_3_parm(real x, real a[], real *y, real dyda[])
-{
- /* Fit to function
- *
- * y = a2 exp(-x/a1) + (1-a2) exp(-x/a3)
- *
- */
-
- real e1, e2;
-
- e1 = exp(-x/a[1]);
- e2 = exp(-x/a[3]);
- *y = a[2]*e1 + (1-a[2])*e2;
- dyda[1] = x*a[2]*e1/sqr(a[1]);
- dyda[2] = e1-e2;
- dyda[3] = x*(1-a[2])*e2/sqr(a[3]);
-}
-
-static void exp_5_parm(real x, real a[], real *y, real dyda[])
-{
- /* Fit to function
- *
- * y = a1 exp(-x/a2) + a3 exp(-x/a4) + a5
- *
- */
-
- real e1, e2;
-
- e1 = exp(-x/a[2]);
- e2 = exp(-x/a[4]);
- *y = a[1]*e1 + a[3]*e2 + a[5];
-
- if (debug)
- {
- fprintf(debug, "exp_5_parm called: x = %10.3f y = %10.3f\n"
- "a = ( %8.3f %8.3f %8.3f %8.3f %8.3f)\n",
- x, *y, a[1], a[2], a[3], a[4], a[5]);
- }
- dyda[1] = e1;
- dyda[2] = x*e1/sqr(a[2]);
- dyda[3] = e2;
- dyda[4] = x*e2/sqr(a[4]);
- dyda[5] = 0;
-}
-
-static void exp_7_parm(real x, real a[], real *y, real dyda[])
-{
- /* Fit to function
- *
- * y = a1 exp(-x/a2) + a3 exp(-x/a4) + a5 exp(-x/a6) + a7
- *
- */
-
- real e1, e2, e3;
-
- e1 = exp(-x/a[2]);
- e2 = exp(-x/a[4]);
- e3 = exp(-x/a[6]);
- *y = a[1]*e1 + a[3]*e2 + a[5]*e3 + a[7];
-
- dyda[1] = e1;
- dyda[2] = x*e1/sqr(a[2]);
- dyda[3] = e2;
- dyda[4] = x*e2/sqr(a[4]);
- dyda[5] = e3;
- dyda[6] = x*e3/sqr(a[6]);
- dyda[7] = 0;
-}
-
-static void exp_9_parm(real x, real a[], real *y, real dyda[])
-{
- /* Fit to function
- *
- * y = a1 exp(-x/a2) + a3 exp(-x/a4) + a5 exp(-x/a6) + a7
- *
- */
-
- real e1, e2, e3, e4;
-
- e1 = exp(-x/a[2]);
- e2 = exp(-x/a[4]);
- e3 = exp(-x/a[6]);
- e4 = exp(-x/a[8]);
- *y = a[1]*e1 + a[3]*e2 + a[5]*e3 + a[7]*e4 + a[9];
-
- dyda[1] = e1;
- dyda[2] = x*e1/sqr(a[2]);
- dyda[3] = e2;
- dyda[4] = x*e2/sqr(a[4]);
- dyda[5] = e3;
- dyda[6] = x*e3/sqr(a[6]);
- dyda[7] = e4;
- dyda[8] = x*e4/sqr(a[8]);
- dyda[9] = 0;
-}
-
-static void vac_2_parm(real x, real a[], real *y, real dyda[])
-{
- /* Fit to function
- *
- * y = 1/2 (1 - 1/w) exp(-(1+w)v) + 1/2 (1 + 1/w) exp(-(1-w)v)
- *
- * = exp(-v) (cosh(wv) + 1/w sinh(wv))
- *
- * v = x/(2 a1)
- * w = sqrt(1 - a2)
- *
- * For tranverse current autocorrelation functions:
- * a1 = tau
- * a2 = 4 tau (eta/rho) k^2
- *
- */
-
- double v, det, omega, omega2, em, ec, es;
-
- v = x/(2*a[1]);
- det = 1 - a[2];
- em = exp(-v);
- if (det != 0)
- {
- omega2 = fabs(det);
- omega = sqrt(omega2);
- if (det > 0)
- {
- ec = em*0.5*(exp(omega*v)+exp(-omega*v));
- es = em*0.5*(exp(omega*v)-exp(-omega*v))/omega;
- }
- else
- {
- ec = em*cos(omega*v);
- es = em*sin(omega*v)/omega;
- }
- *y = ec + es;
- dyda[2] = (v/det*ec+(v-1/det)*es)/(-2.0);
- dyda[1] = (1-det)*v/a[1]*es;
- }
- else
- {
- *y = (1+v)*em;
- dyda[2] = -v*v*em*(0.5+v/6);
- dyda[1] = v*v/a[1]*em;
- }
-}
-
-static void errest_3_parm(real x, real a[], real *y, real dyda[])
-{
- real e1, e2, v1, v2;
-
- if (a[1])
- {
- e1 = exp(-x/a[1]) - 1;
- }
- else
- {
- e1 = 0;
- }
- if (a[3])
- {
- e2 = exp(-x/a[3]) - 1;
- }
- else
- {
- e2 = 0;
- }
-
- if (x > 0)
- {
- v1 = 2*a[1]*(e1*a[1]/x + 1);
- v2 = 2*a[3]*(e2*a[3]/x + 1);
- *y = a[2]*v1 + (1-a[2])*v2;
- dyda[1] = 2* a[2] *(v1/a[1] + e1);
- dyda[3] = 2*(1 - a[2])*(v2/a[3] + e2);
- dyda[2] = (v1 - v2);
- }
- else
- {
- *y = 0;
- dyda[1] = 0;
- dyda[3] = 0;
- dyda[2] = 0;
- }
-}
-
-typedef void (*myfitfn)(real x, real a[], real *y, real dyda[]);
-myfitfn mfitfn[effnNR] = {
- exp_one_parm, exp_one_parm, exp_two_parm, exp_3_parm, vac_2_parm,
- exp_5_parm, exp_7_parm, exp_9_parm, erffit, errest_3_parm
-};
-
-real fit_function(int eFitFn, real *parm, real x)
-{
- static real y, dum[8];
-
- mfitfn[eFitFn](x, parm-1, &y, dum);
-
- return y;
-}
-
-/* lmfit_exp supports up to 3 parameter fitting of exponential functions */
-static gmx_bool lmfit_exp(int nfit, real x[], real y[], real dy[], real ftol,
- real parm[], real dparm[], gmx_bool bVerbose,
- int eFitFn, int fix)
-{
- real chisq, ochisq, alamda;
- real *a, **covar, **alpha, *dum;
- gmx_bool bCont;
- int i, j, ma, mfit, *lista, *ia;
-
- if ((eFitFn < 0) || (eFitFn >= effnNR))
- {
- gmx_fatal(FARGS, "fitfn = %d, should be in 0..%d (%s,%d)",
- effnNR-1, eFitFn, __FILE__, __LINE__);
- }
-
- ma = mfit = nfp_ffn[eFitFn]; /* number of parameters to fit */
- snew(a, ma+1);
- snew(covar, ma+1);
- snew(alpha, ma+1);
- snew(lista, ma+1);
- snew(ia, ma+1);
- snew(dum, ma+1);
- for (i = 1; (i < ma+1); i++)
- {
- lista[i] = i;
- ia[i] = 1; /* fixed bug B.S.S 19/11 */
- snew(covar[i], ma+1);
- snew(alpha[i], ma+1);
- }
- if (fix)
- {
- if (bVerbose)
- {
- fprintf(stderr, "Will keep parameters fixed during fit procedure: %d\n",
- fix);
- }
- for (i = 0; i < ma; i++)
- {
- if (fix & 1<<i)
- {
- ia[i+1] = 0;
- }
- }
- }
- if (debug)
- {
- fprintf(debug, "%d parameter fit\n", mfit);
- }
-
- /* Initial params */
- alamda = -1; /* Starting value */
- chisq = 1e12;
- for (i = 0; (i < mfit); i++)
- {
- a[i+1] = parm[i];
- }
-
- j = 0;
- if (bVerbose)
- {
- fprintf(stderr, "%4s %10s %10s %10s %10s %10s %10s\n",
- "Step", "chi^2", "Lambda", "A1", "A2", "A3", "A4");
- }
- do
- {
- ochisq = chisq;
- /* mrqmin(x-1,y-1,dy-1,nfit,a,ma,lista,mfit,covar,alpha,
- * &chisq,expfn[mfit-1],&alamda)
- */
- if (!mrqmin_new(x-1, y-1, dy-1, nfit, a, ia, ma, covar, alpha, &chisq,
- mfitfn[eFitFn], &alamda))
- {
- return FALSE;
- }
-
- if (bVerbose)
- {
- fprintf(stderr, "%4d %10.5e %10.5e %10.5e",
- j, chisq, alamda, a[1]);
- if (mfit > 1)
- {
- fprintf(stderr, " %10.5e", a[2]);
- }
- if (mfit > 2)
- {
- fprintf(stderr, " %10.5e", a[3]);
- }
- if (mfit > 3)
- {
- fprintf(stderr, " %10.5e", a[4]);
- }
- fprintf(stderr, "\n");
- }
- j++;
- bCont = ((fabs(ochisq - chisq) > fabs(ftol*chisq)) ||
- ((ochisq == chisq)));
- }
- while (bCont && (alamda != 0.0) && (j < 50));
- if (bVerbose)
- {
- fprintf(stderr, "\n");
- }
-
- /* Now get the covariance matrix out */
- alamda = 0;
-
- /* mrqmin(x-1,y-1,dy-1,nfit,a,ma,lista,mfit,covar,alpha,
- * &chisq,expfn[mfit-1],&alamda)
- */
- if (!mrqmin_new(x-1, y-1, dy-1, nfit, a, ia, ma, covar, alpha, &chisq,
- mfitfn[eFitFn], &alamda))
- {
- return FALSE;
- }
-
- for (j = 0; (j < mfit); j++)
- {
- parm[j] = a[j+1];
- dparm[j] = covar[j+1][j+1];
- }
-
- for (i = 0; (i < ma+1); i++)
- {
- sfree(covar[i]);
- sfree(alpha[i]);
- }
- sfree(a);
- sfree(covar);
- sfree(alpha);
- sfree(lista);
- sfree(dum);
-
- return TRUE;
-}
-
-real do_lmfit(int ndata, real c1[], real sig[], real dt, real x0[],
- real begintimefit, real endtimefit, const output_env_t oenv,
- gmx_bool bVerbose, int eFitFn, real fitparms[], int fix)
-{
- FILE *fp;
- char buf[32];
-
- int i, j, nparm, nfitpnts;
- real integral, ttt;
- real *parm, *dparm;
- real *x, *y, *dy;
- real ftol = 1e-4;
-
- nparm = nfp_ffn[eFitFn];
- if (debug)
- {
- fprintf(debug, "There are %d points to fit %d vars!\n", ndata, nparm);
- fprintf(debug, "Fit to function %d from %g through %g, dt=%g\n",
- eFitFn, begintimefit, endtimefit, dt);
- }
-
- snew(x, ndata);
- snew(y, ndata);
- snew(dy, ndata);
-
- j = 0;
- for (i = 0; i < ndata; i++)
- {
- ttt = x0 ? x0[i] : dt*i;
- if (ttt >= begintimefit && ttt <= endtimefit)
- {
- x[j] = ttt;
- y[j] = c1[i];
-
- /* mrqmin does not like sig to be zero */
- if (sig[i] < 1.0e-7)
- {
- dy[j] = 1.0e-7;
- }
- else
- {
- dy[j] = sig[i];
- }
- if (debug)
- {
- fprintf(debug, "j= %d, i= %d, x= %g, y= %g, dy= %g\n",
- j, i, x[j], y[j], dy[j]);
- }
- j++;
- }
- }
- nfitpnts = j;
- integral = 0;
- if (nfitpnts < nparm)
- {
- fprintf(stderr, "Not enough data points for fitting!\n");
- }
- else
- {
- snew(parm, nparm);
- snew(dparm, nparm);
- if (fitparms)
- {
- for (i = 0; (i < nparm); i++)
- {
- parm[i] = fitparms[i];
- }
- }
-
- if (!lmfit_exp(nfitpnts, x, y, dy, ftol, parm, dparm, bVerbose, eFitFn, fix))
- {
- fprintf(stderr, "Fit failed!\n");
- }
- else if (nparm <= 3)
- {
- /* Compute the integral from begintimefit */
- if (nparm == 3)
- {
- integral = (parm[0]*myexp(begintimefit, parm[1], parm[0]) +
- parm[2]*myexp(begintimefit, 1-parm[1], parm[2]));
- }
- else if (nparm == 2)
- {
- integral = parm[0]*myexp(begintimefit, parm[1], parm[0]);
- }
- else if (nparm == 1)
- {
- integral = parm[0]*myexp(begintimefit, 1, parm[0]);
- }
- else
- {
- gmx_fatal(FARGS, "nparm = %d in file %s, line %d",
- nparm, __FILE__, __LINE__);
- }
-
- /* Generate THE output */
- if (bVerbose)
- {
- fprintf(stderr, "FIT: # points used in fit is: %d\n", nfitpnts);
- fprintf(stderr, "FIT: %21s%21s%21s\n",
- "parm0 ", "parm1 (ps) ", "parm2 (ps) ");
- fprintf(stderr, "FIT: ------------------------------------------------------------\n");
- fprintf(stderr, "FIT: %8.3g +/- %8.3g%9.4g +/- %8.3g%8.3g +/- %8.3g\n",
- parm[0], dparm[0], parm[1], dparm[1], parm[2], dparm[2]);
- fprintf(stderr, "FIT: Integral (calc with fitted function) from %g ps to inf. is: %g\n",
- begintimefit, integral);
-
- sprintf(buf, "test%d.xvg", nfitpnts);
- fp = xvgropen(buf, "C(t) + Fit to C(t)", "Time (ps)", "C(t)", oenv);
- fprintf(fp, "# parm0 = %g, parm1 = %g, parm2 = %g\n",
- parm[0], parm[1], parm[2]);
- for (j = 0; (j < nfitpnts); j++)
- {
- ttt = x0 ? x0[j] : dt*j;
- fprintf(fp, "%10.5e %10.5e %10.5e\n",
- ttt, c1[j], fit_function(eFitFn, parm, ttt));
- }
- xvgrclose(fp);
- }
- }
- if (fitparms)
- {
- for (i = 0; (i < nparm); i++)
- {
- fitparms[i] = parm[i];
- }
- }
- sfree(parm);
- sfree(dparm);
- }
-
- sfree(x);
- sfree(y);
- sfree(dy);
-
- return integral;
-}
-
-void do_expfit(int ndata, real c1[], real dt, real begintimefit, real endtimefit)
-{
- int i, n;
- real *x, *y, *Dy;
- real aa, bb, saa, sbb, A, tau, dA, dtau;
-
- fprintf(stderr, "Will fit data from %g (ps) to %g (ps).\n",
- begintimefit, endtimefit);
-
- snew(x, ndata); /* allocate the maximum necessary space */
- snew(y, ndata);
- snew(Dy, ndata);
- n = 0;
-
- for (i = 0; (i < ndata); i++)
- {
- if ( (dt*i >= begintimefit) && (dt*i <= endtimefit) )
- {
- x[n] = dt*i;
- y[n] = c1[i];
- Dy[n] = 0.5;
- fprintf(stderr, "n= %d, i= %d, x= %g, y= %g\n", n, i, x[n], y[n]);
- n++;
- }
- }
- fprintf(stderr, "# of data points used in the fit is : %d\n\n", n);
- expfit(n, x, y, Dy, &aa, &saa, &bb, &sbb);
-
- A = exp(aa);
- dA = exp(aa)*saa;
- tau = -1.0/bb;
- dtau = sbb/sqr(bb);
- fprintf(stderr, "Fitted to y=exp(a+bx):\n");
- fprintf(stderr, "a = %10.5f\t b = %10.5f", aa, bb);
- fprintf(stderr, "\n");
- fprintf(stderr, "Fitted to y=Aexp(-x/tau):\n");
- fprintf(stderr, "A = %10.5f\t tau = %10.5f\n", A, tau);
- fprintf(stderr, "dA = %10.5f\t dtau = %10.5f\n", dA, dtau);
-}
-
-
-void expfit(int n, real *x, real *y, real *Dy, real *a, real *sa,
- real *b, real *sb)
-{
- real *w, *ly, A, SA, B, SB;
- int i;
- real sum, xbar, ybar, Sxx, Sxy, wr2, chi2, gamma, Db;
-
-#define ZERO 0.0
-#define ONE 1.0
-#define ONEP5 1.5
-#define TWO 2.0
-
-#define sqr(x) ((x)*(x))
-
- /*allocate memory */
- snew(w, n);
- snew(ly, n);
-
- /* Calculate weights and values of ln(y). */
- for (i = 0; (i < n); i++)
- {
- w[i] = sqr(y[i]/Dy[i]);
- ly[i] = log(y[i]);
- }
-
- /* The weighted averages of x and y: xbar and ybar. */
- sum = ZERO;
- xbar = ZERO;
- ybar = ZERO;
- for (i = 0; (i < n); i++)
- {
- sum += w[i];
- xbar += w[i]*x[i];
- ybar += w[i]*ly[i];
- }
- xbar /= sum;
- ybar /= sum;
-
- /* The centered product sums Sxx and Sxy, and hence A and B. */
- Sxx = ZERO;
- Sxy = ZERO;
- for (i = 0; (i < n); i++)
- {
- Sxx += w[i]*sqr(x[i]-xbar);
- Sxy += w[i]*(x[i]-xbar)*(ly[i]-ybar);
- }
- B = Sxy/Sxx;
- A = ybar-B*xbar;
-
- /* Chi-squared (chi2) and gamma. */
- chi2 = ZERO;
- gamma = ZERO;
- for (i = 0; (i < n); i++)
- {
- wr2 = w[i]*sqr(ly[i]-A-B*x[i]);
- chi2 += wr2;
- gamma += wr2*(x[i]-xbar);
- }
-
- /* Refined values of A and B. Also SA and SB. */
- Db = -ONEP5*gamma/Sxx;
- B += Db;
- A -= ONEP5*chi2/sum-xbar*Db;
- SB = sqrt((chi2/(n-2))/Sxx);
- SA = SB*sqrt(Sxx/sum+sqr(xbar));
- *a = A;
- *b = B;
- *sa = SA;
- *sb = SB;
-}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include "fitahx.h"
-#include "vec.h"
#include "gromacs/math/do_fit.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
static void my_calc_xcm(int nbb, atom_id bbind[], rvec x[], rvec xcm)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define _fitahx_h
-#include "typedefs.h"
-#include "hxprops.h"
+#include "gromacs/gmxana/hxprops.h"
+#include "gromacs/legacyheaders/typedefs.h"
extern real fit_ahx(int nres, t_bb bb[], int natoms, int nall, atom_id allindex[],
rvec x[], int nca, atom_id caindex[], gmx_bool bFit);
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <math.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
#include "geminate.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include <math.h>
+#include <stdlib.h>
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
static void missing_code_message()
{
/* This returns the real-valued index(!) to an ACF, equidistant on a log scale. */
static double getLogIndex(const int i, const t_gemParams *params)
{
- return (exp(((double)(i)) * params->logQuota) -1);
+ return gmx_expm1(((double)(i)) * params->logQuota);
}
extern t_gemParams *init_gemParams(const double sigma, const double D,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _GEMINATE_H
#define _GEMINATE_H
+#include <stddef.h>
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
enum {
gemNULL, gemNONE, gemDD, gemAD, gemAA, gemA4, gemNR
};
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int
gmx_rama(int argc, char *argv[]);
-int
-gmx_rdf(int argc, char *argv[]);
-
int
gmx_rotmat(int argc, char *argv[]);
int
gmx_pme_error(int argc, char *argv[]);
-int
-gmx_options(int argc, char *argv[]);
-
int
gmx_sans(int argc, char *argv[]);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include <stdlib.h>
#include <string.h>
+#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
-#include "copyrite.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/cstringutil.h"
-#include "vec.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
#include "gromacs/statistics/statistics.h"
-#include "gromacs/commandline/pargs.h"
-#include "typedefs.h"
-#include "xvgr.h"
-#include "macros.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static const char *etitles[] = { "E-docked", "Free Energy" };
{
fprintf(fp, "%12lf\n", bFreeSort ? pdbf[i]->efree : pdbf[i]->edocked);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <math.h>
+#include <stdlib.h>
#include <string.h>
+
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
-#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/matio.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "rmpbc.h"
-#include "txtdump.h"
-#include "eigio.h"
-#include "physics.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/math/do_fit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void calc_entropy_qh(FILE *fp, int n, real eigval[], real temp, int nskip)
{
lambda = eigval[i]*AMU;
w = sqrt(BOLTZMANN*temp/lambda)/NANO;
hwkT = (hbar*w)/(BOLTZMANN*temp);
- dS = (hwkT/(exp(hwkT) - 1) - log(1-exp(-hwkT)));
+ dS = (hwkT/gmx_expm1(hwkT) - gmx_log1p(-exp(-hwkT)));
S += dS;
if (debug)
{
fprintf(out, "%5d %5.3f\n", eignr2[x]+1, overlap/noutvec);
}
- gmx_ffclose(out);
+ xvgrclose(out);
}
static void project(const char *trajfile, t_topology *top, int ePBC, matrix topbox,
for (v = 0; v < noutvec; v++)
{
sprintf(str, "vec %d", eignr[outvec[v]]+1);
- ylabel[v] = strdup(str);
+ ylabel[v] = gmx_strdup(str);
}
sprintf(str, "projection on eigenvectors (%s)", proj_unit);
write_xvgr_graphs(projfile, noutvec, 1, str, NULL, output_env_get_xvgr_tlabel(oenv),
}
fprintf(xvgrout, "%10.5f %10.5f\n", inprod[0][i], inprod[noutvec-1][i]);
}
- gmx_ffclose(xvgrout);
+ xvgrclose(xvgrout);
}
if (threedplotfile)
init_t_atoms(&atoms, nframes, FALSE);
snew(x, nframes);
snew(b, nframes);
- atnm = strdup("C");
- resnm = strdup("PRJ");
+ atnm = gmx_strdup("C");
+ resnm = gmx_strdup("PRJ");
if (nframes > 10000)
{
{
v = outvec[g];
sprintf(str, "vec %d", eignr[v]+1);
- ylabel[g] = strdup(str);
+ ylabel[g] = gmx_strdup(str);
snew(y[g], 4);
for (s = 0; s < 4; s++)
{
gmx_fatal(FARGS, "Selected vector %d is larger than the number of eigenvalues (%d)", eignr[v]+1, neig);
}
sprintf(str, "vec %d", eignr[v]+1);
- ylabel[g] = strdup(str);
+ ylabel[g] = gmx_strdup(str);
snew(y[g], natoms);
for (i = 0; i < natoms; i++)
{
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv,
- PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
+ PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "copyrite.h"
-#include "gromacs/fileio/futil.h"
-#include "readinp.h"
-#include "txtdump.h"
-#include "gstat.h"
-#include "gromacs/statistics/statistics.h"
-#include "xvgr.h"
-#include "gmx_ana.h"
-#include "geminate.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/correlationfunctions/autocorr.h"
+#include "gromacs/correlationfunctions/expfit.h"
+#include "gromacs/correlationfunctions/integrate.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/geminate.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/linearalgebra/matrix.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/statistics/statistics.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
/* must correspond to char *avbar_opt[] declared in main() */
enum {
fprintf(stdout, "First time is not larger than 0, using index number as time for power fit\n");
for (i = 0; i < n; i++)
{
- x[i] = log(i+1);
+ x[i] = gmx_log1p(i);
}
}
}
fprintf(stdout, "\n");
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
static void regression_analysis(int n, gmx_bool bXYdy,
fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
static int real_comp(const void *a, const void *b)
}
}
-static real anal_ee_inf(real *parm, real T)
+static real anal_ee_inf(double *parm, real T)
{
return sqrt(parm[1]*2*parm[0]/T+parm[3]*2*parm[2]/T);
}
double blav, var;
char **leg;
real *tbs, *ybs, rtmp, dens, *fitsig, twooe, tau1_est, tau_sig;
- real fitparm[4];
+ double fitparm[4];
real ee, a, tau1, tau2;
if (n < 4)
if (bFitAc)
{
- int fitlen;
- real *ac, acint, ac_fit[4];
+ int fitlen;
+ real *ac, acint;
+ double ac_fit[4];
snew(ac, n);
for (i = 0; i < n; i++)
sfree(fitsig);
sfree(ybs);
sfree(tbs);
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
static void luzar_correl(int nn, real *time, int nset, real **val, real temp,
int ny, real *x0, real **val,
int npargs, t_pargs *ppa, const output_env_t oenv)
{
- real *c1 = NULL, *sig = NULL, *fitparm;
- real tendfit, tbeginfit;
- int i, efitfn, nparm;
+ real *c1 = NULL, *sig = NULL;
+ double *fitparm;
+ real tendfit, tbeginfit;
+ int i, efitfn, nparm;
efitfn = get_acffitfn();
- nparm = nfp_ffn[efitfn];
+ nparm = effnNparams(efitfn);
fprintf(out, "Will fit to the following function:\n");
- fprintf(out, "%s\n", longs_ffn[efitfn]);
+ fprintf(out, "%s\n", effnDescription(efitfn));
c1 = val[n];
if (bYdy)
{
}
sfree(ctd);
sfree(td);
+ xvgrclose(fp);
}
else
{
sfree(ctd);
sfree(ctdGem);
sfree(td);
+ xvgrclose(fp);
}
int gmx_analyze(int argc, char *argv[])
fprintf(out, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
}
- gmx_ffclose(out);
+ xvgrclose(out);
fprintf(stderr, "\r%d, time=%g\n", j-1, (j-1)*dt);
}
if (ccfile)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
-#include "physics.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/commandline/pargs.h"
-#include "copyrite.h"
-#include "vec.h"
-#include "index.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "xvgr.h"
-#include "gstat.h"
+#include "gromacs/correlationfunctions/autocorr.h"
#include "gromacs/fileio/trnio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void dump_dih_trn(int nframes, int nangles, real **dih, const char *fn,
real *time)
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs,
&oenv))
{
}
fprintf(out, "\n");
}
- gmx_ffclose(out);
+ xvgrclose(out);
}
if (opt2bSet("-or", NFILE, fnm))
{
fprintf(out, "%10.5f %10.3f\n", time[i], trans_frac[i]);
tfrac += trans_frac[i];
}
- gmx_ffclose(out);
+ xvgrclose(out);
tfrac /= nframes;
fprintf(stderr, "Average trans fraction: %g\n", tfrac);
fprintf(out, "%10g %10f\n", 180.0, angstat[0]*norm_fac);
}
- gmx_ffclose(out);
+ xvgrclose(out);
do_view(oenv, opt2fn("-od", NFILE, fnm), "-nxy");
if (bAver)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <math.h>
-#include <string.h>
#include <ctype.h>
-#include <math.h>
#include <float.h>
+#include <math.h>
+#include <stdlib.h>
+#include <string.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/commandline/pargs.h"
-#include "macros.h"
#include "gromacs/fileio/enxio.h"
-#include "physics.h"
-#include "gmx_fatal.h"
-#include "xvgr.h"
-#include "gmx_ana.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/utility/cstringutil.h"
-#include "names.h"
-#include "mdebin.h"
+#include "gromacs/utility/dir_separator.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/snprintf.h"
/* Structure for the names of lambda vector components */
str += sprintf(str, "dH/dl");
if (strlen(lv->lc->names[lv->dhdl]) > 0)
{
- str += sprintf(str, " (%s)", lv->lc->names[lv->dhdl]);
+ sprintf(str, " (%s)", lv->lc->names[lv->dhdl]);
}
}
}
{
lambda_vec_print_short(results[nresults-1].b->native_lambda, buf);
fprintf(fpi, xvg2format, buf, dg_tot);
- gmx_ffclose(fpi);
+ xvgrclose(fpi);
+ }
+ if (fpb != NULL)
+ {
+ xvgrclose(fpb);
}
do_view(oenv, opt2fn_null("-o", NFILE, fnm), "-xydy");
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <math.h>
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
-#include "xvgr.h"
-#include "rmpbc.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "physics.h"
-#include "gmx_ana.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define MAX_ENDS 3
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
{
close_trx(fpdb);
}
- gmx_ffclose(flen);
- gmx_ffclose(fdist);
- gmx_ffclose(fz);
- gmx_ffclose(ftilt);
- gmx_ffclose(ftiltr);
- gmx_ffclose(ftiltl);
+ xvgrclose(flen);
+ xvgrclose(fdist);
+ xvgrclose(fz);
+ xvgrclose(ftilt);
+ xvgrclose(ftiltr);
+ xvgrclose(ftiltl);
if (bKink)
{
- gmx_ffclose(fkink);
- gmx_ffclose(fkinkr);
- gmx_ffclose(fkinkl);
+ xvgrclose(fkink);
+ xvgrclose(fkinkr);
+ xvgrclose(fkinkl);
}
return 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <stdio.h>
+#include "gmxpre.h"
+
#include <math.h>
+#include <stdio.h>
+#include <string.h>
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/correlationfunctions/autocorr.h"
#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/pdbio.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
-#include "gstat.h"
-#include "macros.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
-#include "physics.h"
-#include "index.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
-#include <string.h>
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "gromacs/fileio/matio.h"
#include "gmx_ana.h"
static gmx_bool bAllowed(real phi, real psi)
return j;
}
-static void histogramming(FILE *log, int nbin, gmx_residuetype_t rt,
+static void histogramming(FILE *log, int nbin, gmx_residuetype_t *rt,
int nf, int maxchi, real **dih,
int nlist, t_dlist dlist[],
atom_id index[],
snew(leg, NJC);
for (i = 0; (i < NKKKPHI); i++)
{
- leg[i] = strdup(kkkphi[i].name);
+ leg[i] = gmx_strdup(kkkphi[i].name);
}
for (i = 0; (i < NKKKPSI); i++)
{
- leg[i+NKKKPHI] = strdup(kkkpsi[i].name);
+ leg[i+NKKKPHI] = gmx_strdup(kkkpsi[i].name);
}
for (i = 0; (i < NKKKCHI); i++)
{
- leg[i+NKKKPHI+NKKKPSI] = strdup(kkkchi1[i].name);
+ leg[i+NKKKPHI+NKKKPSI] = gmx_strdup(kkkchi1[i].name);
}
xvgr_legend(fp, NJC, (const char**)leg, oenv);
fprintf(fp, "%5s ", "#Res.");
}
fprintf(fp, "\n");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
for (i = 0; (i < NJC); i++)
{
sfree(leg[i]);
}
}
fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
- gmx_ffclose(fp);
+ xvgrclose(fp);
if (bSSHisto)
{
for (k = 0; (k < 3); k++)
{
gmx_ffclose(gp);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
if (bOm)
{
sprintf(fn, "ramomega%s.xpm", dlist[i].name);
{
fprintf(fp, "%10g %10g\n", RAD2DEG*dih[Xi1][j], RAD2DEG*dih[Xi2][j]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
else
{
char *leg[edMax];
#define NLEG asize(leg)
- leg[0] = strdup("Phi");
- leg[1] = strdup("Psi");
- leg[2] = strdup("Omega");
- leg[3] = strdup("Chi1");
- leg[4] = strdup("Chi2");
- leg[5] = strdup("Chi3");
- leg[6] = strdup("Chi4");
- leg[7] = strdup("Chi5");
- leg[8] = strdup("Chi6");
+ leg[0] = gmx_strdup("Phi");
+ leg[1] = gmx_strdup("Psi");
+ leg[2] = gmx_strdup("Omega");
+ leg[3] = gmx_strdup("Chi1");
+ leg[4] = gmx_strdup("Chi2");
+ leg[5] = gmx_strdup("Chi3");
+ leg[6] = gmx_strdup("Chi4");
+ leg[7] = gmx_strdup("Chi5");
+ leg[8] = gmx_strdup("Chi6");
/* Print order parameters */
fp = xvgropen(fn, "Dihedral Rotamer Transitions", "Residue", "Transitions/ns",
/* fprintf(fp,"%12s\n",dlist[i].name); this confuses xmgrace */
fprintf(fp, "\n");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
static void order_params(FILE *log,
for (i = 0; i < NLEG; i++)
{
- leg[i] = strdup(const_leg[i]);
+ leg[i] = gmx_strdup(const_leg[i]);
}
/* Print order parameters */
fprintf(fp, "\n");
/* fprintf(fp,"%12s\n",dlist[i].name); this confuses xmgrace */
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
if (NULL != pdbfn)
{
gmx_bool bDo_rt, bDo_oh, bDo_ot, bDo_jc;
real dt = 0, traj_t_ns;
output_env_t oenv;
- gmx_residuetype_t rt;
+ gmx_residuetype_t *rt;
atom_id isize, *index;
int ndih, nactdih, nf;
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs,
&oenv))
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/utility/cstringutil.h"
-#include "vec.h"
-#include "macros.h"
-#include "index.h"
-#include "gromacs/random/random.h"
-#include "pbc.h"
-#include "rmpbc.h"
-#include "xvgr.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/matio.h"
-#include "cmat.h"
+#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trnio.h"
-#include "viewit.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/cmat.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/linearalgebra/eigensolver.h"
#include "gromacs/math/do_fit.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/random/random.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
/* print to two file pointers at once (i.e. stderr and log) */
static gmx_inline
int *nb;
} t_nnb;
-void pr_energy(FILE *fp, real e)
-{
- fprintf(fp, "Energy: %8.4f\n", e);
-}
-
void cp_index(int nn, int from[], int to[])
{
int i;
if (NULL != fp)
{
- fclose(fp);
+ xvgrclose(fp);
}
}
{
fprintf(fp, "%5d %5d\n", i+1, ntrans[i]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
sfree(ntrans);
for (i = 0; i < clust->ncl; i++)
gmx_bool bFit, FILE *log, t_rgb rlo, t_rgb rhi,
const output_env_t oenv)
{
- FILE *fp = NULL;
+ FILE *size_fp = NULL;
char buf[STRLEN], buf1[40], buf2[40], buf3[40], *trxsfn;
t_trxstatus *trxout = NULL;
t_trxstatus *trxsout = NULL;
if (clustidfn)
{
- fp = xvgropen(clustidfn, "Clusters", output_env_get_xvgr_tlabel(oenv), "Cluster #", oenv);
+ FILE *fp = xvgropen(clustidfn, "Clusters", output_env_get_xvgr_tlabel(oenv), "Cluster #", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ s0 symbol 2\n");
{
fprintf(fp, "%8g %8d\n", time[i], clust->cl[i]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
if (sizefn)
{
- fp = xvgropen(sizefn, "Cluster Sizes", "Cluster #", "# Structures", oenv);
+ size_fp = xvgropen(sizefn, "Cluster Sizes", "Cluster #", "# Structures", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
- fprintf(fp, "@g%d type %s\n", 0, "bar");
+ fprintf(size_fp, "@g%d type %s\n", 0, "bar");
}
}
snew(structure, nf);
}
if (sizefn)
{
- fprintf(fp, "%8d %8d\n", cl, nstr);
+ fprintf(size_fp, "%8d %8d\n", cl, nstr);
}
clrmsd = 0;
midstr = 0;
{
sfree(trxsfn);
}
+
+ if (size_fp)
+ {
+ xvgrclose(size_fp);
+ }
}
static void convert_mat(t_matrix *mat, t_mat *rms)
{ efXVG, "-sz", "clust-size", ffOPTWR},
{ efXPM, "-tr", "clust-trans", ffOPTWR},
{ efXVG, "-ntr", "clust-trans", ffOPTWR},
- { efXVG, "-clid", "clust-id.xvg", ffOPTWR},
+ { efXVG, "-clid", "clust-id", ffOPTWR},
{ efTRX, "-cl", "clusters.pdb", ffOPTWR }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
&oenv))
{
{
fprintf(fp, "%10d %10g\n", i, eigenvalues[i]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
break;
case m_monte_carlo:
orig = init_mat(rms->nn, FALSE);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2007, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "rmpbc.h"
#include "gromacs/commandline/pargs.h"
-#include "xvgr.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "index.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "calcgrid.h"
-#include "nrnb.h"
-#include "physics.h"
-#include "coulomb.h"
-#include "pme.h"
-#include "gstat.h"
-#include "gromacs/fileio/matio.h"
-#include "mtop_util.h"
-#include "gmx_ana.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
static void clust_size(const char *ndx, const char *trx, const char *xpm,
const char *xpmw, const char *ncl, const char *acl,
{
index[i] = i;
}
- gname = strdup("mols");
+ gname = gmx_strdup("mols");
}
else
{
}
while (read_next_frame(oenv, status, &fr));
close_trx(status);
- gmx_ffclose(fp);
- gmx_ffclose(gp);
- gmx_ffclose(hp);
- gmx_ffclose(tp);
+ xvgrclose(fp);
+ xvgrclose(gp);
+ xvgrclose(hp);
+ xvgrclose(tp);
gmx_mtop_atomlookup_destroy(alook);
nhisto += (int)((j+1)*nelem/n_x);
}
fprintf(fp, "%5d %8.3f\n", j+1, 0.0);
- gmx_ffclose(fp);
+ xvgrclose(fp);
fprintf(stderr, "Total number of atoms in clusters = %d\n", nhisto);
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
-#include "gromacs/fileio/filenm.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "typedefs.h"
-#include "xvgr.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
-#include "vec.h"
-#include "index.h"
-#include "pbc.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/filenm.h"
#include "gromacs/fileio/pdbio.h"
-#include "txtdump.h"
-#include "viewit.h"
-#include "rmpbc.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
void calc_rm_cm(int isize, atom_id index[], t_atoms *atoms, rvec x[], rvec xcm)
{
{
if (debug)
{
- fprintf(debug, "{%d %d}", *i1+bFW ? dx : dy, *i2+bFW ? dy : dx );
+ fprintf(debug, "{%d %d}", *i1 + (bFW ? dx : dy), *i2 + (bFW ? dy : dx) );
}
if (bFW)
{
{ efTPS, "-f1", "conf1.gro", ffREAD },
{ efSTX, "-f2", "conf2", ffREAD },
{ efSTO, "-o", "fit.pdb", ffWRITE },
- { efNDX, "-n1", "fit1.ndx", ffOPTRD },
- { efNDX, "-n2", "fit2.ndx", ffOPTRD },
- { efNDX, "-no", "match.ndx", ffOPTWR }
+ { efNDX, "-n1", "fit1", ffOPTRD },
+ { efNDX, "-n2", "fit2", ffOPTRD },
+ { efNDX, "-no", "match", ffOPTWR }
};
#define NFILE asize(fnm)
real *msds;
- if (!parse_common_args(&argc, argv, PCA_BE_NICE | PCA_CAN_VIEW,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
fprintf(fp, "[ Match_%s_%s ]\n", conf1file, groupnames1);
for (i = 0; i < isize1; i++)
{
- fprintf(fp, "%4u%s", index1[i]+1, (i%15 == 14 || i == isize1-1) ? "\n" : " ");
+ fprintf(fp, "%4d%s", index1[i]+1, (i%15 == 14 || i == isize1-1) ? "\n" : " ");
}
fprintf(fp, "[ Match_%s_%s ]\n", conf2file, groupnames2);
for (i = 0; i < isize2; i++)
{
- fprintf(fp, "%4u%s", index2[i]+1, (i%15 == 14 || i == isize2-1) ? "\n" : " ");
+ fprintf(fp, "%4d%s", index2[i]+1, (i%15 == 14 || i == isize2-1) ? "\n" : " ");
}
}
}
if (warn < 20)
{
fprintf(stderr,
- "Warning: atomnames at index %d don't match: %u %s, %u %s\n",
+ "Warning: atomnames at index %d don't match: %d %s, %d %s\n",
i+1, index1[i]+1, name1, index2[i]+1, name2);
}
warn++;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
-#include <time.h>
-
-#ifdef HAVE_SYS_TIME_H
-#include <sys/time.h>
-#endif
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/trnio.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "rmpbc.h"
-#include "txtdump.h"
#include "gromacs/fileio/matio.h"
-#include "eigio.h"
-#include "physics.h"
-#include "gmx_ana.h"
-#include "gromacs/utility/cstringutil.h"
+#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/trxio.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/linearalgebra/eigensolver.h"
#include "gromacs/math/do_fit.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/sysinfo.h"
int gmx_covar(int argc, char *argv[])
{
int d, dj, nfit;
atom_id *index, *ifit;
gmx_bool bDiffMass1, bDiffMass2;
- time_t now;
char timebuf[STRLEN];
t_rgb rlo, rmi, rhi;
real *eigenvectors;
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
{
fprintf (out, "%10d %g\n", (int)i+1, eigenvalues[ndim-1-i]);
}
- gmx_ffclose(out);
+ xvgrclose(out);
if (bFit)
{
out = gmx_ffopen(logfile, "w");
- time(&now);
- gmx_ctime_r(&now, timebuf, STRLEN);
+ gmx_format_current_time(timebuf, STRLEN);
fprintf(out, "Covariance analysis log, written %s\n", timebuf);
fprintf(out, "Program: %s\n", argv[0]);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2008,2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include <assert.h>
+#include <stdlib.h>
#include "gromacs/commandline/pargs.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "xvgr.h"
-#include "rmpbc.h"
-#include "pbc.h"
-#include "physics.h"
-#include "index.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
#include "gromacs/statistics/statistics.h"
-#include "gmx_ana.h"
-#include "macros.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#define SQR(x) (pow(x, 2.0))
#define EPSI0 (EPSILON0*E_CHARGE*E_CHARGE*AVOGADRO/(KILO*NANO)) /* EPSILON0 in SI units */
xshfr[i] = 0.0;
}
}
-
+ assert(time != NULL);
if (nfr == 0)
{ efTPS, NULL, NULL, ffREAD }, /* this is for the topology */
{ efNDX, NULL, NULL, ffOPTRD },
{ efTRX, "-f", NULL, ffREAD }, /* and this for the trajectory */
- { efXVG, "-o", "current.xvg", ffWRITE },
- { efXVG, "-caf", "caf.xvg", ffOPTWR },
- { efXVG, "-dsp", "dsp.xvg", ffWRITE },
- { efXVG, "-md", "md.xvg", ffWRITE },
- { efXVG, "-mj", "mj.xvg", ffWRITE},
- { efXVG, "-mc", "mc.xvg", ffOPTWR }
+ { efXVG, "-o", "current", ffWRITE },
+ { efXVG, "-caf", "caf", ffOPTWR },
+ { efXVG, "-dsp", "dsp", ffWRITE },
+ { efXVG, "-md", "md", ffWRITE },
+ { efXVG, "-mj", "mj", ffWRITE },
+ { efXVG, "-mc", "mc", ffOPTWR }
};
#define NFILE asize(fnm)
temp, trust, bfit, efit, bvit, evit, status, isize, nmols, nshift,
index0, indexm, mass2, qmol, eps_rf, oenv);
- gmx_ffclose(fmj);
- gmx_ffclose(fmd);
- gmx_ffclose(fmjdsp);
- if (bACF)
- {
- gmx_ffclose(outf);
- }
- if (bINT)
+ xvgrclose(fmj);
+ xvgrclose(fmd);
+ xvgrclose(fmjdsp);
+ if (fr.bV)
{
- gmx_ffclose(mcor);
+ if (bACF)
+ {
+ xvgrclose(outf);
+ }
+ xvgrclose(fcur);
+ if (bINT)
+ {
+ xvgrclose(mcor);
+ }
}
return 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <math.h>
-#include <ctype.h>
+#include "gmxpre.h"
-#include "sysstuff.h"
+#include <ctype.h>
+#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "gromacs/utility/cstringutil.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "gstat.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+
#include "gromacs/commandline/pargs.h"
-#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "physics.h"
-#include "gmx_ana.h"
-#include "macros.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
char *atomname;
gmx_fatal(FARGS, "Invalid line in datafile at line %d\n", i+1);
}
(*eltab)[i].nr_el = tempnr;
- (*eltab)[i].atomname = strdup(tempname);
+ (*eltab)[i].atomname = gmx_strdup(tempname);
}
gmx_ffclose(in);
slice = (z / (*slWidth));
}
sought.nr_el = 0;
- sought.atomname = strdup(*(top->atoms.atomname[index[n][i]]));
+ sought.atomname = gmx_strdup(*(top->atoms.atomname[index[n][i]]));
/* now find the number of electrons. This is not efficient. */
found = (t_electron *)
fprintf(den, "\n");
}
- gmx_ffclose(den);
+ xvgrclose(den);
}
int gmx_density(int argc, char *argv[])
t_filenm fnm[] = { /* files for g_density */
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efDAT, "-ei", "electrons", ffOPTRD }, /* file with nr. of electrons */
{ efXVG, "-o", "density", ffWRITE },
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs,
&oenv))
{
/* Calculate axis */
axis = toupper(axtitle[0]) - 'X';
- top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC); /* read topology file */
if (dens_opt[0][0] == 'n')
{
for (i = 0; (i < top->atoms.nr); i++)
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "princ.h"
-#include "rmpbc.h"
-#include "txtdump.h"
+#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gstat.h"
-#include "gromacs/fileio/matio.h"
-#include "pbc.h"
-#include "gmx_ana.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
int gmx_densmap(int argc, char *argv[])
{
npargs = asize(pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, npargs, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
{
n1 = (int)(2*amax/bin + 0.5);
nradial = (int)(rmax/bin + 0.5);
+ /* cppcheck-suppress zerodiv fixed in 1.68-dev */
invspa = n1/(2*amax);
+ /* cppcheck-suppress zerodiv fixed in 1.68-dev */
invspz = nradial/rmax;
if (bMirror)
{
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <ctype.h>
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
-#include "gromacs/utility/cstringutil.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "gstat.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/commandline/pargs.h"
-#include "index.h"
+#include "gromacs/correlationfunctions/autocorr.h"
+#include "gromacs/correlationfunctions/expfit.h"
+#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "physics.h"
-#include "gromacs/fileio/matio.h"
-#include "dens_filter.h"
-#include "binsearch.h"
-#include "powerspect.h"
-#include "gmx_ana.h"
-#include "copyrite.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/binsearch.h"
+#include "gromacs/gmxana/dens_filter.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/powerspect.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#ifdef GMX_DOUBLE
#define FLOOR(x) ((int) floor(x))
t_interf ****intf2, const output_env_t oenv)
{
/*Returns two pointers to 3D arrays of t_interf structs containing (position,thickness) of the interface(s)*/
- FILE *xvg;
- real *zDensavg; /* zDensavg[z]*/
- int i, j, k, n;
- int xysize;
- int ndx1, ndx2, *zperm;
- real densmid;
- real splitpoint, startpoint, endpoint;
- real *sigma1, *sigma2;
- real beginfit1[4];
- real beginfit2[4];
- real *fit1 = NULL, *fit2 = NULL;
- const real *avgfit1;
- const real *avgfit2;
- const real onehalf = 1.00/2.00;
- t_interf ***int1 = NULL, ***int2 = NULL; /*Interface matrices [t][x,y] - last index in row-major order*/
+ FILE *xvg;
+ real *zDensavg; /* zDensavg[z]*/
+ int i, j, k, n;
+ int xysize;
+ int ndx1, ndx2, *zperm;
+ real densmid;
+ real splitpoint, startpoint, endpoint;
+ real *sigma1, *sigma2;
+ double beginfit1[4];
+ double beginfit2[4];
+ double *fit1 = NULL, *fit2 = NULL;
+ const double *avgfit1;
+ const double *avgfit2;
+ const real onehalf = 1.00/2.00;
+ t_interf ***int1 = NULL, ***int2 = NULL; /*Interface matrices [t][x,y] - last index in row-major order*/
/*Create int1(t,xy) and int2(t,xy) arrays with correct number of interf_t elements*/
xysize = xslices*yslices;
snew(int1, tblocks);
sfree(yticks);
}
-static void writeraw(t_interf ***int1, t_interf ***int2, int tblocks, int xbins, int ybins, char **fnms)
+static void writeraw(t_interf ***int1, t_interf ***int2, int tblocks,
+ int xbins, int ybins, char **fnms,
+ const output_env_t oenv)
{
FILE *raw1, *raw2;
int i, j, n;
gmx::BinaryInformationSettings settings;
settings.generatedByHeader(true);
settings.linePrefix("# ");
- gmx::printBinaryInformation(raw1, gmx::getProgramContext(), settings);
- gmx::printBinaryInformation(raw2, gmx::getProgramContext(), settings);
+ gmx::printBinaryInformation(raw1, output_env_get_program_context(oenv),
+ settings);
+ gmx::printBinaryInformation(raw2, output_env_get_program_context(oenv),
+ settings);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
fprintf(raw1, "# Legend: nt nx ny\n# Xbin Ybin Z t\n");
t_filenm fnm[] = {
- { efTPX, "-s", NULL, ffREAD }, /* this is for the topology */
+ { efTPR, "-s", NULL, ffREAD }, /* this is for the topology */
{ efTRX, "-f", NULL, ffREAD }, /* and this for the trajectory */
{ efNDX, "-n", NULL, ffREAD}, /* this is to select groups */
{ efDAT, "-o", "Density4D", ffOPTWR}, /* This is for outputting the entire 4D densityfield in binary format */
bRawOut = opt2bSet("-or", NFILE, fnm);
bGraph = opt2bSet("-og", NFILE, fnm);
bOut = opt2bSet("-o", NFILE, fnm);
- top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
snew(grpname, 1);
snew(index, 1);
snew(ngx, 1);
{
gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfxpm);
}
- writeraw(surf1, surf2, tblock, xslices, yslices, rawfiles);
+ writeraw(surf1, surf2, tblock, xslices, yslices, rawfiles, oenv);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
-
-#include "copyrite.h"
-#include "typedefs.h"
-#include "gstat.h"
+#include <string.h>
+
+#include "gromacs/correlationfunctions/expfit.h"
+#include "gromacs/correlationfunctions/integrate.h"
+#include "gromacs/fft/fft.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "xvgr.h"
-#include "correl.h"
-#include "gmx_ana.h"
-#include "gmx_fatal.h"
-
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/math/gmxcomplex.h"
#include "gromacs/math/utilities.h"
+#include "gmx_ana.h"
/* Determines at which point in the array the fit should start */
int calc_nbegin(int nx, real x[], real tbegin)
t_complex *tmp, gw, hw, kw;
int i, nnx, nxsav;
real fac, nu, dt, *ptr, maxeps, numax;
+ gmx_fft_t fft;
+ int fftcode;
nxsav = nx;
/*while ((dy[nx-1] == 0.0) && (nx > 0))
{
nnx *= 2;
}
+
snew(tmp, 2*nnx);
printf("Doing FFT of %d points\n", nnx);
for (i = 0; (i < nx); i++)
{
tmp[i].re = dy[i];
}
- ptr = &tmp[0].re;
- four1(ptr-1, nnx, -1);
-
+ if ((fftcode = gmx_fft_init_1d_real(&fft, nnx,
+ GMX_FFT_FLAG_NONE)) != 0)
+ {
+ gmx_fatal(FARGS, "gmx_fft_init_1d_real returned %d", fftcode);
+ }
+ if ((fftcode = gmx_fft_1d_real(fft, GMX_FFT_COMPLEX_TO_REAL,
+ (void *)tmp, (void *)tmp)) != 0)
+ {
+ gmx_fatal(FARGS, "gmx_fft_1d_real returned %d", fftcode);
+ }
+ gmx_fft_destroy(fft);
dt = x[1]-x[0];
if (epsRF == 0)
{
}
printf("MAXEPS = %10.5e at frequency %10.5e GHz (tauD = %8.1f ps)\n",
maxeps, numax, 1000/(2*M_PI*numax));
- gmx_ffclose(fp);
- gmx_ffclose(cp);
+ xvgrclose(fp);
+ xvgrclose(cp);
sfree(tmp);
}
#define NFILE asize(fnm)
output_env_t oenv;
int i, j, nx, ny, nxtail, eFitFn, nfitparm;
- real dt, integral, fitintegral, *fitparms, fac, rffac;
+ real dt, integral, fitintegral, fac, rffac;
+ double *fitparms;
double **yd;
real **y;
const char *legend[] = { "Correlation", "Std. Dev.", "Fit", "Combined", "Derivative" };
- static int fix = 0, bFour = 0, bX = 1, nsmooth = 3;
+ static int fix = 0, bX = 1, nsmooth = 3;
static real tendInt = 5.0, tbegin = 5.0, tend = 500.0;
static real A = 0.5, tau1 = 10.0, tau2 = 1.0, eps0 = 80, epsRF = 78.5, tail = 500.0;
real lambda;
t_pargs pa[] = {
- { "-fft", FALSE, etBOOL, {&bFour},
- "use fast fourier transform for correlation function" },
{ "-x1", FALSE, etBOOL, {&bX},
"use first column as [IT]x[it]-axis rather than first data set" },
{ "-eint", FALSE, etREAL, {&tendInt},
"Number of points for smoothing" }
};
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
eFitFn = sffn2effn(s_ffn);
- nfitparm = nfp_ffn[eFitFn];
+ nfitparm = effnNparams(eFitFn);
snew(fitparms, 4);
fitparms[0] = tau1;
if (nfitparm > 1)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <string.h>
+#include "gmxpre.h"
+
#include <math.h>
+#include <string.h>
#include <algorithm>
-#include "macros.h"
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "pbc.h"
-#include "bondf.h"
-#include "gromacs/fileio/futil.h"
-#include "xvgr.h"
-#include "txtdump.h"
-#include "gromacs/statistics/statistics.h"
-#include "gstat.h"
-#include "index.h"
-#include "gromacs/random/random.h"
-#include "names.h"
-#include "physics.h"
-#include "calcmu.h"
+#include "gromacs/correlationfunctions/autocorr.h"
#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/matio.h"
-#include "gmx_ana.h"
-#include "copyrite.h"
#include "gromacs/fileio/trxio.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/calcmu.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/random/random.h"
+#include "gromacs/statistics/statistics.h"
+#include "gromacs/topology/index.h"
#include "gromacs/utility/exceptions.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define e2d(x) ENM2DEBYE*(x)
#define EANG2CM E_CHARGE*1.0e-10 /* e Angstrom to Coulomb meter */
/* Swap x0 and x1 */
x0 = x1;
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
gmx_bool read_mu_from_enx(ener_file_t fmu, int Vol, ivec iMu, rvec mu, real *vol,
slab_dipole[i][ZZ]/nframes,
mutot);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
do_view(oenv, fn, "-autoscale xy -nxy");
}
gmx::BinaryInformationSettings settings;
settings.generatedByHeader(true);
settings.linePrefix("# ");
- gmx::printBinaryInformation(dip3d, gmx::getProgramContext(),
+ gmx::printBinaryInformation(dip3d, output_env_get_program_context(oenv),
settings);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
close_trj(status);
}
- gmx_ffclose(outmtot);
- gmx_ffclose(outaver);
- gmx_ffclose(outeps);
+ xvgrclose(outmtot);
+ xvgrclose(outaver);
+ xvgrclose(outeps);
if (fnadip)
{
- gmx_ffclose(adip);
+ xvgrclose(adip);
}
if (cosaver)
{
- gmx_ffclose(caver);
+ xvgrclose(caver);
}
if (dip3d)
fprintf(outdd, "%10g %10f\n",
(i*mu_max)/ndipbin, dipole_bin[i]/(double)teller);
}
- gmx_ffclose(outdd);
+ xvgrclose(outdd);
sfree(dipole_bin);
}
if (bGkr)
t_filenm fnm[] = {
{ efEDR, "-en", NULL, ffOPTRD },
{ efTRX, "-f", NULL, ffREAD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-o", "Mtot", ffWRITE },
{ efXVG, "-eps", "epsilon", ffWRITE },
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
snew(top, 1);
- ePBC = read_tpx_top(ftp2fn(efTPX, NFILE, fnm), NULL, box,
+ ePBC = read_tpx_top(ftp2fn(efTPR, NFILE, fnm), NULL, box,
&natoms, NULL, NULL, NULL, top);
snew(gnx, ncos);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "typedefs.h"
-#include "macros.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "vec.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/utility/smalloc.h"
-#include "nrnb.h"
-#include "disre.h"
#include "gromacs/commandline/pargs.h"
-#include "force.h"
-#include "gstat.h"
-#include "main.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/pdbio.h"
-#include "index.h"
-#include "mdatoms.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "mdrun.h"
-#include "names.h"
-#include "gromacs/fileio/matio.h"
-#include "mtop_util.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/math/do_fit.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
int n;
gmx_rmpbc_t gpbc = NULL;
t_filenm fnm[] = {
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efXVG, "-ds", "drsum", ffWRITE },
{ efXVG, "-da", "draver", ffWRITE },
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
init5(ntop);
}
- read_tpxheader(ftp2fn(efTPX, NFILE, fnm), &header, FALSE, NULL, NULL);
+ read_tpxheader(ftp2fn(efTPR, NFILE, fnm), &header, FALSE, NULL, NULL);
snew(xtop, header.natoms);
- read_tpx(ftp2fn(efTPX, NFILE, fnm), &ir, box, &ntopatoms, xtop, NULL, NULL, &mtop);
+ read_tpx(ftp2fn(efTPR, NFILE, fnm), &ir, box, &ntopatoms, xtop, NULL, NULL, &mtop);
bPDB = opt2bSet("-q", NFILE, fnm);
if (bPDB)
{
if (ftp2bSet(efNDX, NFILE, fnm))
{
+ /* TODO: Nothing is written to this file if -c is provided, but it is
+ * still opened... */
rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
xvg = xvgropen(opt2fn("-dr", NFILE, fnm), "Individual Restraints", "Time (ps)",
"nm", oenv);
}
dump_disre_matrix(opt2fn_null("-x", NFILE, fnm), &dr, fcd.disres.nres,
j, &top->idef, &mtop, max_dr, nlevels, bThird);
- gmx_ffclose(out);
- gmx_ffclose(aver);
- gmx_ffclose(numv);
- gmx_ffclose(maxxv);
- if (isize > 0)
- {
- gmx_ffclose(xvg);
- do_view(oenv, opt2fn("-dr", NFILE, fnm), "-nxy");
- }
+ xvgrclose(out);
+ xvgrclose(aver);
+ xvgrclose(numv);
+ xvgrclose(maxxv);
do_view(oenv, opt2fn("-dn", NFILE, fnm), "-nxy");
do_view(oenv, opt2fn("-da", NFILE, fnm), "-nxy");
do_view(oenv, opt2fn("-ds", NFILE, fnm), "-nxy");
do_view(oenv, opt2fn("-dm", NFILE, fnm), "-nxy");
}
+ if (isize > 0)
+ {
+ xvgrclose(xvg);
+ if (!clust)
+ {
+ do_view(oenv, opt2fn("-dr", NFILE, fnm), "-nxy");
+ }
+ }
gmx_log_close(fplog);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include <stdlib.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/strdb.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "mshift.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gmx_fatal.h"
-#include "xvgr.h"
#include "gromacs/fileio/matio.h"
-#include "index.h"
-#include "gstat.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/strdb.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "viewit.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/dir_separator.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static int strip_dssp(char *dsspfile, int nres,
gmx_bool bPhobres[], real t,
int i;
- OOO = strdup("O");
+ OOO = gmx_strdup("O");
for (i = 0; (i < atoms->nr); i++)
{
leg[0] = "Structure";
for (s = 0; s < (size_t)mat->nmap; s++)
{
- leg[s+1] = strdup(map[s].desc);
+ leg[s+1] = gmx_strdup(map[s].desc);
}
fp = xvgropen(outfile, "Secondary Structure",
}
fprintf(fp, "\n");
- gmx_ffclose(fp);
+ xvgrclose(fp);
sfree(leg);
sfree(count);
}
gmx_bool *bPhbres, bDoAccSurf;
real t;
int i, j, natoms, nframe = 0;
- matrix box;
+ matrix box = {{0}};
int gnx;
char *grpnm, *ss_str;
atom_id *index;
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv,
- PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT | PCA_BE_NICE,
+ PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
mat.map = NULL;
- mat.nmap = getcmap(libopen(opt2fn("-map", NFILE, fnm)),
- opt2fn("-map", NFILE, fnm), &(mat.map));
+ mat.nmap = readcmap(opt2fn("-map", NFILE, fnm), &(mat.map));
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
if (natoms > atoms->nr)
write_pdbfile_indexed(tapein, NULL, atoms, x, ePBC, box, ' ', -1, gnx, index, NULL, TRUE);
gmx_ffclose(tapein);
-#ifdef GMX_NO_SYSTEM
- printf("Warning-- No calls to system(3) supported on this platform.");
- printf("Warning-- Skipping execution of 'system(\"%s\")'.", dssp);
- exit(1);
-#else
if (0 != system(dssp))
{
gmx_fatal(FARGS, "Failed to execute command: %s\n",
"Try specifying your dssp version with the -ver option.", dssp);
}
-#endif
/* strip_dssp returns the number of lines found in the dssp file, i.e.
* the number of residues plus the separator lines */
close_trj(status);
if (fTArea)
{
- gmx_ffclose(fTArea);
+ xvgrclose(fTArea);
}
gmx_rmpbc_done(gpbc);
{
fprintf(acc, "%5d %10g %10g\n", i+1, av_area[i], norm_av_area[i]);
}
- gmx_ffclose(acc);
+ xvgrclose(acc);
}
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <stdio.h>
+#include "gmxpre.h"
+
#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/correlationfunctions/autocorr.h"
+#include "gromacs/correlationfunctions/integrate.h"
+#include "gromacs/fft/fft.h"
#include "gromacs/fileio/confio.h"
-#include "copyrite.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
-#include "gstat.h"
-#include "macros.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
-#include "physics.h"
-#include "index.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/commandline/pargs.h"
-#include <string.h>
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "correl.h"
#include "gmx_ana.h"
-#include "gromacs/fft/fft.h"
-#include "gromacs/fileio/trxio.h"
enum {
VACF, MVACF, DOS, DOS_SOLID, DOS_DIFF, DOS_CP, DOS_S, DOS_A, DOS_E, DOS_NR
}
else
{
- return bhn/(exp(bhn)-1) - log(1-exp(-bhn));
+ return bhn/gmx_expm1(bhn) - gmx_log1p(-exp(-bhn));
}
}
}
else
{
- return bhn/2 + bhn/(exp(bhn)-1)-1;
+ return bhn/2 + bhn/gmx_expm1(bhn)-1;
}
}
t_filenm fnm[] = {
{ efTRN, "-f", NULL, ffREAD },
- { efTPX, "-s", NULL, ffREAD },
+ { efTPR, "-s", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-vacf", "vacf", ffWRITE },
{ efXVG, "-mvacf", "mvacf", ffWRITE },
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, npargs, ppa, asize(desc), desc,
asize(bugs), bugs, &oenv))
{
please_cite(fplog, "Pascal2011a");
please_cite(fplog, "Caleman2011b");
- read_tps_conf(ftp2fn(efTPX, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box,
+ read_tps_conf(ftp2fn(efTPR, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box,
TRUE);
V = det(box);
tmass = 0;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "copyrite.h"
-#include "gromacs/fileio/filenm.h"
-#include "macros.h"
-#include "pbc.h"
-#include "gromacs/utility/smalloc.h"
+#include "gmxpre.h"
+
#include "gromacs/commandline/pargs.h"
-#include "vec.h"
-#include "xvgr.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/trx.h"
#include "gromacs/fileio/trxio.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
int gmx_dyecoupl(int argc, char *argv[])
{
int ndon, nacc;
atom_id *donindex, *accindex;
char *grpnm;
- t_atoms *atoms = NULL;
t_trxstatus *status;
t_trxframe fr;
rrange, krange, rincr, kincr, Rfrac;
int rkcount = 0, rblocksallocated = 0, kblocksallocated = 0;
- if (!parse_common_args(&argc, argv, PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT | PCA_BE_NICE, NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ if (!parse_common_args(&argc, argv, PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
}
printf("Select group with donor atom pairs defining the transition moment\n");
- get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &ndon, &donindex, &grpnm);
+ get_index(NULL, ftp2fn_null(efNDX, NFILE, fnm), 1, &ndon, &donindex, &grpnm);
printf("Select group with acceptor atom pairs defining the transition moment\n");
- get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &nacc, &accindex, &grpnm);
+ get_index(NULL, ftp2fn_null(efNDX, NFILE, fnm), 1, &nacc, &accindex, &grpnm);
/*check if groups are identical*/
grident = TRUE;
if (bRKout)
{
- gmx_ffclose(rkfp);
+ xvgrclose(rkfp);
}
if (bDatout)
if (bInstEffout)
{
- gmx_ffclose(iefp);
+ xvgrclose(iefp);
}
fprintf(rhfp, "%12.7f %12.7f\n", (i + 0.5) * rincr + rmin,
rhist[i]);
}
- gmx_ffclose(rhfp);
+ xvgrclose(rhfp);
}
if (bKhistout)
fprintf(khfp, "%12.7f %12.7f\n", (i + 0.5) * kincr + kmin,
khist[i]);
}
- gmx_ffclose(khfp);
+ xvgrclose(khfp);
}
printf("\nAverages:\n");
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "gromacs/math/3dview.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/utility/smalloc.h"
-#include "index.h"
#include "gromacs/fileio/confio.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "physics.h"
-#include "gmx_ana.h"
-#include "macros.h"
#include "gromacs/fileio/trxio.h"
-
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/3dtransforms.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static void rot_conf(t_atoms *atoms, rvec x[], rvec v[], real trans, real angle,
rvec head, rvec tail, int isize, atom_id index[],
/* Now the total rotation matrix: */
/* Rotate a couple of times */
- rotate(ZZ, -phi, Rz);
- rotate(YY, M_PI/2-theta, Ry);
- rotate(XX, angle*DEG2RAD, Rx);
+ gmx_mat4_init_rotation(ZZ, -phi, Rz);
+ gmx_mat4_init_rotation(YY, M_PI/2-theta, Ry);
+ gmx_mat4_init_rotation(XX, angle*DEG2RAD, Rx);
Rx[WW][XX] = trans;
- rotate(YY, theta-M_PI/2, Rinvy);
- rotate(ZZ, phi, Rinvz);
+ gmx_mat4_init_rotation(YY, theta-M_PI/2, Rinvy);
+ gmx_mat4_init_rotation(ZZ, phi, Rinvz);
- mult_matrix(temp1, Ry, Rz);
- mult_matrix(temp2, Rinvy, Rx);
- mult_matrix(temp3, temp2, temp1);
- mult_matrix(Mtot, Rinvz, temp3);
+ gmx_mat4_mmul(temp1, Ry, Rz);
+ gmx_mat4_mmul(temp2, Rinvy, Rx);
+ gmx_mat4_mmul(temp3, temp2, temp1);
+ gmx_mat4_mmul(Mtot, Rinvz, temp3);
- print_m4(debug, "Rz", Rz);
- print_m4(debug, "Ry", Ry);
- print_m4(debug, "Rx", Rx);
- print_m4(debug, "Rinvy", Rinvy);
- print_m4(debug, "Rinvz", Rinvz);
- print_m4(debug, "Mtot", Mtot);
+ if (debug)
+ {
+ gmx_mat4_print(debug, "Rz", Rz);
+ gmx_mat4_print(debug, "Ry", Ry);
+ gmx_mat4_print(debug, "Rx", Rx);
+ gmx_mat4_print(debug, "Rinvy", Rinvy);
+ gmx_mat4_print(debug, "Rinvz", Rinvz);
+ gmx_mat4_print(debug, "Mtot", Mtot);
+ }
for (i = 0; (i < isize); i++)
{
ai = index[i];
- m4_op(Mtot, xout[ai], xv);
+ gmx_mat4_transform_point(Mtot, xout[ai], xv);
rvec_add(xv, xcm, xout[ai]);
- m4_op(Mtot, v[ai], xv);
+ gmx_mat4_transform_point(Mtot, v[ai], xv);
copy_rvec(xv, vout[ai]);
}
}
return 0;
}
+ if (maxangle == 0)
+ {
+ gmx_fatal(FARGS, "maxangle not given");
+ }
+
get_stx_coordnum (opt2fn("-f", NFILE, fnm), &natoms);
init_t_atoms(&atoms, natoms, TRUE);
snew(x, natoms);
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/confio.h"
-#include "symtab.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/strdb.h"
-#include "index.h"
-#include "vec.h"
-#include "typedefs.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
-#include "physics.h"
-#include "atomprop.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "pbc.h"
-#include "princ.h"
-#include "txtdump.h"
-#include "viewit.h"
-#include "rmpbc.h"
-#include "gmx_ana.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
typedef struct
{
for (i = 1; (i < 12); i++)
{
fprintf(out,
- "%-6s%5u %-4.4s%3.3s %c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f\n",
+ "%-6s%5d %-4.4s%3.3s %c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f\n",
"ATOM ", natoms + 1 + i, "CA", "LEG", space, nres + 1, space,
(xmin + (i * 0.12)) * 10, ymin * 10, zmin * 10, 1.0, bfac_min
+ ((i - 1.0) * (bfac_max - bfac_min) / 10));
gmx_fatal(FARGS, "Output file should be a .pdb file"
" when using the -grasp option\n");
}
- if ((bMead || bGrasp) && !((fn2ftp(infile) == efTPR) ||
- (fn2ftp(infile) == efTPA) ||
- (fn2ftp(infile) == efTPB)))
+ if ((bMead || bGrasp) && (fn2ftp(infile) != efTPR))
{
- gmx_fatal(FARGS, "Input file should be a .tp[abr] file"
+ gmx_fatal(FARGS, "Input file should be a .tpr file"
" when using the -mead option\n");
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <string.h>
+#include "gmxpre.h"
+
#include <math.h>
+#include <stdlib.h>
+#include <string.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
#include "gromacs/commandline/pargs.h"
-#include "disre.h"
-#include "names.h"
-#include "macros.h"
-#include "gmx_fatal.h"
#include "gromacs/fileio/enxio.h"
-#include "vec.h"
-#include "gmx_ana.h"
#include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#define TIME_EXPLICIT 0
#define TIME_CONTINUE 1
"Stop on errors in the file" }
};
- if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa),
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa),
pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
nset = 0;
timestep = 0.0;
snew(fnms, argc);
- nfile = 0;
lastfilestep = 0;
laststep = startstep = 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <string.h>
+#include "gmxpre.h"
+
#include <math.h>
+#include <string.h>
-#include "gromacs/utility/cstringutil.h"
-#include "typedefs.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/enxio.h"
#include "gromacs/commandline/pargs.h"
-#include "names.h"
-#include "macros.h"
-#include "xvgr.h"
-#include "gstat.h"
-#include "physics.h"
+#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/strdb.h"
-#include "gmx_ana.h"
#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static int search_str2(int nstr, char **str, char *key)
t_filenm fnm[] = {
{ efEDR, "-f", NULL, ffOPTRD },
- { efDAT, "-groups", "groups.dat", ffREAD },
- { efDAT, "-eref", "eref.dat", ffOPTRD },
- { efXPM, "-emat", "emat", ffWRITE },
+ { efDAT, "-groups", "groups", ffREAD },
+ { efDAT, "-eref", "eref", ffOPTRD },
+ { efXPM, "-emat", "emat", ffWRITE },
{ efXVG, "-etot", "energy", ffWRITE }
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
fprintf(out, "\n");
}
- gmx_ffclose(out);
+ xvgrclose(out);
}
else
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "typedefs.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/enxio.h"
#include "gromacs/commandline/pargs.h"
-#include "names.h"
-#include "copyrite.h"
-#include "macros.h"
-#include "xvgr.h"
-#include "gstat.h"
-#include "physics.h"
+#include "gromacs/correlationfunctions/autocorr.h"
+#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "viewit.h"
-#include "mtop_util.h"
-#include "gmx_ana.h"
-#include "mdebin.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static real minthird = -1.0/3.0, minsixth = -1.0/6.0;
j = 0;
for (k = 0; k < nre; k++)
{
- newnm[k] = strdup(nm[k].name);
+ newnm[k] = gmx_strdup(nm[k].name);
/* Insert dashes in all the names */
while ((ptr = strchr(newnm[k], ' ')) != NULL)
{
fprintf(vout, "%10d %10.5e\n", j, mypow(violaver[j]/nframes, minthird));
}
#endif
- gmx_ffclose(vout);
+ xvgrclose(vout);
fprintf(stdout, "\nSum of violations averaged over simulation: %g nm\n",
sumt);
}
fprintf(fp1, "\n");
}
- gmx_ffclose(fp0);
- gmx_ffclose(fp1);
+ xvgrclose(fp0);
+ xvgrclose(fp1);
}
typedef struct {
intBulk += 0.5*(eneset[11][i-1] + eneset[11][i])*factor;
fprintf(fp, "%10g %10g %10g\n", (i*Dt), integral, intBulk);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
for (i = 0; i < 12; i++)
{
}
if (fp)
{
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
sfree(fr);
}
t_filenm fnm[] = {
{ efEDR, "-f", NULL, ffREAD },
{ efEDR, "-f2", NULL, ffOPTRD },
- { efTPX, "-s", NULL, ffOPTRD },
+ { efTPR, "-s", NULL, ffOPTRD },
{ efXVG, "-o", "energy", ffWRITE },
{ efXVG, "-viol", "violaver", ffOPTWR },
{ efXVG, "-pairs", "pairs", ffOPTWR },
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
if (!parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END | PCA_BE_NICE,
+ PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END,
NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
if (bSum)
{
- leg[nset] = strdup("Sum");
+ leg[nset] = gmx_strdup("Sum");
xvgr_legend(out, nset+1, (const char**)leg, oenv);
}
else
if (bORIRE || bOTEN)
{
- get_orires_parms(ftp2fn(efTPX, NFILE, fnm), &nor, &nex, &or_label, &oobs);
+ get_orires_parms(ftp2fn(efTPR, NFILE, fnm), &nor, &nex, &or_label, &oobs);
}
if (bORIRE)
for (j = 0; j < 3; j++)
{
sprintf(buf, "eig%d", j+1);
- otenleg[(bOvec ? 12 : 3)*i+j] = strdup(buf);
+ otenleg[(bOvec ? 12 : 3)*i+j] = gmx_strdup(buf);
}
if (bOvec)
{
for (j = 0; j < 9; j++)
{
sprintf(buf, "vec%d%s", j/3+1, j%3 == 0 ? "x" : (j%3 == 1 ? "y" : "z"));
- otenleg[12*i+3+j] = strdup(buf);
+ otenleg[12*i+3+j] = gmx_strdup(buf);
}
}
}
}
else if (bDisRe)
{
- nbounds = get_bounds(ftp2fn(efTPX, NFILE, fnm), &bounds, &index, &pair, &npairs,
+ nbounds = get_bounds(ftp2fn(efTPR, NFILE, fnm), &bounds, &index, &pair, &npairs,
&mtop, &top, &ir);
snew(violaver, npairs);
out = xvgropen(opt2fn("-o", NFILE, fnm), "Sum of Violations",
}
else if (bDHDL)
{
- get_dhdl_parms(ftp2fn(efTPX, NFILE, fnm), &ir);
+ get_dhdl_parms(ftp2fn(efTPR, NFILE, fnm), &ir);
}
/* Initiate energies and set them to zero */
close_enx(fp);
if (out)
{
- gmx_ffclose(out);
+ xvgrclose(out);
}
if (bDRAll)
{
- gmx_ffclose(fp_pairs);
+ xvgrclose(fp_pairs);
}
if (bORT)
{
- gmx_ffclose(fort);
+ xvgrclose(fort);
}
if (bODT)
{
- gmx_ffclose(fodt);
+ xvgrclose(fodt);
}
if (bORA)
{
{
fprintf(out, "%5d %g\n", or_label[i], orient[i]/norfr);
}
- gmx_ffclose(out);
+ xvgrclose(out);
}
if (bODA)
{
{
fprintf(out, "%5d %g\n", or_label[i], orient[i]/norfr-oobs[i]);
}
- gmx_ffclose(out);
+ xvgrclose(out);
}
if (bODR)
{
{
fprintf(out, "%5d %g\n", or_label[i], sqrt(odrms[i]/norfr));
}
- gmx_ffclose(out);
+ xvgrclose(out);
}
if (bOTEN)
{
- gmx_ffclose(foten);
+ xvgrclose(foten);
}
if (bDisRe)
{
if (fp_dhdl)
{
- gmx_ffclose(fp_dhdl);
+ gmx_fio_fclose(fp_dhdl);
printf("\n\nWrote %d lambda values with %d samples as ",
dh_lambdas, dh_samples);
if (dh_hists > 0)
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <math.h>
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "princ.h"
-#include "rmpbc.h"
-#include "gmx_ana.h"
-
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/smalloc.h"
int gmx_filter(int argc, char *argv[])
{
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <ctype.h>
+#include <stdlib.h>
#include <string.h>
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "gromacs/fileio/confio.h"
#include "gromacs/commandline/pargs.h"
-#include "pbc.h"
-#include "force.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/math/utilities.h"
-#include "macros.h"
-#include "vec.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/tpxio.h"
-#include "mdrun.h"
-#include "main.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/random/random.h"
-#include "index.h"
-#include "mtop_util.h"
-#include "gmx_ana.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void insert_ion(int nsa, int *nwater,
gmx_bool bSet[], int repl[], atom_id index[],
char *str;
int i;
- str = strdup(mname);
+ str = gmx_strdup(mname);
i = strlen(str)-1;
while (i > 1 && (isdigit(str[i]) || (str[i] == '+') || (str[i] == '-')))
{
if (np)
{
snew(pptr, 1);
- pptr[0] = strdup(p_name);
+ pptr[0] = gmx_strdup(p_name);
snew(paptr, 1);
paptr[0] = aname(p_name);
}
if (nn)
{
snew(nptr, 1);
- nptr[0] = strdup(n_name);
+ nptr[0] = gmx_strdup(n_name);
snew(naptr, 1);
naptr[0] = aname(n_name);
}
}
/* Store this molecules section line */
srenew(mol_line, nmol_line+1);
- mol_line[nmol_line] = strdup(buf);
+ mol_line[nmol_line] = gmx_strdup(buf);
nmol_line++;
}
}
output_env_t oenv;
gmx_rng_t rng;
t_filenm fnm[] = {
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efSTO, "-o", NULL, ffWRITE },
{ efTOP, "-p", "topol", ffOPTRW }
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
/* Read atom positions and charges */
- read_tps_conf(ftp2fn(efTPX, NFILE, fnm), title, &top, &ePBC, &x, &v, box, FALSE);
+ read_tps_conf(ftp2fn(efTPR, NFILE, fnm), title, &top, &ePBC, &x, &v, box, FALSE);
atoms = top.atoms;
/* Compute total charge */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "sysstuff.h"
-#include "gromacs/commandline/pargs.h"
#include <string.h>
-#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
+
+#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/futil.h"
-#include "macros.h"
-#include "vec.h"
-#include "index.h"
-#include "gmx_fatal.h"
-#include "gmx_ana.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
int gmx_genpr(int argc, char *argv[])
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "princ.h"
-#include "rmpbc.h"
-#include "txtdump.h"
+#include "gromacs/correlationfunctions/autocorr.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gstat.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#include "gmx_ana.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
-
real calc_gyro(rvec x[], int gnx, atom_id index[], t_atom atom[], real tm,
rvec gvec, rvec d, gmx_bool bQ, gmx_bool bRot, gmx_bool bMOI, matrix trans)
{
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
gmx_rmpbc_done(gpbc);
}
- gmx_ffclose(out);
+ xvgrclose(out);
if (bACF)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-
-#include "sysstuff.h"
#include <string.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "princ.h"
-#include "rmpbc.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+
#include "gromacs/commandline/pargs.h"
-#include "index.h"
-#include "gmx_ana.h"
#include "gromacs/fileio/trxio.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
/****************************************************************************/
/* This program calculates the ordering of water molecules across a box, as */
factor*dipole[slice][ZZ], order[slice]);
}
- gmx_ffclose(ord);
+ xvgrclose(ord);
}
int gmx_h2order(int argc, char *argv[])
{ efTRX, "-f", NULL, ffREAD }, /* trajectory file */
{ efNDX, NULL, NULL, ffREAD }, /* index file */
{ efNDX, "-nm", NULL, ffOPTRD }, /* index with micelle atoms */
- { efTPX, NULL, NULL, ffREAD }, /* topology file */
+ { efTPR, NULL, NULL, ffREAD }, /* topology file */
{ efXVG, "-o", "order", ffWRITE }, /* xvgr output file */
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE, NFILE,
+ PCA_CAN_VIEW | PCA_CAN_TIME, NFILE,
fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
bMicel = opt2bSet("-nm", NFILE, fnm);
- top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC); /* read topology file */
rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &ngx, &index, &grpname);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <math.h>
+#include "gmxpre.h"
-/*#define HAVE_NN_LOOPS*/
+#include "config.h"
-#include "gromacs/commandline/pargs.h"
-#include "copyrite.h"
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "physics.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "index.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "gstat.h"
-#include "gromacs/utility/cstringutil.h"
-#include "pbc.h"
-#include "correl.h"
-#include "gmx_ana.h"
-#include "geminate.h"
+#include <math.h>
-#include "gromacs/fileio/futil.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/correlationfunctions/autocorr.h"
+#include "gromacs/correlationfunctions/crosscorr.h"
+#include "gromacs/correlationfunctions/expfit.h"
+#include "gromacs/correlationfunctions/integrate.h"
#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/geminate.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/snprintf.h"
+
+#include "geminate.h"
+
+/*#define HAVE_NN_LOOPS*/
typedef short int t_E;
typedef int t_EEst;
{
int i;
- if (ISDON(datable[id]) || !datable)
+ if (!datable || ISDON(datable[id]))
{
if (ddd->dptr[id] == NOTSET) /* New donor */
{
integral += x1;
}
integral *= dt;
- gmx_ffclose(fp);
+ xvgrclose(fp);
printf("%s lifetime = %.2f ps\n", bContact ? "Contact" : "HB", integral);
printf("Note that the lifetime obtained in this manner is close to useless\n");
printf("Use the -ac option instead and check the Forward lifetime\n");
static void smooth_tail(int n, real t[], real c[], real sigma_c[], real start,
const output_env_t oenv)
{
- FILE *fp;
- real e_1, fitparm[4];
- int i;
+ FILE *fp;
+ real e_1;
+ double fitparm[4];
+ int i;
e_1 = exp(-1);
for (i = 0; (i < n); i++)
fitparm[0] = 10;
}
fitparm[1] = 0.95;
- do_lmfit(n, c, sigma_c, 0, t, start, t[n-1], oenv, bDebugMode(), effnEXP2, fitparm, 0);
+ do_lmfit(n, c, sigma_c, 0, t, start, t[n-1], oenv, bDebugMode(),
+ effnEXP2, fitparm, 0);
}
void analyse_corr(int n, real t[], real ct[], real nt[], real kt[],
static void normalizeACF(real *ct, real *gt, int nhb, int len)
{
- real ct_fac, gt_fac;
+ real ct_fac, gt_fac = 0;
int i;
/* Xu and Berne use the same normalization constant */
ct_fac = 1.0/ct[0];
- gt_fac = (nhb == 0) ? 0 : 1.0/(real)nhb;
+ if (nhb != 0)
+ {
+ gt_fac = 1.0/(real)nhb;
+ }
printf("Normalization for c(t) = %g for gh(t) = %g\n", ct_fac, gt_fac);
for (i = 0; i < len; i++)
fprintf(fp, "%10g %10g %10g %10g %10g\n",
hb->time[j]-hb->time[0], ct[j], cct[j], ght[j], kt[j]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
analyse_corr(nn, hb->time, ct, ght, kt, NULL, NULL, NULL,
fit_start, temp, smooth_tail_start, oenv);
/*set_hb(hb->hbmap[i][j]->h[m],nframes-hb->hbmap[i][j]->n0,HB_NO);*/
}
-static void analyse_donor_props(const char *fn, t_hbdata *hb, int nframes, real t,
- const output_env_t oenv)
+static FILE *open_donor_properties_file(const char *fn,
+ t_hbdata *hb,
+ const output_env_t oenv)
{
- static FILE *fp = NULL;
- const char *leg[] = { "Nbound", "Nfree" };
- int i, j, k, nbound, nb, nhtot;
+ FILE *fp = NULL;
+ const char *leg[] = { "Nbound", "Nfree" };
- if (!fn)
+ if (!fn || !hb)
{
- return;
+ return NULL;
}
- if (!fp)
+
+ fp = xvgropen(fn, "Donor properties", output_env_get_xvgr_tlabel(oenv), "Number", oenv);
+ xvgr_legend(fp, asize(leg), leg, oenv);
+
+ return fp;
+}
+
+static void analyse_donor_properties(FILE *fp, t_hbdata *hb, int nframes, real t)
+{
+ int i, j, k, nbound, nb, nhtot;
+
+ if (!fp || !hb)
{
- fp = xvgropen(fn, "Donor properties", output_env_get_xvgr_tlabel(oenv), "Number", oenv);
- xvgr_legend(fp, asize(leg), leg, oenv);
+ return;
}
nbound = 0;
nhtot = 0;
for (i = 0; i < isize[grp]; i++)
{
fprintf(fp, (i%15) ? " " : "\n");
- fprintf(fp, " %4u", index[grp][i]+1);
+ fprintf(fp, " %4d", index[grp][i]+1);
}
fprintf(fp, "\n");
/*
{
for (j = 0; (j < hb->d.nhydro[i]); j++)
{
- fprintf(fp, " %4u %4u", hb->d.don[i]+1,
+ fprintf(fp, " %4d %4d", hb->d.don[i]+1,
hb->d.hydro[i][j]+1);
}
fprintf(fp, "\n");
if (hb->a.grp[i] == grp)
{
fprintf(fp, (i%15 && !first) ? " " : "\n");
- fprintf(fp, " %4u", hb->a.acc[i]+1);
+ fprintf(fp, " %4d", hb->a.acc[i]+1);
first = FALSE;
}
}
sprintf(as, "%s", mkatomname(atoms, aaa));
if (bContact)
{
- fprintf(fp, " %6u %6u\n", ddd+1, aaa+1);
+ fprintf(fp, " %6d %6d\n", ddd+1, aaa+1);
if (fplog)
{
fprintf(fplog, "%12s %12s\n", ds, as);
{
hhh = hb->d.hydro[i][m];
sprintf(hs, "%s", mkatomname(atoms, hhh));
- fprintf(fp, " %6u %6u %6u\n", ddd+1, hhh+1, aaa+1);
+ fprintf(fp, " %6d %6d %6d\n", ddd+1, hhh+1, aaa+1);
if (fplog)
{
fprintf(fplog, "%12s %12s %12s\n", ds, hs, as);
};
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
/* { efNDX, "-sel", "select", ffOPTRD },*/
{ efXVG, "-num", "hbnum", ffWRITE },
int grp, nabin, nrbin, bin, resdist, ihb;
char **leg;
t_hbdata *hb, *hbptr;
- FILE *fp, *fpins = NULL, *fpnhb = NULL;
+ FILE *fp, *fpins = NULL, *fpnhb = NULL, *donor_properties = NULL;
t_gridcell ***grid;
t_ncell *icell, *jcell, *kcell;
ivec ngrid;
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE, NFILE, fnm, npargs,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, npargs,
ppa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
hb = mk_hbdata(bHBmap, opt2bSet("-dan", NFILE, fnm), bMerge || bContact, bGem, gemmode);
/* get topology */
- read_tpx_top(ftp2fn(efTPX, NFILE, fnm), &ir, box, &natoms, NULL, NULL, NULL, &top);
+ read_tpx_top(ftp2fn(efTPR, NFILE, fnm), &ir, box, &natoms, NULL, NULL, NULL, &top);
snew(grpnames, grNR);
snew(index, grNR);
/*if (bSelected)
snew(donors[gr0D], dons[gr0D].nrd);*/
+ donor_properties = open_donor_properties_file(opt2fn_null("-don", NFILE, fnm), hb, oenv);
+
if (bHBmap)
{
printf("Making hbmap structure...");
#pragma omp barrier
#pragma omp single
{
- if (hb != NULL)
- {
- analyse_donor_props(opt2fn_null("-don", NFILE, fnm), hb, k, t, oenv);
- }
+ analyse_donor_properties(donor_properties, hb, k, t);
}
#pragma omp single
free_grid(ngrid, &grid);
close_trj(status);
+
+ if (donor_properties)
+ {
+ xvgrclose(donor_properties);
+ }
+
if (fpnhb)
{
- gmx_ffclose(fpnhb);
+ xvgrclose(fpnhb);
}
/* Compute maximum possible number of different hbonds */
aver_nhb += hb->nhb[i];
aver_dist += hb->ndist[i];
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
aver_nhb /= nframes;
aver_dist /= nframes;
/* Print HB distance distribution */
{
fprintf(fp, "%10g %10g\n", (i+0.5)*rbin, rdist[i]/(rbin*(real)sum));
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
/* Print HB angle distribution */
{
fprintf(fp, "%10g %10g\n", (i+0.5)*abin, adist[i]/(abin*(real)sum));
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
/* Print HB in alpha-helix */
}
fprintf(fp, "\n");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
if (!bNN)
{
gmx_fatal(FARGS, "Could not initiate t_gemParams params.");
}
}
- gemstring = strdup(gemType[hb->per->gemtype]);
+ gemstring = gmx_strdup(gemType[hb->per->gemtype]);
do_hbac(opt2fn("-ac", NFILE, fnm), hb, nDump,
bMerge, bContact, fit_start, temp, r2cut > 0, smooth_tail_start, oenv,
gemstring, nThreads, NN, bBallistic, bGemFit);
{
t_matrix mat;
int id, ia, hh, x, y;
+ mat.flags = mat.y0 = 0;
if ((nframes > 0) && (hb->nrhb > 0))
{
if (USE_THIS_GROUP(j) )
{
sprintf(buf, "Donors %s", grpnames[j]);
- legnames[i++] = strdup(buf);
+ legnames[i++] = gmx_strdup(buf);
sprintf(buf, "Acceptors %s", grpnames[j]);
- legnames[i++] = strdup(buf);
+ legnames[i++] = gmx_strdup(buf);
}
}
if (i != nleg)
}
fprintf(fp, "\n");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
return 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
+#include <string.h>
+#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
-#include "gmx_fatal.h"
-#include "fitahx.h"
-#include "gromacs/fileio/futil.h"
-#include "gstat.h"
-#include "hxprops.h"
-#include "macros.h"
-#include "gromacs/math/utilities.h"
-#include "pbc.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "physics.h"
-#include "index.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/fitahx.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/hxprops.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/commandline/pargs.h"
-#include <string.h>
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "gmx_ana.h"
int gmx_helix(int argc, char *argv[])
{
gmx_rmpbc_t gpbc = NULL;
gmx_bool bRange;
t_filenm fnm[] = {
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efSTO, "-cz", "zconf", ffWRITE },
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
bRange = (opt2parg_bSet("-ahxstart", asize(pa), pa) &&
opt2parg_bSet("-ahxend", asize(pa), pa));
- top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
natoms = read_first_x(oenv, &status, opt2fn("-f", NFILE, fnm), &t, &x, box);
/* Read reference frame from tpx file to compute helix length */
snew(xref, top->atoms.nr);
- read_tpx(ftp2fn(efTPX, NFILE, fnm),
+ read_tpx(ftp2fn(efTPR, NFILE, fnm),
NULL, NULL, &natoms, xref, NULL, NULL, NULL);
calc_hxprops(nres, bb, xref);
do_start_end(nres, bb, &nbb, bbindex, &nca, caindex, bRange, rStart, rEnd);
for (i = 0; (i < efhNR); i++)
{
- gmx_ffclose(xf[i].fp);
+ xvgrclose(xf[i].fp);
if (xf[i].bfp2)
{
- gmx_ffclose(xf[i].fp2);
+ xvgrclose(xf[i].fp2);
}
do_view(oenv, xf[i].filenm, "-nxy");
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "xvgr.h"
#include "gromacs/commandline/pargs.h"
-#include "vec.h"
-#include "index.h"
-#include "pbc.h"
-#include "gmx_fatal.h"
-#include "gstat.h"
-#include "pbc.h"
-#include "gmx_ana.h"
-
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
int gmx_helixorient(int argc, char *argv[])
{
#define NPA asize(pa)
t_filenm fnm[] = {
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efDAT, "-oaxis", "helixaxis", ffWRITE },
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
- top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
for (i = 0; i < 3; i++)
{
gmx_ffclose(fpaxis);
gmx_ffclose(fpcenter);
- gmx_ffclose(fptilt);
- gmx_ffclose(fprotation);
+ xvgrclose(fptilt);
+ xvgrclose(fprotation);
gmx_ffclose(fprise);
gmx_ffclose(fpradius);
gmx_ffclose(fptwist);
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
-#include "typedefs.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "gstat.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
+#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/matio.h"
-#include "binsearch.h"
-#include "powerspect.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/binsearch.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/powerspect.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
/* Print name of first atom in all groups in index file */
static void print_types(atom_id index[], atom_id a[], int ngrps,
fprintf(stderr, "Using following groups: \n");
for (i = 0; i < ngrps; i++)
{
- fprintf(stderr, "Groupname: %s First atomname: %s First atomnr %u\n",
+ fprintf(stderr, "Groupname: %s First atomname: %s First atomnr %d\n",
groups[i], *(top->atoms.atomname[a[index[i]]]), a[index[i]]);
}
fprintf(stderr, "\n");
t_filenm fnm[] = { /* files for g_order */
{ efTRX, "-f", NULL, ffREAD }, /* trajectory file */
{ efNDX, "-n", NULL, ffREAD }, /* index file */
- { efTPX, "-s", NULL, ffREAD }, /* topology file */
+ { efTPR, "-s", NULL, ffREAD }, /* topology file */
{ efXPM, "-o", "intf", ffWRMULT}, /* XPM- surface maps */
{ efOUT, "-or", "raw", ffOPTWRMULT }, /* xvgr output file */
{ efOUT, "-Spect", "intfspect", ffOPTWRMULT}, /* Fourier spectrum interfaces */
int nfspect, nfxpm, nfraw;
output_env_t oenv;
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
ndxfnm = ftp2fn(efNDX, NFILE, fnm);
- tpsfnm = ftp2fn(efTPX, NFILE, fnm);
+ tpsfnm = ftp2fn(efTPR, NFILE, fnm);
trxfnm = ftp2fn(efTRX, NFILE, fnm);
/* Calculate axis */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include <math.h>
#include <stdio.h>
#include <stdlib.h>
-#include <math.h>
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "gromacs/fileio/futil.h"
-#include "txtdump.h"
#include "gromacs/fileio/enxio.h"
-#include "gstat.h"
-#include "xvgr.h"
-#include "gmx_ana.h"
#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
int nlj, nqq;
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
}
close_enx(fp);
- gmx_ffclose(out);
+ xvgrclose(out);
fprintf(stderr, "\n");
if (nframes > 0)
* on the code from g_anaeig. You can reach him as olange@gwdg.de. He
* probably also holds copyright to the following code.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include <ctype.h>
#include <math.h>
#include <stdlib.h>
-#include <ctype.h>
#include <string.h>
-#include "readinp.h"
+
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/matio.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "rmpbc.h"
-#include "txtdump.h"
-#include "eigio.h"
-#include "index.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
typedef struct
{
printf("\n");
}
- EigvecFile = NULL;
EigvecFile = opt2fn("-f", NFILE, fnm);
/*read eigenvectors from eigvec.trr*/
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <ctype.h>
#include <string.h>
-#include "sysstuff.h"
-#include "gromacs/fileio/futil.h"
-#include "macros.h"
-#include "gromacs/utility/cstringutil.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
-#include "typedefs.h"
-#include "index.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "index.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
/* It's not nice to have size limits, but we should not spend more time
* on this ancient tool, but instead use the new selection library.
{
c = (*string)[0];
(*string)++;
- s = strdup((*string));
+ s = gmx_strdup((*string));
sp = strchr(s, c);
if (sp != NULL)
{
{
block->index[i] = block->index[i+1]-shift;
}
- name = strdup((*gn)[nr]);
+ name = gmx_strdup((*gn)[nr]);
sfree((*gn)[nr]);
for (i = nr; i < block->nr-1; i++)
{
{
sprintf(buf, "%s_%s_%d", (*gn)[sel_nr], name, atoms->resinfo[resind].nr);
}
- (*gn)[block->nr-1] = strdup(buf);
+ (*gn)[block->nr-1] = gmx_strdup(buf);
}
block->a[block->nra] = a;
block->nra++;
{
rvec_sub(x[ca_end], x[i], vec);
}
+ else
+ {
+ break;
+ }
}
- while ((i < natoms) && (norm(vec) < 0.45));
+ while (norm(vec) < 0.45);
end[nchain] = ca_end;
while ((end[nchain]+1 < natoms) &&
srenew(block->index, block->nr+1);
srenew(*gn, block->nr);
sprintf(buf, "%s_chain%d", (*gn)[sel_nr], j+1);
- (*gn)[block->nr-1] = strdup(buf);
+ (*gn)[block->nr-1] = gmx_strdup(buf);
for (i = block->index[sel_nr]; i < block->index[sel_nr+1]; i++)
{
a = block->a[i];
{
sscanf(string, "%s", gname);
sfree((*gn)[sel_nr]);
- (*gn)[sel_nr] = strdup(gname);
+ (*gn)[sel_nr] = gmx_strdup(gname);
}
}
}
copy2block(nr, index, block);
srenew(*gn, block->nr);
newgroup = block->nr-1;
- (*gn)[newgroup] = strdup(gname);
+ (*gn)[newgroup] = gmx_strdup(gname);
}
else
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
-#include "macros.h"
-#include "vec.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/fileio/filenm.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/filenm.h"
#include "gromacs/fileio/matio.h"
-#include "xvgr.h"
-#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "rmpbc.h"
-#include "pbc.h"
-#include "gmx_ana.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define FARAWAY 10000
int **nmat, **totnmat;
real *mean_n;
int *tot_n;
- matrix box;
+ matrix box = {{0}};
output_env_t oenv;
gmx_rmpbc_t gpbc = NULL;
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE, NFILE, fnm,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm,
asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
fprintf(fp, "%3d %8.3f %3d %8.3f %3d %8.3f\n",
i+1, ratio, tot_n[i], mean_n[i], natm[i], mean_n[i]/natm[i]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
return 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <stdlib.h>
-
-#include "sysstuff.h"
#include <string.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+
#include "gromacs/commandline/pargs.h"
-#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "rmpbc.h"
-#include "gmx_ana.h"
-#include "names.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void periodic_dist(int ePBC,
gmx_rmpbc_done(gpbc);
}
- gmx_ffclose(out);
+ xvgrclose(out);
fprintf(stdout,
"\nThe shortest periodic distance is %g (nm) at time %g (%s),\n"
{
snew(leg, 1);
sprintf(buf, "Internal in %s", grpn[0]);
- leg[0] = strdup(buf);
+ leg[0] = gmx_strdup(buf);
xvgr_legend(dist, 0, (const char**)leg, oenv);
if (num)
{
for (k = i+1; (k < ng); k++, j++)
{
sprintf(buf, "%s-%s", grpn[i], grpn[k]);
- leg[j] = strdup(buf);
+ leg[j] = gmx_strdup(buf);
}
}
xvgr_legend(dist, j, (const char**)leg, oenv);
for (i = 0; (i < ng-1); i++)
{
sprintf(buf, "%s-%s", grpn[0], grpn[i+1]);
- leg[i] = strdup(buf);
+ leg[i] = gmx_strdup(buf);
}
xvgr_legend(dist, ng-1, (const char**)leg, oenv);
if (num)
while (read_next_x(oenv, status, &t, x0, box));
close_trj(status);
- gmx_ffclose(dist);
+ xvgrclose(dist);
if (num)
{
- gmx_ffclose(num);
+ xvgrclose(num);
}
if (atm)
{
{
close_trx(trxout);
}
+ if (respertime)
+ {
+ xvgrclose(respertime);
+ }
if (nres && !bEachResEachTime)
{
}
fprintf(res, "\n");
}
+ xvgrclose(res);
}
sfree(x0);
"each direction is considered, giving a total of 26 shifts.",
"It also plots the maximum distance within the group and the lengths",
"of the three box vectors.[PAR]",
- "Also [gmx-distance] calculates distances."
+ "Also [gmx-distance] and [gmx-pairdist] calculate distances."
};
const char *bugs[] = {
"The [TT]-pi[tt] option is very slow."
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
+
#include "gromacs/commandline/pargs.h"
-#include "macros.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
#include "gromacs/fileio/trxio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static int calc_ntype(int nft, int *ft, t_idef *idef)
{
gmx_fatal(FARGS, "Unsupported function type '%s' selected",
interaction_function[ftype].longname);
}
- grpnames[ind] = strdup(buf);
+ grpnames[ind] = gmx_strdup(buf);
ind++;
}
}
int *nr;
char **grpnames;
t_filenm fnm[] = {
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, "angle", ffWRITE }
};
#define NFILE asize(fnm)
ft = select_ftype(opt[0], &nft, &mult);
- top = read_top(ftp2fn(efTPX, NFILE, fnm), NULL);
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), NULL);
ntype = calc_ntype(nft, ft, &(top->idef));
snew(grpnames, ntype);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
#include "gromacs/fileio/confio.h"
-#include "xvgr.h"
-#include "index.h"
-#include "gmx_ana.h"
-#include "gmx_fatal.h"
#include "gromacs/fileio/trxio.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/math/do_fit.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static real dointerp(int n, rvec x1[], rvec x2[], rvec xx[],
int I, int N, real first, real last)
if (bRMS)
{
- gmx_ffclose(fp);
+ xvgrclose(fp);
do_view(oenv, opt2fn("-or", NFILE, fnm), "-nxy");
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
-#include "typedefs.h"
-#include "xvgr.h"
-#include "gstat.h"
-#include "gromacs/statistics/statistics.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "pbc.h"
-#include "vec.h"
-#include "gromacs/fileio/confio.h"
-#include "gmx_ana.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/statistics/statistics.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define FACTOR 1000.0 /* Convert nm^2/ps to 10e-5 cm^2/s */
/* NORMAL = total diffusion coefficient (default). X,Y,Z is diffusion
}
fprintf(out, "\n");
}
- gmx_ffclose(out);
+ xvgrclose(out);
}
/* called from corr_loop, to do the main calculations */
}
}
}
- gmx_ffclose(out);
+ xvgrclose(out);
do_view(oenv, fn, "-graphtype bar");
/* Compute variance, stddev and error */
output_env_t oenv;
if (!parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END | PCA_TIME_UNIT | PCA_BE_NICE,
+ PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "copyrite.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "gstat.h"
-#include "txtdump.h"
-#include "eigio.h"
-#include "mtop_util.h"
-#include "physics.h"
-#include "main.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/mtxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/linearalgebra/eigensolver.h"
-#include "gromacs/linearalgebra/mtxio.h"
#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static double cv_corr(double nu, double T)
{
t_filenm fnm[] = {
{ efMTX, "-f", "hessian", ffREAD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efXVG, "-of", "eigenfreq", ffWRITE },
{ efXVG, "-ol", "eigenval", ffWRITE },
{ efXVG, "-os", "spectrum", ffOPTWR },
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, 0,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
/* Read tpr file for volume and number of harmonic terms */
- read_tpxheader(ftp2fn(efTPX, NFILE, fnm), &tpx, TRUE, &version, &generation);
+ read_tpxheader(ftp2fn(efTPR, NFILE, fnm), &tpx, TRUE, &version, &generation);
snew(top_x, tpx.natoms);
- read_tpx(ftp2fn(efTPX, NFILE, fnm), NULL, box, &natoms,
+ read_tpx(ftp2fn(efTPR, NFILE, fnm), NULL, box, &natoms,
top_x, NULL, NULL, &mtop);
if (bCons)
{
{
fprintf (out, "%6d %15g\n", begin+i, eigenvalues[i]);
}
- gmx_ffclose(out);
+ xvgrclose(out);
if (opt2bSet("-qc", NFILE, fnm))
qutot += qu;
}
}
- gmx_ffclose(out);
+ xvgrclose(out);
if (NULL != spec)
{
for (j = 0; (j < maxspec); j++)
{
fprintf(spec, "%10g %10g\n", 1.0*j, spectrum[j]);
}
- gmx_ffclose(spec);
+ xvgrclose(spec);
}
if (NULL != qc)
{
nharm, nvsite);
printf("Total correction to cV = %g J/mol K\n", qcvtot);
printf("Total correction to H = %g kJ/mol\n", qutot);
- gmx_ffclose(qc);
+ xvgrclose(qc);
please_cite(stdout, "Caleman2011b");
}
/* Writing eigenvectors. Note that if mass scaling was used, the eigenvectors
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "txtdump.h"
-#include "physics.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
-#include "eigio.h"
-#include "gmx_ana.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
int gmx_nmens(int argc, char *argv[])
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, 0,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
+#include <stdlib.h>
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "txtdump.h"
-#include "physics.h"
-#include "eigio.h"
-#include "gmx_ana.h"
+#include "gromacs/gmxana/eigio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
int gmx_nmtraj(int argc, char *argv[])
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, 0,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2006, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "typedefs.h"
-#include "macros.h"
-#include "gromacs/commandline/pargs.h"
-
-/*
- * This program is needed to create the files:
- * options.html
- * options.tex
- * for the html and latex manuals.
- * It should be ran with the option: -hidden
- */
-
-int
-gmx_options(int argc, char *argv[])
-{
- const char *desc[] = {
- "GROMACS programs have some standard options,",
- "of which some are hidden by default:"
- };
-
- const char *bugs[] = {
- "If the configuration script found Motif or Lesstif on your system, "
- "you can use the graphical interface (if not, you will get an error):[BR]"
- "[TT]-X[tt] gmx_bool [TT]no[tt] Use dialog box GUI to edit command line options",
-
- "Optional files are not used unless the option is set, in contrast to "
- "non-optional files, where the default file name is used when the "
- "option is not set.",
-
- "All GROMACS programs will accept file options without a file extension "
- "or filename being specified. In such cases the default filenames will "
- "be used. With multiple input file types, such as generic structure "
- "format, the directory will be searched for files of each type with the "
- "supplied or default name. When no such file is found, or with output "
- "files the first file type will be used.",
-
- "All GROMACS programs with the exception of [TT]mdrun[tt] "
- "and [TT]eneconv[tt] check if the command line options "
- "are valid. If this is not the case, the program will be halted.",
-
- "Enumerated options (enum) should be used with one of the arguments "
- "listed in the option description, the argument may be abbreviated. "
- "The first match to the shortest argument in the list will be selected.",
-
- "Vector options can be used with 1 or 3 parameters. When only one "
- "parameter is supplied the two others are also set to this value.",
-
- "All GROMACS programs can read compressed or g-zipped files. There "
- "might be a problem with reading compressed [TT].xtc[tt], "
- "[TT].trr[tt] and [TT].trj[tt] files, but these will not compress "
- "very well anyway.",
-
- "Most GROMACS programs can process a trajectory with fewer atoms than "
- "the run input or structure file, but only if the trajectory consists "
- "of the first n atoms of the run input or structure file.",
-
- "Many GROMACS programs will accept the [TT]-tu[tt] option to set the "
- "time units to use in output files (e.g. for [TT]xmgr[tt] graphs or "
- "[TT]xpm[tt] matrices) and in all time options."
- };
-
- output_env_t oenv = NULL;
- if (!parse_common_args(&argc, argv, 0,
- 0, NULL, 0, NULL, asize(desc), desc, asize(bugs), bugs, &oenv))
- {
- return 0;
- }
-
- return 0;
-}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "gstat.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/commandline/pargs.h"
-#include "index.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/confio.h"
-#include "cmat.h"
-#include "gmx_ana.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/cmat.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
/****************************************************************************/
/* This program calculates the order parameter per atom for an interface or */
sfree(index);
sfree(isize);
- gmx_ffclose(fpsg);
- gmx_ffclose(fpsk);
+ xvgrclose(fpsg);
+ xvgrclose(fpsk);
fpsg = xvgropen(sgslfn,
"S\\sg\\N Angle Order Parameter / Slab", "(nm)", "S\\sg\\N",
fprintf(fpsk, "%10g %10g\n", (i+0.5)*box[slice_dim][slice_dim]/nslice,
sk_slice_tot[i]/nframes);
}
- gmx_ffclose(fpsg);
- gmx_ffclose(fpsk);
+ xvgrclose(fpsg);
+ xvgrclose(fpsk);
}
fprintf(stderr, "Using following groups: \n");
for (i = 0; i < ngrps; i++)
{
- fprintf(stderr, "Groupname: %s First atomname: %s First atomnr %u\n",
+ fprintf(stderr, "Groupname: %s First atomname: %s First atomnr %d\n",
groups[i], *(top->atoms.atomname[a[index[i]]]), a[index[i]]);
}
fprintf(stderr, "\n");
0.333 * order[atom][YY]));
}
- gmx_ffclose(ord);
- gmx_ffclose(slOrd);
}
+ xvgrclose(ord);
+ xvgrclose(slOrd);
}
void write_bfactors(t_filenm *fnm, int nfile, atom_id *index, atom_id *a, int nslices, int ngrps, real **order, t_topology *top, real **distvals, output_env_t oenv)
{ efTRX, "-f", NULL, ffREAD }, /* trajectory file */
{ efNDX, "-n", NULL, ffREAD }, /* index file */
{ efNDX, "-nr", NULL, ffREAD }, /* index for radial axis calculation */
- { efTPX, NULL, NULL, ffREAD }, /* topology file */
+ { efTPR, NULL, NULL, ffREAD }, /* topology file */
{ efXVG, "-o", "order", ffWRITE }, /* xvgr output file */
{ efXVG, "-od", "deuter", ffWRITE }, /* xvgr output file */
{ efPDB, "-ob", NULL, ffWRITE }, /* write Scd as B factors to PDB if permolecule */
const char *sgfnm, *skfnm, *ndxfnm, *tpsfnm, *trxfnm;
output_env_t oenv;
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
sgfnm = opt2fn_null("-Sg", NFILE, fnm);
skfnm = opt2fn_null("-Sk", NFILE, fnm);
ndxfnm = opt2fn_null("-n", NFILE, fnm);
- tpsfnm = ftp2fn(efTPX, NFILE, fnm);
+ tpsfnm = ftp2fn(efTPR, NFILE, fnm);
trxfnm = ftp2fn(efTRX, NFILE, fnm);
/* Calculate axis */
fprintf(stderr, "Taking carbons as unsaturated!\n");
}
- top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC); /* read topology file */
block = init_index(ftp2fn(efNDX, NFILE, fnm), &grpname);
index = block->index; /* get indices from t_block block */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
+#include "config.h"
+
#include <algorithm>
#include "gromacs/commandline/pargs.h"
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "copyrite.h"
#include "gromacs/fileio/tpxio.h"
-#include "readinp.h"
-#include "calcgrid.h"
-#include "checkpoint.h"
-#include "gmx_ana.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/calcgrid.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/calculate-ewald-splitting-coefficient.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
-#include "physics.h"
-#include "mdatoms.h"
-#include "coulomb.h"
-#include "mtop_util.h"
-#include "network.h"
-#include "main.h"
-#include "macros.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
-/* We use the same defines as in mvdata.c here */
+/* We use the same defines as in broadcaststructs.cpp here */
#define block_bc(cr, d) gmx_bcast( sizeof(d), &(d), (cr))
#define nblock_bc(cr, nr, d) gmx_bcast((nr)*sizeof((d)[0]), (d), (cr))
#define snew_bc(cr, d, nr) { if (!MASTER(cr)) {snew((d), (nr)); }}
static t_filenm fnm[] = {
- { efTPX, "-s", NULL, ffREAD },
+ { efTPR, "-s", NULL, ffREAD },
{ efOUT, "-o", "error", ffWRITE },
- { efTPX, "-so", "tuned", ffOPTWR }
+ { efTPR, "-so", "tuned", ffOPTWR }
};
output_env_t oenv = NULL;
#define NFILE asize(fnm)
cr = init_commrec();
-#ifdef GMX_LIB_MPI
- MPI_Barrier(MPI_COMM_WORLD);
-#endif
PCA_Flags = PCA_NOEXIT_ON_ARGS;
- PCA_Flags |= (MASTER(cr) ? 0 : PCA_QUIET);
if (!parse_common_args(&argc, argv, PCA_Flags,
NFILE, fnm, asize(pa), pa, asize(desc), desc,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
-#include "physics.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/commandline/pargs.h"
-#include "vec.h"
-#include "index.h"
-#include "macros.h"
-#include "xvgr.h"
-#include "rmpbc.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void gyro_eigen(double **gyr, double *eig, double **eigv, int *ord)
{
};
t_filenm fnm[] = {
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-o", "polystat", ffWRITE },
gmx_rmpbc_t gpbc = NULL;
if (!parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
snew(top, 1);
- ePBC = read_tpx_top(ftp2fn(efTPX, NFILE, fnm),
+ ePBC = read_tpx_top(ftp2fn(efTPR, NFILE, fnm),
NULL, box, &natoms, NULL, NULL, NULL, top);
fprintf(stderr, "Select a group of polymer mainchain atoms:\n");
for (d2 = 0; d2 < DIM; d2++)
{
sprintf(buf, "eig%d %c", d+1, 'x'+d2);
- legp[d*DIM+d2] = strdup(buf);
+ legp[d*DIM+d2] = gmx_strdup(buf);
}
}
xvgr_legend(outv, DIM*DIM, (const char**)legp, oenv);
close_trx(status);
- gmx_ffclose(out);
+ xvgrclose(out);
if (outv)
{
- gmx_ffclose(outv);
+ xvgrclose(outv);
}
if (outp)
{
- gmx_ffclose(outp);
+ xvgrclose(outp);
}
sum_eed2_tot /= frame;
{
fprintf(outi, "%d %8.4f\n", i+1, intd[i]);
}
- gmx_ffclose(outi);
+ xvgrclose(outi);
}
do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <math.h>
#include <ctype.h>
-
-#include "sysstuff.h"
+#include <math.h>
#include <string.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "princ.h"
-#include "rmpbc.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+
#include "gromacs/commandline/pargs.h"
-#include "index.h"
-#include "gmx_ana.h"
-#include "gromacs/utility/cstringutil.h"
#include "gromacs/fileio/trxio.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define EPS0 8.85419E-12
#define ELC 1.60219E-19
fprintf(fie, "\n");
}
- gmx_ffclose(pot);
- gmx_ffclose(cha);
- gmx_ffclose(fie);
+ xvgrclose(pot);
+ xvgrclose(cha);
+ xvgrclose(fie);
}
int gmx_potential(int argc, char *argv[])
t_filenm fnm[] = { /* files for g_order */
{ efTRX, "-f", NULL, ffREAD }, /* trajectory file */
{ efNDX, NULL, NULL, ffREAD }, /* index file */
- { efTPX, NULL, NULL, ffREAD }, /* topology file */
+ { efTPR, NULL, NULL, ffREAD }, /* topology file */
{ efXVG, "-o", "potential", ffWRITE }, /* xvgr output file */
{ efXVG, "-oc", "charge", ffWRITE }, /* xvgr output file */
{ efXVG, "-of", "field", ffWRITE }, /* xvgr output file */
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs,
&oenv))
{
/* Calculate axis */
axis = toupper(axtitle[0]) - 'X';
- top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC); /* read topology file */
snew(grpname, ngrps);
snew(index, ngrps);
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "princ.h"
-#include "rmpbc.h"
-#include "txtdump.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gstat.h"
-#include "gmx_ana.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
void
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv,
- PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
+ PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "sysstuff.h"
#include <string.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "physics.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
+
#include "gromacs/commandline/pargs.h"
-#include "index.h"
-#include "nrama.h"
-#include "gmx_ana.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/nrama.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void plot_rama(FILE *out, t_xrama *xr)
output_env_t oenv;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efXVG, NULL, "rama", ffWRITE }
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, 0, NULL, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
snew(xr, 1);
- init_rama(oenv, ftp2fn(efTRX, NFILE, fnm), ftp2fn(efTPX, NFILE, fnm), xr, 3);
+ init_rama(oenv, ftp2fn(efTRX, NFILE, fnm), ftp2fn(efTPR, NFILE, fnm), xr, 3);
out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Ramachandran Plot", "Phi", "Psi", oenv);
xvgr_line_props(out, 0, elNone, ecFrank, oenv);
}
while (new_data(xr));
fprintf(stderr, "\n");
- gmx_ffclose(out);
+ xvgrclose(out);
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), NULL);
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "xvgr.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "physics.h"
-#include "index.h"
-#include "gromacs/utility/smalloc.h"
-#include "calcgrid.h"
-#include "nrnb.h"
-#include "coulomb.h"
-#include "gstat.h"
-#include "gromacs/fileio/matio.h"
-#include "gmx_ana.h"
-#include "names.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
-
-static void check_box_c(matrix box)
-{
- if (fabs(box[ZZ][XX]) > GMX_REAL_EPS*box[ZZ][ZZ] ||
- fabs(box[ZZ][YY]) > GMX_REAL_EPS*box[ZZ][ZZ])
- {
- gmx_fatal(FARGS,
- "The last box vector is not parallel to the z-axis: %f %f %f",
- box[ZZ][XX], box[ZZ][YY], box[ZZ][ZZ]);
- }
-}
-
-static void calc_comg(int is, int *coi, int *index, gmx_bool bMass, t_atom *atom,
- rvec *x, rvec *x_comg)
-{
- int c, i, d;
- rvec xc;
- real mtot, m;
-
- if (bMass && atom == NULL)
- {
- gmx_fatal(FARGS, "No masses available while mass weighting was requested");
- }
-
- for (c = 0; c < is; c++)
- {
- clear_rvec(xc);
- mtot = 0;
- for (i = coi[c]; i < coi[c+1]; i++)
- {
- if (bMass)
- {
- m = atom[index[i]].m;
- for (d = 0; d < DIM; d++)
- {
- xc[d] += m*x[index[i]][d];
- }
- mtot += m;
- }
- else
- {
- rvec_inc(xc, x[index[i]]);
- mtot += 1.0;
- }
- }
- svmul(1/mtot, xc, x_comg[c]);
- }
-}
-
-static void split_group(int isize, int *index, char *grpname,
- t_topology *top, char type,
- int *is_out, int **coi_out)
-{
- t_block *mols = NULL;
- t_atom *atom = NULL;
- int is, *coi;
- int cur, mol, res, i, a, i1;
-
- /* Split up the group in molecules or residues */
- switch (type)
- {
- case 'm':
- mols = &top->mols;
- break;
- case 'r':
- atom = top->atoms.atom;
- break;
- default:
- gmx_fatal(FARGS, "Unknown rdf option '%s'", type);
- }
- snew(coi, isize+1);
- is = 0;
- cur = -1;
- mol = 0;
- for (i = 0; i < isize; i++)
- {
- a = index[i];
- if (type == 'm')
- {
- /* Check if the molecule number has changed */
- i1 = mols->index[mol+1];
- while (a >= i1)
- {
- mol++;
- i1 = mols->index[mol+1];
- }
- if (mol != cur)
- {
- coi[is++] = i;
- cur = mol;
- }
- }
- else if (type == 'r')
- {
- /* Check if the residue index has changed */
- res = atom[a].resind;
- if (res != cur)
- {
- coi[is++] = i;
- cur = res;
- }
- }
- }
- coi[is] = i;
- srenew(coi, is+1);
- printf("Group '%s' of %d atoms consists of %d %s\n",
- grpname, isize, is,
- (type == 'm' ? "molecules" : "residues"));
-
- *is_out = is;
- *coi_out = coi;
-}
-
-static void do_rdf(const char *fnNDX, const char *fnTPS, const char *fnTRX,
- const char *fnRDF, const char *fnCNRDF, const char *fnHQ,
- gmx_bool bCM, const char *close,
- const char **rdft, gmx_bool bXY, gmx_bool bPBC, gmx_bool bNormalize,
- real cutoff, real binwidth, real fade, int ng,
- const output_env_t oenv)
-{
- FILE *fp;
- t_trxstatus *status;
- char outf1[STRLEN], outf2[STRLEN];
- char title[STRLEN], gtitle[STRLEN], refgt[30];
- int g, natoms, i, ii, j, k, nbin, j0, j1, n, nframes;
- int **count;
- char **grpname;
- int *isize, isize_cm = 0, nrdf = 0, max_i, isize0, isize_g;
- atom_id **index, *index_cm = NULL;
- gmx_int64_t *sum;
- real t, rmax2, cut2, r, r2, r2ii, invhbinw, normfac;
- real segvol, spherevol, prev_spherevol, **rdf;
- rvec *x, dx, *x0 = NULL, *x_i1, xi;
- real *inv_segvol, invvol, invvol_sum, rho;
- gmx_bool bClose, *bExcl, bTop, bNonSelfExcl;
- matrix box, box_pbc;
- int **npairs;
- atom_id ix, jx, ***pairs;
- t_topology *top = NULL;
- int ePBC = -1, ePBCrdf = -1;
- t_block *mols = NULL;
- t_blocka *excl;
- t_atom *atom = NULL;
- t_pbc pbc;
- gmx_rmpbc_t gpbc = NULL;
- int *is = NULL, **coi = NULL, cur, mol, i1, res, a;
-
- excl = NULL;
-
- bClose = (close[0] != 'n');
-
- if (fnTPS)
- {
- snew(top, 1);
- bTop = read_tps_conf(fnTPS, title, top, &ePBC, &x, NULL, box, TRUE);
- if (bTop && !(bCM || bClose))
- {
- /* get exclusions from topology */
- excl = &(top->excls);
- }
- }
- snew(grpname, ng+1);
- snew(isize, ng+1);
- snew(index, ng+1);
- fprintf(stderr, "\nSelect a reference group and %d group%s\n",
- ng, ng == 1 ? "" : "s");
- if (fnTPS)
- {
- get_index(&(top->atoms), fnNDX, ng+1, isize, index, grpname);
- atom = top->atoms.atom;
- }
- else
- {
- rd_index(fnNDX, ng+1, isize, index, grpname);
- }
-
- if (bCM || bClose)
- {
- snew(is, 1);
- snew(coi, 1);
- if (bClose)
- {
- split_group(isize[0], index[0], grpname[0], top, close[0], &is[0], &coi[0]);
- }
- }
- if (rdft[0][0] != 'a')
- {
- /* Split up all the groups in molecules or residues */
- srenew(is, ng+1);
- srenew(coi, ng+1);
- for (g = ((bCM || bClose) ? 1 : 0); g < ng+1; g++)
- {
- split_group(isize[g], index[g], grpname[g], top, rdft[0][0], &is[g], &coi[g]);
- }
- }
-
- if (bCM)
- {
- is[0] = 1;
- snew(coi[0], is[0]+1);
- coi[0][0] = 0;
- coi[0][1] = isize[0];
- isize0 = is[0];
- snew(x0, isize0);
- }
- else if (bClose || rdft[0][0] != 'a')
- {
- isize0 = is[0];
- snew(x0, isize0);
- }
- else
- {
- isize0 = isize[0];
- }
-
- natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
- if (!natoms)
- {
- gmx_fatal(FARGS, "Could not read coordinates from statusfile\n");
- }
- if (fnTPS)
- {
- /* check with topology */
- if (natoms > top->atoms.nr)
- {
- gmx_fatal(FARGS, "Trajectory (%d atoms) does not match topology (%d atoms)",
- natoms, top->atoms.nr);
- }
- }
- /* check with index groups */
- for (i = 0; i < ng+1; i++)
- {
- for (j = 0; j < isize[i]; j++)
- {
- if (index[i][j] >= natoms)
- {
- gmx_fatal(FARGS, "Atom index (%d) in index group %s (%d atoms) larger "
- "than number of atoms in trajectory (%d atoms)",
- index[i][j], grpname[i], isize[i], natoms);
- }
- }
- }
-
- /* initialize some handy things */
- if (ePBC == -1)
- {
- ePBC = guess_ePBC(box);
- }
- copy_mat(box, box_pbc);
- if (bXY)
- {
- check_box_c(box);
- switch (ePBC)
- {
- case epbcXYZ:
- case epbcXY: ePBCrdf = epbcXY; break;
- case epbcNONE: ePBCrdf = epbcNONE; break;
- default:
- gmx_fatal(FARGS, "xy-rdf's are not supported for pbc type'%s'",
- EPBC(ePBC));
- break;
- }
- /* Make sure the z-height does not influence the cut-off */
- box_pbc[ZZ][ZZ] = 2*max(box[XX][XX], box[YY][YY]);
- }
- else
- {
- ePBCrdf = ePBC;
- }
- if (bPBC)
- {
- rmax2 = 0.99*0.99*max_cutoff2(bXY ? epbcXY : epbcXYZ, box_pbc);
- }
- else
- {
- rmax2 = sqr(3*max(box[XX][XX], max(box[YY][YY], box[ZZ][ZZ])));
- }
- if (debug)
- {
- fprintf(debug, "rmax2 = %g\n", rmax2);
- }
-
- /* We use the double amount of bins, so we can correctly
- * write the rdf and rdf_cn output at i*binwidth values.
- */
- nbin = (int)(sqrt(rmax2) * 2 / binwidth);
- invhbinw = 2.0 / binwidth;
- cut2 = sqr(cutoff);
-
- snew(count, ng);
- snew(pairs, ng);
- snew(npairs, ng);
-
- snew(bExcl, natoms);
- max_i = 0;
- for (g = 0; g < ng; g++)
- {
- if (isize[g+1] > max_i)
- {
- max_i = isize[g+1];
- }
-
- /* this is THE array */
- snew(count[g], nbin+1);
-
- /* make pairlist array for groups and exclusions */
- snew(pairs[g], isize[0]);
- snew(npairs[g], isize[0]);
- for (i = 0; i < isize[0]; i++)
- {
- /* We can only have exclusions with atomic rdfs */
- if (!(bCM || bClose || rdft[0][0] != 'a'))
- {
- ix = index[0][i];
- for (j = 0; j < natoms; j++)
- {
- bExcl[j] = FALSE;
- }
- /* exclusions? */
- if (excl)
- {
- for (j = excl->index[ix]; j < excl->index[ix+1]; j++)
- {
- bExcl[excl->a[j]] = TRUE;
- }
- }
- k = 0;
- snew(pairs[g][i], isize[g+1]);
- bNonSelfExcl = FALSE;
- for (j = 0; j < isize[g+1]; j++)
- {
- jx = index[g+1][j];
- if (!bExcl[jx])
- {
- pairs[g][i][k++] = jx;
- }
- else if (ix != jx)
- {
- /* Check if we have exclusions other than self exclusions */
- bNonSelfExcl = TRUE;
- }
- }
- if (bNonSelfExcl)
- {
- npairs[g][i] = k;
- srenew(pairs[g][i], npairs[g][i]);
- }
- else
- {
- /* Save a LOT of memory and some cpu cycles */
- npairs[g][i] = -1;
- sfree(pairs[g][i]);
- }
- }
- else
- {
- npairs[g][i] = -1;
- }
- }
- }
- sfree(bExcl);
-
- snew(x_i1, max_i);
- nframes = 0;
- invvol_sum = 0;
- if (bPBC && (NULL != top))
- {
- gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
- }
-
- do
- {
- /* Must init pbc every step because of pressure coupling */
- copy_mat(box, box_pbc);
- if (bPBC)
- {
- if (top != NULL)
- {
- gmx_rmpbc(gpbc, natoms, box, x);
- }
- if (bXY)
- {
- check_box_c(box);
- clear_rvec(box_pbc[ZZ]);
- }
- set_pbc(&pbc, ePBCrdf, box_pbc);
-
- if (bXY)
- {
- /* Set z-size to 1 so we get the surface iso the volume */
- box_pbc[ZZ][ZZ] = 1;
- }
- }
- invvol = 1/det(box_pbc);
- invvol_sum += invvol;
-
- if (bCM)
- {
- /* Calculate center of mass of the whole group */
- calc_comg(is[0], coi[0], index[0], TRUE, atom, x, x0);
- }
- else if (!bClose && rdft[0][0] != 'a')
- {
- calc_comg(is[0], coi[0], index[0], rdft[0][6] == 'm', atom, x, x0);
- }
-
- for (g = 0; g < ng; g++)
- {
- if (rdft[0][0] == 'a')
- {
- /* Copy the indexed coordinates to a continuous array */
- for (i = 0; i < isize[g+1]; i++)
- {
- copy_rvec(x[index[g+1][i]], x_i1[i]);
- }
- }
- else
- {
- /* Calculate the COMs/COGs and store in x_i1 */
- calc_comg(is[g+1], coi[g+1], index[g+1], rdft[0][6] == 'm', atom, x, x_i1);
- }
-
- for (i = 0; i < isize0; i++)
- {
- if (bClose)
- {
- /* Special loop, since we need to determine the minimum distance
- * over all selected atoms in the reference molecule/residue.
- */
- if (rdft[0][0] == 'a')
- {
- isize_g = isize[g+1];
- }
- else
- {
- isize_g = is[g+1];
- }
- for (j = 0; j < isize_g; j++)
- {
- r2 = 1e30;
- /* Loop over the selected atoms in the reference molecule */
- for (ii = coi[0][i]; ii < coi[0][i+1]; ii++)
- {
- if (bPBC)
- {
- pbc_dx(&pbc, x[index[0][ii]], x_i1[j], dx);
- }
- else
- {
- rvec_sub(x[index[0][ii]], x_i1[j], dx);
- }
- if (bXY)
- {
- r2ii = dx[XX]*dx[XX] + dx[YY]*dx[YY];
- }
- else
- {
- r2ii = iprod(dx, dx);
- }
- if (r2ii < r2)
- {
- r2 = r2ii;
- }
- }
- if (r2 > cut2 && r2 <= rmax2)
- {
- count[g][(int)(sqrt(r2)*invhbinw)]++;
- }
- }
- }
- else
- {
- /* Real rdf between points in space */
- if (bCM || rdft[0][0] != 'a')
- {
- copy_rvec(x0[i], xi);
- }
- else
- {
- copy_rvec(x[index[0][i]], xi);
- }
- if (rdft[0][0] == 'a' && npairs[g][i] >= 0)
- {
- /* Expensive loop, because of indexing */
- for (j = 0; j < npairs[g][i]; j++)
- {
- jx = pairs[g][i][j];
- if (bPBC)
- {
- pbc_dx(&pbc, xi, x[jx], dx);
- }
- else
- {
- rvec_sub(xi, x[jx], dx);
- }
-
- if (bXY)
- {
- r2 = dx[XX]*dx[XX] + dx[YY]*dx[YY];
- }
- else
- {
- r2 = iprod(dx, dx);
- }
- if (r2 > cut2 && r2 <= rmax2)
- {
- count[g][(int)(sqrt(r2)*invhbinw)]++;
- }
- }
- }
- else
- {
- /* Cheaper loop, no exclusions */
- if (rdft[0][0] == 'a')
- {
- isize_g = isize[g+1];
- }
- else
- {
- isize_g = is[g+1];
- }
- for (j = 0; j < isize_g; j++)
- {
- if (bPBC)
- {
- pbc_dx(&pbc, xi, x_i1[j], dx);
- }
- else
- {
- rvec_sub(xi, x_i1[j], dx);
- }
- if (bXY)
- {
- r2 = dx[XX]*dx[XX] + dx[YY]*dx[YY];
- }
- else
- {
- r2 = iprod(dx, dx);
- }
- if (r2 > cut2 && r2 <= rmax2)
- {
- count[g][(int)(sqrt(r2)*invhbinw)]++;
- }
- }
- }
- }
- }
- }
- nframes++;
- }
- while (read_next_x(oenv, status, &t, x, box));
- fprintf(stderr, "\n");
-
- if (bPBC && (NULL != top))
- {
- gmx_rmpbc_done(gpbc);
- }
-
- close_trj(status);
-
- sfree(x);
-
- /* Average volume */
- invvol = invvol_sum/nframes;
-
- /* Calculate volume of sphere segments or length of circle segments */
- snew(inv_segvol, (nbin+1)/2);
- prev_spherevol = 0;
- for (i = 0; (i < (nbin+1)/2); i++)
- {
- r = (i + 0.5)*binwidth;
- if (bXY)
- {
- spherevol = M_PI*r*r;
- }
- else
- {
- spherevol = (4.0/3.0)*M_PI*r*r*r;
- }
- segvol = spherevol-prev_spherevol;
- inv_segvol[i] = 1.0/segvol;
- prev_spherevol = spherevol;
- }
-
- snew(rdf, ng);
- for (g = 0; g < ng; g++)
- {
- /* We have to normalize by dividing by the number of frames */
- if (rdft[0][0] == 'a')
- {
- normfac = 1.0/(nframes*invvol*isize0*isize[g+1]);
- }
- else
- {
- normfac = 1.0/(nframes*invvol*isize0*is[g+1]);
- }
-
- /* Do the normalization */
- nrdf = max((nbin+1)/2, 1+2*fade/binwidth);
- snew(rdf[g], nrdf);
- for (i = 0; i < (nbin+1)/2; i++)
- {
- r = i*binwidth;
- if (i == 0)
- {
- j = count[g][0];
- }
- else
- {
- j = count[g][i*2-1] + count[g][i*2];
- }
- if ((fade > 0) && (r >= fade))
- {
- rdf[g][i] = 1 + (j*inv_segvol[i]*normfac-1)*exp(-16*sqr(r/fade-1));
- }
- else
- {
- if (bNormalize)
- {
- rdf[g][i] = j*inv_segvol[i]*normfac;
- }
- else
- {
- rdf[g][i] = j/(binwidth*isize0*nframes);
- }
- }
- }
- for (; (i < nrdf); i++)
- {
- rdf[g][i] = 1.0;
- }
- }
-
- if (rdft[0][0] == 'a')
- {
- sprintf(gtitle, "Radial distribution");
- }
- else
- {
- sprintf(gtitle, "Radial distribution of %s %s",
- rdft[0][0] == 'm' ? "molecule" : "residue",
- rdft[0][6] == 'm' ? "COM" : "COG");
- }
- fp = xvgropen(fnRDF, gtitle, "r", "", oenv);
- if (bCM)
- {
- sprintf(refgt, " %s", "COM");
- }
- else if (bClose)
- {
- sprintf(refgt, " closest atom in %s.", close);
- }
- else
- {
- sprintf(refgt, "%s", "");
- }
- if (ng == 1)
- {
- if (output_env_get_print_xvgr_codes(oenv))
- {
- fprintf(fp, "@ subtitle \"%s%s - %s\"\n", grpname[0], refgt, grpname[1]);
- }
- }
- else
- {
- if (output_env_get_print_xvgr_codes(oenv))
- {
- fprintf(fp, "@ subtitle \"reference %s%s\"\n", grpname[0], refgt);
- }
- xvgr_legend(fp, ng, (const char**)(grpname+1), oenv);
- }
- for (i = 0; (i < nrdf); i++)
- {
- fprintf(fp, "%10g", i*binwidth);
- for (g = 0; g < ng; g++)
- {
- fprintf(fp, " %10g", rdf[g][i]);
- }
- fprintf(fp, "\n");
- }
- gmx_ffclose(fp);
-
- do_view(oenv, fnRDF, NULL);
-
- /* h(Q) function: fourier transform of rdf */
- if (fnHQ)
- {
- int nhq = 401;
- real *hq, *integrand, Q;
-
- /* Get a better number density later! */
- rho = isize[1]*invvol;
- snew(hq, nhq);
- snew(integrand, nrdf);
- for (i = 0; (i < nhq); i++)
- {
- Q = i*0.5;
- integrand[0] = 0;
- for (j = 1; (j < nrdf); j++)
- {
- r = j*binwidth;
- integrand[j] = (Q == 0) ? 1.0 : sin(Q*r)/(Q*r);
- integrand[j] *= 4.0*M_PI*rho*r*r*(rdf[0][j]-1.0);
- }
- hq[i] = print_and_integrate(debug, nrdf, binwidth, integrand, NULL, 0);
- }
- fp = xvgropen(fnHQ, "h(Q)", "Q(/nm)", "h(Q)", oenv);
- for (i = 0; (i < nhq); i++)
- {
- fprintf(fp, "%10g %10g\n", i*0.5, hq[i]);
- }
- gmx_ffclose(fp);
- do_view(oenv, fnHQ, NULL);
- sfree(hq);
- sfree(integrand);
- }
-
- if (fnCNRDF)
- {
- normfac = 1.0/(isize0*nframes);
- fp = xvgropen(fnCNRDF, "Cumulative Number RDF", "r", "number", oenv);
- if (ng == 1)
- {
- if (output_env_get_print_xvgr_codes(oenv))
- {
- fprintf(fp, "@ subtitle \"%s-%s\"\n", grpname[0], grpname[1]);
- }
- }
- else
- {
- if (output_env_get_print_xvgr_codes(oenv))
- {
- fprintf(fp, "@ subtitle \"reference %s\"\n", grpname[0]);
- }
- xvgr_legend(fp, ng, (const char**)(grpname+1), oenv);
- }
- snew(sum, ng);
- for (i = 0; (i <= nbin/2); i++)
- {
- fprintf(fp, "%10g", i*binwidth);
- for (g = 0; g < ng; g++)
- {
- fprintf(fp, " %10g", (real)((double)sum[g]*normfac));
- if (i*2+1 < nbin)
- {
- sum[g] += count[g][i*2] + count[g][i*2+1];
- }
- }
- fprintf(fp, "\n");
- }
- gmx_ffclose(fp);
- sfree(sum);
-
- do_view(oenv, fnCNRDF, NULL);
- }
-
- for (g = 0; g < ng; g++)
- {
- sfree(rdf[g]);
- }
- sfree(rdf);
-}
-
-
-int gmx_rdf(int argc, char *argv[])
-{
- const char *desc[] = {
- "The structure of liquids can be studied by either neutron or X-ray",
- "scattering. The most common way to describe liquid structure is by a",
- "radial distribution function. However, this is not easy to obtain from",
- "a scattering experiment.[PAR]",
- "[THISMODULE] calculates radial distribution functions in different ways.",
- "The normal method is around a (set of) particle(s), the other methods",
- "are around the center of mass of a set of particles ([TT]-com[tt])",
- "or to the closest particle in a set ([TT]-surf[tt]).",
- "With all methods, the RDF can also be calculated around axes parallel",
- "to the [IT]z[it]-axis with option [TT]-xy[tt].",
- "With option [TT]-surf[tt] normalization can not be used.[PAR]",
- "The option [TT]-rdf[tt] sets the type of RDF to be computed.",
- "Default is for atoms or particles, but one can also select center",
- "of mass or geometry of molecules or residues. In all cases, only",
- "the atoms in the index groups are taken into account.",
- "For molecules and/or the center of mass option, a run input file",
- "is required.",
- "Weighting other than COM or COG can currently only be achieved",
- "by providing a run input file with different masses.",
- "Options [TT]-com[tt] and [TT]-surf[tt] also work in conjunction",
- "with [TT]-rdf[tt].[PAR]",
- "If a run input file is supplied ([TT]-s[tt]) and [TT]-rdf[tt] is set",
- "to [TT]atom[tt], exclusions defined",
- "in that file are taken into account when calculating the RDF.",
- "The option [TT]-cut[tt] is meant as an alternative way to avoid",
- "intramolecular peaks in the RDF plot.",
- "It is however better to supply a run input file with a higher number of",
- "exclusions. For e.g. benzene a topology, setting nrexcl to 5",
- "would eliminate all intramolecular contributions to the RDF.",
- "Note that all atoms in the selected groups are used, also the ones",
- "that don't have Lennard-Jones interactions.[PAR]",
- "Option [TT]-cn[tt] produces the cumulative number RDF,",
- "i.e. the average number of particles within a distance r.[PAR]"
- };
- static gmx_bool bCM = FALSE, bXY = FALSE, bPBC = TRUE, bNormalize = TRUE;
- static real cutoff = 0, binwidth = 0.002, fade = 0.0;
- static int ngroups = 1;
-
- static const char *closet[] = { NULL, "no", "mol", "res", NULL };
- static const char *rdft[] = { NULL, "atom", "mol_com", "mol_cog", "res_com", "res_cog", NULL };
-
- t_pargs pa[] = {
- { "-bin", FALSE, etREAL, {&binwidth},
- "Binwidth (nm)" },
- { "-com", FALSE, etBOOL, {&bCM},
- "RDF with respect to the center of mass of first group" },
- { "-surf", FALSE, etENUM, {closet},
- "RDF with respect to the surface of the first group" },
- { "-rdf", FALSE, etENUM, {rdft},
- "RDF type" },
- { "-pbc", FALSE, etBOOL, {&bPBC},
- "Use periodic boundary conditions for computing distances. Without PBC the maximum range will be three times the largest box edge." },
- { "-norm", FALSE, etBOOL, {&bNormalize},
- "Normalize for volume and density" },
- { "-xy", FALSE, etBOOL, {&bXY},
- "Use only the x and y components of the distance" },
- { "-cut", FALSE, etREAL, {&cutoff},
- "Shortest distance (nm) to be considered"},
- { "-ng", FALSE, etINT, {&ngroups},
- "Number of secondary groups to compute RDFs around a central group" },
- { "-fade", FALSE, etREAL, {&fade},
- "From this distance onwards the RDF is tranformed by g'(r) = 1 + [g(r)-1] exp(-(r/fade-1)^2 to make it go to 1 smoothly. If fade is 0.0 nothing is done." }
- };
-#define NPA asize(pa)
- const char *fnTPS, *fnNDX;
- output_env_t oenv;
-
- t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffOPTRD },
- { efNDX, NULL, NULL, ffOPTRD },
- { efXVG, "-o", "rdf", ffWRITE },
- { efXVG, "-cn", "rdf_cn", ffOPTWR },
- { efXVG, "-hq", "hq", ffOPTWR },
- };
-#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
- {
- return 0;
- }
-
- if (bCM || closet[0][0] != 'n' || rdft[0][0] == 'm' || rdft[0][6] == 'm')
- {
- fnTPS = ftp2fn(efTPS, NFILE, fnm);
- }
- else
- {
- fnTPS = ftp2fn_null(efTPS, NFILE, fnm);
- }
- fnNDX = ftp2fn_null(efNDX, NFILE, fnm);
-
- if (!fnTPS && !fnNDX)
- {
- gmx_fatal(FARGS, "Neither index file nor topology file specified\n"
- "Nothing to do!");
- }
-
- if (closet[0][0] != 'n')
- {
- if (bCM)
- {
- gmx_fatal(FARGS, "Can not have both -com and -surf");
- }
- if (bNormalize)
- {
- fprintf(stderr, "Turning of normalization because of option -surf\n");
- bNormalize = FALSE;
- }
- }
-
- do_rdf(fnNDX, fnTPS, ftp2fn(efTRX, NFILE, fnm),
- opt2fn("-o", NFILE, fnm), opt2fn_null("-cn", NFILE, fnm),
- opt2fn_null("-hq", NFILE, fnm),
- bCM, closet[0], rdft, bXY, bPBC, bNormalize, cutoff, binwidth, fade, ngroups,
- oenv);
-
- return 0;
-}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "gromacs/utility/smalloc.h"
#include <math.h>
-#include "macros.h"
-#include "typedefs.h"
-#include "xvgr.h"
-#include "copyrite.h"
+#include <stdlib.h>
+
#include "gromacs/commandline/pargs.h"
-#include "vec.h"
-#include "index.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
-#include "princ.h"
-#include "rmpbc.h"
#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "cmat.h"
-#include "viewit.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/cmat.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void norm_princ(t_atoms *atoms, int isize, atom_id *index, int natoms,
rvec *x)
int ePBC;
t_iatom *iatom = NULL;
- matrix box;
+ matrix box = {{0}};
rvec *x, *xp, *xm = NULL, **mat_x = NULL, **mat_x2, *mat_x2_j = NULL, vec1,
vec2;
t_trxstatus *status;
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW
- | PCA_BE_NICE, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
&oenv))
{
return 0;
}
fprintf(fp, "\n");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
if (bMirror)
{
}
fprintf(fp, "\n");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
if (bAv)
{
fprintf(fp, "%10d %10g\n", j, rlstot/teller);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
if (bNorm)
{
fprintf(fp, "%10d %10g\n", j, rlsnorm[j]/teller);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
do_view(oenv, opt2fn_null("-a", NFILE, fnm), "-graphtype bar");
do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "names.h"
#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/strdb.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/strdb.h"
-#include "vec.h"
-#include "macros.h"
-#include "index.h"
-#include "pbc.h"
-#include "xvgr.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/matio.h"
-#include "gmx_ana.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void calc_dist(int nind, atom_id index[], rvec x[], int ePBC, matrix box,
{
lp += n;
snew(equiv[neq], 1);
- equiv[neq][0].nname = strdup(atomname);
+ equiv[neq][0].nname = gmx_strdup(atomname);
while (sscanf(lp, "%d %s %s %n", &resnr, resname, atomname, &n) == 3)
{
/* this is not efficient, but I'm lazy (again) */
srenew(equiv[neq], na+1);
equiv[neq][na].rnr = resnr-1;
- equiv[neq][na].rname = strdup(resname);
- equiv[neq][na].aname = strdup(atomname);
+ equiv[neq][na].rname = gmx_strdup(resname);
+ equiv[neq][na].aname = gmx_strdup(atomname);
if (na > 0)
{
equiv[neq][na].nname = NULL;
}
if (bFound)
{
- *nname = strdup(equiv[i-1][0].nname);
+ *nname = gmx_strdup(equiv[i-1][0].nname);
}
return bFound;
rnrj, *atoms->resinfo[rnrj].name, *atoms->atomname[index[j]]);
if (nnm[i] && bEquiv)
{
- nnm[j] = strdup(nnm[i]);
+ nnm[j] = gmx_strdup(nnm[i]);
}
if (bEquiv)
{
noe_gr[gi].anr = index[i];
if (nnm[i])
{
- noe_gr[gi].aname = strdup(nnm[i]);
+ noe_gr[gi].aname = gmx_strdup(nnm[i]);
}
else
{
- noe_gr[gi].aname = strdup(*atoms->atomname[index[i]]);
+ noe_gr[gi].aname = gmx_strdup(*atoms->atomname[index[i]]);
if (noe_index[i] == noe_index[i+1])
{
noe_gr[gi].aname[strlen(noe_gr[gi].aname)-1] = '*';
}
}
noe_gr[gi].rnr = atoms->atom[index[i]].resind;
- noe_gr[gi].rname = strdup(*atoms->resinfo[noe_gr[gi].rnr].name);
+ noe_gr[gi].rname = gmx_strdup(*atoms->resinfo[noe_gr[gi].rnr].name);
/* dump group definitions */
if (debug)
{
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
- gmx_ffclose(fp);
+ xvgrclose(fp);
close_trj(status);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "gromacs/utility/smalloc.h"
#include <math.h>
-#include "macros.h"
-#include "typedefs.h"
-#include "xvgr.h"
+
#include "gromacs/commandline/pargs.h"
-#include "vec.h"
-#include "index.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
-#include "princ.h"
-#include "rmpbc.h"
-#include "gromacs/fileio/confio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/linearalgebra/eigensolver.h"
#include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static real find_pdb_bfac(t_atoms *atoms, t_resinfo *ri, char *atomnm)
{
}
}
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
static void average_residues(double f[], double **U, int uind,
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, asize(pargs), pargs, asize(desc), desc, 0, NULL,
&oenv))
{
pdb_bfac);
}
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
else
{
bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, sqrt(rmsf[i]));
}
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
for (i = 0; i < isize; i++)
bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, sqrt(rmsf[i]));
}
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
if (opt2bSet("-oq", NFILE, fnm))
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
-#include "physics.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
+
#include "gromacs/commandline/pargs.h"
-#include "index.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "xvgr.h"
-#include "gstat.h"
-#include "vec.h"
-#include "gmx_ana.h"
+#include "gromacs/correlationfunctions/autocorr.h"
#include "gromacs/fileio/trxio.h"
-
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
int gmx_rotacf(int argc, char *argv[])
{
int ePBC;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffREAD },
{ efXVG, "-o", "rotacf", ffWRITE }
};
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
"these can not be atom doublets\n");
}
- top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
snew(c1, nvec);
for (i = 0; (i < nvec); i++)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "rmpbc.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void get_refx(output_env_t oenv, const char *trxfn, int nfitdim, int skip,
int gnx, int *index,
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
close_trj(status);
- gmx_ffclose(out);
+ xvgrclose(out);
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <math.h>
#include <string.h>
-#include "macros.h"
-#include "vec.h"
-#include "sysstuff.h"
-#include "typedefs.h"
+#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/filenm.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "pbc.h"
-#include "xvgr.h"
-#include "gmx_ana.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
typedef struct {
char *label;
*(atoms->resinfo[resnr].name),
atoms->resinfo[resnr].nr,
anr+1);
- cg[ncg].label = strdup(buf);
+ cg[ncg].label = gmx_strdup(buf);
ncg++;
}
}
};
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
};
#define NFILE asize(fnm)
matrix box;
output_env_t oenv;
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
- top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
cg = mk_charge(&top->atoms, &(top->cgs), &ncg);
snew(cgdist, ncg);
snew(nWithin, ncg);
{
fprintf(fp, "%10g %10g\n", time[k], cgdist[i][j][k]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
}
}
}
for (m = 0; (m < 3); m++)
{
- gmx_ffclose(out[m]);
+ xvgrclose(out[m]);
if (nset[m] == 0)
{
remove(fn[m]);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "xvgr.h"
-#include "copyrite.h"
-#include "gromacs/commandline/pargs.h"
-#include "index.h"
-#include "gstat.h"
-#include "gmx_ana.h"
-#include "nsfactor.h"
+#include "config.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/matio.h"
+#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxana/nsfactor.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
int gmx_sans(int argc, char *argv[])
{
#define NFILE asize(fnm)
t_filenm fnm[] = {
- { efTPX, "-s", NULL, ffREAD },
+ { efTPR, "-s", NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efDAT, "-d", "nsfactor", ffOPTRD },
nthreads = gmx_omp_get_max_threads();
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
/* Try to read files */
fnDAT = ftp2fn(efDAT, NFILE, fnm);
- fnTPX = ftp2fn(efTPX, NFILE, fnm);
+ fnTPX = ftp2fn(efTPR, NFILE, fnm);
fnTRX = ftp2fn(efTRX, NFILE, fnm);
gnsf = gmx_neutronstructurefactors_init(fnDAT);
fprintf(fp, "%10.6f%10.6f\n", prframecurrent->r[i], prframecurrent->gr[i]);
}
done_filenms(NFILE, fnmdup);
- fclose(fp);
+ xvgrclose(fp);
sfree(hdr);
sfree(suffix);
sfree(fnmdup);
fprintf(fp, "%10.6f%10.6f\n", sqframecurrent->q[i], sqframecurrent->s[i]);
}
done_filenms(NFILE, fnmdup);
- fclose(fp);
+ xvgrclose(fp);
sfree(hdr);
sfree(suffix);
sfree(fnmdup);
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "xvgr.h"
-#include "copyrite.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/tpxio.h"
-#include "physics.h"
-#include "index.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/sfactor.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/utility/smalloc.h"
-#include "calcgrid.h"
-#include "nrnb.h"
-#include "coulomb.h"
-#include "gstat.h"
-#include "gromacs/fileio/matio.h"
-#include "gmx_ana.h"
-#include "names.h"
-#include "sfactor.h"
int gmx_saxs(int argc, char *argv[])
{
{ efXVG, "-sq", "sq", ffWRITE },
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <math.h>
+#include <stdlib.h>
#include <string.h>
+
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "gromacs/fileio/futil.h"
-#include "readinp.h"
-#include "txtdump.h"
-#include "gstat.h"
-#include "xvgr.h"
-#include "physics.h"
-#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/matio.h"
-#include "gmx_ana.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static int index2(int *ibox, int x, int y)
index = index3(ibox, i, j, k);
if (P[index] > 0)
{
- fprintf(fp, "%-6s%5u %-4.4s%3.3s %4d %8.3f%8.3f%8.3f%6.2f%6.2f\n",
+ fprintf(fp, "%-6s%5d %-4.4s%3.3s %4d %8.3f%8.3f%8.3f%6.2f%6.2f\n",
"ATOM", (index+1) %10000, "H", "H", (index+1)%10000,
xxx[XX], xxx[YY], xxx[ZZ], 1.0, W[index]);
}
}
fprintf(fp, "\n");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
int gmx_sham(int argc, char *argv[])
int npargs;
npargs = asize(pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
NFILE, fnm, npargs, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <stdio.h>
#include <math.h>
+#include <stdio.h>
-#include "typedefs.h"
#include "gromacs/commandline/pargs.h"
-#include "xvgr.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/pdbio.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "pbc.h"
-#include "physics.h"
-#include "names.h"
-#include "txtdump.h"
#include "gromacs/fileio/trnio.h"
-#include "symtab.h"
-#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
real pot(real x, real qq, real c6, real cn, int npow)
{
oldx = x;
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), NULL);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "macros.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gstat.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gmx_ana.h"
-
-#include "gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static void calc_com_pbc(int nrefat, t_topology *top, rvec x[], t_pbc *pbc,
atom_id index[], rvec xref, gmx_bool bPBC)
{ efTRX, NULL, NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
- { efXVG, NULL, "sori.xvg", ffWRITE },
- { efXVG, "-no", "snor.xvg", ffWRITE },
- { efXVG, "-ro", "sord.xvg", ffWRITE },
- { efXVG, "-co", "scum.xvg", ffWRITE },
- { efXVG, "-rc", "scount.xvg", ffWRITE }
+ { efXVG, NULL, "sori", ffWRITE },
+ { efXVG, "-no", "snor", ffWRITE },
+ { efXVG, "-ro", "sord", ffWRITE },
+ { efXVG, "-co", "scum", ffWRITE },
+ { efXVG, "-rc", "scount", ffWRITE }
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
{
fprintf(fp, "%g %g\n", (i+0.5)*binwidth-1, 2*normfac*hist1[i]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
sprintf(str, "Solvent normal orientation between %g and %g nm", rmin, rmax);
fp = xvgropen(opt2fn("-no", NFILE, fnm), str, "cos(\\8q\\4\\s2\\N)", "", oenv);
{
fprintf(fp, "%g %g\n", (i+0.5)*binwidth, normfac*hist2[i]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
sprintf(str, "Solvent orientation");
histn[i] ? histi1[i]/histn[i] : 0,
histn[i] ? histi2[i]/histn[i] : 0);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
sprintf(str, "Cumulative solvent orientation");
fp = xvgropen(opt2fn("-co", NFILE, fnm), str, "r (nm)", "", oenv);
c2 += histi2[i]*normfac;
fprintf(fp, "%g %g %g\n", (i+1)*rbinw, c1, c2);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
sprintf(str, "Solvent distribution");
fp = xvgropen(opt2fn("-rc", NFILE, fnm), str, "r (nm)", "molecules/nm", oenv);
{
fprintf(fp, "%g %g\n", (i+0.5)*rbinw, histn[i]*normfac);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);
do_view(oenv, opt2fn("-no", NFILE, fnm), NULL);
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
+#include "gmxpre.h"
+#include <math.h>
+#include <stdlib.h>
#include "gromacs/commandline/pargs.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include <math.h>
-#include "index.h"
-#include "pbc.h"
-#include "rmpbc.h"
-#include "gmx_ana.h"
-#include "macros.h"
-
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/smalloc.h"
static const double bohr = 0.529177249; /* conversion factor to compensate for VMD plugin conversion... */
-static void mequit(void)
-{
- printf("Memory allocation error\n");
- exit(1);
-}
-
int gmx_spatial(int argc, char *argv[])
{
const char *desc[] = {
MINBIN[i] -= (double)iNAB*rBINWIDTH;
nbin[i] = (long)ceil((MAXBIN[i]-MINBIN[i])/rBINWIDTH);
}
- bin = (long ***)malloc(nbin[XX]*sizeof(long **));
- if (!bin)
- {
- mequit();
- }
+ snew(bin, nbin[XX]);
for (i = 0; i < nbin[XX]; ++i)
{
- bin[i] = (long **)malloc(nbin[YY]*sizeof(long *));
- if (!bin[i])
- {
- mequit();
- }
+ snew(bin[i], nbin[YY]);
for (j = 0; j < nbin[YY]; ++j)
{
- bin[i][j] = (long *)calloc(nbin[ZZ], sizeof(long));
- if (!bin[i][j])
- {
- mequit();
- }
+ snew(bin[i][j], nbin[ZZ]);
}
}
copy_mat(box, box_pbc);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "macros.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gstat.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "index.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "physics.h"
-#include "gmx_ana.h"
-
-#include "gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static void calc_com_pbc(int nrefat, t_topology *top, rvec x[], t_pbc *pbc,
atom_id index[], rvec xref, int ePBC)
t_filenm fnm[] = {
{ efTRX, NULL, NULL, ffREAD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
- { efXVG, NULL, "scdist.xvg", ffWRITE }
+ { efXVG, NULL, "scdist", ffWRITE }
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
snew(top, 1);
snew(ir, 1);
- read_tpx_top(ftp2fn(efTPX, NFILE, fnm),
+ read_tpx_top(ftp2fn(efTPR, NFILE, fnm),
ir, box, &natoms, NULL, NULL, NULL, top);
/* get index groups */
nmol += hist[i];
fprintf(fp, "%g %g\n", i*bw, nmol/nf);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <stdio.h>
+#include "gmxpre.h"
#include <math.h>
+#include <stdio.h>
+#include <string.h>
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/correlationfunctions/autocorr.h"
+#include "gromacs/correlationfunctions/expfit.h"
#include "gromacs/fileio/confio.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
-#include "gstat.h"
-#include "macros.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
-#include "physics.h"
-#include "index.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/commandline/pargs.h"
-#include <string.h>
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "gmx_ana.h"
-#include "gromacs/fileio/trxio.h"
-
#define NK 24
#define NPK 4
{
FILE *fp, *fp_vk, *fp_cub = NULL;
int nk, ntc;
- real **tcaf, **tcafc = NULL, eta;
+ real **tcaf, **tcafc = NULL, eta, *sig;
int i, j, k, kc;
int ncorr;
- real fitparms[3], *sig;
+ double fitparms[3];
nk = kset_c[nkc];
ntc = nk*NPK;
}
fprintf(fp, "\n");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
do_view(oenv, fn_trans, "-nxy");
}
}
fprintf(fp, "\n");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
do_view(oenv, fn_tc, "-nxy");
if (fn_cub)
}
fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
do_view(oenv, fn_tcf, "-nxy");
if (fn_cub)
fprintf(fp_cub, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
fprintf(fp_vk, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
- gmx_ffclose(fp_cub);
+ xvgrclose(fp_cub);
do_view(oenv, fn_cub, "-nxy");
}
- gmx_ffclose(fp_vk);
+ xvgrclose(fp_vk);
do_view(oenv, fn_vk, "-nxy");
}
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
+#include <stdlib.h>
#include <string.h>
+
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
-#include "mshift.h"
-#include "xvgr.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "rmpbc.h"
-#include "physics.h"
-#include "gromacs/fileio/confio.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/linearalgebra/nrjac.h"
-#include "gmx_fatal.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void low_print_data(FILE *fp, real time, rvec x[], int n, atom_id *index,
gmx_bool bDim[], const char *sffmt)
fprintf(fp, "%-5d %10.3f %10.3f %10.3f\n", 1+i,
sum[index[i]][XX], sum[index[i]][YY], sum[index[i]][ZZ]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
max = 0;
maxi = 0;
for (i = 0; i < isize; i++)
{
fprintf(fp, "%10.3e %10d\n", i*binwidth, histo[i]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
int gmx_traj(int argc, char *argv[])
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
- { efXVG, "-ox", "coord.xvg", ffOPTWR },
- { efTRX, "-oxt", "coord.xtc", ffOPTWR },
- { efXVG, "-ov", "veloc.xvg", ffOPTWR },
- { efXVG, "-of", "force.xvg", ffOPTWR },
- { efXVG, "-ob", "box.xvg", ffOPTWR },
- { efXVG, "-ot", "temp.xvg", ffOPTWR },
- { efXVG, "-ekt", "ektrans.xvg", ffOPTWR },
- { efXVG, "-ekr", "ekrot.xvg", ffOPTWR },
- { efXVG, "-vd", "veldist.xvg", ffOPTWR },
- { efPDB, "-cv", "veloc.pdb", ffOPTWR },
- { efPDB, "-cf", "force.pdb", ffOPTWR },
- { efXVG, "-av", "all_veloc.xvg", ffOPTWR },
- { efXVG, "-af", "all_force.xvg", ffOPTWR }
+ { efXVG, "-ox", "coord", ffOPTWR },
+ { efTRX, "-oxt", "coord", ffOPTWR },
+ { efXVG, "-ov", "veloc", ffOPTWR },
+ { efXVG, "-of", "force", ffOPTWR },
+ { efXVG, "-ob", "box", ffOPTWR },
+ { efXVG, "-ot", "temp", ffOPTWR },
+ { efXVG, "-ekt", "ektrans", ffOPTWR },
+ { efXVG, "-ekr", "ekrot", ffOPTWR },
+ { efXVG, "-vd", "veldist", ffOPTWR },
+ { efPDB, "-cv", "veloc", ffOPTWR },
+ { efPDB, "-cf", "force", ffOPTWR },
+ { efXVG, "-av", "all_veloc", ffOPTWR },
+ { efXVG, "-af", "all_force", ffOPTWR }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv,
- PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
+ PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
if (bOX)
{
- gmx_ffclose(outx);
+ xvgrclose(outx);
}
if (bOXT)
{
}
if (bOV)
{
- gmx_ffclose(outv);
+ xvgrclose(outv);
}
if (bOF)
{
- gmx_ffclose(outf);
+ xvgrclose(outf);
}
if (bOB)
{
- gmx_ffclose(outb);
+ xvgrclose(outb);
}
if (bOT)
{
- gmx_ffclose(outt);
+ xvgrclose(outt);
}
if (bEKT)
{
- gmx_ffclose(outekt);
+ xvgrclose(outekt);
}
if (bEKR)
{
- gmx_ffclose(outekr);
+ xvgrclose(outekr);
}
if (bVD)
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <string.h>
#include <math.h>
-#include "macros.h"
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
+#include <stdlib.h>
+#include <string.h>
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/tngio.h"
#include "gromacs/fileio/tngio_for_tools.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/confio.h"
-#include "names.h"
-#include "index.h"
-#include "vec.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xtcio.h"
-#include "rmpbc.h"
-#include "pbc.h"
-#include "xvgr.h"
-#include "gmx_ana.h"
-
-#include "gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define TIME_EXPLICIT 0
#define TIME_CONTINUE 1
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_BE_NICE | PCA_TIME_UNIT, NFILE, fnm,
+ if (!parse_common_args(&argc, argv, PCA_TIME_UNIT, NFILE, fnm,
asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
{
if (nfile_out != nset)
{
- char *buf = strdup(fnms_out[0]);
+ char *buf = gmx_strdup(fnms_out[0]);
snew(fnms_out, nset);
for (i = 0; (i < nset); i++)
{
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <string.h>
#include <math.h>
+#include <stdlib.h>
+#include <string.h>
-#include "copyrite.h"
-#include "macros.h"
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/tngio_for_tools.h"
#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/tngio_for_tools.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/confio.h"
-#include "names.h"
-#include "index.h"
-#include "vec.h"
+#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xtcio.h"
-#include "rmpbc.h"
-#include "pbc.h"
-#include "viewit.h"
-#include "xvgr.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/math/do_fit.h"
-#include "gmx_fatal.h"
-
-#ifdef HAVE_UNISTD_H
-#include <unistd.h>
-#endif
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
enum {
euSel, euRect, euTric, euCompact, euNR
{
if (debug)
{
- fprintf(debug, "\nShifting position of residue %d (atoms %u-%u) "
+ fprintf(debug, "\nShifting position of residue %d (atoms %d-%d) "
"by %g,%g,%g\n", atom[res_start].resind+1,
res_start+1, res_end+1, shift[XX], shift[YY], shift[ZZ]);
}
void check_trn(const char *fn)
{
- if ((fn2ftp(fn) != efTRJ) && (fn2ftp(fn) != efTRR))
+ if (fn2ftp(fn) != efTRR)
{
gmx_fatal(FARGS, "%s is not a trajectory file, exiting\n", fn);
}
}
-#ifndef GMX_NATIVE_WINDOWS
void do_trunc(const char *fn, real t0)
{
t_fileio *in;
gmx_fatal(FARGS, "You forgot to set the truncation time");
}
- /* Check whether this is a .trj file */
+ /* Check whether this is a .trr file */
check_trn(fn);
in = open_trn(fn, "r");
{
fprintf(stderr, "Once again, I'm gonna DO this...\n");
close_trn(in);
- if (0 != truncate(fn, fpos))
+ if (0 != gmx_truncate(fn, fpos))
{
gmx_fatal(FARGS, "Error truncating file %s", fn);
}
}
}
}
-#endif
/*! \brief Read a full molecular topology if useful and available.
*
"[PAR]",
"The following formats are supported for input and output:",
- "[TT].xtc[tt], [TT].trr[tt], [TT].trj[tt], [TT].gro[tt], [TT].g96[tt]",
+ "[TT].xtc[tt], [TT].trr[tt], [TT].gro[tt], [TT].g96[tt]",
"and [TT].pdb[tt].",
"The file formats are detected from the file extension.",
"The precision of [TT].xtc[tt] and [TT].gro[tt] output is taken from the",
"input file for [TT].xtc[tt], [TT].gro[tt] and [TT].pdb[tt],",
"and from the [TT]-ndec[tt] option for other input formats. The precision",
"is always taken from [TT]-ndec[tt], when this option is set.",
- "All other formats have fixed precision. [TT].trr[tt] and [TT].trj[tt]",
+ "All other formats have fixed precision. [TT].trr[tt]",
"output can be single or double precision, depending on the precision",
"of the [THISMODULE] binary.",
"Note that velocities are only supported in",
- "[TT].trr[tt], [TT].trj[tt], [TT].gro[tt] and [TT].g96[tt] files.[PAR]",
+ "[TT].trr[tt], [TT].gro[tt] and [TT].g96[tt] files.[PAR]",
"Option [TT]-sep[tt] can be used to write every frame to a separate",
"[TT].gro, .g96[tt] or [TT].pdb[tt] file. By default, all frames all written to one file.",
"can reduce the number of frames while using low-pass frequency",
"filtering, this reduces aliasing of high frequency motions.[PAR]",
- "Using [TT]-trunc[tt] [THISMODULE] can truncate [TT].trj[tt] in place, i.e.",
+ "Using [TT]-trunc[tt] [THISMODULE] can truncate [TT].trr[tt] in place, i.e.",
"without copying the file. This is useful when a run has crashed",
"during disk I/O (i.e. full disk), or when two contiguous",
"trajectories must be concatenated without having double frames.[PAR]",
{ &bVels }, "Read and write velocities if possible" },
{ "-force", FALSE, etBOOL,
{ &bForce }, "Read and write forces if possible" },
-#ifndef GMX_NATIVE_WINDOWS
{ "-trunc", FALSE, etTIME,
{ &ttrunc },
"Truncate input trajectory file after this time (%t)" },
-#endif
{ "-exec", FALSE, etSTR,
{ &exec_command },
"Execute command for every output frame with the "
if (!parse_common_args(&argc, argv,
PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
- PCA_TIME_UNIT | PCA_BE_NICE,
+ PCA_TIME_UNIT,
NFILE, fnm, NPA, pa, asize(desc), desc,
0, NULL, &oenv))
{
if (ttrunc != -1)
{
-#ifndef GMX_NATIVE_WINDOWS
do_trunc(in_file, ttrunc);
-#endif
}
else
{
{
/* check if velocities are possible in input and output files */
ftpin = fn2ftp(in_file);
- bVels = (ftp == efTRR || ftp == efTRJ || ftp == efGRO ||
+ bVels = (ftp == efTRR || ftp == efGRO ||
ftp == efG96 || ftp == efTNG)
- && (ftpin == efTRR || ftpin == efTRJ || ftpin == efGRO ||
+ && (ftpin == efTRR || ftpin == efGRO ||
ftpin == efG96 || ftpin == efTNG || ftpin == efCPT);
}
if (bSeparate || bSplit)
{
gmx_fatal(FARGS, "Output file name '%s' does not contain a '.'", out_file);
}
- outf_base = strdup(out_file);
+ outf_base = gmx_strdup(out_file);
outf_base[outf_ext - out_file] = '\0';
}
useatoms.nr = nout;
}
/* select what to read */
- if (ftp == efTRR || ftp == efTRJ)
+ if (ftp == efTRR)
{
flags = TRX_READ_X;
}
break;
case efXTC:
case efTRR:
- case efTRJ:
out = NULL;
if (!bSplit && !bSubTraj)
{
if (bWriteFrame)
{
+ /* We should avoid modifying the input frame,
+ * but since here we don't have the output frame yet,
+ * we introduce a temporary output frame time variable.
+ */
+ real frout_time;
+
+ frout_time = fr.time;
/* calc new time */
if (bTimeStep)
{
- fr.time = tzero+frame*timestep;
+ frout_time = tzero + frame*timestep;
}
else
if (bSetTime)
{
- fr.time += tshift;
+ frout_time += tshift;
}
if (bTDump)
{
fprintf(stderr, "\nDumping frame at t= %g %s\n",
- output_env_conv_time(oenv, fr.time), output_env_get_time_unit(oenv));
+ output_env_conv_time(oenv, frout_time), output_env_get_time_unit(oenv));
}
/* check for writing at each delta_t */
{
if (!bRound)
{
- bDoIt = bRmod(fr.time, tzero, delta_t);
+ bDoIt = bRmod(frout_time, tzero, delta_t);
}
else
{
/* round() is not C89 compatible, so we do this: */
- bDoIt = bRmod(floor(fr.time+0.5), floor(tzero+0.5),
+ bDoIt = bRmod(floor(frout_time+0.5), floor(tzero+0.5),
floor(delta_t+0.5));
}
}
if ( ((outframe % SKIP) == 0) || (outframe < SKIP) )
{
fprintf(stderr, " -> frame %6d time %8.3f \r",
- outframe, output_env_conv_time(oenv, fr.time));
+ outframe, output_env_conv_time(oenv, frout_time));
}
if (!bPFit)
}
/* Copy the input trxframe struct to the output trxframe struct */
frout = fr;
+ frout.time = frout_time;
frout.bV = (frout.bV && bVels);
frout.bF = (frout.bF && bForce);
frout.natoms = nout;
if (!bRound)
{
- bSplitHere = bSplit && bRmod(fr.time, tzero, split_t);
+ bSplitHere = bSplit && bRmod(frout.time, tzero, split_t);
}
else
{
/* round() is not C89 compatible, so we do this: */
- bSplitHere = bSplit && bRmod(floor(fr.time+0.5),
+ bSplitHere = bSplit && bRmod(floor(frout.time+0.5),
floor(tzero+0.5),
floor(split_t+0.5));
}
write_tng_frame(trxout, &frout);
// TODO when trjconv behaves better: work how to read and write lambda
break;
- case efTRJ:
case efTRR:
case efXTC:
if (bSplitHere)
case efG96:
case efPDB:
sprintf(title, "Generated by trjconv : %s t= %9.5f",
- top_title, fr.time);
+ top_title, frout.time);
if (bSeparate || bSplitHere)
{
out = gmx_ffopen(out_file2, "w");
char c[255];
sprintf(c, "%s %d", exec_command, file_nr-1);
/*fprintf(stderr,"Executing '%s'\n",c);*/
-#ifdef GMX_NO_SYSTEM
- printf("Warning-- No calls to system(3) supported on this platform.");
- printf("Warning-- Skipping execution of 'system(\"%s\")'.", c);
-#else
if (0 != system(c))
{
gmx_fatal(FARGS, "Error executing command: %s", c);
}
-#endif
}
outframe++;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
+#include <stdlib.h>
#include <string.h>
+
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "princ.h"
-#include "rmpbc.h"
-#include "txtdump.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gmx_ana.h"
-
-#include "gmx_fatal.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
atom_id i;
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
if (fp)
{
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
gmx_rmpbc_done(gpbc);
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
+#include <stdlib.h>
#include <time.h>
+
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
#include "gromacs/commandline/pargs.h"
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "copyrite.h"
#include "gromacs/fileio/tpxio.h"
-#include "gromacs/utility/cstringutil.h"
-#include "readinp.h"
-#include "calcgrid.h"
-#include "checkpoint.h"
-#include "macros.h"
-#include "gmx_ana.h"
-#include "names.h"
-#include "perf_est.h"
-#include "inputrec.h"
-#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/calcgrid.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/inputrec.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/perf_est.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/math/utilities.h"
-
-#include "gmx_fatal.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/utility/baseversion.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* Enum for situations that can occur during log file parsing, the
* corresponding string entries can be found in do_the_tests() in
* const char* ParseLog[] */
+/* TODO clean up CamelCasing of these enum names */
enum {
eParselogOK,
eParselogNotFound,
eParselogTPXVersion,
eParselogNotParallel,
eParselogLargePrimeFactor,
+ eParselogMismatchOfNumberOfPPRanksAndAvailableGPUs,
+ eParselogGpuProblem,
eParselogFatal,
eParselogNr
};
/* Wrapper for system calls */
static int gmx_system_call(char *command)
{
-#ifdef GMX_NO_SYSTEM
- gmx_fatal(FARGS, "No calls to system(3) supported on this platform. Attempted to call:\n'%s'\n", command);
-#else
return ( system(command) );
-#endif
}
}
-static gmx_bool is_equal(real a, real b)
-{
- real diff, eps = 1.0e-7;
-
-
- diff = a - b;
-
- if (diff < 0.0)
- {
- diff = -diff;
- }
-
- if (diff < eps)
- {
- return TRUE;
- }
- else
- {
- return FALSE;
- }
-}
-
-
static void remove_if_exists(const char *fn)
{
if (gmx_fexist(fn))
}
break;
case eFoundDDStr:
+ /* Even after the "Domain decomposition grid" string was found,
+ * it could be that mdrun had to quit due to some error. */
+ if (str_starts(line, "Incorrect launch configuration: mismatching number of"))
+ {
+ fclose(fp);
+ return eParselogMismatchOfNumberOfPPRanksAndAvailableGPUs;
+ }
+ else if (str_starts(line, "Some of the requested GPUs do not exist"))
+ {
+ fclose(fp);
+ return eParselogGpuProblem;
+ }
/* Look for PME mesh/force balance (not necessarily present, though) */
- if (str_starts(line, matchstrbal))
+ else if (str_starts(line, matchstrbal))
{
sscanf(&line[strlen(matchstrbal)], "%f", &(perfdata->PME_f_load[test_nr]));
}
/* Look for matchstring */
- if (str_starts(line, matchstring))
+ else if (str_starts(line, matchstring))
{
iFound = eFoundAccountingStr;
}
fprintf(fp, "\n");
/* Only mention settings if they were modified: */
- bRefinedCoul = !is_equal(info->rcoulomb[k_win], info->rcoulomb[0]);
- bRefinedVdW = !is_equal(info->rvdw[k_win], info->rvdw[0] );
+ bRefinedCoul = !gmx_within_tol(info->rcoulomb[k_win], info->rcoulomb[0], GMX_REAL_EPS);
+ bRefinedVdW = !gmx_within_tol(info->rvdw[k_win], info->rvdw[0], GMX_REAL_EPS);
bRefinedGrid = !(info->nkx[k_win] == info->nkx[0] &&
info->nky[k_win] == info->nky[0] &&
info->nkz[k_win] == info->nkz[0]);
{
if ( (cp = getenv("MPIRUN")) != NULL)
{
- *cmd_mpirun = strdup(cp);
+ *cmd_mpirun = gmx_strdup(cp);
}
else
{
- *cmd_mpirun = strdup(def_mpirun);
+ *cmd_mpirun = gmx_strdup(def_mpirun);
}
}
else
{
- *cmd_mpirun = strdup(empty_mpirun);
+ *cmd_mpirun = gmx_strdup(empty_mpirun);
}
if ( (cp = getenv("MDRUN" )) != NULL)
{
- *cmd_mdrun = strdup(cp);
+ *cmd_mdrun = gmx_strdup(cp);
}
else
{
- *cmd_mdrun = strdup(def_mdrun);
+ *cmd_mdrun = gmx_strdup(def_mdrun);
}
}
/* Check that the commands will run mdrun (perhaps via mpirun) by
- * running a very quick test simulation. Requires MPI environment to
- * be available if applicable. */
+ * running a very quick test simulation. Requires MPI environment or
+ * GPU support to be available if applicable. */
+/* TODO implement feature to parse the log file to get the list of
+ compatible GPUs from mdrun, if the user of gmx tune-pme has not
+ given one. */
static void check_mdrun_works(gmx_bool bThreads,
const char *cmd_mpirun,
const char *cmd_np,
- const char *cmd_mdrun)
+ const char *cmd_mdrun,
+ gmx_bool bNeedGpuSupport)
{
char *command = NULL;
char *cp;
/* This string should always be identical to the one in copyrite.c,
* gmx_print_version_info() in the defined(GMX_MPI) section */
- const char match_mpi[] = "MPI library: MPI";
- const char match_mdrun[] = "Executable: ";
- gmx_bool bMdrun = FALSE;
- gmx_bool bMPI = FALSE;
+ const char match_mpi[] = "MPI library: MPI";
+ const char match_mdrun[] = "Executable: ";
+ const char match_gpu[] = "GPU support: enabled";
+ gmx_bool bMdrun = FALSE;
+ gmx_bool bMPI = FALSE;
+ gmx_bool bHaveGpuSupport = FALSE;
/* Run a small test to see whether mpirun + mdrun work */
fprintf(stdout, "Making sure that mdrun can be executed. ");
{
bMPI = TRUE;
}
+ if (str_starts(line, match_gpu) )
+ {
+ bHaveGpuSupport = TRUE;
+ }
}
}
fclose(fp);
filename);
}
+ if (bNeedGpuSupport && !bHaveGpuSupport)
+ {
+ gmx_fatal(FARGS, "The mdrun executable did not have the expected GPU support.");
+ }
+
fprintf(stdout, "passed.\n");
/* Clean up ... */
sfree(command);
}
+/*! \brief Helper struct so we can parse the string with eligible GPU
+ IDs outside do_the_tests. */
+typedef struct eligible_gpu_ids
+{
+ int n; /**< Length of ids */
+ int *ids; /**< Array of length n. NULL if no GPUs in use */
+} t_eligible_gpu_ids;
+
+/* Handles the no-GPU case by emitting an empty string. */
+static char *make_gpu_id_command_line(int numRanks, int numPmeRanks, const t_eligible_gpu_ids *gpu_ids)
+{
+ char *command_line, *flag = "-gpu_id ", *ptr;
+ int flag_length;
+
+ /* Reserve enough room for the option name, enough single-digit
+ GPU ids (since that is currently all that is possible to use
+ with mdrun), and a terminating NULL. */
+ flag_length = strlen(flag);
+ snew(command_line, flag_length + numRanks + 1);
+ ptr = command_line;
+
+ /* If the user has given no eligible GPU IDs, or we're trying the
+ * default behaviour, then there is nothing for g_tune_pme to give
+ * to mdrun -gpu_id */
+ if (gpu_ids->n > 0 && numPmeRanks > -1)
+ {
+ int numPpRanks, max_num_ranks_for_each_GPU;
+ int gpu_id, rank;
+
+ /* Write the option flag */
+ strcpy(ptr, flag);
+ ptr += flag_length;
+
+ numPpRanks = numRanks - numPmeRanks;
+ max_num_ranks_for_each_GPU = numPpRanks / gpu_ids->n;
+ if (max_num_ranks_for_each_GPU * gpu_ids->n != numPpRanks)
+ {
+ /* Some GPUs will receive more work than others, which
+ * we choose to be those with the lowest indices */
+ max_num_ranks_for_each_GPU++;
+ }
+
+ /* Loop over all eligible GPU ids */
+ for (gpu_id = 0, rank = 0; gpu_id < gpu_ids->n; gpu_id++)
+ {
+ int rank_for_this_GPU;
+ /* Loop over all PP ranks for GPU with ID gpu_id, building the
+ assignment string. */
+ for (rank_for_this_GPU = 0;
+ rank_for_this_GPU < max_num_ranks_for_each_GPU && rank < numPpRanks;
+ rank++, rank_for_this_GPU++)
+ {
+ *ptr = '0' + gpu_ids->ids[gpu_id];
+ ptr++;
+ }
+ }
+ }
+ *ptr = '\0';
+
+ return command_line;
+}
static void launch_simulation(
- gmx_bool bLaunch, /* Should the simulation be launched? */
- FILE *fp, /* General log file */
- gmx_bool bThreads, /* whether to use threads */
- char *cmd_mpirun, /* Command for mpirun */
- char *cmd_np, /* Switch for -np or -ntmpi or empty */
- char *cmd_mdrun, /* Command for mdrun */
- char *args_for_mdrun, /* Arguments for mdrun */
- const char *simulation_tpr, /* This tpr will be simulated */
- int nPMEnodes) /* Number of PME nodes to use */
+ gmx_bool bLaunch, /* Should the simulation be launched? */
+ FILE *fp, /* General log file */
+ gmx_bool bThreads, /* whether to use threads */
+ char *cmd_mpirun, /* Command for mpirun */
+ char *cmd_np, /* Switch for -np or -ntmpi or empty */
+ char *cmd_mdrun, /* Command for mdrun */
+ char *args_for_mdrun, /* Arguments for mdrun */
+ const char *simulation_tpr, /* This tpr will be simulated */
+ int nnodes, /* Number of ranks to use */
+ int nPMEnodes, /* Number of PME ranks to use */
+ const t_eligible_gpu_ids *gpu_ids) /* Struct containing GPU IDs for
+ * constructing mdrun command lines */
{
- char *command;
+ char *command, *cmd_gpu_ids;
/* Make enough space for the system call command,
- * (100 extra chars for -npme ... etc. options should suffice): */
- snew(command, strlen(cmd_mpirun)+strlen(cmd_mdrun)+strlen(cmd_np)+strlen(args_for_mdrun)+strlen(simulation_tpr)+100);
+ * (200 extra chars for -npme ... etc. options should suffice): */
+ snew(command, strlen(cmd_mpirun)+strlen(cmd_mdrun)+strlen(cmd_np)+strlen(args_for_mdrun)+strlen(simulation_tpr)+200);
+
+ cmd_gpu_ids = make_gpu_id_command_line(nnodes, nPMEnodes, gpu_ids);
/* Note that the -passall options requires args_for_mdrun to be at the end
* of the command line string */
if (bThreads)
{
- sprintf(command, "%s%s-npme %d -s %s %s",
- cmd_mdrun, cmd_np, nPMEnodes, simulation_tpr, args_for_mdrun);
+ sprintf(command, "%s%s-npme %d -s %s %s %s",
+ cmd_mdrun, cmd_np, nPMEnodes, simulation_tpr, args_for_mdrun, cmd_gpu_ids);
}
else
{
- sprintf(command, "%s%s%s -npme %d -s %s %s",
- cmd_mpirun, cmd_np, cmd_mdrun, nPMEnodes, simulation_tpr, args_for_mdrun);
+ sprintf(command, "%s%s%s -npme %d -s %s %s %s",
+ cmd_mpirun, cmd_np, cmd_mdrun, nPMEnodes, simulation_tpr, args_for_mdrun, cmd_gpu_ids);
}
fprintf(fp, "%s this command line to launch the simulation:\n\n%s", bLaunch ? "Using" : "Please use", command);
{
/* Determine which Coulomb radii rc to use in the benchmarks */
add = (rmax-rmin)/(*ntprs-1);
- if (is_equal(rmin, info->rcoulomb[0]))
+ if (gmx_within_tol(rmin, info->rcoulomb[0], GMX_REAL_EPS))
{
ir->rcoulomb = rmin + j*add;
}
- else if (is_equal(rmax, info->rcoulomb[0]))
+ else if (gmx_within_tol(rmax, info->rcoulomb[0], GMX_REAL_EPS))
{
ir->rcoulomb = rmin + (j-1)*add;
}
fprintf(fp, " %-14s\n", fn_bench_tprs[j]);
/* Make it clear to the user that some additional settings were modified */
- if (!is_equal(ir->rvdw, info->rvdw[0])
- || !is_equal(ir->rlistlong, info->rlistlong[0]) )
+ if (!gmx_within_tol(ir->rvdw, info->rvdw[0], GMX_REAL_EPS)
+ || !gmx_within_tol(ir->rlistlong, info->rlistlong[0], GMX_REAL_EPS) )
{
bNote = TRUE;
}
sfree(msg );
}
-
static void do_the_tests(
- FILE *fp, /* General g_tune_pme output file */
- char **tpr_names, /* Filenames of the input files to test */
- int maxPMEnodes, /* Max fraction of nodes to use for PME */
- int minPMEnodes, /* Min fraction of nodes to use for PME */
- int npme_fixed, /* If >= -1, test fixed number of PME
- * nodes only */
- const char *npmevalues_opt, /* Which -npme values should be tested */
- t_perf **perfdata, /* Here the performance data is stored */
- int *pmeentries, /* Entries in the nPMEnodes list */
- int repeats, /* Repeat each test this often */
- int nnodes, /* Total number of nodes = nPP + nPME */
- int nr_tprs, /* Total number of tpr files to test */
- gmx_bool bThreads, /* Threads or MPI? */
- char *cmd_mpirun, /* mpirun command string */
- char *cmd_np, /* "-np", "-n", whatever mpirun needs */
- char *cmd_mdrun, /* mdrun command string */
- char *cmd_args_bench, /* arguments for mdrun in a string */
- const t_filenm *fnm, /* List of filenames from command line */
- int nfile, /* Number of files specified on the cmdl. */
- int presteps, /* DLB equilibration steps, is checked */
- gmx_int64_t cpt_steps, /* Time step counter in the checkpoint */
- gmx_bool bCheck) /* Check whether benchmark mdrun works */
+ FILE *fp, /* General g_tune_pme output file */
+ char **tpr_names, /* Filenames of the input files to test */
+ int maxPMEnodes, /* Max fraction of nodes to use for PME */
+ int minPMEnodes, /* Min fraction of nodes to use for PME */
+ int npme_fixed, /* If >= -1, test fixed number of PME
+ * nodes only */
+ const char *npmevalues_opt, /* Which -npme values should be tested */
+ t_perf **perfdata, /* Here the performace data is stored */
+ int *pmeentries, /* Entries in the nPMEnodes list */
+ int repeats, /* Repeat each test this often */
+ int nnodes, /* Total number of nodes = nPP + nPME */
+ int nr_tprs, /* Total number of tpr files to test */
+ gmx_bool bThreads, /* Threads or MPI? */
+ char *cmd_mpirun, /* mpirun command string */
+ char *cmd_np, /* "-np", "-n", whatever mpirun needs */
+ char *cmd_mdrun, /* mdrun command string */
+ char *cmd_args_bench, /* arguments for mdrun in a string */
+ const t_filenm *fnm, /* List of filenames from command line */
+ int nfile, /* Number of files specified on the cmdl. */
+ int presteps, /* DLB equilibration steps, is checked */
+ gmx_int64_t cpt_steps, /* Time step counter in the checkpoint */
+ gmx_bool bCheck, /* Check whether benchmark mdrun works */
+ const t_eligible_gpu_ids *gpu_ids) /* Struct containing GPU IDs for
+ * constructing mdrun command lines */
{
int i, nr, k, ret, count = 0, totaltests;
int *nPMEnodes = NULL;
char buf[STRLEN];
gmx_bool bResetProblem = FALSE;
gmx_bool bFirst = TRUE;
-
+ gmx_bool bUsingGpus = 0 < gpu_ids->n;
/* This string array corresponds to the eParselog enum type at the start
* of this file */
"TPX version conflict!",
"mdrun was not started in parallel!",
"Number of PP ranks has a prime factor that is too large.",
+ "The number of PP ranks did not suit the number of GPUs.",
+ "Some GPUs were not detected or are incompatible.",
"An error occured."
};
char str_PME_f_load[13];
/* Loop over various numbers of PME nodes: */
for (i = 0; i < *pmeentries; i++)
{
+ char *cmd_gpu_ids = NULL;
+
pd = &perfdata[k][i];
+ cmd_gpu_ids = make_gpu_id_command_line(nnodes, nPMEnodes[i], gpu_ids);
+
/* Loop over the repeats for each scenario: */
for (nr = 0; nr < repeats; nr++)
{
* the -passall (if set) options requires cmd_args_bench to be
* at the end of the command line string */
snew(pd->mdrun_cmd_line, cmdline_length);
- sprintf(pd->mdrun_cmd_line, "%s-npme %d -s %s %s",
- cmd_stub, pd->nPMEnodes, tpr_names[k], cmd_args_bench);
+ sprintf(pd->mdrun_cmd_line, "%s-npme %d -s %s %s %s",
+ cmd_stub, pd->nPMEnodes, tpr_names[k], cmd_args_bench, cmd_gpu_ids);
/* To prevent that all benchmarks fail due to a show-stopper argument
* on the mdrun command line, we make a quick check first.
* decomposition can be found (e.g. for large prime numbers) */
if (bFirst && bCheck)
{
- make_sure_it_runs(pd->mdrun_cmd_line, cmdline_length, fp, fnm, nfile);
+ /* TODO This check is really for a functional
+ * .tpr, and if we need it, it should take place
+ * for every .tpr, and the logic for it should be
+ * immediately inside the loop over k, not in
+ * this inner loop. */
+ char *temporary_cmd_line;
+
+ snew(temporary_cmd_line, cmdline_length);
+ /* TODO -npme 0 is more likely to succeed at low
+ parallelism than the default of -npme -1, but
+ is more likely to fail at the scaling limit
+ when the PP domains may be too small. "mpirun
+ -np 1 mdrun" is probably a reasonable thing to
+ do for this check, but it'll be easier to
+ implement that after some refactoring of how
+ the number of MPI ranks is managed. */
+ sprintf(temporary_cmd_line, "%s-npme 0 -nb cpu -s %s %s",
+ cmd_stub, tpr_names[k], cmd_args_bench);
+ make_sure_it_runs(temporary_cmd_line, cmdline_length, fp, fnm, nfile);
}
bFirst = FALSE;
break;
}
} /* end of repeats loop */
+ sfree(cmd_gpu_ids);
} /* end of -npme loop */
} /* end of tpr file loop */
/* Add test scenarios if rmin or rmax were set */
if (*ntprs <= 2)
{
- if (!is_equal(*rmin, rcoulomb) && (*ntprs == 1) )
+ if (!gmx_within_tol(*rmin, rcoulomb, GMX_REAL_EPS) && (*ntprs == 1) )
{
(*ntprs)++;
fprintf(stderr, "NOTE: Setting -rmin to %g changed -ntpr to %d\n",
*rmin, *ntprs);
}
- if (!is_equal(*rmax, rcoulomb) && (*ntprs == 1) )
+ if (!gmx_within_tol(*rmax, rcoulomb, GMX_REAL_EPS) && (*ntprs == 1) )
{
(*ntprs)++;
fprintf(stderr, "NOTE: Setting -rmax to %g changed -ntpr to %d\n",
}
old = *ntprs;
/* If one of rmin, rmax is set, we need 2 tpr files at minimum */
- if (!is_equal(*rmax, rcoulomb) || !is_equal(*rmin, rcoulomb) )
+ if (!gmx_within_tol(*rmax, rcoulomb, GMX_REAL_EPS) || !gmx_within_tol(*rmin, rcoulomb, GMX_REAL_EPS) )
{
*ntprs = max(*ntprs, 2);
}
/* If both rmin, rmax are set, we need 3 tpr files at minimum */
- if (!is_equal(*rmax, rcoulomb) && !is_equal(*rmin, rcoulomb) )
+ if (!gmx_within_tol(*rmax, rcoulomb, GMX_REAL_EPS) && !gmx_within_tol(*rmin, rcoulomb, GMX_REAL_EPS) )
{
*ntprs = max(*ntprs, 3);
}
if (*ntprs > 1)
{
- if (is_equal(*rmin, rcoulomb) && is_equal(rcoulomb, *rmax)) /* We have just a single rc */
+ if (gmx_within_tol(*rmin, rcoulomb, GMX_REAL_EPS) && gmx_within_tol(rcoulomb, *rmax, GMX_REAL_EPS)) /* We have just a single rc */
{
fprintf(stderr, "WARNING: Resetting -ntpr to 1 since no Coulomb radius scaling is requested.\n"
"Please set rmin < rmax to test Coulomb radii in the [rmin, rmax] interval\n"
"(options [TT]-b[tt]*), these will be automatically deleted after each test.[PAR]",
"If you want the simulation to be started automatically with the",
"optimized parameters, use the command line option [TT]-launch[tt].[PAR]",
+ "Basic support for GPU-enabled [TT]mdrun[tt] exists. Give a string containing the IDs",
+ "of the GPUs that you wish to use in the optimization in the [TT]-gpu_id[tt]",
+ "command-line argument. Unlike [TT]mdrun -gpu_id[tt], this does not imply a mapping",
+ "but merely the eligible set. [TT]g_tune_pme[tt] will construct calls to",
+ "mdrun that use this set appropriately, assuming that PP ranks with low indices",
+ "should map to GPUs with low indices, and increasing both monotonically",
+ "over the respective sets.[PAR]",
};
int nnodes = 1;
int sim_part = 1; /* For benchmarks with checkpoint files */
char bbuf[STRLEN];
+
/* Default program names if nothing else is found */
- char *cmd_mpirun = NULL, *cmd_mdrun = NULL;
- char *cmd_args_bench, *cmd_args_launch;
- char *cmd_np = NULL;
+ char *cmd_mpirun = NULL, *cmd_mdrun = NULL;
+ char *cmd_args_bench, *cmd_args_launch;
+ char *cmd_np = NULL;
+
+ /* IDs of GPUs that are eligible for computation */
+ char *eligible_gpu_ids = NULL;
+ t_eligible_gpu_ids *gpu_ids = NULL;
- t_perf **perfdata = NULL;
- t_inputinfo *info;
- int i;
- FILE *fp;
- t_commrec *cr;
+ t_perf **perfdata = NULL;
+ t_inputinfo *info;
+ int i;
+ FILE *fp;
+ t_commrec *cr;
/* Print out how long the tuning took */
double seconds;
/* g_tune_pme */
{ efOUT, "-p", "perf", ffWRITE },
{ efLOG, "-err", "bencherr", ffWRITE },
- { efTPX, "-so", "tuned", ffWRITE },
+ { efTPR, "-so", "tuned", ffWRITE },
/* mdrun: */
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efTRN, "-o", NULL, ffWRITE },
{ efCOMPRESSED, "-x", NULL, ffOPTWR },
{ efCPT, "-cpi", NULL, ffOPTRD },
"Run the benchmarks or just create the input [TT].tpr[tt] files?" },
{ "-check", FALSE, etBOOL, {&bCheck},
"Before the benchmark runs, check whether mdrun works in parallel" },
+ { "-gpu_id", FALSE, etSTR, {&eligible_gpu_ids},
+ "List of GPU device id-s that are eligible for use (unlike mdrun, does not imply any mapping)" },
/******************/
/* mdrun options: */
/******************/
maxPMEfraction, minPMEfraction, npme_fixed,
bench_nsteps, fnm, NFILE, sim_part, presteps,
asize(pa), pa);
+ /* Check any GPU IDs passed make sense, and fill the data structure for them */
+ snew(gpu_ids, 1);
+ parse_digits_from_plain_string(eligible_gpu_ids, &gpu_ids->n, &gpu_ids->ids);
/* Determine the maximum and minimum number of PME nodes to test,
* the actual list of settings is build in do_the_tests(). */
get_program_paths(bThreads, &cmd_mpirun, &cmd_mdrun);
if (bBenchmark && repeats > 0)
{
- check_mdrun_works(bThreads, cmd_mpirun, cmd_np, cmd_mdrun);
+ check_mdrun_works(bThreads, cmd_mpirun, cmd_np, cmd_mdrun, NULL != eligible_gpu_ids);
}
/* Print some header info to file */
sep_line(fp);
fprintf(fp, "\n P E R F O R M A N C E R E S U L T S\n");
sep_line(fp);
- fprintf(fp, "%s for Gromacs %s\n", ShortProgram(), GromacsVersion());
+ fprintf(fp, "%s for Gromacs %s\n", output_env_get_program_display_name(oenv),
+ gmx_version());
if (!bThreads)
{
fprintf(fp, "Number of ranks : %d\n", nnodes);
{
do_the_tests(fp, tpr_names, maxPMEnodes, minPMEnodes, npme_fixed, npmevalues_opt[0], perfdata, &pmeentries,
repeats, nnodes, ntprs, bThreads, cmd_mpirun, cmd_np, cmd_mdrun,
- cmd_args_bench, fnm, NFILE, presteps, cpt_steps, bCheck);
+ cmd_args_bench, fnm, NFILE, presteps, cpt_steps, bCheck, gpu_ids);
fprintf(fp, "\nTuning took%8.1f minutes.\n", (gmx_gettime()-seconds)/60.0);
/* Now start the real simulation if the user requested it ... */
launch_simulation(bLaunch, fp, bThreads, cmd_mpirun, cmd_np, cmd_mdrun,
- cmd_args_launch, simulation_tpr, best_npme);
+ cmd_args_launch, simulation_tpr, nnodes, best_npme, gpu_ids);
}
gmx_ffclose(fp);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include <assert.h>
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/fileio/futil.h"
-#include "index.h"
-#include "typedefs.h"
-#include "xvgr.h"
-#include "gstat.h"
+#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "vec.h"
-#include "gromacs/fileio/matio.h"
-#include "gmx_ana.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
int gmx_vanhove(int argc, char *argv[])
FILE *fp;
t_rgb rlo = {1, 1, 1}, rhi = {0, 0, 0};
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
srenew(sbox, nalloc);
srenew(sx, nalloc);
}
+ assert(time != NULL); assert(sbox != NULL);
time[nfr] = t;
copy_mat(box, sbox[nfr]);
for (fbin = 0; fbin < nr; fbin++)
{
sprintf(buf, "%g ps", (fbin + 1)*fshift*dt);
- legend[fbin] = strdup(buf);
+ legend[fbin] = gmx_strdup(buf);
}
xvgr_legend(fp, nr, (const char**)legend, oenv);
for (i = 0; i < nalloc; i++)
}
fprintf(fp, "\n");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
if (otfile)
{
fprintf(fp, "%g %g\n", f*dt, (real)pt[f]/(tcount[f]*isize));
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
do_view(oenv, matfile, NULL);
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <stdio.h>
+#include "gmxpre.h"
+
#include <math.h>
+#include <stdio.h>
+#include <string.h>
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/correlationfunctions/autocorr.h"
+#include "gromacs/fft/fft.h"
#include "gromacs/fileio/confio.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
-#include "gstat.h"
-#include "macros.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
-#include "physics.h"
-#include "index.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/commandline/pargs.h"
-#include <string.h>
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "xvgr.h"
#include "gmx_ana.h"
-#include "gromacs/fft/fft.h"
-#include "gromacs/fileio/trxio.h"
static void index_atom2mol(int *n, atom_id *index, t_block *mols)
{
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Jochen Hub <jhub@gwdg.de>
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <ctype.h>
#include <stdio.h>
#include <sstream>
#include "gromacs/commandline/pargs.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "copyrite.h"
#include "gromacs/fileio/tpxio.h"
-#include "names.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
-#include "gmx_ana.h"
-#include "macros.h"
#include "gromacs/utility/cstringutil.h"
-#include "xvgr.h"
-
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
//! longest file names allowed in input files
#define WHAM_MAXFILELEN 2048
fprintf(fp, "\n");
}
printf("Wrote cumulative distribution functions to %s\n", fn);
- gmx_ffclose(fp);
+ xvgrclose(fp);
sfree(fn);
sfree(buf);
}
fprintf(fp, "\n");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
printf("Wrote %s\n", fn);
if (bs_index >= 0)
{
}
fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(opt->oenv) ? "&" : "");
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
/* write average and stddev */
fp = xvgropen(fnres, "Average and stddev from bootstrapping", xlabel, ylabel, opt->oenv);
stddev = (tmp >= 0.) ? sqrt(tmp) : 0.; /* Catch rouding errors */
fprintf(fp, "%e\t%e\t%e\n", (i+0.5)*opt->dz+opt->min, bsProfiles_av [i], stddev);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
printf("Wrote boot strap result to %s\n", fnres);
}
printf(" done\n");
if (fpcorr)
{
- gmx_ffclose(fpcorr);
+ xvgrclose(fpcorr);
}
/* plot IACT along reaction coordinate */
}
}
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
printf("Wrote %s\n", fn);
}
{
fprintf(fp, "%g %g\n", (j+0.5)*dz+opt->min, pot[j]);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
printf("verbose mode: wrote %s with PMF from interated forces\n", "pmfintegrated.xvg");
}
opt.stepchange = 100;
opt.stepUpdateContrib = 100;
- if (!parse_common_args(&argc, argv, PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, 0,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &opt.oenv))
{
return 0;
}
fprintf(histout, "\n");
}
- gmx_ffclose(histout);
+ xvgrclose(histout);
printf("Wrote %s\n", opt2fn("-hist", NFILE, fnm));
if (opt.bHistOnly)
{
{
fprintf(profout, "%e\t%e\n", (double)(i+0.5)/opt.bins*(opt.max-opt.min)+opt.min, profile[i]);
}
- gmx_ffclose(profout);
+ xvgrclose(profout);
printf("Wrote %s\n", opt2fn("-o", NFILE, fnm));
/* Bootstrap Method */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
-#include "physics.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "pbc.h"
-#include "index.h"
-#include "gstat.h"
-#include "gmx_fatal.h"
-#include "gmx_ana.h"
-
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/strdb.h"
#include "gromacs/fileio/writeps.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static gmx_bool *bPhobics(int nres, char *resnm[])
{
int i, nres;
char **resnm;
- if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
else if (strcmp(argv[i], "-T") == 0)
{
- title = strdup(argv[++i]);
+ title = gmx_strdup(argv[++i]);
fprintf(stderr, "Title will be '%s'\n", title);
}
else if (strcmp(argv[i], "-nn") == 0)
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include <math.h>
#include <stdio.h>
#include <stdlib.h>
-#include <math.h>
-#include "typedefs.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "gromacs/utility/smalloc.h"
-#include "viewit.h"
-#include "gmx_ana.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/writeps.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define FUDGE 1.2
#define DDD 2
for (j = 0; (j < ntx); j++)
{
sprintf(buf, "%g", mat[i].axis_x[j]);
- xtick[j] = strdup(buf);
+ xtick[j] = gmx_strdup(buf);
}
ps_strfont(ps, psr->X.tickfont, psr->X.tickfontsize);
for (x = 0; (x < ntx); x++)
for (j = 0; (j < nty); j++)
{
sprintf(buf, "%g", mat[i].axis_y[j]);
- ytick[j] = strdup(buf);
+ ytick[j] = gmx_strdup(buf);
}
for (y = 0; (y < nty); y++)
sfree(mat[i].map);
mat[i].nmap = nmap;
mat[i].map = map;
- if (mat2 && (strcmp(mat[i].title, mat2[i].title) != 0))
+ if (strcmp(mat[i].title, mat2[i].title) != 0)
{
sprintf(mat[i].title+strlen(mat[i].title), " / %s", mat2[i].title);
}
- if (mat2 && (strcmp(mat[i].legend, mat2[i].legend) != 0))
+ if (strcmp(mat[i].legend, mat2[i].legend) != 0)
{
sprintf(mat[i].legend+strlen(mat[i].legend), " / %s", mat2[i].legend);
}
#ifndef GMX_GMXANA_GSTAT_H
#define GMX_GMXANA_GSTAT_H
-#include "../legacyheaders/typedefs.h"
-#include "../commandline/pargs.h"
-#include "../legacyheaders/oenv.h"
-#include "../legacyheaders/mshift.h"
-#include "../legacyheaders/rmpbc.h"
-#include "../legacyheaders/index.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/topology/index.h"
#ifdef __cplusplus
extern "C" {
#endif
-/***********************************************
- *
- * A U T O C O R R E L A T I O N
- *
- ***********************************************/
-
-real LegendreP(real x, unsigned long m);
-
-#define eacNormal (1<<0)
-#define eacCos (1<<1)
-#define eacVector (1<<2)
-#define eacRcross (1<<3 | eacVector)
-#define eacP0 (1<<4 | eacVector)
-#define eacP1 (1<<5 | eacVector)
-#define eacP2 (1<<6 | eacVector)
-#define eacP3 (1<<7 | eacVector)
-#define eacP4 (1<<8 | eacVector)
-#define eacIden (1<<9)
-
-enum {
- effnNONE, effnEXP1, effnEXP2, effnEXP3, effnVAC,
- effnEXP5, effnEXP7, effnEXP9, effnERF, effnERREST, effnNR
-};
+struct gmx_residuetype_t;
/* must correspond with 'leg' g_chi.c:727 */
enum {
} t_dlist;
-extern const int nfp_ffn[effnNR];
-
-extern const char *s_ffn[effnNR+2];
-
-extern const char *longs_ffn[effnNR];
-
-int sffn2effn(const char **sffn);
-/* Returns the ffn enum corresponding to the selected enum option in sffn */
-
-t_pargs *add_acf_pargs(int *npargs, t_pargs *pa);
-/* Add options for autocorr to the current set of options.
- * *npargs must be initialised to the number of elements in pa,
- * it will be incremented appropriately.
- */
-
-void cross_corr(int n, real f[], real g[], real corr[]);
-/* Simple minded cross correlation algorithm */
-
-real fit_acf(int ncorr, int fitfn, const output_env_t oenv, gmx_bool bVerbose,
- real tbeginfit, real tendfit, real dt, real c1[], real *fit);
-/* Fit an ACF to a given function */
-
-void do_autocorr(const char *fn, const output_env_t oenv,
- const char *title,
- int nframes, int nitem, real **c1,
- real dt, unsigned long mode, gmx_bool bAver);
-/* Calls low_do_autocorr (see below). After calling add_acf_pargs */
-
-void low_do_autocorr(const char *fn, const output_env_t oenv,
- const char *title, int nframes, int nitem,
- int nout, real **c1, real dt, unsigned long mode,
- int nrestart, gmx_bool bAver, gmx_bool bNormalize,
- gmx_bool bVerbose, real tbeginfit, real tendfit,
- int nfitparm);
-/*
- * do_autocorr calculates autocorrelation functions for many things.
- * It takes a 2 d array containing nitem arrays of length nframes
- * for each item the ACF is calculated.
- *
- * A number of "modes" exist for computation of the ACF
- *
- * if (mode == eacNormal) {
- * C(t) = < X (tau) * X (tau+t) >
- * }
- * else if (mode == eacCos) {
- * C(t) = < cos (X(tau) - X(tau+t)) >
- * }
- * else if (mode == eacIden) { **not fully supported yet**
- * C(t) = < (X(tau) == X(tau+t)) >
- * }
- * else if (mode == eacVector) {
- * C(t) = < X(tau) * X(tau+t)
- * }
- * else if (mode == eacP1) {
- * C(t) = < cos (X(tau) * X(tau+t) >
- * }
- * else if (mode == eacP2) {
- * C(t) = 1/2 * < 3 cos (X(tau) * X(tau+t) - 1 >
- * }
- * else if (mode == eacRcross) {
- * C(t) = < ( X(tau) * X(tau+t) )^2 >
- * }
- *
- * For modes eacVector, eacP1, eacP2 and eacRcross the input should be
- * 3 x nframes long, where each triplet is taken as a 3D vector
- *
- * For mode eacCos inputdata must be in radians, not degrees!
- *
- * Other parameters are:
- *
- * fn is output filename (.xvg) where the correlation function(s) are printed
- * title is the title in the output file
- * nframes is the number of frames in the time series
- * nitem is the number of items
- * c1 is an array of dimension [ 0 .. nitem-1 ] [ 0 .. nframes-1 ]
- * on output, this array is filled with the correlation function
- * to reduce storage
- * nrestart is the number of steps between restarts for direct ACFs
- * (i.e. without FFT) When set to 1 all points are used as
- * time origin for averaging
- * dt is the time between frames
- * bAver If set, all ndih C(t) functions are averaged into a single
- * C(t)
- * (bFour If set, will use fast fourier transform (FFT) for evaluating
- * the ACF: removed option, now on the command line only)
- * bNormalize If set, all ACFs will be normalized to start at 0
- * nskip Determines whether steps a re skipped in the output
- */
-
typedef struct {
const char *name; /* Description of the J coupling constant */
real A, B, C; /* Karplus coefficients */
*
*/
-
-/***********************************************
- *
- * F I T R O U T I N E S
- *
- ***********************************************/
-void do_expfit(int ndata, real c1[], real dt,
- real begintimefit, real endtimefit);
-
-void expfit(int n, real x[], real y[], real Dy[],
- real *a, real *sa,
- real *b, real *sb);
-/* This procedure fits y=exp(a+bx) for n (x,y) pairs to determine a and b.
- * The uncertainties in the y values must be in the vector Dy.
- * The standard deviations of a and b, sa and sb, are also calculated.
- *
- * Routine from Computers in physics, 7(3) (1993), p. 280-285.
- */
-
void ana_dih_trans(const char *fn_trans, const char *fn_histo,
real **dih, int nframes, int nangles,
const char *grpname, real *time, gmx_bool bRb,
* Read a trajectory and calculate angles and dihedrals.
*
* trj_fn file name of trajectory
- * tpb_fn file name of tpb file
* bAngles do we have to read angles or dihedrals
* bSaveAll do we have to store all in the dih array
* bRb do we have Ryckaert-Bellemans dihedrals (trans = 0)
* normhisto normalized output histogram
*/
-real fit_function(int eFitFn, real *parm, real x);
-/* Returns the value of fit function eFitFn at x */
-
-/* Use Levenberg-Marquardt method to fit to a nfitparm parameter exponential */
-/* or to a transverse current autocorrelation function */
-/* Or: "There is no KILL like OVERKILL", Dr. Ir. D. van der Spoel */
-real do_lmfit(int ndata, real c1[], real sig[], real dt, real *x,
- real begintimefit, real endtimefit, const output_env_t oenv,
- gmx_bool bVerbose, int eFitFn, real fitparms[], int fix);
-/* Returns integral.
- * If x == NULL, the timestep dt will be used to create a time axis.
- * fix fixes fit parameter i at it's starting value, when the i'th bit
- * of fix is set.
- */
-
-real evaluate_integral(int n, real x[], real y[], real dy[],
- real aver_start, real *stddev);
-/* Integrate data in y, and, if given, use dy as weighting
- * aver_start should be set to a value where the function has
- * converged to 0.
- */
-
-real print_and_integrate(FILE *fp, int n, real dt,
- real c[], real *fit, int nskip);
-/* Integrate the data in c[] from 0 to n using trapezium rule.
- * If fp != NULL output is written to it
- * nskip determines whether all elements are written to the output file
- * (written when i % nskip == 0)
- * If fit != NULL the fit is also written.
- */
-
-int get_acfnout(void);
-/* Return the output length for the correlation function
- * Works only AFTER do_auto_corr has been called!
- */
-
-int get_acffitfn(void);
-/* Return the fit function type.
- * Works only AFTER do_auto_corr has been called!
- */
-
/* Routines from pp2shift (anadih.c etc.) */
void do_pp2shifts(FILE *fp, int nframes,
t_dlist *mk_dlist(FILE *log,
t_atoms *atoms, int *nlist,
gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bHChi,
- int maxchi, int r0, gmx_residuetype_t rt);
+ int maxchi, int r0, struct gmx_residuetype_t *rt);
void pr_dlist(FILE *fp, int nl, t_dlist dl[], real dt, int printtype,
gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bOmega, int maxchi);
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "hxprops.h"
#include <math.h>
#include <string.h>
-#include "typedefs.h"
-#include "macros.h"
-#include "physics.h"
-#include "vec.h"
-#include "index.h"
-#include "hxprops.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "bondf.h"
-
-#include "gmx_fatal.h"
real ellipticity(int nres, t_bb bb[])
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define _hxprops_h
#include <stdio.h>
-#include "typedefs.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
#define PHI_AHX (-55.0)
#define PSI_AHX (-45.0)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _interf_h
#define _interf_h
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
typedef struct {
real Z; /* Interface height-coordinate */
* \author Mark Abraham <mark.j.abraham@gmail.com>
*/
+#include "gmxpre.h"
+
+#include "config.h"
+
#include "gromacs/gmxana/gmx_ana.h"
-#include "testutils/integrationtests.h"
-#include "testutils/cmdlinetest.h"
#include "gromacs/utility/arrayref.h"
-#include "config.h"
+#include "testutils/cmdlinetest.h"
+#include "testutils/integrationtests.h"
namespace
{
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-
-#include "types/simple.h"
-
-static void nrerror(const char error_text[], gmx_bool bExit)
-{
- fprintf(stderr, "Numerical Recipes run-time error...\n");
- fprintf(stderr, "%s\n", error_text);
- if (bExit)
- {
- fprintf(stderr, "...now exiting to system...\n");
- exit(1);
- }
-}
-
-/* dont use the keyword vector - it will clash with the
- * altivec extensions used for powerpc processors.
- */
-
-static real *rvector(int nl, int nh)
-{
- real *v;
-
- v = (real *)malloc((unsigned) (nh-nl+1)*sizeof(real));
- if (!v)
- {
- nrerror("allocation failure in rvector()", TRUE);
- }
- return v-nl;
-}
-
-static int *ivector(int nl, int nh)
-{
- int *v;
-
- v = (int *)malloc((unsigned) (nh-nl+1)*sizeof(int));
- if (!v)
- {
- nrerror("allocation failure in ivector()", TRUE);
- }
- return v-nl;
-}
-
-
-static real **matrix1(int nrl, int nrh, int ncl, int nch)
-{
- int i;
- real **m;
-
- m = (real **) malloc((unsigned) (nrh-nrl+1)*sizeof(real*));
- if (!m)
- {
- nrerror("allocation failure 1 in matrix1()", TRUE);
- }
- m -= nrl;
-
- for (i = nrl; i <= nrh; i++)
- {
- m[i] = (real *) malloc((unsigned) (nch-ncl+1)*sizeof(real));
- if (!m[i])
- {
- nrerror("allocation failure 2 in matrix1()", TRUE);
- }
- m[i] -= ncl;
- }
- return m;
-}
-
-static double **dmatrix(int nrl, int nrh, int ncl, int nch)
-{
- int i;
- double **m;
-
- m = (double **) malloc((unsigned) (nrh-nrl+1)*sizeof(double*));
- if (!m)
- {
- nrerror("allocation failure 1 in dmatrix()", TRUE);
- }
- m -= nrl;
-
- for (i = nrl; i <= nrh; i++)
- {
- m[i] = (double *) malloc((unsigned) (nch-ncl+1)*sizeof(double));
- if (!m[i])
- {
- nrerror("allocation failure 2 in dmatrix()", TRUE);
- }
- m[i] -= ncl;
- }
- return m;
-}
-
-static int **imatrix1(int nrl, int nrh, int ncl, int nch)
-{
- int i, **m;
-
- m = (int **)malloc((unsigned) (nrh-nrl+1)*sizeof(int*));
- if (!m)
- {
- nrerror("allocation failure 1 in imatrix1()", TRUE);
- }
- m -= nrl;
-
- for (i = nrl; i <= nrh; i++)
- {
- m[i] = (int *)malloc((unsigned) (nch-ncl+1)*sizeof(int));
- if (!m[i])
- {
- nrerror("allocation failure 2 in imatrix1()", TRUE);
- }
- m[i] -= ncl;
- }
- return m;
-}
-
-
-
-static real **submatrix(real **a, int oldrl, int oldrh, int oldcl,
- int newrl, int newcl)
-{
- int i, j;
- real **m;
-
- m = (real **) malloc((unsigned) (oldrh-oldrl+1)*sizeof(real*));
- if (!m)
- {
- nrerror("allocation failure in submatrix()", TRUE);
- }
- m -= newrl;
-
- for (i = oldrl, j = newrl; i <= oldrh; i++, j++)
- {
- m[j] = a[i]+oldcl-newcl;
- }
-
- return m;
-}
-
-
-
-static void free_vector(real *v, int nl)
-{
- free((char*) (v+nl));
-}
-
-static void free_ivector(int *v, int nl)
-{
- free((char*) (v+nl));
-}
-
-static void free_dvector(int *v, int nl)
-{
- free((char*) (v+nl));
-}
-
-
-
-static void free_matrix(real **m, int nrl, int nrh, int ncl)
-{
- int i;
-
- for (i = nrh; i >= nrl; i--)
- {
- free((char*) (m[i]+ncl));
- }
- free((char*) (m+nrl));
-}
-
-static real **convert_matrix(real *a, int nrl, int nrh, int ncl, int nch)
-{
- int i, j, nrow, ncol;
- real **m;
-
- nrow = nrh-nrl+1;
- ncol = nch-ncl+1;
- m = (real **) malloc((unsigned) (nrow)*sizeof(real*));
- if (!m)
- {
- nrerror("allocation failure in convert_matrix()", TRUE);
- }
- m -= nrl;
- for (i = 0, j = nrl; i <= nrow-1; i++, j++)
- {
- m[j] = a+ncol*i-ncl;
- }
- return m;
-}
-
-
-
-static void free_convert_matrix(real **b, int nrl)
-{
- free((char*) (b+nrl));
-}
-
-#define SWAP(a, b) {real temp = (a); (a) = (b); (b) = temp; }
-
-static void dump_mat(int n, real **a)
-{
- int i, j;
-
- for (i = 1; (i <= n); i++)
- {
- for (j = 1; (j <= n); j++)
- {
- fprintf(stderr, " %10.3f", a[i][j]);
- }
- fprintf(stderr, "\n");
- }
-}
-
-gmx_bool gaussj(real **a, int n, real **b, int m)
-{
- int *indxc, *indxr, *ipiv;
- int i, icol = 0, irow = 0, j, k, l, ll;
- real big, dum, pivinv;
-
- indxc = ivector(1, n);
- indxr = ivector(1, n);
- ipiv = ivector(1, n);
- for (j = 1; j <= n; j++)
- {
- ipiv[j] = 0;
- }
- for (i = 1; i <= n; i++)
- {
- big = 0.0;
- for (j = 1; j <= n; j++)
- {
- if (ipiv[j] != 1)
- {
- for (k = 1; k <= n; k++)
- {
- if (ipiv[k] == 0)
- {
- if (fabs(a[j][k]) >= big)
- {
- big = fabs(a[j][k]);
- irow = j;
- icol = k;
- }
- }
- else if (ipiv[k] > 1)
- {
- nrerror("GAUSSJ: Singular Matrix-1", FALSE);
- return FALSE;
- }
- }
- }
- }
- ++(ipiv[icol]);
- if (irow != icol)
- {
- for (l = 1; l <= n; l++)
- {
- SWAP(a[irow][l], a[icol][l]);
- }
- for (l = 1; l <= m; l++)
- {
- SWAP(b[irow][l], b[icol][l]);
- }
- }
- indxr[i] = irow;
- indxc[i] = icol;
- if (a[icol][icol] == 0.0)
- {
- fprintf(stderr, "irow = %d, icol = %d\n", irow, icol);
- dump_mat(n, a);
- nrerror("GAUSSJ: Singular Matrix-2", FALSE);
- return FALSE;
- }
- pivinv = 1.0/a[icol][icol];
- a[icol][icol] = 1.0;
- for (l = 1; l <= n; l++)
- {
- a[icol][l] *= pivinv;
- }
- for (l = 1; l <= m; l++)
- {
- b[icol][l] *= pivinv;
- }
- for (ll = 1; ll <= n; ll++)
- {
- if (ll != icol)
- {
- dum = a[ll][icol];
- a[ll][icol] = 0.0;
- for (l = 1; l <= n; l++)
- {
- a[ll][l] -= a[icol][l]*dum;
- }
- for (l = 1; l <= m; l++)
- {
- b[ll][l] -= b[icol][l]*dum;
- }
- }
- }
- }
- for (l = n; l >= 1; l--)
- {
- if (indxr[l] != indxc[l])
- {
- for (k = 1; k <= n; k++)
- {
- SWAP(a[k][indxr[l]], a[k][indxc[l]]);
- }
- }
- }
- free_ivector(ipiv, 1);
- free_ivector(indxr, 1);
- free_ivector(indxc, 1);
-
- return TRUE;
-}
-
-#undef SWAP
-
-
-static void covsrt(real **covar, int ma, int lista[], int mfit)
-{
- int i, j;
- real swap;
-
- for (j = 1; j < ma; j++)
- {
- for (i = j+1; i <= ma; i++)
- {
- covar[i][j] = 0.0;
- }
- }
- for (i = 1; i < mfit; i++)
- {
- for (j = i+1; j <= mfit; j++)
- {
- if (lista[j] > lista[i])
- {
- covar[lista[j]][lista[i]] = covar[i][j];
- }
- else
- {
- covar[lista[i]][lista[j]] = covar[i][j];
- }
- }
- }
- swap = covar[1][1];
- for (j = 1; j <= ma; j++)
- {
- covar[1][j] = covar[j][j];
- covar[j][j] = 0.0;
- }
- covar[lista[1]][lista[1]] = swap;
- for (j = 2; j <= mfit; j++)
- {
- covar[lista[j]][lista[j]] = covar[1][j];
- }
- for (j = 2; j <= ma; j++)
- {
- for (i = 1; i <= j-1; i++)
- {
- covar[i][j] = covar[j][i];
- }
- }
-}
-
-#define SWAP(a, b) {swap = (a); (a) = (b); (b) = swap; }
-
-static void covsrt_new(real **covar, int ma, int ia[], int mfit)
-/* Expand in storage the covariance matrix covar, so as to take
- * into account parameters that are being held fixed. (For the
- * latter, return zero covariances.)
- */
-{
- int i, j, k;
- real swap;
- for (i = mfit+1; i <= ma; i++)
- {
- for (j = 1; j <= i; j++)
- {
- covar[i][j] = covar[j][i] = 0.0;
- }
- }
- k = mfit;
- for (j = ma; j >= 1; j--)
- {
- if (ia[j])
- {
- for (i = 1; i <= ma; i++)
- {
- SWAP(covar[i][k], covar[i][j]);
- }
- for (i = 1; i <= ma; i++)
- {
- SWAP(covar[k][i], covar[j][i]);
- }
- k--;
- }
- }
-}
-#undef SWAP
-
-static void mrqcof(real x[], real y[], real sig[], int ndata, real a[],
- int ma, int lista[], int mfit,
- real **alpha, real beta[], real *chisq,
- void (*funcs)(real, real *, real *, real *))
-{
- int k, j, i;
- real ymod, wt, sig2i, dy, *dyda;
-
- dyda = rvector(1, ma);
- for (j = 1; j <= mfit; j++)
- {
- for (k = 1; k <= j; k++)
- {
- alpha[j][k] = 0.0;
- }
- beta[j] = 0.0;
- }
- *chisq = 0.0;
- for (i = 1; i <= ndata; i++)
- {
- (*funcs)(x[i], a, &ymod, dyda);
- sig2i = 1.0/(sig[i]*sig[i]);
- dy = y[i]-ymod;
- for (j = 1; j <= mfit; j++)
- {
- wt = dyda[lista[j]]*sig2i;
- for (k = 1; k <= j; k++)
- {
- alpha[j][k] += wt*dyda[lista[k]];
- }
- beta[j] += dy*wt;
- }
- (*chisq) += dy*dy*sig2i;
- }
- for (j = 2; j <= mfit; j++)
- {
- for (k = 1; k <= j-1; k++)
- {
- alpha[k][j] = alpha[j][k];
- }
- }
- free_vector(dyda, 1);
-}
-
-
-gmx_bool mrqmin(real x[], real y[], real sig[], int ndata, real a[],
- int ma, int lista[], int mfit,
- real **covar, real **alpha, real *chisq,
- void (*funcs)(real, real *, real *, real *),
- real *alamda)
-{
- int k, kk, j, ihit;
- static real *da, *atry, **oneda, *beta, ochisq;
-
- if (*alamda < 0.0)
- {
- oneda = matrix1(1, mfit, 1, 1);
- atry = rvector(1, ma);
- da = rvector(1, ma);
- beta = rvector(1, ma);
- kk = mfit+1;
- for (j = 1; j <= ma; j++)
- {
- ihit = 0;
- for (k = 1; k <= mfit; k++)
- {
- if (lista[k] == j)
- {
- ihit++;
- }
- }
- if (ihit == 0)
- {
- lista[kk++] = j;
- }
- else if (ihit > 1)
- {
- nrerror("Bad LISTA permutation in MRQMIN-1", FALSE);
- return FALSE;
- }
- }
- if (kk != ma+1)
- {
- nrerror("Bad LISTA permutation in MRQMIN-2", FALSE);
- return FALSE;
- }
- *alamda = 0.001;
- mrqcof(x, y, sig, ndata, a, ma, lista, mfit, alpha, beta, chisq, funcs);
- ochisq = (*chisq);
- }
- for (j = 1; j <= mfit; j++)
- {
- for (k = 1; k <= mfit; k++)
- {
- covar[j][k] = alpha[j][k];
- }
- covar[j][j] = alpha[j][j]*(1.0+(*alamda));
- oneda[j][1] = beta[j];
- }
- if (!gaussj(covar, mfit, oneda, 1))
- {
- return FALSE;
- }
- for (j = 1; j <= mfit; j++)
- {
- da[j] = oneda[j][1];
- }
- if (*alamda == 0.0)
- {
- covsrt(covar, ma, lista, mfit);
- free_vector(beta, 1);
- free_vector(da, 1);
- free_vector(atry, 1);
- free_matrix(oneda, 1, mfit, 1);
- return TRUE;
- }
- for (j = 1; j <= ma; j++)
- {
- atry[j] = a[j];
- }
- for (j = 1; j <= mfit; j++)
- {
- atry[lista[j]] = a[lista[j]]+da[j];
- }
- mrqcof(x, y, sig, ndata, atry, ma, lista, mfit, covar, da, chisq, funcs);
- if (*chisq < ochisq)
- {
- *alamda *= 0.1;
- ochisq = (*chisq);
- for (j = 1; j <= mfit; j++)
- {
- for (k = 1; k <= mfit; k++)
- {
- alpha[j][k] = covar[j][k];
- }
- beta[j] = da[j];
- a[lista[j]] = atry[lista[j]];
- }
- }
- else
- {
- *alamda *= 10.0;
- *chisq = ochisq;
- }
- return TRUE;
-}
-
-
-gmx_bool mrqmin_new(real x[], real y[], real sig[], int ndata, real a[],
- int ia[], int ma, real **covar, real **alpha, real *chisq,
- void (*funcs)(real, real [], real *, real []),
- real *alamda)
-/* Levenberg-Marquardt method, attempting to reduce the value Chi^2
- * of a fit between a set of data points x[1..ndata], y[1..ndata]
- * with individual standard deviations sig[1..ndata], and a nonlinear
- * function dependent on ma coefficients a[1..ma]. The input array
- * ia[1..ma] indicates by nonzero entries those components of a that
- * should be fitted for, and by zero entries those components that
- * should be held fixed at their input values. The program returns
- * current best-fit values for the parameters a[1..ma], and
- * Chi^2 = chisq. The arrays covar[1..ma][1..ma], alpha[1..ma][1..ma]
- * are used as working space during most iterations. Supply a routine
- * funcs(x,a,yfit,dyda,ma) that evaluates the fitting function yfit,
- * and its derivatives dyda[1..ma] with respect to the fitting
- * parameters a at x. On the first call provide an initial guess for
- * the parameters a, and set alamda < 0 for initialization (which then
- * sets alamda=.001). If a step succeeds chisq becomes smaller and
- * alamda de-creases by a factor of 10. If a step fails alamda grows by
- * a factor of 10. You must call this routine repeatedly until
- * convergence is achieved. Then, make one final call with alamda=0,
- * so that covar[1..ma][1..ma] returns the covariance matrix, and alpha
- * the curvature matrix.
- * (Parameters held fixed will return zero covariances.)
- */
-{
- void covsrt(real **covar, int ma, int ia[], int mfit);
- gmx_bool gaussj(real **a, int n, real **b, int m);
- void mrqcof_new(real x[], real y[], real sig[], int ndata, real a[],
- int ia[], int ma, real **alpha, real beta[], real *chisq,
- void (*funcs)(real, real [], real *, real []));
- int j, k, l;
- static int mfit;
- static real ochisq, *atry, *beta, *da, **oneda;
-
- if (*alamda < 0.0) /* Initialization. */
- {
- atry = rvector(1, ma);
- beta = rvector(1, ma);
- da = rvector(1, ma);
- for (mfit = 0, j = 1; j <= ma; j++)
- {
- if (ia[j])
- {
- mfit++;
- }
- }
- oneda = matrix1(1, mfit, 1, 1);
- *alamda = 0.001;
- mrqcof_new(x, y, sig, ndata, a, ia, ma, alpha, beta, chisq, funcs);
- ochisq = (*chisq);
- for (j = 1; j <= ma; j++)
- {
- atry[j] = a[j];
- }
- }
- for (j = 1; j <= mfit; j++) /* Alter linearized fitting matrix, by augmenting. */
- {
- for (k = 1; k <= mfit; k++)
- {
- covar[j][k] = alpha[j][k]; /* diagonal elements. */
- }
- covar[j][j] = alpha[j][j]*(1.0+(*alamda));
- oneda[j][1] = beta[j];
- }
- if (!gaussj(covar, mfit, oneda, 1)) /* Matrix solution. */
- {
- return FALSE;
- }
- for (j = 1; j <= mfit; j++)
- {
- da[j] = oneda[j][1];
- }
- if (*alamda == 0.0) /* Once converged, evaluate covariance matrix. */
- {
- covsrt_new(covar, ma, ia, mfit);
- free_matrix(oneda, 1, mfit, 1);
- free_vector(da, 1);
- free_vector(beta, 1);
- free_vector(atry, 1);
- return TRUE;
- }
- for (j = 0, l = 1; l <= ma; l++) /* Did the trial succeed? */
- {
- if (ia[l])
- {
- atry[l] = a[l]+da[++j];
- }
- }
- mrqcof_new(x, y, sig, ndata, atry, ia, ma, covar, da, chisq, funcs);
- if (*chisq < ochisq)
- {
- /* Success, accept the new solution. */
- *alamda *= 0.1;
- ochisq = (*chisq);
- for (j = 1; j <= mfit; j++)
- {
- for (k = 1; k <= mfit; k++)
- {
- alpha[j][k] = covar[j][k];
- }
- beta[j] = da[j];
- }
- for (l = 1; l <= ma; l++)
- {
- a[l] = atry[l];
- }
- }
- else /* Failure, increase alamda and return. */
- {
- *alamda *= 10.0;
- *chisq = ochisq;
- }
- return TRUE;
-}
-
-void mrqcof_new(real x[], real y[], real sig[], int ndata, real a[],
- int ia[], int ma, real **alpha, real beta[], real *chisq,
- void (*funcs)(real, real [], real *, real[]))
-/* Used by mrqmin to evaluate the linearized fitting matrix alpha, and
- * vector beta as in (15.5.8), and calculate Chi^2.
- */
-{
- int i, j, k, l, m, mfit = 0;
- real ymod, wt, sig2i, dy, *dyda;
-
- dyda = rvector(1, ma);
- for (j = 1; j <= ma; j++)
- {
- if (ia[j])
- {
- mfit++;
- }
- }
- for (j = 1; j <= mfit; j++) /* Initialize (symmetric) alpha), beta. */
- {
- for (k = 1; k <= j; k++)
- {
- alpha[j][k] = 0.0;
- }
- beta[j] = 0.0;
- }
- *chisq = 0.0;
- for (i = 1; i <= ndata; i++) /* Summation loop over all data. */
- {
- (*funcs)(x[i], a, &ymod, dyda);
- sig2i = 1.0/(sig[i]*sig[i]);
- dy = y[i]-ymod;
- for (j = 0, l = 1; l <= ma; l++)
- {
- if (ia[l])
- {
- wt = dyda[l]*sig2i;
- for (j++, k = 0, m = 1; m <= l; m++)
- {
- if (ia[m])
- {
- alpha[j][++k] += wt*dyda[m];
- }
- }
- beta[j] += dy*wt;
- }
- }
- *chisq += dy*dy*sig2i; /* And find Chi^2. */
- }
- for (j = 2; j <= mfit; j++) /* Fill in the symmetric side. */
- {
- for (k = 1; k < j; k++)
- {
- alpha[k][j] = alpha[j][k];
- }
- }
- free_vector(dyda, 1);
-}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include "nrama.h"
+
#include <math.h>
-#include "sysstuff.h"
+#include <stdlib.h>
+
+#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "bondf.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
-#include "rmpbc.h"
static const char *pp_pat[] = { "C", "N", "CA", "C", "N" };
#define NPP (sizeof(pp_pat)/sizeof(pp_pat[0]))
xr->pp[xr->npp].bShow = FALSE;
sprintf(buf, "%s-%d", *atoms->resinfo[atoms->atom[ff[1]].resind].name,
atoms->resinfo[atoms->atom[ff[1]].resind].nr);
- xr->pp[xr->npp].label = strdup(buf);
+ xr->pp[xr->npp].label = gmx_strdup(buf);
xr->npp++;
}
#ifndef GMX_GMXANA_NRAMA_H
#define GMX_GMXANA_NRAMA_H
-#include "typedefs.h"
-#include "oenv.h"
-#include "mshift.h"
-#include "../fileio/trxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <string.h>
+#include "gmxpre.h"
-#include "gromacs/random/random.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "vec.h"
#include "nsfactor.h"
-#include "gromacs/fileio/futil.h"
+#include "config.h"
+
+#include <string.h>
+
#include "gromacs/fileio/strdb.h"
-#include "gmx_fatal.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/random/random.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
void check_binwidth(real binwidth)
{
i = line_no;
if (sscanf(line, "%s %d %d %lf", atomnm, &p, &n, &slength) == 4)
{
- gnsf->atomnm[i] = strdup(atomnm);
+ gnsf->atomnm[i] = gmx_strdup(atomnm);
gnsf->n[i] = n;
gnsf->p[i] = p;
gnsf->slength[i] = slength;
#ifndef _nsfactor_h
#define _nsfactor_h
-#include "index.h"
-#include "types/simple.h"
-#include "oenv.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_topology;
+
typedef struct gmx_neutron_atomic_structurefactors_t {
int nratoms;
int *p; /* proton number */
} gmx_neutron_atomic_structurefactors_t;
typedef struct gmx_sans_t {
- t_topology *top; /* topology */
- double *slength; /* scattering length for this topology */
+ struct t_topology *top; /* topology */
+ double *slength; /* scattering length for this topology */
} gmx_sans_t;
typedef struct gmx_radial_distribution_histogram_t {
gmx_neutron_atomic_structurefactors_t *gmx_neutronstructurefactors_init(const char *datfn);
-gmx_sans_t *gmx_sans_init(t_topology *top, gmx_neutron_atomic_structurefactors_t *gnsf);
+gmx_sans_t *gmx_sans_init(struct t_topology *top, gmx_neutron_atomic_structurefactors_t *gnsf);
gmx_radial_distribution_histogram_t *calc_radial_distribution_histogram (gmx_sans_t *gsans,
rvec *x,
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fft/fft.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
-#include "interf.h"
#include "powerspect.h"
+#include "gromacs/fft/fft.h"
+#include "gromacs/gmxana/interf.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
+
void addtoavgenergy(t_complex *list, real *result, int size, int tsteps)
{
int i;
/*Prepare data structures for FFT, with time averaging of power spectrum*/
if ( (status = gmx_fft_init_2d_real(&fftp, xbins, ybins, GMX_FFT_FLAG_NONE) ) != 0)
{
- free(fftp);
gmx_fatal(status, __FILE__, __LINE__, "Error allocating FFT");
}
gmx_ffclose(datfile1);
gmx_ffclose(datfile2);
- free(ftspect1);
- free(ftspect2);
+ sfree(ftspect1);
+ sfree(ftspect2);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _powerspect_h
#define _powerspect_h
-#include "typedefs.h"
-#include "interf.h"
+#include "gromacs/gmxana/interf.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C"
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <stdlib.h>
#include <math.h>
-#include "typedefs.h"
-#include "gromacs/fileio/futil.h"
-#include "macros.h"
-#include "physics.h"
-#include "gromacs/utility/smalloc.h"
-#include "gstat.h"
+#include <stdlib.h>
+
#include "gromacs/fileio/matio.h"
-#include "copyrite.h"
-#include "gmx_fatal.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
int nx, ny;
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "txtdump.h"
#include "princ.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
static void m_op(matrix mat, rvec x)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_GMXANA_PRINC_H
+#define GMX_GMXANA_PRINC_H
-#ifndef _princ_h
-#define _princ_h
-
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/math/utilities.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "macros.h"
-#include "index.h"
+#include "sfactor.h"
+
+#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/strdb.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "typedefs.h"
-#include "oenv.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "xvgr.h"
-#include "gromacs/fileio/matio.h"
-#include "names.h"
-#include "sfactor.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
typedef struct gmx_structurefactors {
t_complex ***t;
int i, j;
- t = (t_complex ***)calloc(x, sizeof(t_complex**));
- if (!t)
- {
- exit(fprintf(stderr, "\nallocation error"));
- }
- t[0] = (t_complex **)calloc(x*y, sizeof(t_complex*));
- if (!t[0])
- {
- exit(fprintf(stderr, "\nallocation error"));
- }
- t[0][0] = (t_complex *)calloc(x*y*z, sizeof(t_complex));
- if (!t[0][0])
- {
- exit(fprintf(stderr, "\nallocation error"));
- }
+ snew(t, x);
+ snew(t[0], x*y);
+ snew(t[0][0], x*y*z);
for (j = 1; j < y; j++)
{
}
}
}
- sfree (counter); free(tmpSF[0][0]); free(tmpSF[0]); free(tmpSF);
+ sfree(counter);
+ sfree(tmpSF[0][0]);
+ sfree(tmpSF[0]);
+ sfree(tmpSF);
}
if (sscanf(line, "%s %d %lf %lf %lf %lf %lf %lf %lf %lf %lf",
atomn, &p, &a1, &a2, &a3, &a4, &b1, &b2, &b3, &b4, &c) == 11)
{
- gsf->atomnm[i] = strdup(atomn);
+ gsf->atomnm[i] = gmx_strdup(atomn);
gsf->p[i] = p;
snew(gsf->a[i], 4);
snew(gsf->b[i], 4);
{
copy_rvec (fr->x[index[i]], pos[i].x);
}
-
- positions = (reduced_atom_t *)pos;
}
}
}
- gmx_ffclose (fp);
+ xvgrclose (fp);
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
#ifndef _sfactor_h
#define _sfactor_h
-
-#include "index.h"
-#include "types/simple.h"
-#include "../math/gmxcomplex.h"
-#include "oenv.h"
-
-
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/gmxcomplex.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_topology;
+struct t_trxframe;
typedef struct gmx_structurefactors gmx_structurefactors_t;
int return_atom_type (const char *name, gmx_structurefactors_t *gsf);
-void rearrange_atoms (reduced_atom_t * positions, t_trxframe *fr, atom_id * index,
- int isize, t_topology * top, gmx_bool flag, gmx_structurefactors_t *gsf);
+void rearrange_atoms (reduced_atom_t * positions, struct t_trxframe *fr, atom_id * index,
+ int isize, struct t_topology * top, gmx_bool flag, gmx_structurefactors_t *gsf);
int do_scattering_intensity (const char* fnTPS, const char* fnNDX,
const char* fnXVG, const char *fnTRX,
# conditionally built, so we cannot use a GLOB_RECURSE here.
file(GLOB GMXLIB_SOURCES *.c *.cpp)
-# Files called xxx_test.c are test drivers with a main() function for module xxx.c,
-# so they should not be included in the library
-file(GLOB_RECURSE NOT_GMXLIB_SOURCES *_test.c *\#*)
-list(REMOVE_ITEM GMXLIB_SOURCES ${NOT_GMXLIB_SOURCES})
-
# gpu utils + cuda tools module
if(GMX_GPU)
# The log file output queries Cuda if GPU support is enabled
add_subdirectory(cuda_tools)
- add_subdirectory(gpu_utils)
- set(GMX_GPU_LIBRARIES ${GMX_GPU_LIBRARIES} gpu_utils cuda_tools PARENT_SCOPE)
+ add_subdirectory(gpu_utils)
endif()
set(GMXLIB_SOURCES ${GMXLIB_SOURCES} ${NONBONDED_SOURCES} PARENT_SCOPE)
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/calcgrid.h"
#include <math.h>
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "calcgrid.h"
/* The grid sizes below are based on timing of a 3D cubic grid in fftw
* compiled with SSE using 4 threads in fft5d.c.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/chargegroup.h"
#include <math.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "pbc.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "chargegroup.h"
void calc_chargegroup_radii(const gmx_mtop_t *mtop, rvec *x,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2008,2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* The source code in this file should be thread-safe.
Please keep it that way. */
+#include "gmxpre.h"
+#include "gromacs/legacyheaders/checkpoint.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "config.h"
+#include <errno.h>
+#include <stdlib.h>
#include <string.h>
-#include <time.h>
-
-#ifdef HAVE_SYS_TIME_H
-#include <sys/time.h>
-#endif
-
-#ifdef HAVE_UNISTD_H
-#include <unistd.h>
-#endif
+#include <fcntl.h>
#ifdef GMX_NATIVE_WINDOWS
-/* _chsize_s */
#include <io.h>
#include <sys/locking.h>
#endif
-#include "copyrite.h"
-#include "names.h"
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "txtdump.h"
-#include "vec.h"
-#include "network.h"
-#include "checkpoint.h"
-#include "main.h"
-#include "gromacs/utility/cstringutil.h"
-#include <fcntl.h>
-
+#include "buildinfo.h"
#include "gromacs/fileio/filenm.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/xdrf.h"
#include "gromacs/fileio/xdr_datatype.h"
+#include "gromacs/fileio/xdrf.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
#include "gromacs/utility/baseversion.h"
-#include "gmx_fatal.h"
-
-#include "buildinfo.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/sysinfo.h"
#ifdef GMX_FAHCORE
#include "corewrap.h"
"accumulated_plus", "accumulated_minus", "accumulated_plus_2", "accumulated_minus_2", "Tij", "Tij_empirical"
};
-#ifdef GMX_NATIVE_WINDOWS
-static int
-gmx_wintruncate(const char *filename, __int64 size)
-{
-#ifdef GMX_FAHCORE
- /*we do this elsewhere*/
- return 0;
-#else
- FILE *fp;
- int rc;
-
- fp = fopen(filename, "rb+");
-
- if (fp == NULL)
- {
- return -1;
- }
-
-#ifdef _MSC_VER
- return _chsize_s( fileno(fp), size);
-#else
- return _chsize( fileno(fp), size);
-#endif
-#endif
-}
-#endif
-
-
enum {
ecprREAL, ecprRVEC, ecprMATRIX
};
{
if (dtc == xdr_datatype_double)
{
+ /* cppcheck-suppress invalidPointerCast
+ * Only executed if real is anyhow double */
vd = (double *)vp;
}
else
static int do_cpte_real(XDR *xd, int cptp, int ecpt, int sflags,
real *r, FILE *list)
{
- int n;
-
return do_cpte_reals_low(xd, cptp, ecpt, sflags, 1, NULL, &r, list, ecprREAL);
}
bool_t res = 0;
int dtc = xdr_datatype_int;
int *vp, *va = NULL;
- int nf, dt, i;
+ int nf, dt;
nf = n;
res = xdr_int(xd, &nf);
bool_t res = 0;
int dtc = xdr_datatype_double;
double *vp, *va = NULL;
- int nf, dt, i;
+ int nf, dt;
nf = n;
res = xdr_int(xd, &nf);
static int do_cpte_rvecs(XDR *xd, int cptp, int ecpt, int sflags,
int n, rvec **v, FILE *list)
{
- int n3;
-
return do_cpte_reals_low(xd, cptp, ecpt, sflags,
n*DIM, NULL, (real **)v, list, ecprRVEC);
}
matrix v, FILE *list)
{
real *vr;
- real ret;
+ int ret;
vr = (real *)&(v[0][0]);
ret = do_cpte_reals_low(xd, cptp, ecpt, sflags,
int n, real **v, FILE *list)
{
int i;
- real *vr;
- real ret, reti;
+ int ret, reti;
char name[CPTSTRLEN];
ret = 0;
}
for (i = 0; i < n; i++)
{
- reti = 0;
- vr = v[i];
reti = do_cpte_reals_low(xd, cptp, ecpt, sflags, n, NULL, &(v[i]), NULL, ecprREAL);
if (list && reti == 0)
{
sprintf(name, "%s[%d]", st_names(cptp, ecpt), i);
pr_reals(list, 0, name, v[i], n);
}
- if (reti == 0)
+ if (reti != 0)
{
- ret = 0;
+ ret = reti;
}
}
return ret;
bool_t res = 0;
int magic;
int idum = 0;
- int i;
char *fhost;
if (bRead)
{
enerhist->ener_sum_sim[i] = enerhist->ener_sum[i];
}
- fflags |= (1<<eenhENERGY_SUM_SIM);
}
if ( (fflags & (1<<eenhENERGY_NSUM)) &&
{
/* Assume we have an old file format and copy nsum to nsteps */
enerhist->nsteps = enerhist->nsum;
- fflags |= (1<<eenhENERGY_NSTEPS);
}
if ( (fflags & (1<<eenhENERGY_NSUM_SIM)) &&
!(fflags & (1<<eenhENERGY_NSTEPS_SIM)))
{
/* Assume we have an old file format and copy nsum to nsteps */
enerhist->nsteps_sim = enerhist->nsum_sim;
- fflags |= (1<<eenhENERGY_NSTEPS_SIM);
}
return ret;
static int do_cpt_EDstate(XDR *xd, gmx_bool bRead,
edsamstate_t *EDstate, FILE *list)
{
- int i, j;
+ int i;
int ret = 0;
char buf[STRLEN];
gmx_file_position_t **p_outputfiles, int *nfiles,
FILE *list, int file_version)
{
- int i, j;
+ int i;
gmx_off_t offset;
gmx_off_t mask = 0xFFFFFFFFL;
int offset_high, offset_low;
int double_prec;
char *fprog;
char *fntemp; /* the temporary checkpoint file name */
- time_t now;
char timebuf[STRLEN];
- int nppnodes, npmenodes, flag_64bit;
+ int nppnodes, npmenodes;
char buf[1024], suffix[5+STEPSTRSIZE], sbuf[STEPSTRSIZE];
gmx_file_position_t *outputfiles;
int noutputfiles;
char *ftime;
- int flags_eks, flags_enh, flags_dfh, i;
+ int flags_eks, flags_enh, flags_dfh;
t_fileio *ret;
if (DOMAINDECOMP(cr))
snew(fntemp, strlen(fn));
strcpy(fntemp, fn);
#endif
- time(&now);
- gmx_ctime_r(&now, timebuf, STRLEN);
+ gmx_format_current_time(timebuf, STRLEN);
if (fplog)
{
*/
int gmx_major, gmx_minor;
int cpt_major, cpt_minor;
- sscanf(gmx_version(), "VERSION %d.%d", &gmx_major, &gmx_minor);
- sscanf(version, "VERSION %d.%d", &cpt_major, &cpt_minor);
- version_differs = (gmx_major != cpt_major || gmx_minor != cpt_minor);
+ sscanf(gmx_version(), "VERSION %5d.%5d", &gmx_major, &gmx_minor);
+ int ret = sscanf(version, "VERSION %5d.%5d", &cpt_major, &cpt_minor);
+ version_differs = (ret < 2 || gmx_major != cpt_major ||
+ gmx_minor != cpt_minor);
}
check_string(fplog, "Build time", BUILD_TIME, btime, &mm);
int file_version;
char *version, *btime, *buser, *bhost, *fprog, *ftime;
int double_prec;
- char filename[STRLEN], buf[STEPSTRSIZE];
- int nppnodes, eIntegrator_f, nppnodes_f, npmenodes_f;
+ char buf[STEPSTRSIZE];
+ int eIntegrator_f, nppnodes_f, npmenodes_f;
ivec dd_nc_f;
int natoms, ngtc, nnhpres, nhchainlength, nlambda, fflags, flags_eks, flags_enh, flags_dfh;
int d;
if (!PAR(cr))
{
- nppnodes = 1;
cr->npmenodes = 0;
}
else if (cr->nnodes == nppnodes_f + npmenodes_f)
{
cr->npmenodes = npmenodes_f;
}
- nppnodes = cr->nnodes - cr->npmenodes;
+ int nppnodes = cr->nnodes - cr->npmenodes;
if (nppnodes == nppnodes_f)
{
for (d = 0; d < DIM; d++)
}
}
}
- else
- {
- /* The number of PP nodes has not been set yet */
- nppnodes = -1;
- }
if (fflags != state->flags)
{
if (i != 0) /*log file is already seeked to correct position */
{
-#ifdef GMX_NATIVE_WINDOWS
- rc = gmx_wintruncate(outputfiles[i].filename, outputfiles[i].offset);
-#else
- rc = truncate(outputfiles[i].filename, outputfiles[i].offset);
-#endif
+#if !defined(GMX_NATIVE_WINDOWS) || !defined(GMX_FAHCORE)
+ /* For FAHCORE, we do this elsewhere*/
+ rc = gmx_truncate(outputfiles[i].filename, outputfiles[i].offset);
if (rc != 0)
{
gmx_fatal(FARGS, "Truncation of file %s failed. Cannot do appending because of this failure.", outputfiles[i].filename);
}
+#endif
}
}
}
ivec dd_nc;
t_state state;
int flags_eks, flags_enh, flags_dfh;
- int indent;
- int i, j;
int ret;
gmx_file_position_t *outputfiles;
int nfiles;
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-
-struct gmx_invsqrtdata
-{
- unsigned int exptab[256]; /*!< Exponential lookup table */
- unsigned int fracttab[4096]; /*!< Mantissa lookup table */
-};
-
-
-struct gmx_invsqrtdata
-F77_FUNC(gmxinvsqrtdata, GMXINVSQRTDATA) =
-{
- /* data for exponent table - 256 floats */
- {
- 0x5f000000, 0x5e800000, 0x5e800000, 0x5e000000,
- 0x5e000000, 0x5d800000, 0x5d800000, 0x5d000000,
- 0x5d000000, 0x5c800000, 0x5c800000, 0x5c000000,
- 0x5c000000, 0x5b800000, 0x5b800000, 0x5b000000,
- 0x5b000000, 0x5a800000, 0x5a800000, 0x5a000000,
- 0x5a000000, 0x59800000, 0x59800000, 0x59000000,
- 0x59000000, 0x58800000, 0x58800000, 0x58000000,
- 0x58000000, 0x57800000, 0x57800000, 0x57000000,
- 0x57000000, 0x56800000, 0x56800000, 0x56000000,
- 0x56000000, 0x55800000, 0x55800000, 0x55000000,
- 0x55000000, 0x54800000, 0x54800000, 0x54000000,
- 0x54000000, 0x53800000, 0x53800000, 0x53000000,
- 0x53000000, 0x52800000, 0x52800000, 0x52000000,
- 0x52000000, 0x51800000, 0x51800000, 0x51000000,
- 0x51000000, 0x50800000, 0x50800000, 0x50000000,
- 0x50000000, 0x4f800000, 0x4f800000, 0x4f000000,
- 0x4f000000, 0x4e800000, 0x4e800000, 0x4e000000,
- 0x4e000000, 0x4d800000, 0x4d800000, 0x4d000000,
- 0x4d000000, 0x4c800000, 0x4c800000, 0x4c000000,
- 0x4c000000, 0x4b800000, 0x4b800000, 0x4b000000,
- 0x4b000000, 0x4a800000, 0x4a800000, 0x4a000000,
- 0x4a000000, 0x49800000, 0x49800000, 0x49000000,
- 0x49000000, 0x48800000, 0x48800000, 0x48000000,
- 0x48000000, 0x47800000, 0x47800000, 0x47000000,
- 0x47000000, 0x46800000, 0x46800000, 0x46000000,
- 0x46000000, 0x45800000, 0x45800000, 0x45000000,
- 0x45000000, 0x44800000, 0x44800000, 0x44000000,
- 0x44000000, 0x43800000, 0x43800000, 0x43000000,
- 0x43000000, 0x42800000, 0x42800000, 0x42000000,
- 0x42000000, 0x41800000, 0x41800000, 0x41000000,
- 0x41000000, 0x40800000, 0x40800000, 0x40000000,
- 0x40000000, 0x3f800000, 0x3f800000, 0x3f000000,
- 0x3f000000, 0x3e800000, 0x3e800000, 0x3e000000,
- 0x3e000000, 0x3d800000, 0x3d800000, 0x3d000000,
- 0x3d000000, 0x3c800000, 0x3c800000, 0x3c000000,
- 0x3c000000, 0x3b800000, 0x3b800000, 0x3b000000,
- 0x3b000000, 0x3a800000, 0x3a800000, 0x3a000000,
- 0x3a000000, 0x39800000, 0x39800000, 0x39000000,
- 0x39000000, 0x38800000, 0x38800000, 0x38000000,
- 0x38000000, 0x37800000, 0x37800000, 0x37000000,
- 0x37000000, 0x36800000, 0x36800000, 0x36000000,
- 0x36000000, 0x35800000, 0x35800000, 0x35000000,
- 0x35000000, 0x34800000, 0x34800000, 0x34000000,
- 0x34000000, 0x33800000, 0x33800000, 0x33000000,
- 0x33000000, 0x32800000, 0x32800000, 0x32000000,
- 0x32000000, 0x31800000, 0x31800000, 0x31000000,
- 0x31000000, 0x30800000, 0x30800000, 0x30000000,
- 0x30000000, 0x2f800000, 0x2f800000, 0x2f000000,
- 0x2f000000, 0x2e800000, 0x2e800000, 0x2e000000,
- 0x2e000000, 0x2d800000, 0x2d800000, 0x2d000000,
- 0x2d000000, 0x2c800000, 0x2c800000, 0x2c000000,
- 0x2c000000, 0x2b800000, 0x2b800000, 0x2b000000,
- 0x2b000000, 0x2a800000, 0x2a800000, 0x2a000000,
- 0x2a000000, 0x29800000, 0x29800000, 0x29000000,
- 0x29000000, 0x28800000, 0x28800000, 0x28000000,
- 0x28000000, 0x27800000, 0x27800000, 0x27000000,
- 0x27000000, 0x26800000, 0x26800000, 0x26000000,
- 0x26000000, 0x25800000, 0x25800000, 0x25000000,
- 0x25000000, 0x24800000, 0x24800000, 0x24000000,
- 0x24000000, 0x23800000, 0x23800000, 0x23000000,
- 0x23000000, 0x22800000, 0x22800000, 0x22000000,
- 0x22000000, 0x21800000, 0x21800000, 0x21000000,
- 0x21000000, 0x20800000, 0x20800000, 0x20000000,
- 0x20000000, 0x1f800000, 0x1f800000, 0x1f000000
- },
- /* data for fraction table - 4096 floats */
- {
- 0x3504f3, 0x34f9a4, 0x34ee57, 0x34e30c, 0x34d7c3, 0x34cc7c, 0x34c137, 0x34b5f5,
- 0x34aab4, 0x349f76, 0x34943a, 0x348900, 0x347dc7, 0x347291, 0x34675e, 0x345c2c,
- 0x3450fc, 0x3445ce, 0x343aa3, 0x342f79, 0x342452, 0x34192c, 0x340e09, 0x3402e8,
- 0x33f7c9, 0x33ecac, 0x33e191, 0x33d678, 0x33cb61, 0x33c04c, 0x33b539, 0x33aa28,
- 0x339f19, 0x33940d, 0x338902, 0x337df9, 0x3372f3, 0x3367ee, 0x335cec, 0x3351eb,
- 0x3346ed, 0x333bf0, 0x3330f6, 0x3325fd, 0x331b07, 0x331013, 0x330520, 0x32fa30,
- 0x32ef41, 0x32e455, 0x32d96b, 0x32ce82, 0x32c39c, 0x32b8b7, 0x32add5, 0x32a2f5,
- 0x329816, 0x328d3a, 0x32825f, 0x327787, 0x326cb0, 0x3261dc, 0x325709, 0x324c38,
- 0x32416a, 0x32369d, 0x322bd2, 0x32210a, 0x321643, 0x320b7e, 0x3200bb, 0x31f5fa,
- 0x31eb3b, 0x31e07e, 0x31d5c3, 0x31cb0a, 0x31c053, 0x31b59d, 0x31aaea, 0x31a038,
- 0x319589, 0x318adb, 0x318030, 0x317586, 0x316ade, 0x316038, 0x315594, 0x314af2,
- 0x314052, 0x3135b4, 0x312b18, 0x31207d, 0x3115e5, 0x310b4e, 0x3100b9, 0x30f627,
- 0x30eb96, 0x30e107, 0x30d67a, 0x30cbee, 0x30c165, 0x30b6dd, 0x30ac58, 0x30a1d4,
- 0x309752, 0x308cd2, 0x308254, 0x3077d8, 0x306d5e, 0x3062e5, 0x30586e, 0x304dfa,
- 0x304387, 0x303916, 0x302ea7, 0x302439, 0x3019ce, 0x300f64, 0x3004fc, 0x2ffa96,
- 0x2ff032, 0x2fe5d0, 0x2fdb6f, 0x2fd111, 0x2fc6b4, 0x2fbc59, 0x2fb200, 0x2fa7a9,
- 0x2f9d53, 0x2f9300, 0x2f88ae, 0x2f7e5e, 0x2f7410, 0x2f69c3, 0x2f5f79, 0x2f5530,
- 0x2f4ae9, 0x2f40a4, 0x2f3661, 0x2f2c1f, 0x2f21df, 0x2f17a1, 0x2f0d65, 0x2f032b,
- 0x2ef8f2, 0x2eeebc, 0x2ee487, 0x2eda53, 0x2ed022, 0x2ec5f2, 0x2ebbc5, 0x2eb199,
- 0x2ea76e, 0x2e9d46, 0x2e931f, 0x2e88fa, 0x2e7ed7, 0x2e74b5, 0x2e6a96, 0x2e6078,
- 0x2e565c, 0x2e4c41, 0x2e4229, 0x2e3812, 0x2e2dfd, 0x2e23e9, 0x2e19d8, 0x2e0fc8,
- 0x2e05ba, 0x2dfbad, 0x2df1a3, 0x2de79a, 0x2ddd93, 0x2dd38d, 0x2dc989, 0x2dbf87,
- 0x2db587, 0x2dab89, 0x2da18c, 0x2d9791, 0x2d8d97, 0x2d83a0, 0x2d79aa, 0x2d6fb6,
- 0x2d65c3, 0x2d5bd2, 0x2d51e3, 0x2d47f6, 0x2d3e0a, 0x2d3420, 0x2d2a38, 0x2d2051,
- 0x2d166c, 0x2d0c89, 0x2d02a8, 0x2cf8c8, 0x2ceeea, 0x2ce50d, 0x2cdb33, 0x2cd15a,
- 0x2cc782, 0x2cbdad, 0x2cb3d9, 0x2caa06, 0x2ca036, 0x2c9667, 0x2c8c99, 0x2c82ce,
- 0x2c7904, 0x2c6f3b, 0x2c6575, 0x2c5bb0, 0x2c51ed, 0x2c482b, 0x2c3e6b, 0x2c34ad,
- 0x2c2af0, 0x2c2135, 0x2c177b, 0x2c0dc4, 0x2c040e, 0x2bfa59, 0x2bf0a6, 0x2be6f5,
- 0x2bdd46, 0x2bd398, 0x2bc9eb, 0x2bc041, 0x2bb698, 0x2bacf0, 0x2ba34b, 0x2b99a6,
- 0x2b9004, 0x2b8663, 0x2b7cc4, 0x2b7326, 0x2b698a, 0x2b5ff0, 0x2b5657, 0x2b4cc0,
- 0x2b432a, 0x2b3996, 0x2b3004, 0x2b2673, 0x2b1ce4, 0x2b1357, 0x2b09cb, 0x2b0040,
- 0x2af6b7, 0x2aed30, 0x2ae3ab, 0x2ada27, 0x2ad0a4, 0x2ac724, 0x2abda4, 0x2ab427,
- 0x2aaaab, 0x2aa130, 0x2a97b7, 0x2a8e40, 0x2a84ca, 0x2a7b56, 0x2a71e3, 0x2a6872,
- 0x2a5f03, 0x2a5595, 0x2a4c29, 0x2a42be, 0x2a3955, 0x2a2fed, 0x2a2687, 0x2a1d23,
- 0x2a13c0, 0x2a0a5e, 0x2a00fe, 0x29f7a0, 0x29ee43, 0x29e4e8, 0x29db8e, 0x29d236,
- 0x29c8e0, 0x29bf8b, 0x29b637, 0x29ace5, 0x29a395, 0x299a46, 0x2990f8, 0x2987ad,
- 0x297e62, 0x297519, 0x296bd2, 0x29628c, 0x295948, 0x295005, 0x2946c4, 0x293d85,
- 0x293446, 0x292b0a, 0x2921cf, 0x291895, 0x290f5d, 0x290626, 0x28fcf1, 0x28f3be,
- 0x28ea8c, 0x28e15b, 0x28d82c, 0x28cefe, 0x28c5d2, 0x28bca8, 0x28b37f, 0x28aa57,
- 0x28a131, 0x28980c, 0x288ee9, 0x2885c7, 0x287ca7, 0x287389, 0x286a6b, 0x286150,
- 0x285835, 0x284f1c, 0x284605, 0x283cef, 0x2833db, 0x282ac8, 0x2821b7, 0x2818a7,
- 0x280f98, 0x28068b, 0x27fd80, 0x27f475, 0x27eb6d, 0x27e266, 0x27d960, 0x27d05c,
- 0x27c759, 0x27be57, 0x27b557, 0x27ac59, 0x27a35c, 0x279a60, 0x279166, 0x27886d,
- 0x277f76, 0x277680, 0x276d8c, 0x276499, 0x275ba7, 0x2752b7, 0x2749c9, 0x2740db,
- 0x2737f0, 0x272f05, 0x27261c, 0x271d35, 0x27144f, 0x270b6a, 0x270287, 0x26f9a5,
- 0x26f0c4, 0x26e7e5, 0x26df08, 0x26d62c, 0x26cd51, 0x26c477, 0x26bba0, 0x26b2c9,
- 0x26a9f4, 0x26a120, 0x26984e, 0x268f7d, 0x2686ad, 0x267ddf, 0x267512, 0x266c47,
- 0x26637d, 0x265ab4, 0x2651ed, 0x264927, 0x264063, 0x2637a0, 0x262ede, 0x26261e,
- 0x261d5f, 0x2614a2, 0x260be6, 0x26032b, 0x25fa72, 0x25f1ba, 0x25e903, 0x25e04e,
- 0x25d79a, 0x25cee7, 0x25c636, 0x25bd87, 0x25b4d8, 0x25ac2b, 0x25a37f, 0x259ad5,
- 0x25922c, 0x258985, 0x2580de, 0x257839, 0x256f96, 0x2566f4, 0x255e53, 0x2555b3,
- 0x254d15, 0x254479, 0x253bdd, 0x253343, 0x252aaa, 0x252213, 0x25197d, 0x2510e8,
- 0x250855, 0x24ffc3, 0x24f732, 0x24eea3, 0x24e615, 0x24dd88, 0x24d4fc, 0x24cc72,
- 0x24c3ea, 0x24bb62, 0x24b2dc, 0x24aa57, 0x24a1d4, 0x249952, 0x2490d1, 0x248852,
- 0x247fd3, 0x247756, 0x246edb, 0x246661, 0x245de8, 0x245570, 0x244cfa, 0x244485,
- 0x243c11, 0x24339f, 0x242b2e, 0x2422be, 0x241a4f, 0x2411e2, 0x240976, 0x24010c,
- 0x23f8a2, 0x23f03a, 0x23e7d4, 0x23df6e, 0x23d70a, 0x23cea7, 0x23c646, 0x23bde6,
- 0x23b587, 0x23ad29, 0x23a4cc, 0x239c71, 0x239417, 0x238bbf, 0x238368, 0x237b12,
- 0x2372bd, 0x236a69, 0x236217, 0x2359c6, 0x235177, 0x234928, 0x2340db, 0x23388f,
- 0x233045, 0x2327fb, 0x231fb3, 0x23176c, 0x230f27, 0x2306e2, 0x22fe9f, 0x22f65e,
- 0x22ee1d, 0x22e5de, 0x22dda0, 0x22d563, 0x22cd28, 0x22c4ed, 0x22bcb4, 0x22b47c,
- 0x22ac46, 0x22a411, 0x229bdd, 0x2293aa, 0x228b78, 0x228348, 0x227b19, 0x2272eb,
- 0x226abe, 0x226293, 0x225a69, 0x225240, 0x224a18, 0x2241f2, 0x2239cc, 0x2231a8,
- 0x222985, 0x222164, 0x221944, 0x221124, 0x220907, 0x2200ea, 0x21f8ce, 0x21f0b4,
- 0x21e89b, 0x21e083, 0x21d86d, 0x21d057, 0x21c843, 0x21c030, 0x21b81e, 0x21b00e,
- 0x21a7fe, 0x219ff0, 0x2197e3, 0x218fd8, 0x2187cd, 0x217fc4, 0x2177bc, 0x216fb5,
- 0x2167af, 0x215faa, 0x2157a7, 0x214fa5, 0x2147a4, 0x213fa4, 0x2137a5, 0x212fa8,
- 0x2127ac, 0x211fb1, 0x2117b7, 0x210fbe, 0x2107c7, 0x20ffd0, 0x20f7db, 0x20efe7,
- 0x20e7f5, 0x20e003, 0x20d813, 0x20d023, 0x20c835, 0x20c048, 0x20b85d, 0x20b072,
- 0x20a889, 0x20a0a1, 0x2098ba, 0x2090d4, 0x2088ef, 0x20810b, 0x207929, 0x207148,
- 0x206968, 0x206189, 0x2059ab, 0x2051cf, 0x2049f3, 0x204219, 0x203a40, 0x203268,
- 0x202a91, 0x2022bb, 0x201ae7, 0x201313, 0x200b41, 0x200370, 0x1ffba0, 0x1ff3d1,
- 0x1fec04, 0x1fe437, 0x1fdc6c, 0x1fd4a2, 0x1fccd9, 0x1fc511, 0x1fbd4a, 0x1fb584,
- 0x1fadc0, 0x1fa5fc, 0x1f9e3a, 0x1f9679, 0x1f8eb9, 0x1f86fa, 0x1f7f3c, 0x1f777f,
- 0x1f6fc4, 0x1f680a, 0x1f6050, 0x1f5898, 0x1f50e1, 0x1f492b, 0x1f4176, 0x1f39c3,
- 0x1f3210, 0x1f2a5f, 0x1f22af, 0x1f1aff, 0x1f1351, 0x1f0ba4, 0x1f03f8, 0x1efc4e,
- 0x1ef4a4, 0x1eecfb, 0x1ee554, 0x1eddae, 0x1ed608, 0x1ece64, 0x1ec6c1, 0x1ebf1f,
- 0x1eb77f, 0x1eafdf, 0x1ea840, 0x1ea0a3, 0x1e9906, 0x1e916b, 0x1e89d1, 0x1e8238,
- 0x1e7aa0, 0x1e7309, 0x1e6b73, 0x1e63de, 0x1e5c4a, 0x1e54b8, 0x1e4d26, 0x1e4596,
- 0x1e3e06, 0x1e3678, 0x1e2eeb, 0x1e275f, 0x1e1fd4, 0x1e184a, 0x1e10c1, 0x1e0939,
- 0x1e01b3, 0x1dfa2d, 0x1df2a8, 0x1deb25, 0x1de3a2, 0x1ddc21, 0x1dd4a1, 0x1dcd22,
- 0x1dc5a3, 0x1dbe26, 0x1db6aa, 0x1daf2f, 0x1da7b6, 0x1da03d, 0x1d98c5, 0x1d914e,
- 0x1d89d9, 0x1d8264, 0x1d7af1, 0x1d737e, 0x1d6c0d, 0x1d649c, 0x1d5d2d, 0x1d55bf,
- 0x1d4e52, 0x1d46e5, 0x1d3f7a, 0x1d3810, 0x1d30a7, 0x1d293f, 0x1d21d8, 0x1d1a73,
- 0x1d130e, 0x1d0baa, 0x1d0447, 0x1cfce6, 0x1cf585, 0x1cee25, 0x1ce6c7, 0x1cdf69,
- 0x1cd80d, 0x1cd0b1, 0x1cc957, 0x1cc1fe, 0x1cbaa5, 0x1cb34e, 0x1cabf8, 0x1ca4a2,
- 0x1c9d4e, 0x1c95fb, 0x1c8ea9, 0x1c8758, 0x1c8008, 0x1c78b8, 0x1c716a, 0x1c6a1d,
- 0x1c62d1, 0x1c5b86, 0x1c543c, 0x1c4cf3, 0x1c45ab, 0x1c3e65, 0x1c371f, 0x1c2fda,
- 0x1c2896, 0x1c2153, 0x1c1a11, 0x1c12d0, 0x1c0b90, 0x1c0452, 0x1bfd14, 0x1bf5d7,
- 0x1bee9b, 0x1be760, 0x1be027, 0x1bd8ee, 0x1bd1b6, 0x1bca7f, 0x1bc349, 0x1bbc15,
- 0x1bb4e1, 0x1badae, 0x1ba67c, 0x1b9f4c, 0x1b981c, 0x1b90ed, 0x1b89bf, 0x1b8292,
- 0x1b7b67, 0x1b743c, 0x1b6d12, 0x1b65e9, 0x1b5ec1, 0x1b579a, 0x1b5074, 0x1b4950,
- 0x1b422c, 0x1b3b09, 0x1b33e7, 0x1b2cc6, 0x1b25a6, 0x1b1e87, 0x1b1769, 0x1b104c,
- 0x1b0930, 0x1b0215, 0x1afafb, 0x1af3e2, 0x1aecc9, 0x1ae5b2, 0x1ade9c, 0x1ad787,
- 0x1ad073, 0x1ac95f, 0x1ac24d, 0x1abb3c, 0x1ab42b, 0x1aad1c, 0x1aa60d, 0x1a9f00,
- 0x1a97f3, 0x1a90e8, 0x1a89dd, 0x1a82d4, 0x1a7bcb, 0x1a74c3, 0x1a6dbd, 0x1a66b7,
- 0x1a5fb2, 0x1a58ae, 0x1a51ab, 0x1a4aa9, 0x1a43a8, 0x1a3ca8, 0x1a35a9, 0x1a2eab,
- 0x1a27ae, 0x1a20b1, 0x1a19b6, 0x1a12bc, 0x1a0bc2, 0x1a04ca, 0x19fdd2, 0x19f6dc,
- 0x19efe6, 0x19e8f2, 0x19e1fe, 0x19db0b, 0x19d419, 0x19cd28, 0x19c638, 0x19bf49,
- 0x19b85b, 0x19b16e, 0x19aa82, 0x19a396, 0x199cac, 0x1995c3, 0x198eda, 0x1987f3,
- 0x19810c, 0x197a26, 0x197342, 0x196c5e, 0x19657b, 0x195e99, 0x1957b8, 0x1950d8,
- 0x1949f8, 0x19431a, 0x193c3d, 0x193560, 0x192e85, 0x1927aa, 0x1920d1, 0x1919f8,
- 0x191320, 0x190c49, 0x190573, 0x18fe9e, 0x18f7ca, 0x18f0f7, 0x18ea24, 0x18e353,
- 0x18dc82, 0x18d5b3, 0x18cee4, 0x18c816, 0x18c149, 0x18ba7d, 0x18b3b2, 0x18ace8,
- 0x18a61f, 0x189f56, 0x18988f, 0x1891c8, 0x188b03, 0x18843e, 0x187d7a, 0x1876b7,
- 0x186ff5, 0x186934, 0x186274, 0x185bb4, 0x1854f6, 0x184e38, 0x18477c, 0x1840c0,
- 0x183a05, 0x18334b, 0x182c92, 0x1825da, 0x181f23, 0x18186c, 0x1811b7, 0x180b02,
- 0x18044e, 0x17fd9b, 0x17f6e9, 0x17f038, 0x17e988, 0x17e2d9, 0x17dc2a, 0x17d57d,
- 0x17ced0, 0x17c824, 0x17c179, 0x17bacf, 0x17b426, 0x17ad7e, 0x17a6d6, 0x17a030,
- 0x17998a, 0x1792e5, 0x178c41, 0x17859e, 0x177efc, 0x17785b, 0x1771ba, 0x176b1b,
- 0x17647c, 0x175dde, 0x175741, 0x1750a5, 0x174a0a, 0x17436f, 0x173cd6, 0x17363d,
- 0x172fa5, 0x17290f, 0x172278, 0x171be3, 0x17154f, 0x170ebb, 0x170829, 0x170197,
- 0x16fb06, 0x16f476, 0x16ede7, 0x16e759, 0x16e0cb, 0x16da3e, 0x16d3b3, 0x16cd28,
- 0x16c69e, 0x16c014, 0x16b98c, 0x16b305, 0x16ac7e, 0x16a5f8, 0x169f73, 0x1698ef,
- 0x16926c, 0x168be9, 0x168568, 0x167ee7, 0x167867, 0x1671e8, 0x166b6a, 0x1664ec,
- 0x165e70, 0x1657f4, 0x165179, 0x164aff, 0x164486, 0x163e0d, 0x163796, 0x16311f,
- 0x162aa9, 0x162434, 0x161dc0, 0x16174d, 0x1610da, 0x160a68, 0x1603f8, 0x15fd88,
- 0x15f718, 0x15f0aa, 0x15ea3c, 0x15e3d0, 0x15dd64, 0x15d6f9, 0x15d08e, 0x15ca25,
- 0x15c3bc, 0x15bd55, 0x15b6ee, 0x15b087, 0x15aa22, 0x15a3be, 0x159d5a, 0x1596f7,
- 0x159095, 0x158a34, 0x1583d3, 0x157d74, 0x157715, 0x1570b7, 0x156a5a, 0x1563fd,
- 0x155da2, 0x155747, 0x1550ed, 0x154a94, 0x15443c, 0x153de4, 0x15378e, 0x153138,
- 0x152ae3, 0x15248e, 0x151e3b, 0x1517e8, 0x151197, 0x150b45, 0x1504f5, 0x14fea6,
- 0x14f857, 0x14f209, 0x14ebbc, 0x14e570, 0x14df25, 0x14d8da, 0x14d290, 0x14cc47,
- 0x14c5ff, 0x14bfb7, 0x14b971, 0x14b32b, 0x14ace6, 0x14a6a1, 0x14a05e, 0x149a1b,
- 0x1493d9, 0x148d98, 0x148758, 0x148118, 0x147ada, 0x14749c, 0x146e5f, 0x146822,
- 0x1461e7, 0x145bac, 0x145572, 0x144f38, 0x144900, 0x1442c8, 0x143c91, 0x14365b,
- 0x143026, 0x1429f1, 0x1423be, 0x141d8b, 0x141758, 0x141127, 0x140af6, 0x1404c6,
- 0x13fe97, 0x13f869, 0x13f23b, 0x13ec0f, 0x13e5e3, 0x13dfb7, 0x13d98d, 0x13d363,
- 0x13cd3a, 0x13c712, 0x13c0eb, 0x13bac4, 0x13b49e, 0x13ae79, 0x13a855, 0x13a231,
- 0x139c0e, 0x1395ec, 0x138fcb, 0x1389ab, 0x13838b, 0x137d6c, 0x13774e, 0x137130,
- 0x136b13, 0x1364f8, 0x135edc, 0x1358c2, 0x1352a8, 0x134c8f, 0x134677, 0x134060,
- 0x133a49, 0x133433, 0x132e1e, 0x13280a, 0x1321f6, 0x131be3, 0x1315d1, 0x130fc0,
- 0x1309af, 0x13039f, 0x12fd90, 0x12f782, 0x12f174, 0x12eb67, 0x12e55b, 0x12df50,
- 0x12d945, 0x12d33b, 0x12cd32, 0x12c72a, 0x12c122, 0x12bb1b, 0x12b515, 0x12af10,
- 0x12a90b, 0x12a307, 0x129d04, 0x129702, 0x129100, 0x128aff, 0x1284ff, 0x127eff,
- 0x127900, 0x127302, 0x126d05, 0x126708, 0x12610d, 0x125b11, 0x125517, 0x124f1d,
- 0x124925, 0x12432c, 0x123d35, 0x12373e, 0x123148, 0x122b53, 0x12255e, 0x121f6b,
- 0x121978, 0x121385, 0x120d94, 0x1207a3, 0x1201b3, 0x11fbc3, 0x11f5d4, 0x11efe6,
- 0x11e9f9, 0x11e40d, 0x11de21, 0x11d836, 0x11d24b, 0x11cc62, 0x11c679, 0x11c090,
- 0x11baa9, 0x11b4c2, 0x11aedc, 0x11a8f7, 0x11a312, 0x119d2e, 0x11974b, 0x119168,
- 0x118b87, 0x1185a6, 0x117fc5, 0x1179e5, 0x117407, 0x116e28, 0x11684b, 0x11626e,
- 0x115c92, 0x1156b6, 0x1150dc, 0x114b02, 0x114529, 0x113f50, 0x113978, 0x1133a1,
- 0x112dca, 0x1127f5, 0x112220, 0x111c4b, 0x111678, 0x1110a5, 0x110ad3, 0x110501,
- 0x10ff30, 0x10f960, 0x10f391, 0x10edc2, 0x10e7f4, 0x10e226, 0x10dc5a, 0x10d68e,
- 0x10d0c3, 0x10caf8, 0x10c52e, 0x10bf65, 0x10b99c, 0x10b3d5, 0x10ae0e, 0x10a847,
- 0x10a281, 0x109cbc, 0x1096f8, 0x109134, 0x108b72, 0x1085af, 0x107fee, 0x107a2d,
- 0x10746d, 0x106ead, 0x1068ee, 0x106330, 0x105d73, 0x1057b6, 0x1051fa, 0x104c3e,
- 0x104684, 0x1040ca, 0x103b10, 0x103558, 0x102fa0, 0x1029e8, 0x102432, 0x101e7c,
- 0x1018c6, 0x101312, 0x100d5e, 0x1007ab, 0x1001f8, 0xffc46, 0xff695, 0xff0e4,
- 0xfeb35, 0xfe585, 0xfdfd7, 0xfda29, 0xfd47c, 0xfcecf, 0xfc923, 0xfc378,
- 0xfbdce, 0xfb824, 0xfb27b, 0xfacd2, 0xfa72a, 0xfa183, 0xf9bdd, 0xf9637,
- 0xf9092, 0xf8aed, 0xf854a, 0xf7fa6, 0xf7a04, 0xf7462, 0xf6ec1, 0xf6920,
- 0xf6381, 0xf5de1, 0xf5843, 0xf52a5, 0xf4d08, 0xf476b, 0xf41cf, 0xf3c34,
- 0xf369a, 0xf3100, 0xf2b66, 0xf25ce, 0xf2036, 0xf1a9f, 0xf1508, 0xf0f72,
- 0xf09dd, 0xf0448, 0xefeb4, 0xef921, 0xef38e, 0xeedfc, 0xee86b, 0xee2da,
- 0xedd4a, 0xed7ba, 0xed22b, 0xecc9d, 0xec710, 0xec183, 0xebbf7, 0xeb66b,
- 0xeb0e0, 0xeab56, 0xea5cc, 0xea043, 0xe9abb, 0xe9533, 0xe8fac, 0xe8a26,
- 0xe84a0, 0xe7f1b, 0xe7996, 0xe7413, 0xe6e8f, 0xe690d, 0xe638b, 0xe5e0a,
- 0xe5889, 0xe5309, 0xe4d8a, 0xe480b, 0xe428d, 0xe3d0f, 0xe3792, 0xe3216,
- 0xe2c9b, 0xe2720, 0xe21a5, 0xe1c2c, 0xe16b3, 0xe113a, 0xe0bc3, 0xe064c,
- 0xe00d5, 0xdfb5f, 0xdf5ea, 0xdf075, 0xdeb01, 0xde58e, 0xde01b, 0xddaa9,
- 0xdd538, 0xdcfc7, 0xdca57, 0xdc4e7, 0xdbf78, 0xdba0a, 0xdb49c, 0xdaf2f,
- 0xda9c2, 0xda457, 0xd9eeb, 0xd9981, 0xd9417, 0xd8ead, 0xd8945, 0xd83dc,
- 0xd7e75, 0xd790e, 0xd73a8, 0xd6e42, 0xd68dd, 0xd6379, 0xd5e15, 0xd58b2,
- 0xd534f, 0xd4ded, 0xd488c, 0xd432b, 0xd3dcb, 0xd386c, 0xd330d, 0xd2dae,
- 0xd2851, 0xd22f4, 0xd1d97, 0xd183b, 0xd12e0, 0xd0d86, 0xd082c, 0xd02d2,
- 0xcfd79, 0xcf821, 0xcf2ca, 0xced73, 0xce81c, 0xce2c7, 0xcdd72, 0xcd81d,
- 0xcd2c9, 0xccd76, 0xcc823, 0xcc2d1, 0xcbd7f, 0xcb82f, 0xcb2de, 0xcad8f,
- 0xca83f, 0xca2f1, 0xc9da3, 0xc9856, 0xc9309, 0xc8dbd, 0xc8871, 0xc8326,
- 0xc7ddc, 0xc7892, 0xc7349, 0xc6e01, 0xc68b9, 0xc6372, 0xc5e2b, 0xc58e5,
- 0xc539f, 0xc4e5a, 0xc4916, 0xc43d2, 0xc3e8f, 0xc394c, 0xc340a, 0xc2ec9,
- 0xc2988, 0xc2448, 0xc1f08, 0xc19c9, 0xc148b, 0xc0f4d, 0xc0a10, 0xc04d3,
- 0xbff97, 0xbfa5b, 0xbf521, 0xbefe6, 0xbeaad, 0xbe573, 0xbe03b, 0xbdb03,
- 0xbd5cb, 0xbd095, 0xbcb5e, 0xbc629, 0xbc0f4, 0xbbbbf, 0xbb68b, 0xbb158,
- 0xbac25, 0xba6f3, 0xba1c1, 0xb9c90, 0xb9760, 0xb9230, 0xb8d01, 0xb87d2,
- 0xb82a4, 0xb7d76, 0xb7849, 0xb731d, 0xb6df1, 0xb68c6, 0xb639b, 0xb5e71,
- 0xb5948, 0xb541f, 0xb4ef6, 0xb49cf, 0xb44a7, 0xb3f81, 0xb3a5b, 0xb3535,
- 0xb3010, 0xb2aec, 0xb25c8, 0xb20a5, 0xb1b82, 0xb1660, 0xb113e, 0xb0c1d,
- 0xb06fd, 0xb01dd, 0xafcbe, 0xaf79f, 0xaf281, 0xaed64, 0xae847, 0xae32a,
- 0xade0e, 0xad8f3, 0xad3d8, 0xacebe, 0xac9a4, 0xac48b, 0xabf73, 0xaba5b,
- 0xab544, 0xab02d, 0xaab17, 0xaa601, 0xaa0ec, 0xa9bd7, 0xa96c3, 0xa91b0,
- 0xa8c9d, 0xa878a, 0xa8279, 0xa7d67, 0xa7857, 0xa7347, 0xa6e37, 0xa6928,
- 0xa641a, 0xa5f0c, 0xa59fe, 0xa54f2, 0xa4fe5, 0xa4ada, 0xa45ce, 0xa40c4,
- 0xa3bba, 0xa36b0, 0xa31a7, 0xa2c9f, 0xa2797, 0xa2290, 0xa1d89, 0xa1883,
- 0xa137d, 0xa0e78, 0xa0974, 0xa0470, 0x9ff6c, 0x9fa69, 0x9f567, 0x9f065,
- 0x9eb64, 0x9e663, 0x9e163, 0x9dc63, 0x9d764, 0x9d266, 0x9cd68, 0x9c86a,
- 0x9c36d, 0x9be71, 0x9b975, 0x9b47a, 0x9af7f, 0x9aa85, 0x9a58b, 0x9a092,
- 0x99b9a, 0x996a1, 0x991aa, 0x98cb3, 0x987bd, 0x982c7, 0x97dd1, 0x978dc,
- 0x973e8, 0x96ef4, 0x96a01, 0x9650e, 0x9601c, 0x95b2b, 0x9563a, 0x95149,
- 0x94c59, 0x94769, 0x9427a, 0x93d8c, 0x9389e, 0x933b1, 0x92ec4, 0x929d8,
- 0x924ec, 0x92001, 0x91b16, 0x9162c, 0x91142, 0x90c59, 0x90770, 0x90288,
- 0x8fda1, 0x8f8ba, 0x8f3d3, 0x8eeed, 0x8ea08, 0x8e523, 0x8e03e, 0x8db5b,
- 0x8d677, 0x8d194, 0x8ccb2, 0x8c7d0, 0x8c2ef, 0x8be0e, 0x8b92e, 0x8b44e,
- 0x8af6f, 0x8aa91, 0x8a5b2, 0x8a0d5, 0x89bf8, 0x8971b, 0x8923f, 0x88d64,
- 0x88889, 0x883ae, 0x87ed4, 0x879fb, 0x87522, 0x87049, 0x86b71, 0x8669a,
- 0x861c3, 0x85ced, 0x85817, 0x85341, 0x84e6d, 0x84998, 0x844c5, 0x83ff1,
- 0x83b1e, 0x8364c, 0x8317a, 0x82ca9, 0x827d8, 0x82308, 0x81e39, 0x81969,
- 0x8149b, 0x80fcd, 0x80aff, 0x80632, 0x80165, 0x7fc99, 0x7f7cd, 0x7f302,
- 0x7ee37, 0x7e96d, 0x7e4a4, 0x7dfdb, 0x7db12, 0x7d64a, 0x7d182, 0x7ccbb,
- 0x7c7f5, 0x7c32f, 0x7be69, 0x7b9a4, 0x7b4df, 0x7b01b, 0x7ab58, 0x7a695,
- 0x7a1d2, 0x79d10, 0x7984f, 0x7938e, 0x78ecd, 0x78a0d, 0x7854d, 0x7808e,
- 0x77bd0, 0x77712, 0x77254, 0x76d97, 0x768da, 0x7641e, 0x75f63, 0x75aa8,
- 0x755ed, 0x75133, 0x74c79, 0x747c0, 0x74308, 0x73e50, 0x73998, 0x734e1,
- 0x7302a, 0x72b74, 0x726be, 0x72209, 0x71d55, 0x718a0, 0x713ed, 0x70f3a,
- 0x70a87, 0x705d5, 0x70123, 0x6fc72, 0x6f7c1, 0x6f311, 0x6ee61, 0x6e9b2,
- 0x6e503, 0x6e055, 0x6dba7, 0x6d6f9, 0x6d24d, 0x6cda0, 0x6c8f4, 0x6c449,
- 0x6bf9e, 0x6baf4, 0x6b64a, 0x6b1a0, 0x6acf7, 0x6a84f, 0x6a3a7, 0x69eff,
- 0x69a58, 0x695b2, 0x6910c, 0x68c66, 0x687c1, 0x6831d, 0x67e78, 0x679d5,
- 0x67532, 0x6708f, 0x66bed, 0x6674b, 0x662aa, 0x65e09, 0x65969, 0x654c9,
- 0x65029, 0x64b8a, 0x646ec, 0x6424e, 0x63db1, 0x63914, 0x63477, 0x62fdb,
- 0x62b40, 0x626a5, 0x6220a, 0x61d70, 0x618d6, 0x6143d, 0x60fa4, 0x60b0c,
- 0x60674, 0x601dd, 0x5fd46, 0x5f8b0, 0x5f41a, 0x5ef85, 0x5eaf0, 0x5e65b,
- 0x5e1c7, 0x5dd34, 0x5d8a1, 0x5d40e, 0x5cf7c, 0x5caea, 0x5c659, 0x5c1c9,
- 0x5bd38, 0x5b8a9, 0x5b419, 0x5af8a, 0x5aafc, 0x5a66e, 0x5a1e1, 0x59d54,
- 0x598c7, 0x5943b, 0x58fb0, 0x58b24, 0x5869a, 0x58210, 0x57d86, 0x578fd,
- 0x57474, 0x56feb, 0x56b64, 0x566dc, 0x56255, 0x55dcf, 0x55949, 0x554c3,
- 0x5503e, 0x54bb9, 0x54735, 0x542b1, 0x53e2e, 0x539ab, 0x53529, 0x530a7,
- 0x52c25, 0x527a4, 0x52324, 0x51ea4, 0x51a24, 0x515a5, 0x51126, 0x50ca8,
- 0x5082a, 0x503ad, 0x4ff30, 0x4fab4, 0x4f638, 0x4f1bc, 0x4ed41, 0x4e8c6,
- 0x4e44c, 0x4dfd3, 0x4db59, 0x4d6e0, 0x4d268, 0x4cdf0, 0x4c979, 0x4c502,
- 0x4c08b, 0x4bc15, 0x4b79f, 0x4b32a, 0x4aeb5, 0x4aa41, 0x4a5cd, 0x4a15a,
- 0x49ce7, 0x49874, 0x49402, 0x48f91, 0x48b1f, 0x486af, 0x4823e, 0x47dce,
- 0x4795f, 0x474f0, 0x47082, 0x46c14, 0x467a6, 0x46339, 0x45ecc, 0x45a60,
- 0x455f4, 0x45189, 0x44d1e, 0x448b3, 0x44449, 0x43fdf, 0x43b76, 0x4370d,
- 0x432a5, 0x42e3d, 0x429d6, 0x4256f, 0x42108, 0x41ca2, 0x4183c, 0x413d7,
- 0x40f72, 0x40b0e, 0x406aa, 0x40247, 0x3fde4, 0x3f981, 0x3f51f, 0x3f0bd,
- 0x3ec5c, 0x3e7fb, 0x3e39b, 0x3df3b, 0x3dadb, 0x3d67c, 0x3d21d, 0x3cdbf,
- 0x3c961, 0x3c504, 0x3c0a7, 0x3bc4a, 0x3b7ee, 0x3b393, 0x3af37, 0x3aadd,
- 0x3a682, 0x3a228, 0x39dcf, 0x39976, 0x3951d, 0x390c5, 0x38c6d, 0x38816,
- 0x383bf, 0x37f69, 0x37b13, 0x376bd, 0x37268, 0x36e13, 0x369bf, 0x3656b,
- 0x36117, 0x35cc4, 0x35872, 0x3541f, 0x34fce, 0x34b7c, 0x3472b, 0x342db,
- 0x33e8b, 0x33a3b, 0x335ec, 0x3319d, 0x32d4f, 0x32901, 0x324b3, 0x32066,
- 0x31c1a, 0x317cd, 0x31381, 0x30f36, 0x30aeb, 0x306a1, 0x30256, 0x2fe0d,
- 0x2f9c3, 0x2f57a, 0x2f132, 0x2ecea, 0x2e8a2, 0x2e45b, 0x2e014, 0x2dbce,
- 0x2d788, 0x2d343, 0x2cefd, 0x2cab9, 0x2c675, 0x2c231, 0x2bded, 0x2b9aa,
- 0x2b568, 0x2b125, 0x2ace4, 0x2a8a2, 0x2a461, 0x2a021, 0x29be1, 0x297a1,
- 0x29362, 0x28f23, 0x28ae4, 0x286a6, 0x28269, 0x27e2c, 0x279ef, 0x275b2,
- 0x27176, 0x26d3b, 0x26900, 0x264c5, 0x2608b, 0x25c51, 0x25817, 0x253de,
- 0x24fa6, 0x24b6d, 0x24735, 0x242fe, 0x23ec7, 0x23a90, 0x2365a, 0x23224,
- 0x22def, 0x229ba, 0x22585, 0x22151, 0x21d1d, 0x218ea, 0x214b7, 0x21084,
- 0x20c52, 0x20821, 0x203ef, 0x1ffbe, 0x1fb8e, 0x1f75e, 0x1f32e, 0x1eeff,
- 0x1ead0, 0x1e6a1, 0x1e273, 0x1de45, 0x1da18, 0x1d5eb, 0x1d1bf, 0x1cd93,
- 0x1c967, 0x1c53c, 0x1c111, 0x1bce6, 0x1b8bc, 0x1b493, 0x1b069, 0x1ac40,
- 0x1a818, 0x1a3f0, 0x19fc8, 0x19ba1, 0x1977a, 0x19354, 0x18f2d, 0x18b08,
- 0x186e2, 0x182be, 0x17e99, 0x17a75, 0x17651, 0x1722e, 0x16e0b, 0x169e9,
- 0x165c6, 0x161a5, 0x15d83, 0x15963, 0x15542, 0x15122, 0x14d02, 0x148e3,
- 0x144c4, 0x140a5, 0x13c87, 0x13869, 0x1344c, 0x1302f, 0x12c12, 0x127f6,
- 0x123da, 0x11fbf, 0x11ba4, 0x11789, 0x1136f, 0x10f55, 0x10b3c, 0x10723,
- 0x1030a, 0xfef2, 0xfada, 0xf6c2, 0xf2ab, 0xee95, 0xea7e, 0xe668,
- 0xe253, 0xde3e, 0xda29, 0xd614, 0xd200, 0xcded, 0xc9da, 0xc5c7,
- 0xc1b4, 0xbda2, 0xb990, 0xb57f, 0xb16e, 0xad5e, 0xa94e, 0xa53e,
- 0xa12e, 0x9d1f, 0x9911, 0x9503, 0x90f5, 0x8ce7, 0x88da, 0x84ce,
- 0x80c1, 0x7cb5, 0x78aa, 0x749f, 0x7094, 0x6c89, 0x687f, 0x6476,
- 0x606d, 0x5c64, 0x585b, 0x5453, 0x504b, 0x4c44, 0x483d, 0x4436,
- 0x4030, 0x3c2a, 0x3825, 0x3420, 0x301b, 0x2c17, 0x2813, 0x240f,
- 0x200c, 0x1c09, 0x1807, 0x1405, 0x1003, 0xc02, 0x801, 0x400,
- 0x7fffff, 0x7ff001, 0x7fe006, 0x7fd00d, 0x7fc018, 0x7fb025, 0x7fa036, 0x7f9049,
- 0x7f8060, 0x7f7079, 0x7f6095, 0x7f50b5, 0x7f40d7, 0x7f30fc, 0x7f2124, 0x7f114f,
- 0x7f017e, 0x7ef1af, 0x7ee1e2, 0x7ed219, 0x7ec253, 0x7eb290, 0x7ea2d0, 0x7e9312,
- 0x7e8358, 0x7e73a0, 0x7e63eb, 0x7e543a, 0x7e448b, 0x7e34df, 0x7e2536, 0x7e1590,
- 0x7e05ec, 0x7df64c, 0x7de6ae, 0x7dd714, 0x7dc77c, 0x7db7e7, 0x7da855, 0x7d98c6,
- 0x7d893a, 0x7d79b0, 0x7d6a2a, 0x7d5aa6, 0x7d4b25, 0x7d3ba7, 0x7d2c2c, 0x7d1cb3,
- 0x7d0d3e, 0x7cfdcb, 0x7cee5b, 0x7cdeee, 0x7ccf84, 0x7cc01d, 0x7cb0b8, 0x7ca156,
- 0x7c91f7, 0x7c829b, 0x7c7342, 0x7c63eb, 0x7c5497, 0x7c4546, 0x7c35f8, 0x7c26ad,
- 0x7c1764, 0x7c081e, 0x7bf8db, 0x7be99b, 0x7bda5d, 0x7bcb23, 0x7bbbeb, 0x7bacb5,
- 0x7b9d83, 0x7b8e53, 0x7b7f26, 0x7b6ffc, 0x7b60d4, 0x7b51b0, 0x7b428e, 0x7b336e,
- 0x7b2452, 0x7b1538, 0x7b0621, 0x7af70c, 0x7ae7fb, 0x7ad8ec, 0x7ac9e0, 0x7abad6,
- 0x7aabcf, 0x7a9ccb, 0x7a8dca, 0x7a7ecb, 0x7a6fcf, 0x7a60d5, 0x7a51df, 0x7a42eb,
- 0x7a33f9, 0x7a250b, 0x7a161f, 0x7a0735, 0x79f84f, 0x79e96b, 0x79da89, 0x79cbab,
- 0x79bccf, 0x79adf5, 0x799f1f, 0x79904a, 0x798179, 0x7972aa, 0x7963de, 0x795515,
- 0x79464e, 0x793789, 0x7928c8, 0x791a09, 0x790b4c, 0x78fc92, 0x78eddb, 0x78df27,
- 0x78d075, 0x78c1c5, 0x78b319, 0x78a46e, 0x7895c7, 0x788722, 0x78787f, 0x7869e0,
- 0x785b42, 0x784ca8, 0x783e10, 0x782f7a, 0x7820e7, 0x781257, 0x7803c9, 0x77f53e,
- 0x77e6b5, 0x77d82f, 0x77c9ab, 0x77bb2a, 0x77acac, 0x779e30, 0x778fb6, 0x77813f,
- 0x7772cb, 0x776459, 0x7755ea, 0x77477d, 0x773913, 0x772aab, 0x771c46, 0x770de3,
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- 0x48d2ab, 0x48caf2, 0x48c33a, 0x48bb83, 0x48b3cd, 0x48ac18, 0x48a463, 0x489cb0,
- 0x4894fd, 0x488d4b, 0x48859a, 0x487dea, 0x48763b, 0x486e8d, 0x4866df, 0x485f33,
- 0x485787, 0x484fdd, 0x484833, 0x48408a, 0x4838e2, 0x48313b, 0x482994, 0x4821ef,
- 0x481a4a, 0x4812a6, 0x480b04, 0x480362, 0x47fbc1, 0x47f420, 0x47ec81, 0x47e4e3,
- 0x47dd45, 0x47d5a8, 0x47ce0c, 0x47c672, 0x47bed7, 0x47b73e, 0x47afa6, 0x47a80e,
- 0x47a078, 0x4798e2, 0x47914d, 0x4789b9, 0x478226, 0x477a93, 0x477302, 0x476b71,
- 0x4763e2, 0x475c53, 0x4754c5, 0x474d37, 0x4745ab, 0x473e20, 0x473695, 0x472f0b,
- 0x472783, 0x471ffa, 0x471873, 0x4710ed, 0x470968, 0x4701e3, 0x46fa5f, 0x46f2dc,
- 0x46eb5a, 0x46e3d9, 0x46dc59, 0x46d4d9, 0x46cd5a, 0x46c5dd, 0x46be60, 0x46b6e4,
- 0x46af68, 0x46a7ee, 0x46a074, 0x4698fb, 0x469184, 0x468a0c, 0x468296, 0x467b21,
- 0x4673ac, 0x466c39, 0x4664c6, 0x465d54, 0x4655e3, 0x464e72, 0x464703, 0x463f94,
- 0x463826, 0x4630b9, 0x46294d, 0x4621e2, 0x461a77, 0x46130e, 0x460ba5, 0x46043d,
- 0x45fcd6, 0x45f56f, 0x45ee0a, 0x45e6a5, 0x45df41, 0x45d7de, 0x45d07c, 0x45c91a,
- 0x45c1ba, 0x45ba5a, 0x45b2fb, 0x45ab9d, 0x45a440, 0x459ce4, 0x459588, 0x458e2d,
- 0x4586d3, 0x457f7a, 0x457822, 0x4570ca, 0x456974, 0x45621e, 0x455ac9, 0x455374,
- 0x454c21, 0x4544ce, 0x453d7d, 0x45362c, 0x452edb, 0x45278c, 0x45203e, 0x4518f0,
- 0x4511a3, 0x450a57, 0x45030c, 0x44fbc1, 0x44f477, 0x44ed2e, 0x44e5e6, 0x44de9f,
- 0x44d759, 0x44d013, 0x44c8ce, 0x44c18a, 0x44ba47, 0x44b305, 0x44abc3, 0x44a482,
- 0x449d42, 0x449603, 0x448ec5, 0x448787, 0x44804a, 0x44790e, 0x4471d3, 0x446a99,
- 0x44635f, 0x445c26, 0x4454ee, 0x444db7, 0x444681, 0x443f4b, 0x443816, 0x4430e2,
- 0x4429af, 0x44227c, 0x441b4b, 0x44141a, 0x440cea, 0x4405ba, 0x43fe8c, 0x43f75e,
- 0x43f031, 0x43e905, 0x43e1da, 0x43daaf, 0x43d385, 0x43cc5c, 0x43c534, 0x43be0d,
- 0x43b6e6, 0x43afc0, 0x43a89b, 0x43a177, 0x439a54, 0x439331, 0x438c0f, 0x4384ee,
- 0x437dcd, 0x4376ae, 0x436f8f, 0x436871, 0x436154, 0x435a37, 0x43531b, 0x434c00,
- 0x4344e6, 0x433dcd, 0x4336b4, 0x432f9c, 0x432885, 0x43216f, 0x431a5a, 0x431345,
- 0x430c31, 0x43051e, 0x42fe0b, 0x42f6f9, 0x42efe9, 0x42e8d8, 0x42e1c9, 0x42daba,
- 0x42d3ad, 0x42cca0, 0x42c593, 0x42be88, 0x42b77d, 0x42b073, 0x42a96a, 0x42a261,
- 0x429b59, 0x429452, 0x428d4c, 0x428647, 0x427f42, 0x42783e, 0x42713b, 0x426a39,
- 0x426337, 0x425c36, 0x425536, 0x424e37, 0x424738, 0x42403a, 0x42393d, 0x423241,
- 0x422b45, 0x42244a, 0x421d50, 0x421657, 0x420f5e, 0x420866, 0x42016f, 0x41fa79,
- 0x41f383, 0x41ec8e, 0x41e59a, 0x41dea7, 0x41d7b4, 0x41d0c2, 0x41c9d1, 0x41c2e1,
- 0x41bbf1, 0x41b503, 0x41ae14, 0x41a727, 0x41a03a, 0x41994e, 0x419263, 0x418b79,
- 0x41848f, 0x417da6, 0x4176be, 0x416fd7, 0x4168f0, 0x41620a, 0x415b25, 0x415440,
- 0x414d5c, 0x414679, 0x413f97, 0x4138b6, 0x4131d5, 0x412af5, 0x412415, 0x411d37,
- 0x411659, 0x410f7c, 0x41089f, 0x4101c3, 0x40fae9, 0x40f40e, 0x40ed35, 0x40e65c,
- 0x40df84, 0x40d8ad, 0x40d1d6, 0x40cb00, 0x40c42b, 0x40bd57, 0x40b683, 0x40afb0,
- 0x40a8de, 0x40a20c, 0x409b3b, 0x40946b, 0x408d9c, 0x4086cd, 0x408000, 0x407932,
- 0x407266, 0x406b9a, 0x4064cf, 0x405e05, 0x40573b, 0x405072, 0x4049aa, 0x4042e3,
- 0x403c1c, 0x403556, 0x402e91, 0x4027cc, 0x402109, 0x401a45, 0x401383, 0x400cc1,
- 0x400600, 0x3fff40, 0x3ff880, 0x3ff1c2, 0x3feb03, 0x3fe446, 0x3fdd89, 0x3fd6cd,
- 0x3fd012, 0x3fc957, 0x3fc29d, 0x3fbbe4, 0x3fb52c, 0x3fae74, 0x3fa7bd, 0x3fa107,
- 0x3f9a51, 0x3f939c, 0x3f8ce8, 0x3f8634, 0x3f7f81, 0x3f78cf, 0x3f721e, 0x3f6b6d,
- 0x3f64bd, 0x3f5e0e, 0x3f575f, 0x3f50b1, 0x3f4a04, 0x3f4357, 0x3f3cac, 0x3f3601,
- 0x3f2f56, 0x3f28ac, 0x3f2203, 0x3f1b5b, 0x3f14b3, 0x3f0e0c, 0x3f0766, 0x3f00c1,
- 0x3efa1c, 0x3ef377, 0x3eecd4, 0x3ee631, 0x3edf8f, 0x3ed8ee, 0x3ed24d, 0x3ecbad,
- 0x3ec50e, 0x3ebe6f, 0x3eb7d1, 0x3eb134, 0x3eaa97, 0x3ea3fb, 0x3e9d60, 0x3e96c6,
- 0x3e902c, 0x3e8993, 0x3e82fa, 0x3e7c62, 0x3e75cb, 0x3e6f35, 0x3e689f, 0x3e620a,
- 0x3e5b76, 0x3e54e2, 0x3e4e4f, 0x3e47bd, 0x3e412b, 0x3e3a9a, 0x3e340a, 0x3e2d7a,
- 0x3e26eb, 0x3e205d, 0x3e19cf, 0x3e1342, 0x3e0cb6, 0x3e062b, 0x3dffa0, 0x3df916,
- 0x3df28c, 0x3dec03, 0x3de57b, 0x3ddef4, 0x3dd86d, 0x3dd1e7, 0x3dcb61, 0x3dc4dc,
- 0x3dbe58, 0x3db7d5, 0x3db152, 0x3daad0, 0x3da44f, 0x3d9dce, 0x3d974e, 0x3d90ce,
- 0x3d8a4f, 0x3d83d1, 0x3d7d54, 0x3d76d7, 0x3d705b, 0x3d69e0, 0x3d6365, 0x3d5ceb,
- 0x3d5671, 0x3d4ff9, 0x3d4980, 0x3d4309, 0x3d3c92, 0x3d361c, 0x3d2fa7, 0x3d2932,
- 0x3d22be, 0x3d1c4a, 0x3d15d7, 0x3d0f65, 0x3d08f4, 0x3d0283, 0x3cfc13, 0x3cf5a3,
- 0x3cef34, 0x3ce8c6, 0x3ce259, 0x3cdbec, 0x3cd57f, 0x3ccf14, 0x3cc8a9, 0x3cc23f,
- 0x3cbbd5, 0x3cb56c, 0x3caf04, 0x3ca89c, 0x3ca235, 0x3c9bcf, 0x3c9569, 0x3c8f04,
- 0x3c889f, 0x3c823c, 0x3c7bd8, 0x3c7576, 0x3c6f14, 0x3c68b3, 0x3c6253, 0x3c5bf3,
- 0x3c5593, 0x3c4f35, 0x3c48d7, 0x3c427a, 0x3c3c1d, 0x3c35c1, 0x3c2f66, 0x3c290b,
- 0x3c22b1, 0x3c1c57, 0x3c15ff, 0x3c0fa7, 0x3c094f, 0x3c02f8, 0x3bfca2, 0x3bf64c,
- 0x3beff7, 0x3be9a3, 0x3be34f, 0x3bdcfc, 0x3bd6aa, 0x3bd058, 0x3bca07, 0x3bc3b7,
- 0x3bbd67, 0x3bb718, 0x3bb0c9, 0x3baa7b, 0x3ba42e, 0x3b9de1, 0x3b9795, 0x3b914a,
- 0x3b8aff, 0x3b84b5, 0x3b7e6c, 0x3b7823, 0x3b71db, 0x3b6b93, 0x3b654c, 0x3b5f06,
- 0x3b58c0, 0x3b527b, 0x3b4c36, 0x3b45f3, 0x3b3faf, 0x3b396d, 0x3b332b, 0x3b2cea,
- 0x3b26a9, 0x3b2069, 0x3b1a2a, 0x3b13eb, 0x3b0dad, 0x3b076f, 0x3b0132, 0x3afaf6,
- 0x3af4ba, 0x3aee7f, 0x3ae845, 0x3ae20b, 0x3adbd2, 0x3ad599, 0x3acf61, 0x3ac92a,
- 0x3ac2f3, 0x3abcbd, 0x3ab688, 0x3ab053, 0x3aaa1f, 0x3aa3eb, 0x3a9db8, 0x3a9786,
- 0x3a9154, 0x3a8b23, 0x3a84f2, 0x3a7ec2, 0x3a7893, 0x3a7264, 0x3a6c36, 0x3a6609,
- 0x3a5fdc, 0x3a59b0, 0x3a5384, 0x3a4d59, 0x3a472f, 0x3a4105, 0x3a3adc, 0x3a34b4,
- 0x3a2e8c, 0x3a2864, 0x3a223e, 0x3a1c18, 0x3a15f2, 0x3a0fcd, 0x3a09a9, 0x3a0385,
- 0x39fd62, 0x39f740, 0x39f11e, 0x39eafd, 0x39e4dc, 0x39debc, 0x39d89d, 0x39d27e,
- 0x39cc60, 0x39c642, 0x39c025, 0x39ba09, 0x39b3ed, 0x39add2, 0x39a7b7, 0x39a19d,
- 0x399b84, 0x39956b, 0x398f53, 0x39893b, 0x398324, 0x397d0e, 0x3976f8, 0x3970e3,
- 0x396ace, 0x3964ba, 0x395ea7, 0x395894, 0x395282, 0x394c70, 0x39465f, 0x39404f,
- 0x393a3f, 0x393430, 0x392e21, 0x392813, 0x392206, 0x391bf9, 0x3915ed, 0x390fe1,
- 0x3909d6, 0x3903cb, 0x38fdc1, 0x38f7b8, 0x38f1af, 0x38eba7, 0x38e5a0, 0x38df99,
- 0x38d993, 0x38d38d, 0x38cd88, 0x38c783, 0x38c17f, 0x38bb7c, 0x38b579, 0x38af77,
- 0x38a975, 0x38a374, 0x389d73, 0x389774, 0x389174, 0x388b76, 0x388577, 0x387f7a,
- 0x38797d, 0x387381, 0x386d85, 0x38678a, 0x38618f, 0x385b95, 0x38559b, 0x384fa2,
- 0x3849aa, 0x3843b2, 0x383dbb, 0x3837c5, 0x3831cf, 0x382bd9, 0x3825e4, 0x381ff0,
- 0x3819fd, 0x381409, 0x380e17, 0x380825, 0x380234, 0x37fc43, 0x37f653, 0x37f063,
- 0x37ea74, 0x37e485, 0x37de97, 0x37d8aa, 0x37d2bd, 0x37ccd1, 0x37c6e5, 0x37c0fa,
- 0x37bb10, 0x37b526, 0x37af3d, 0x37a954, 0x37a36c, 0x379d84, 0x37979d, 0x3791b6,
- 0x378bd0, 0x3785eb, 0x378006, 0x377a22, 0x37743e, 0x376e5b, 0x376879, 0x376297,
- 0x375cb5, 0x3756d5, 0x3750f4, 0x374b15, 0x374535, 0x373f57, 0x373979, 0x37339b,
- 0x372dbf, 0x3727e2, 0x372206, 0x371c2b, 0x371651, 0x371077, 0x370a9d, 0x3704c4,
- 0x36feec, 0x36f914, 0x36f33d, 0x36ed66, 0x36e790, 0x36e1ba, 0x36dbe5, 0x36d611,
- 0x36d03d, 0x36ca69, 0x36c497, 0x36bec4, 0x36b8f3, 0x36b321, 0x36ad51, 0x36a781,
- 0x36a1b1, 0x369be2, 0x369614, 0x369046, 0x368a79, 0x3684ac, 0x367ee0, 0x367915,
- 0x36734a, 0x366d7f, 0x3667b5, 0x3661ec, 0x365c23, 0x36565b, 0x365093, 0x364acc,
- 0x364505, 0x363f3f, 0x363979, 0x3633b4, 0x362df0, 0x36282c, 0x362269, 0x361ca6,
- 0x3616e4, 0x361122, 0x360b61, 0x3605a0, 0x35ffe0, 0x35fa20, 0x35f461, 0x35eea3,
- 0x35e8e5, 0x35e328, 0x35dd6b, 0x35d7af, 0x35d1f3, 0x35cc38, 0x35c67d, 0x35c0c3,
- 0x35bb09, 0x35b550, 0x35af98, 0x35a9e0, 0x35a429, 0x359e72, 0x3598bb, 0x359306,
- 0x358d50, 0x35879c, 0x3581e8, 0x357c34, 0x357681, 0x3570ce, 0x356b1c, 0x35656b,
- 0x355fba, 0x355a09, 0x355459, 0x354eaa, 0x3548fb, 0x35434d, 0x353d9f, 0x3537f2,
- 0x353245, 0x352c99, 0x3526ee, 0x352143, 0x351b98, 0x3515ee, 0x351045, 0x350a9c
- }
-};
-
-
-
-/* Shortcuts so we dont have to bother with the structure in C */
-
-/* Pointer to exponential table */
-const unsigned int *
-gmx_invsqrt_exptab = F77_FUNC(gmxinvsqrtdata, GMXINVSQRTDATA).exptab;
-
-/* Pointer to fraction table */
-const unsigned int *
-gmx_invsqrt_fracttab = F77_FUNC(gmxinvsqrtdata, GMXINVSQRTDATA).fracttab;
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#include "conformation-utilities.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "conformation-utilities.h"
#include <math.h>
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
static real dist2(t_pbc *pbc, rvec x, rvec y)
{
#ifndef GMX_CONFORMATION_UTILITIES_H
#define GMX_CONFORMATION_UTILITIES_H
-#include "typedefs.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "copyrite.h"
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/copyrite.h"
-#ifdef HAVE_CONFIG_H
#include "config.h"
-#endif
#include <stdio.h>
#include <stdlib.h>
#ifdef HAVE_LIBMKL
#include <mkl.h>
#endif
-
#ifdef HAVE_EXTRAE
- #include "extrae_user_events.h"
+#include <extrae_user_events.h>
#endif
-
#include <boost/version.hpp>
/* This file is completely threadsafe - keep it that way! */
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/vec.h"
-
+#include "buildinfo.h"
#include "gromacs/fft/fft.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/strdb.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
#include "gromacs/utility/baseversion.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
-
-#include "buildinfo.h"
+#include "gromacs/utility/stringutil.h"
static gmx_bool be_cool(void)
{
};
static const char * const CopyrightText[] = {
"Copyright (c) 1991-2000, University of Groningen, The Netherlands.",
- "Copyright (c) 2001-2014, The GROMACS development team at",
+ "Copyright (c) 2001-2015, The GROMACS development team at",
"Uppsala University, Stockholm University and",
"the Royal Institute of Technology, Sweden.",
"check out http://www.gromacs.org for more information."
fprintf(fp, "MPI library: none\n");
#endif
#ifdef GMX_OPENMP
- fprintf(fp, "OpenMP support: enabled\n");
+ fprintf(fp, "OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = %d)\n", GMX_OPENMP_MAX_THREADS);
#else
fprintf(fp, "OpenMP support: disabled\n");
#endif
#define gmx_stringify2(x) #x
#define gmx_stringify(x) gmx_stringify2(x)
fprintf(fp, "invsqrt routine: %s\n", gmx_stringify(gmx_invsqrt(x)));
-#ifndef __MIC__
fprintf(fp, "SIMD instructions: %s\n", GMX_SIMD_STRING);
-#else
- fprintf(fp, "SIMD instructions: %s\n", "Intel MIC");
-#endif
-
fprintf(fp, "FFT library: %s\n", gmx_fft_get_version_info());
#ifdef HAVE_RDTSCP
fprintf(fp, "RDTSCP usage: enabled\n");
fprintf(fp, "%sGROMACS: %s, %s%s%s\n", prefix, name,
gmx_version(), precisionString, suffix);
const char *const binaryPath = programContext.fullBinaryPath();
- if (binaryPath != NULL && binaryPath[0] != '\0')
+ if (!gmx::isNullOrEmpty(binaryPath))
{
fprintf(fp, "%sExecutable: %s%s\n", prefix, binaryPath, suffix);
}
- const char *const libraryPath = programContext.defaultLibraryDataPath();
- if (libraryPath != NULL && libraryPath[0] != '\0')
+ const gmx::InstallationPrefixInfo installPrefix = programContext.installationPrefix();
+ if (!gmx::isNullOrEmpty(installPrefix.path))
{
- fprintf(fp, "%sLibrary dir: %s%s\n", prefix, libraryPath, suffix);
+ fprintf(fp, "%sData prefix: %s%s%s\n", prefix, installPrefix.path,
+ installPrefix.bSourceLayout ? " (source tree)" : "", suffix);
}
const char *const commandLine = programContext.commandLine();
- if (commandLine != NULL && commandLine[0] != '\0')
+ if (!gmx::isNullOrEmpty(commandLine))
{
fprintf(fp, "%sCommand line:%s\n%s %s%s\n",
prefix, suffix, prefix, commandLine, suffix);
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012, by the GROMACS development team, led by
+# Copyright (c) 2012,2014, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
if(GMX_GPU)
file(GLOB CUDA_TOOLS_SOURCES *.cu)
- CUDA_ADD_LIBRARY(cuda_tools STATIC ${CUDA_TOOLS_SOURCES}
- OPTIONS
- RELWITHDEBINFO -g
- DEBUG -g -D_DEBUG_=1)
+ set(GMXLIB_SOURCES ${GMXLIB_SOURCES} ${CUDA_TOOLS_SOURCES} PARENT_SCOPE)
endif()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <stdio.h>
+
#include <cuda.h>
#include <cuda_runtime_api.h>
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
+#include "cudautils.cuh"
+
#include <stdlib.h>
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "cudautils.cuh"
/*** Generic CUDA data operation wrappers ***/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef CUDAUTILS_CUH
#define CUDAUTILS_CUH
+#include "config.h"
+
#include <stdio.h>
+#ifdef HAVE_NVML
+#include <nvml.h>
+#endif /* HAVE_NVML */
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/* CUDA library and hardware related defines */
/* TODO list some constants instead that can be used for consistency checks to
} \
} while (0)
+/*! Check for NVML error on the return status of a NVML API call. */
+#ifdef HAVE_NVML
+#define HANDLE_NVML_RET_ERR(status, msg) \
+ do { \
+ if (status != NVML_SUCCESS) \
+ { \
+ gmx_warning("%s: %s\n", msg, nvmlErrorString(status)); \
+ } \
+ } while (0)
+#endif /* HAVE_NVML */
#else
#define CU_RET_ERR(status, msg) do { } while (0)
#define CU_CHECK_PREV_ERR() do { } while (0)
#define CU_LAUNCH_ERR(msg) do { } while (0)
#define CU_LAUNCH_ERR_SYNC(msg) do { } while (0)
+#define HANDLE_NVML_RET_ERR(status, msg) do { } while (0)
#endif /* CHECK_CUDA_ERRORS */
typedef struct cuda_dev_info cuda_dev_info_t;
struct cuda_dev_info
{
- int id; /* id of the CUDA device */
- cudaDeviceProp prop; /* CUDA device properties */
- int stat; /* result of the device check */
+ int id; /* id of the CUDA device */
+ cudaDeviceProp prop; /* CUDA device properties */
+ int stat; /* result of the device check */
+ gmx_bool nvml_initialized; /* If NVML was initialized */
+ gmx_bool nvml_ap_clocks_changed; /* If application clocks have been changed */
+#ifdef HAVE_NVML
+ nvmlDevice_t nvml_device_id; /* NVML device id */
+ nvmlEnableState_t nvml_is_restricted; /* Status of application clocks permission */
+#endif /* HAVE_NVML */
};
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include <stdlib.h>
+#include "gmxpre.h"
-#include "cudautils.cuh"
#include "pmalloc_cuda.h"
+#include <stdlib.h>
+
+#include "gromacs/gmxlib/cuda_tools/cudautils.cuh"
+#include "gromacs/utility/cstringutil.h"
+
/*! Allocates nbytes of page-locked memory.
* This memory should always be freed using pfree (or with the page-locked
* free functions provied by the CUDA library).
#ifndef PMALLOC_CUDA_H
#define PMALLOC_CUDA_H
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "config.h"
#include <stdlib.h>
-#include "types/simple.h"
+
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef GMX_GPU
#define FUNC_TERM ;
extern "C" {
#endif
-/*! Allocates nbytes of page-locked memory. */
+/** Allocates nbytes of page-locked memory. */
void pmalloc(void gmx_unused **h_ptr, size_t gmx_unused nbytes) FUNC_TERM
-/*! Allocates nbytes of page-locked memory with write-combining. */
+/** Allocates nbytes of page-locked memory with write-combining. */
void pmalloc_wc(void gmx_unused **h_ptr, size_t gmx_unused nbytes) FUNC_TERM
-/*! Frees page locked memory allocated with pmalloc. */
+/** Frees page locked memory allocated with pmalloc. */
void pfree(void gmx_unused *h_ptr) FUNC_TERM
#ifdef __cplusplus
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/disre.h"
+
+#include "config.h"
#include <math.h>
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "sysstuff.h"
+#include <stdlib.h>
+
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "gromacs/fileio/futil.h"
-#include "xvgr.h"
-#include "gmx_fatal.h"
-#include "bondf.h"
-#include "copyrite.h"
-#include "disre.h"
-#include "main.h"
-#include "mtop_util.h"
void init_disres(FILE *fplog, const gmx_mtop_t *mtop,
t_inputrec *ir, const t_commrec *cr,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#ifdef HAVE_SCHED_H
-# ifndef _GNU_SOURCE
-# define _GNU_SOURCE 1
-# endif
-# include <sched.h>
+/*! \cond */
+#include "gromacs/legacyheaders/gmx_cpuid.h"
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
#endif
+#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include <ctype.h>
+
#ifdef GMX_NATIVE_WINDOWS
/* MSVC definition for __cpuid() */
#ifdef _MSC_VER
/* sysinfo functions */
#include <windows.h>
#endif
+#ifdef HAVE_SCHED_H
+ #include <sched.h>
+#endif
#ifdef HAVE_UNISTD_H
/* sysconf() definition */
#include <unistd.h>
#endif
-#include "gmx_cpuid.h"
-
-
/* For convenience, and to enable configure-time invocation, we keep all architectures
* in a single file, but to avoid repeated ifdefs we set the overall architecture here.
"GenuineIntel",
"AuthenticAMD",
"Fujitsu",
- "IBM"
+ "IBM", /* Used on Power and BlueGene/Q */
+ "ARM"
};
const char *
"GenuineIntel",
"AuthenticAMD",
"Fujitsu",
- "ibm" /* Used on BlueGene/Q */
+ "ibm", /* Used on Power and BlueGene/Q */
+ "AArch64"
};
const char *
"ssse3",
"tdt",
"x2apic",
- "xop"
+ "xop",
+ "arm_neon",
+ "arm_neon_asimd",
+ "QPX",
+ "VMX",
+ "VSX"
};
const char *
"AVX_256",
"AVX2_256",
"Sparc64 HPC-ACE",
- "IBM_QPX"
+ "IBM_QPX",
+ "IBM_VMX",
+ "IBM_VSX",
+ "ARM_NEON",
+ "ARM_NEON_ASIMD"
};
/* Max length of brand string */
-#define GMX_CPUID_BRAND_MAXLEN 256
+#define GMX_CPUID_STRLEN 256
/* Contents of the abstract datatype */
struct gmx_cpuid
{
enum gmx_cpuid_vendor vendor;
- char brand[GMX_CPUID_BRAND_MAXLEN];
+ char brand[GMX_CPUID_STRLEN];
int family;
int model;
int stepping;
static const enum gmx_cpuid_simd compiled_simd = GMX_CPUID_SIMD_X86_SSE4_1;
#elif defined GMX_SIMD_X86_SSE2
static const enum gmx_cpuid_simd compiled_simd = GMX_CPUID_SIMD_X86_SSE2;
+#elif defined GMX_SIMD_ARM_NEON
+static const enum gmx_cpuid_simd compiled_simd = GMX_CPUID_SIMD_ARM_NEON;
+#elif defined GMX_SIMD_ARM_NEON_ASIMD
+static const enum gmx_cpuid_simd compiled_simd = GMX_CPUID_SIMD_ARM_NEON_ASIMD;
#elif defined GMX_SIMD_SPARC64_HPC_ACE
static const enum gmx_cpuid_simd compiled_simd = GMX_CPUID_SIMD_SPARC64_HPC_ACE;
#elif defined GMX_SIMD_IBM_QPX
static const enum gmx_cpuid_simd compiled_simd = GMX_CPUID_SIMD_IBM_QPX;
+#elif defined GMX_SIMD_IBM_VMX
+static const enum gmx_cpuid_simd compiled_simd = GMX_CPUID_SIMD_IBM_VMX;
+#elif defined GMX_SIMD_IBM_VSX
+static const enum gmx_cpuid_simd compiled_simd = GMX_CPUID_SIMD_IBM_VSX;
#elif defined GMX_SIMD_REFERENCE
static const enum gmx_cpuid_simd compiled_simd = GMX_CPUID_SIMD_REFERENCE;
#else
{
int fn, max_stdfn, max_extfn;
unsigned int eax, ebx, ecx, edx;
- char str[GMX_CPUID_BRAND_MAXLEN];
+ char str[GMX_CPUID_STRLEN];
char * p;
/* Find largest standard/extended function input value */
{
p++;
}
- strncpy(cpuid->brand, p, GMX_CPUID_BRAND_MAXLEN);
+ strncpy(cpuid->brand, p, GMX_CPUID_STRLEN);
}
else
{
- strncpy(cpuid->brand, "Unknown CPU brand", GMX_CPUID_BRAND_MAXLEN);
+ strncpy(cpuid->brand, "Unknown CPU brand", GMX_CPUID_STRLEN);
}
/* Find basic CPU properties */
}
}
}
+ free(unique);
return nunique;
}
-
static void
chomp_substring_before_colon(const char *in, char *s, int maxlength)
{
}
}
+static int
+cpuid_check_arm(gmx_cpuid_t cpuid)
+{
+#if defined(__linux__) || defined(__linux)
+ FILE *fp;
+ char buffer[GMX_CPUID_STRLEN], buffer2[GMX_CPUID_STRLEN], buffer3[GMX_CPUID_STRLEN];
+
+ if ( (fp = fopen("/proc/cpuinfo", "r")) != NULL)
+ {
+ while ( (fgets(buffer, sizeof(buffer), fp) != NULL))
+ {
+ chomp_substring_before_colon(buffer, buffer2, GMX_CPUID_STRLEN);
+ chomp_substring_after_colon(buffer, buffer3, GMX_CPUID_STRLEN);
+
+ if (!strcmp(buffer2, "Processor"))
+ {
+ strncpy(cpuid->brand, buffer3, GMX_CPUID_STRLEN);
+ }
+ else if (!strcmp(buffer2, "CPU architecture"))
+ {
+ cpuid->family = strtol(buffer3, NULL, 10);
+ if (!strcmp(buffer3, "AArch64"))
+ {
+ cpuid->family = 8;
+ }
+ }
+ else if (!strcmp(buffer2, "CPU part"))
+ {
+ cpuid->model = strtol(buffer3, NULL, 16);
+ }
+ else if (!strcmp(buffer2, "CPU revision"))
+ {
+ cpuid->stepping = strtol(buffer3, NULL, 10);
+ }
+ else if (!strcmp(buffer2, "Features") && strstr(buffer3, "neon"))
+ {
+ cpuid->feature[GMX_CPUID_FEATURE_ARM_NEON] = 1;
+ }
+ else if (!strcmp(buffer2, "Features") && strstr(buffer3, "asimd"))
+ {
+ cpuid->feature[GMX_CPUID_FEATURE_ARM_NEON_ASIMD] = 1;
+ }
+ }
+ }
+ fclose(fp);
+#else
+# ifdef __aarch64__
+ /* Strange 64-bit non-linux platform. However, since NEON ASIMD is present on all
+ * implementations of AArch64 this far, we assume it is present for now.
+ */
+ cpuid->feature[GMX_CPUID_FEATURE_ARM_NEON_ASIMD] = 1;
+# else
+ /* Strange 32-bit non-linux platform. We cannot assume that neon is present. */
+ cpuid->feature[GMX_CPUID_FEATURE_ARM_NEON] = 0;
+# endif
+#endif
+ return 0;
+}
+
+
+static int
+cpuid_check_ibm(gmx_cpuid_t cpuid)
+{
+#if defined(__linux__) || defined(__linux)
+ FILE *fp;
+ char buffer[GMX_CPUID_STRLEN], before_colon[GMX_CPUID_STRLEN], after_colon[GMX_CPUID_STRLEN];
+
+ if ( (fp = fopen("/proc/cpuinfo", "r")) != NULL)
+ {
+ while ( (fgets(buffer, sizeof(buffer), fp) != NULL))
+ {
+ chomp_substring_before_colon(buffer, before_colon, GMX_CPUID_STRLEN);
+ chomp_substring_after_colon(buffer, after_colon, GMX_CPUID_STRLEN);
+
+ if (!strcmp(before_colon, "cpu") || !strcmp(before_colon, "Processor"))
+ {
+ strncpy(cpuid->brand, after_colon, GMX_CPUID_STRLEN);
+ }
+ if (!strcmp(before_colon, "model name") ||
+ !strcmp(before_colon, "model") ||
+ !strcmp(before_colon, "Processor") ||
+ !strcmp(before_colon, "cpu"))
+ {
+ if (strstr(after_colon, "altivec"))
+ {
+ cpuid->feature[GMX_CPUID_FEATURE_IBM_VMX] = 1;
+
+ if (!strstr(after_colon, "POWER6") && !strstr(after_colon, "Power6") &&
+ !strstr(after_colon, "power6"))
+ {
+ cpuid->feature[GMX_CPUID_FEATURE_IBM_VSX] = 1;
+ }
+ }
+ }
+ }
+ }
+ fclose(fp);
+
+ if (strstr(cpuid->brand, "A2"))
+ {
+ /* BlueGene/Q */
+ cpuid->feature[GMX_CPUID_FEATURE_IBM_QPX] = 1;
+ }
+#else
+ strncpy(cpuid->brand, "Unknown CPU brand", GMX_CPUID_STRLEN);
+ cpuid->feature[GMX_CPUID_FEATURE_IBM_QPX] = 0;
+ cpuid->feature[GMX_CPUID_FEATURE_IBM_VMX] = 0;
+ cpuid->feature[GMX_CPUID_FEATURE_IBM_VSX] = 0;
+#endif
+ return 0;
+}
+
+
/* Try to find the vendor of the current CPU, so we know what specific
* detection routine to call.
*/
unsigned int eax, ebx, ecx, edx;
char vendorstring[13];
FILE * fp;
- char buffer[255], before_colon[255], after_colon[255];
+ char buffer[GMX_CPUID_STRLEN];
+ char before_colon[GMX_CPUID_STRLEN];
+ char after_colon[GMX_CPUID_STRLEN];
/* Set default first */
vendor = GMX_CPUID_VENDOR_UNKNOWN;
while ( (vendor == GMX_CPUID_VENDOR_UNKNOWN) && (fgets(buffer, sizeof(buffer), fp) != NULL))
{
chomp_substring_before_colon(buffer, before_colon, sizeof(before_colon));
- /* Intel/AMD use "vendor_id", IBM "vendor"(?) or "model". Fujitsu "manufacture". Add others if you have them! */
+ /* Intel/AMD use "vendor_id", IBM "vendor", "model", or "cpu". Fujitsu "manufacture".
+ * On ARM there does not seem to be a vendor, but ARM or AArch64 is listed in the Processor string.
+ * Add others if you have them!
+ */
if (!strcmp(before_colon, "vendor_id")
|| !strcmp(before_colon, "vendor")
|| !strcmp(before_colon, "manufacture")
- || !strcmp(before_colon, "model"))
+ || !strcmp(before_colon, "model")
+ || !strcmp(before_colon, "Processor")
+ || !strcmp(before_colon, "cpu"))
{
chomp_substring_after_colon(buffer, after_colon, sizeof(after_colon));
for (i = GMX_CPUID_VENDOR_UNKNOWN; i < GMX_CPUID_NVENDORS; i++)
vendor = i;
}
}
+ /* If we did not find vendor yet, check if it is IBM:
+ * On some Power/PowerPC systems it only says power, not IBM.
+ */
+ if (vendor == GMX_CPUID_VENDOR_UNKNOWN &&
+ ((strstr(after_colon, "POWER") || strstr(after_colon, "Power") ||
+ strstr(after_colon, "power"))))
+ {
+ vendor = GMX_CPUID_VENDOR_IBM;
+ }
}
}
}
fclose(fp);
+#elif defined(__arm__) || defined (__arm) || defined(__aarch64__)
+ /* If we are using ARM on something that is not linux we have to trust the compiler,
+ * and we cannot get the extra info that might be present in /proc/cpuinfo.
+ */
+ vendor = GMX_CPUID_VENDOR_ARM;
#endif
-
return vendor;
}
gmx_cpuid_t cpuid;
int i;
FILE * fp;
- char buffer[255], buffer2[255];
+ char buffer[GMX_CPUID_STRLEN], buffer2[GMX_CPUID_STRLEN];
int found_brand;
cpuid = malloc(sizeof(*cpuid));
cpuid_check_amd_x86(cpuid);
break;
#endif
+ case GMX_CPUID_VENDOR_ARM:
+ cpuid_check_arm(cpuid);
+ break;
+ case GMX_CPUID_VENDOR_IBM:
+ cpuid_check_ibm(cpuid);
+ break;
default:
/* Default value */
- strncpy(cpuid->brand, "Unknown CPU brand", GMX_CPUID_BRAND_MAXLEN);
+ strncpy(cpuid->brand, "Unknown CPU brand", GMX_CPUID_STRLEN);
#if defined(__linux__) || defined(__linux)
/* General Linux. Try to get CPU type from /proc/cpuinfo */
if ( (fp = fopen("/proc/cpuinfo", "r")) != NULL)
/* Intel uses "model name", Fujitsu and IBM "cpu". */
if (!strcmp(buffer2, "model name") || !strcmp(buffer2, "cpu"))
{
- chomp_substring_after_colon(buffer, cpuid->brand, GMX_CPUID_BRAND_MAXLEN);
+ chomp_substring_after_colon(buffer, cpuid->brand, GMX_CPUID_STRLEN);
found_brand = 1;
}
}
}
else if (gmx_cpuid_vendor(cpuid) == GMX_CPUID_VENDOR_IBM)
{
- if (strstr(gmx_cpuid_brand(cpuid), "A2"))
+ if (gmx_cpuid_feature(cpuid, GMX_CPUID_FEATURE_IBM_QPX))
{
tmpsimd = GMX_CPUID_SIMD_IBM_QPX;
}
+ else if (gmx_cpuid_feature(cpuid, GMX_CPUID_FEATURE_IBM_VSX))
+ {
+ /* VSX is better than VMX, so we check it first */
+ tmpsimd = GMX_CPUID_SIMD_IBM_VSX;
+ }
+ else if (gmx_cpuid_feature(cpuid, GMX_CPUID_FEATURE_IBM_VMX))
+ {
+ tmpsimd = GMX_CPUID_SIMD_IBM_VMX;
+ }
+ }
+ else if (gmx_cpuid_vendor(cpuid) == GMX_CPUID_VENDOR_ARM)
+ {
+ if (gmx_cpuid_feature(cpuid, GMX_CPUID_FEATURE_ARM_NEON_ASIMD))
+ {
+ tmpsimd = GMX_CPUID_SIMD_ARM_NEON_ASIMD;
+ }
+ else if (gmx_cpuid_feature(cpuid, GMX_CPUID_FEATURE_ARM_NEON))
+ {
+ tmpsimd = GMX_CPUID_SIMD_ARM_NEON;
+ }
}
return tmpsimd;
}
}
#endif
+
+/*! \endcond */
* Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at h=ttp://www.gromacs.org.
+ * top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/gmx_detect_hardware.h"
+
+#include "config.h"
-#include <stdlib.h>
#include <assert.h>
+#include <errno.h>
+#include <stdlib.h>
#include <string.h>
+#include <string>
+#include <vector>
+
#ifdef HAVE_UNISTD_H
/* For sysconf */
#include <unistd.h>
#endif
-
-#include "types/enums.h"
-#include "types/hw_info.h"
-#include "types/commrec.h"
-#include "gmx_fatal.h"
-#include "gmx_fatal_collective.h"
-#include "md_logging.h"
-#include "gmx_cpuid.h"
-#include "gromacs/utility/smalloc.h"
-#include "gpu_utils.h"
-#include "copyrite.h"
-#include "gmx_detect_hardware.h"
-#include "main.h"
-#include "md_logging.h"
-#include "gromacs/utility/gmxomp.h"
-#include "gromacs/utility/cstringutil.h"
-
-#include "thread_mpi/threads.h"
-
#ifdef GMX_NATIVE_WINDOWS
#include <windows.h>
#endif
+#include "thread_mpi/threads.h"
+
+#include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/gmx_cpuid.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/hw_info.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/sysinfo.h"
+
+
#ifdef GMX_GPU
const gmx_bool bGPUBinary = TRUE;
#else
}
}
-static void print_gpu_use_stats(FILE *fplog,
- const gmx_gpu_info_t *gpu_info,
- const gmx_gpu_opt_t *gpu_opt,
- const t_commrec *cr)
+/*! \brief Helper function for reporting GPU usage information
+ * in the mdrun log file
+ *
+ * \param[in] gpu_info Pointer to per-node GPU info struct
+ * \param[in] gpu_opt Pointer to per-node GPU options struct
+ * \param[in] numPpRanks Number of PP ranks per node
+ * \return String to write to the log file
+ * \throws std::bad_alloc if out of memory */
+static std::string
+makeGpuUsageReport(const gmx_gpu_info_t *gpu_info,
+ const gmx_gpu_opt_t *gpu_opt,
+ size_t numPpRanks)
{
- char sbuf[STRLEN], stmp[STRLEN];
- int i, ngpu_comp, ngpu_use;
-
- ngpu_comp = gpu_info->ncuda_dev_compatible;
- ngpu_use = gpu_opt->ncuda_dev_use;
+ int ngpu_use = gpu_opt->ncuda_dev_use;
+ int ngpu_comp = gpu_info->ncuda_dev_compatible;
/* Issue a note if GPUs are available but not used */
if (ngpu_comp > 0 && ngpu_use < 1)
{
- sprintf(sbuf,
- "%d compatible GPU%s detected in the system, but none will be used.\n"
- "Consider trying GPU acceleration with the Verlet scheme!",
- ngpu_comp, (ngpu_comp > 1) ? "s" : "");
+ return gmx::formatString("%d compatible GPU%s detected in the system, but none will be used.\n"
+ "Consider trying GPU acceleration with the Verlet scheme!\n",
+ ngpu_comp, (ngpu_comp > 1) ? "s" : "");
}
- else
- {
- int ngpu_use_uniq;
-
- ngpu_use_uniq = gmx_count_gpu_dev_unique(gpu_info, gpu_opt);
- sprintf(sbuf, "%d GPU%s %sselected for this run.\n"
- "Mapping of GPU%s to the %d PP rank%s in this node: ",
- ngpu_use_uniq, (ngpu_use_uniq > 1) ? "s" : "",
- gpu_opt->bUserSet ? "user-" : "auto-",
- (ngpu_use > 1) ? "s" : "",
- cr->nrank_pp_intranode,
- (cr->nrank_pp_intranode > 1) ? "s" : "");
+ std::string output;
+ if (!gpu_opt->bUserSet)
+ {
+ // gpu_opt->cuda_dev_compatible is only populated during auto-selection
+ std::string gpuIdsString =
+ formatAndJoin(gmx::constArrayRefFromArray(gpu_opt->cuda_dev_compatible,
+ gpu_opt->ncuda_dev_compatible),
+ ",", gmx::StringFormatter("%d"));
+ bool bPluralGpus = gpu_opt->ncuda_dev_compatible > 1;
+ output += gmx::formatString("%d compatible GPU%s %s present, with ID%s %s\n",
+ gpu_opt->ncuda_dev_compatible,
+ bPluralGpus ? "s" : "",
+ bPluralGpus ? "are" : "is",
+ bPluralGpus ? "s" : "",
+ gpuIdsString.c_str());
+ }
- for (i = 0; i < ngpu_use; i++)
+ {
+ std::vector<int> gpuIdsInUse;
+ for (int i = 0; i < ngpu_use; i++)
{
- sprintf(stmp, "#%d", get_gpu_device_id(gpu_info, gpu_opt, i));
- if (i < ngpu_use - 1)
- {
- strcat(stmp, ", ");
- }
- strcat(sbuf, stmp);
+ gpuIdsInUse.push_back(get_gpu_device_id(gpu_info, gpu_opt, i));
}
- }
- md_print_info(cr, fplog, "%s\n\n", sbuf);
+ std::string gpuIdsString =
+ formatAndJoin(gpuIdsInUse, ",", gmx::StringFormatter("%d"));
+ int numGpusInUse = gmx_count_gpu_dev_unique(gpu_info, gpu_opt);
+ bool bPluralGpus = numGpusInUse > 1;
+
+ output += gmx::formatString("%d GPU%s %sselected for this run.\n"
+ "Mapping of GPU ID%s to the %d PP rank%s in this node: %s\n",
+ numGpusInUse, bPluralGpus ? "s" : "",
+ gpu_opt->bUserSet ? "user-" : "auto-",
+ bPluralGpus ? "s" : "",
+ numPpRanks,
+ (numPpRanks > 1) ? "s" : "",
+ gpuIdsString.c_str());
+ }
+
+ return output;
}
/* Give a suitable fatal error or warning if the build configuration
const gmx_hw_opt_t *hw_opt,
gmx_bool bUseGPU)
{
- int npppn, ntmpi_pp;
- char sbuf[STRLEN], th_or_proc[STRLEN], th_or_proc_plural[STRLEN], pernode[STRLEN];
+ int npppn;
+ char th_or_proc[STRLEN], th_or_proc_plural[STRLEN], pernode[STRLEN];
gmx_bool btMPI, bMPI, bMaxMpiThreadsSet, bNthreadsAuto, bEmulateGPU;
assert(hwinfo);
return;
}
- btMPI = bMPI = FALSE;
- bNthreadsAuto = FALSE;
#if defined(GMX_THREAD_MPI)
+ bMPI = FALSE;
btMPI = TRUE;
bNthreadsAuto = (hw_opt->nthreads_tmpi < 1);
#elif defined(GMX_LIB_MPI)
- bMPI = TRUE;
+ bMPI = TRUE;
+ btMPI = FALSE;
+ bNthreadsAuto = FALSE;
+#else
+ bMPI = FALSE;
+ btMPI = FALSE;
+ bNthreadsAuto = FALSE;
#endif
/* GPU emulation detection is done later, but we need here as well
if (hwinfo->gpu_info.ncuda_dev_compatible > 0)
{
+ std::string gpuUseageReport;
+ try
+ {
+ gpuUseageReport = makeGpuUsageReport(&hwinfo->gpu_info,
+ &hw_opt->gpu_opt,
+ cr->nrank_pp_intranode);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+
/* NOTE: this print is only for and on one physical node */
- print_gpu_use_stats(fplog, &hwinfo->gpu_info, &hw_opt->gpu_opt, cr);
+ md_print_info(cr, fplog, gpuUseageReport.c_str());
}
/* Need to ensure that we have enough GPUs:
gmx_hw_info_t *gmx_detect_hardware(FILE *fplog, const t_commrec *cr,
gmx_bool bDetectGPUs)
{
- gmx_hw_info_t *hw;
int ret;
/* make sure no one else is doing the same thing */
gmx_gpu_opt_t *gpu_opt)
{
int i;
- const char *env;
char sbuf[STRLEN], stmp[STRLEN];
/* Bail if binary is not compiled with GPU acceleration, but this is either
else
{
pick_compatible_gpus(&hwinfo_g->gpu_info, gpu_opt);
-
- if (gpu_opt->ncuda_dev_use > cr->nrank_pp_intranode)
- {
- /* We picked more GPUs than we can use: limit the number.
- * We print detailed messages about this later in
- * gmx_check_hw_runconf_consistency.
- */
- limit_num_gpus_used(gpu_opt, cr->nrank_pp_intranode);
- }
-
- gpu_opt->bUserSet = FALSE;
+ limit_num_gpus_used(gpu_opt, cr->nrank_pp_intranode);
}
/* If the user asked for a GPU, check whether we have a GPU */
}
}
-static void limit_num_gpus_used(gmx_gpu_opt_t *gpu_opt, int count)
+/* If we detected more compatible GPUs than we can use, limit the
+ * number. We print detailed messages about this later in
+ * gmx_check_hw_runconf_consistency.
+ */
+static void limit_num_gpus_used(gmx_gpu_opt_t *gpu_opt, int maxNumberToUse)
{
- int ndev_use;
-
- assert(gpu_opt);
+ GMX_RELEASE_ASSERT(gpu_opt, "Invalid gpu_opt pointer passed");
+ GMX_RELEASE_ASSERT(maxNumberToUse >= 1,
+ gmx::formatString("Invalid limit (%d) for the number of GPUs (detected %d compatible GPUs)",
+ maxNumberToUse, gpu_opt->ncuda_dev_compatible).c_str());
- ndev_use = gpu_opt->ncuda_dev_use;
-
- if (count > ndev_use)
- {
- /* won't increase the # of GPUs */
- return;
- }
-
- if (count < 1)
+ /* Don't increase the number of GPUs used beyond (e.g.) the number
+ of PP ranks */
+ gpu_opt->ncuda_dev_use = std::min(gpu_opt->ncuda_dev_compatible, maxNumberToUse);
+ snew(gpu_opt->cuda_dev_use, gpu_opt->ncuda_dev_use);
+ for (int i = 0; i != gpu_opt->ncuda_dev_use; ++i)
{
- char sbuf[STRLEN];
- sprintf(sbuf, "Limiting the number of GPUs to <1 doesn't make sense (detected %d, %d requested)!",
- ndev_use, count);
- gmx_incons(sbuf);
+ /* TODO: improve this implementation: either sort GPUs or remove the weakest here */
+ gpu_opt->cuda_dev_use[i] = gpu_opt->cuda_dev_compatible[i];
}
-
- /* TODO: improve this implementation: either sort GPUs or remove the weakest here */
- gpu_opt->ncuda_dev_use = count;
}
void gmx_hardware_info_free(gmx_hw_info_t *hwinfo)
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+
+#include "config.h"
+
+#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include <assert.h>
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "gmx_fatal.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "network.h"
-#include "copyrite.h"
-#include "gmx_omp_nthreads.h"
-#include "md_logging.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxomp.h"
/** Structure with the number of threads for each OpenMP multi-threaded
{
"GMX_DEFAULT_NUM_THREADS should never be set",
"GMX_DOMDEC_NUM_THREADS", "GMX_PAIRSEARCH_NUM_THREADS",
- "GMX_NONBONDED_NUM_THREADS", "GMX_BONDED_NUM_THREADS",
+ "GMX_NONBONDED_NUM_THREADS", "GMX_LISTED_FORCES_NUM_THREADS",
"GMX_PME_NUM_THREADS", "GMX_UPDATE_NUM_THREADS",
"GMX_VSITE_NUM_THREADS",
"GMX_LINCS_NUM_THREADS", "GMX_SETTLE_NUM_THREADS"
}
}
-void gmx_omp_nthreads_init(FILE *fplog, t_commrec *cr,
- int nthreads_hw_avail,
- int omp_nthreads_req,
- int omp_nthreads_pme_req,
- gmx_bool gmx_unused bThisNodePMEOnly,
- gmx_bool bFullOmpSupport)
+/*! \brief Helper function for parsing various input about the number
+ of OpenMP threads to use in various modules and deciding what to
+ do about it. */
+static void manage_number_of_openmp_threads(FILE *fplog,
+ const t_commrec *cr,
+ gmx_bool bOMP,
+ int nthreads_hw_avail,
+ int omp_nthreads_req,
+ int omp_nthreads_pme_req,
+ gmx_bool gmx_unused bThisNodePMEOnly,
+ gmx_bool bFullOmpSupport,
+ int nppn,
+ gmx_bool bSepPME)
{
- int nth, nth_pmeonly, gmx_maxth, nppn;
+ int nth;
char *env;
- gmx_bool bSepPME, bOMP;
-
-#ifdef GMX_OPENMP
- bOMP = TRUE;
-#else
- bOMP = FALSE;
-#endif /* GMX_OPENMP */
-
- /* number of MPI processes/threads per physical node */
- nppn = cr->nrank_intranode;
-
- bSepPME = ( (cr->duty & DUTY_PP) && !(cr->duty & DUTY_PME)) ||
- (!(cr->duty & DUTY_PP) && (cr->duty & DUTY_PME));
#ifdef GMX_THREAD_MPI
- /* modth is shared among tMPI threads, so for thread safety do the
- * detection is done on the master only. It is not thread-safe with
- * multiple simulations, but that's anyway not supported by tMPI. */
- if (SIMMASTER(cr))
+ /* modth is shared among tMPI threads, so for thread safety, the
+ * detection is done on the master only. It is not thread-safe
+ * with multiple simulations, but that's anyway not supported by
+ * tMPI. */
+ if (!SIMMASTER(cr))
+ {
+ return;
+ }
#endif
+
+ if (modth.initialized)
{
- /* just return if the initialization has already been done */
- if (modth.initialized)
- {
- return;
- }
+ /* Just return if the initialization has already been
+ done. This could only happen if gmx_omp_nthreads_init() has
+ already been called. */
+ return;
+ }
- /* With full OpenMP support (verlet scheme) set the number of threads
- * per process / default:
- * - 1 if not compiled with OpenMP or
- * - OMP_NUM_THREADS if the env. var is set, or
- * - omp_nthreads_req = #of threads requested by the user on the mdrun
- * command line, otherwise
- * - take the max number of available threads and distribute them
- * on the processes/tMPI threads.
- * ~ The GMX_*_NUM_THREADS env var overrides the number of threads of
- * the respective module and it has to be used in conjunction with
- * OMP_NUM_THREADS.
- *
- * With the group scheme OpenMP multithreading is only supported in PME,
- * for all other modules nthreads is set to 1.
- * The number of PME threads is equal to:
- * - 1 if not compiled with OpenMP or
- * - GMX_PME_NUM_THREADS if defined, otherwise
- * - OMP_NUM_THREADS if defined, otherwise
- * - 1
- */
- nth = 1;
- if ((env = getenv("OMP_NUM_THREADS")) != NULL)
- {
- if (!bOMP && (strncmp(env, "1", 1) != 0))
- {
- gmx_warning("OMP_NUM_THREADS is set, but %s was compiled without OpenMP support!",
- ShortProgram());
- }
- else
- {
- nth = gmx_omp_get_max_threads();
- }
- }
- else if (omp_nthreads_req > 0)
+ /* With full OpenMP support (verlet scheme) set the number of threads
+ * per process / default:
+ * - 1 if not compiled with OpenMP or
+ * - OMP_NUM_THREADS if the env. var is set, or
+ * - omp_nthreads_req = #of threads requested by the user on the mdrun
+ * command line, otherwise
+ * - take the max number of available threads and distribute them
+ * on the processes/tMPI threads.
+ * ~ The GMX_*_NUM_THREADS env var overrides the number of threads of
+ * the respective module and it has to be used in conjunction with
+ * OMP_NUM_THREADS.
+ *
+ * With the group scheme OpenMP multithreading is only supported in PME,
+ * for all other modules nthreads is set to 1.
+ * The number of PME threads is equal to:
+ * - 1 if not compiled with OpenMP or
+ * - GMX_PME_NUM_THREADS if defined, otherwise
+ * - OMP_NUM_THREADS if defined, otherwise
+ * - 1
+ */
+ nth = 1;
+ if ((env = getenv("OMP_NUM_THREADS")) != NULL)
+ {
+ if (!bOMP && (strncmp(env, "1", 1) != 0))
{
- nth = omp_nthreads_req;
+ gmx_warning("OMP_NUM_THREADS is set, but %s was compiled without OpenMP support!",
+ ShortProgram());
}
- else if (bFullOmpSupport && bOMP)
+ else
{
- /* max available threads per node */
- nth = nthreads_hw_avail;
-
- /* divide the threads among the MPI processes/tMPI threads */
- if (nth >= nppn)
- {
- nth /= nppn;
- }
- else
- {
- nth = 1;
- }
+ nth = gmx_omp_get_max_threads();
}
+ }
+ else if (omp_nthreads_req > 0)
+ {
+ nth = omp_nthreads_req;
+ }
+ else if (bFullOmpSupport && bOMP)
+ {
+ /* max available threads per node */
+ nth = nthreads_hw_avail;
- /* now we have the global values, set them:
- * - 1 if not compiled with OpenMP and for the group scheme
- * - nth for the verlet scheme when compiled with OpenMP
- */
- if (bFullOmpSupport && bOMP)
+ /* divide the threads among the MPI processes/tMPI threads */
+ if (nth >= nppn)
{
- modth.gnth = nth;
+ nth /= nppn;
}
else
{
- modth.gnth = 1;
+ nth = 1;
}
+ }
- if (bSepPME)
+ /* now we have the global values, set them:
+ * - 1 if not compiled with OpenMP and for the group scheme
+ * - nth for the verlet scheme when compiled with OpenMP
+ */
+ if (bFullOmpSupport && bOMP)
+ {
+ modth.gnth = nth;
+ }
+ else
+ {
+ modth.gnth = 1;
+ }
+
+ if (bSepPME)
+ {
+ if (omp_nthreads_pme_req > 0)
{
- if (omp_nthreads_pme_req > 0)
- {
- modth.gnth_pme = omp_nthreads_pme_req;
- }
- else
- {
- modth.gnth_pme = nth;
- }
+ modth.gnth_pme = omp_nthreads_pme_req;
}
else
{
- modth.gnth_pme = 0;
+ modth.gnth_pme = nth;
}
+ }
+ else
+ {
+ modth.gnth_pme = 0;
+ }
- /* now set the per-module values */
- modth.nth[emntDefault] = modth.gnth;
- pick_module_nthreads(fplog, emntDomdec, SIMMASTER(cr), bFullOmpSupport, bSepPME);
- pick_module_nthreads(fplog, emntPairsearch, SIMMASTER(cr), bFullOmpSupport, bSepPME);
- pick_module_nthreads(fplog, emntNonbonded, SIMMASTER(cr), bFullOmpSupport, bSepPME);
- pick_module_nthreads(fplog, emntBonded, SIMMASTER(cr), bFullOmpSupport, bSepPME);
- pick_module_nthreads(fplog, emntPME, SIMMASTER(cr), bFullOmpSupport, bSepPME);
- pick_module_nthreads(fplog, emntUpdate, SIMMASTER(cr), bFullOmpSupport, bSepPME);
- pick_module_nthreads(fplog, emntVSITE, SIMMASTER(cr), bFullOmpSupport, bSepPME);
- pick_module_nthreads(fplog, emntLINCS, SIMMASTER(cr), bFullOmpSupport, bSepPME);
- pick_module_nthreads(fplog, emntSETTLE, SIMMASTER(cr), bFullOmpSupport, bSepPME);
-
- /* set the number of threads globally */
- if (bOMP)
- {
+ /* now set the per-module values */
+ modth.nth[emntDefault] = modth.gnth;
+ pick_module_nthreads(fplog, emntDomdec, SIMMASTER(cr), bFullOmpSupport, bSepPME);
+ pick_module_nthreads(fplog, emntPairsearch, SIMMASTER(cr), bFullOmpSupport, bSepPME);
+ pick_module_nthreads(fplog, emntNonbonded, SIMMASTER(cr), bFullOmpSupport, bSepPME);
+ pick_module_nthreads(fplog, emntBonded, SIMMASTER(cr), bFullOmpSupport, bSepPME);
+ pick_module_nthreads(fplog, emntPME, SIMMASTER(cr), bFullOmpSupport, bSepPME);
+ pick_module_nthreads(fplog, emntUpdate, SIMMASTER(cr), bFullOmpSupport, bSepPME);
+ pick_module_nthreads(fplog, emntVSITE, SIMMASTER(cr), bFullOmpSupport, bSepPME);
+ pick_module_nthreads(fplog, emntLINCS, SIMMASTER(cr), bFullOmpSupport, bSepPME);
+ pick_module_nthreads(fplog, emntSETTLE, SIMMASTER(cr), bFullOmpSupport, bSepPME);
+
+ /* set the number of threads globally */
+ if (bOMP)
+ {
#ifndef GMX_THREAD_MPI
- if (bThisNodePMEOnly)
+ if (bThisNodePMEOnly)
+ {
+ gmx_omp_set_num_threads(modth.gnth_pme);
+ }
+ else
+#endif /* GMX_THREAD_MPI */
+ {
+ if (bFullOmpSupport)
{
- gmx_omp_set_num_threads(modth.gnth_pme);
+ gmx_omp_set_num_threads(nth);
}
else
-#endif /* GMX_THREAD_MPI */
{
- if (bFullOmpSupport)
- {
- gmx_omp_set_num_threads(nth);
- }
- else
- {
- gmx_omp_set_num_threads(1);
- }
+ gmx_omp_set_num_threads(1);
}
}
-
- modth.initialized = TRUE;
}
+
+ modth.initialized = TRUE;
+}
+
+/*! \brief Report on the OpenMP settings that will be used */
+static void
+reportOpenmpSettings(FILE *fplog,
+ const t_commrec *cr,
+ gmx_bool bOMP,
+ gmx_bool bFullOmpSupport,
+ gmx_bool bSepPME)
+{
#ifdef GMX_THREAD_MPI
- /* Non-master threads have to wait for the detection to be done. */
- if (PAR(cr))
- {
- MPI_Barrier(cr->mpi_comm_mysim);
- }
+ const char *mpi_str = "per tMPI thread";
+#else
+ const char *mpi_str = "per MPI process";
#endif
/* inform the user about the settings */
- if (bOMP)
+ if (!bOMP)
{
-#ifdef GMX_THREAD_MPI
- const char *mpi_str = "per tMPI thread";
-#else
- const char *mpi_str = "per MPI process";
-#endif
+ return;
+ }
- /* for group scheme we print PME threads info only */
- if (bFullOmpSupport)
- {
- md_print_info(cr, fplog, "Using %d OpenMP thread%s %s\n",
- modth.gnth, modth.gnth > 1 ? "s" : "",
- cr->nnodes > 1 ? mpi_str : "");
- }
- if (bSepPME && modth.gnth_pme != modth.gnth)
- {
- md_print_info(cr, fplog, "Using %d OpenMP thread%s %s for PME\n",
- modth.gnth_pme, modth.gnth_pme > 1 ? "s" : "",
- cr->nnodes > 1 ? mpi_str : "");
- }
+ /* for group scheme we print PME threads info only */
+ if (bFullOmpSupport)
+ {
+ md_print_info(cr, fplog, "Using %d OpenMP thread%s %s\n",
+ modth.gnth, modth.gnth > 1 ? "s" : "",
+ cr->nnodes > 1 ? mpi_str : "");
+ }
+ if (bSepPME && modth.gnth_pme != modth.gnth)
+ {
+ md_print_info(cr, fplog, "Using %d OpenMP thread%s %s for PME\n",
+ modth.gnth_pme, modth.gnth_pme > 1 ? "s" : "",
+ cr->nnodes > 1 ? mpi_str : "");
}
+}
- /* detect and warn about oversubscription
- * TODO: enable this for separate PME nodes as well! */
- if (!bSepPME && cr->rank_pp_intranode == 0)
+/*! \brief Detect and warn about oversubscription of cores.
+ *
+ * \todo This could probably live elsewhere, since it is not specifc
+ * to OpenMP, and only needs modth.gnth.
+ *
+ * \todo Enable this for separate PME nodes as well! */
+static void
+issueOversubscriptionWarning(FILE *fplog,
+ const t_commrec *cr,
+ int nthreads_hw_avail,
+ int nppn,
+ gmx_bool bSepPME)
+{
+ char sbuf[STRLEN], sbuf1[STRLEN], sbuf2[STRLEN];
+
+ if (bSepPME || 0 != cr->rank_pp_intranode)
{
- char sbuf[STRLEN], sbuf1[STRLEN], sbuf2[STRLEN];
+ return;
+ }
- if (modth.gnth*nppn > nthreads_hw_avail)
- {
- sprintf(sbuf, "threads");
- sbuf1[0] = '\0';
- sprintf(sbuf2, "O");
+ if (modth.gnth*nppn > nthreads_hw_avail)
+ {
+ sprintf(sbuf, "threads");
+ sbuf1[0] = '\0';
+ sprintf(sbuf2, "O");
#ifdef GMX_MPI
- if (modth.gnth == 1)
- {
+ if (modth.gnth == 1)
+ {
#ifdef GMX_THREAD_MPI
- sprintf(sbuf, "thread-MPI threads");
+ sprintf(sbuf, "thread-MPI threads");
#else
- sprintf(sbuf, "MPI processes");
- sprintf(sbuf1, " per rank");
- sprintf(sbuf2, "On rank %d: o", cr->sim_nodeid);
+ sprintf(sbuf, "MPI processes");
+ sprintf(sbuf1, " per rank");
+ sprintf(sbuf2, "On rank %d: o", cr->sim_nodeid);
#endif
- }
-#endif
- md_print_warn(cr, fplog,
- "WARNING: %sversubscribing the available %d logical CPU cores%s with %d %s.\n"
- " This will cause considerable performance loss!",
- sbuf2, nthreads_hw_avail, sbuf1, nppn*modth.gnth, sbuf);
}
+#endif
+ md_print_warn(cr, fplog,
+ "WARNING: %sversubscribing the available %d logical CPU cores%s with %d %s.\n"
+ " This will cause considerable performance loss!",
+ sbuf2, nthreads_hw_avail, sbuf1, nppn*modth.gnth, sbuf);
}
}
+void gmx_omp_nthreads_init(FILE *fplog, t_commrec *cr,
+ int nthreads_hw_avail,
+ int omp_nthreads_req,
+ int omp_nthreads_pme_req,
+ gmx_bool bThisNodePMEOnly,
+ gmx_bool bFullOmpSupport)
+{
+ int nth_pmeonly, gmx_maxth, nppn;
+ gmx_bool bSepPME, bOMP;
+
+#ifdef GMX_OPENMP
+ bOMP = TRUE;
+#else
+ bOMP = FALSE;
+#endif /* GMX_OPENMP */
+
+ /* number of MPI processes/threads per physical node */
+ nppn = cr->nrank_intranode;
+
+ bSepPME = ( (cr->duty & DUTY_PP) && !(cr->duty & DUTY_PME)) ||
+ (!(cr->duty & DUTY_PP) && (cr->duty & DUTY_PME));
+
+ manage_number_of_openmp_threads(fplog, cr, bOMP,
+ nthreads_hw_avail,
+ omp_nthreads_req, omp_nthreads_pme_req,
+ bThisNodePMEOnly, bFullOmpSupport,
+ nppn, bSepPME);
+#ifdef GMX_THREAD_MPI
+ /* Non-master threads have to wait for the OpenMP management to be
+ * done, so that code elsewhere that uses OpenMP can be certain
+ * the setup is complete. */
+ if (PAR(cr))
+ {
+ MPI_Barrier(cr->mpi_comm_mysim);
+ }
+#endif
+
+ reportOpenmpSettings(fplog, cr, bOMP, bSepPME, bFullOmpSupport);
+ issueOversubscriptionWarning(fplog, cr, bSepPME, nthreads_hw_avail, nppn);
+}
+
int gmx_omp_nthreads_get(int mod)
{
if (mod < 0 || mod >= emntNR)
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/gmx_thread_affinity.h"
+
+#include "config.h"
+
+#include <assert.h>
+#include <errno.h>
+#include <stdio.h>
+#include <string.h>
+
#ifdef HAVE_SCHED_AFFINITY
-# ifndef _GNU_SOURCE
-# define _GNU_SOURCE 1
-# endif
# include <sched.h>
# include <sys/syscall.h>
#endif
-#include <string.h>
-#include <errno.h>
-#include <assert.h>
-#include <stdio.h>
#include "thread_mpi/threads.h"
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "types/hw_info.h"
-#include "copyrite.h"
-#include "gmx_cpuid.h"
-#include "gmx_omp_nthreads.h"
-#include "md_logging.h"
-#include "gmx_thread_affinity.h"
-
-#include "gmx_fatal.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/gmx_cpuid.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/hw_info.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
static int
get_thread_affinity_layout(FILE *fplog,
* Note that this will only work on Linux as we use a GNU feature.
*/
void
-gmx_check_thread_affinity_set(FILE gmx_unused *fplog,
- const t_commrec gmx_unused *cr,
- gmx_hw_opt_t gmx_unused *hw_opt,
- int gmx_unused nthreads_hw_avail,
- gmx_bool gmx_unused bAfterOpenmpInit)
+gmx_check_thread_affinity_set(FILE *fplog,
+ const t_commrec *cr,
+ gmx_hw_opt_t *hw_opt,
+ int gmx_unused nthreads_hw_avail,
+ gmx_bool bAfterOpenmpInit)
{
#ifdef HAVE_SCHED_AFFINITY
cpu_set_t mask_current;
int i, ret, cpu_count, cpu_set;
gmx_bool bAllSet;
+#endif
#ifdef GMX_LIB_MPI
gmx_bool bAllSet_All;
#endif
assert(hw_opt);
+ if (!bAfterOpenmpInit)
+ {
+ /* Check for externally set OpenMP affinity and turn off internal
+ * pinning if any is found. We need to do this check early to tell
+ * thread-MPI whether it should do pinning when spawning threads.
+ * TODO: the above no longer holds, we should move these checks later
+ */
+ if (hw_opt->thread_affinity != threadaffOFF)
+ {
+ char *message;
+ if (!gmx_omp_check_thread_affinity(&message))
+ {
+ /* TODO: with -pin auto we should only warn when using all cores */
+ md_print_warn(cr, fplog, "%s", message);
+ sfree(message);
+ hw_opt->thread_affinity = threadaffOFF;
+ }
+ }
+
+ /* With thread-MPI this is needed as pinning might get turned off,
+ * which needs to be known before starting thread-MPI.
+ * With thread-MPI hw_opt is processed here on the master rank
+ * and passed to the other ranks later, so we only do this on master.
+ */
+ if (!SIMMASTER(cr))
+ {
+ return;
+ }
+#ifndef GMX_THREAD_MPI
+ return;
+#endif
+ }
+
+#ifdef HAVE_SCHED_GETAFFINITY
if (hw_opt->thread_affinity == threadaffOFF)
{
/* internal affinity setting is off, don't bother checking process affinity */
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-# (slightly sloppy) OS definitions required by memtestG80
-set(_os_def)
-if(UNIX)
- if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
- set(_os_def "-DOSX")
- else() # everything that's UNIX & UNIX-like except OS X
- set(_os_def "-DLINUX")
- endif()
-else()
- if(WIN32)
- set(_os_def "-DWINDOWS")
- else()
- message(FATAL_ERROR " Could not detect OS required for memtestG80.")
- endif()
-endif()
-
-CUDA_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
-set(CUDA_ATTACH_VS_BUILD_RULE_TO_CUDA_FILE OFF)
file(GLOB GPU_UTILS_SOURCES *.cu)
-CUDA_ADD_LIBRARY(gpu_utils STATIC ${GPU_UTILS_SOURCES}
- OPTIONS ${_os_def}
- RELWITHDEBINFO -g
- DEBUG -g -D_DEBUG_=1 )
+set(GMXLIB_SOURCES ${GMXLIB_SOURCES} ${GPU_UTILS_SOURCES} PARENT_SCOPE)
-CUDA_BUILD_CLEAN_TARGET()
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include <stdio.h>
-#include <stdlib.h>
-#include <assert.h>
-
-#include "gromacs/utility/smalloc.h"
-#include "types/hw_info.h"
+#include "gmxpre.h"
#include "gpu_utils.h"
-#include "../cuda_tools/cudautils.cuh"
-#include "memtestG80_core.h"
-/** Amount of memory to be used in quick memtest. */
-#define QUICK_MEM 250
-/** Bit flag with type of tests to run in quick memtest. */
-#define QUICK_TESTS MOD_20_32BIT | LOGIC_4_ITER_SHMEM | RANDOM_BLOCKS
-/** Number of iterations in quick memtest. */
-#define QUICK_ITER 3
+#include "config.h"
-/** Bitflag with all test set on for full memetest. */
-#define FULL_TESTS 0x3FFF
-/** Number of iterations in full memtest. */
-#define FULL_ITER 25
+#include <assert.h>
+#include <stdio.h>
+#include <stdlib.h>
-/** Bit flag with type of tests to run in time constrained memtest. */
-#define TIMED_TESTS MOD_20_32BIT | LOGIC_4_ITER_SHMEM | RANDOM_BLOCKS
+#include "gromacs/gmxlib/cuda_tools/cudautils.cuh"
+#include "gromacs/legacyheaders/types/hw_info.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
/*! \brief
* Max number of devices supported by CUDA (for consistency checking).
}
-/** Bit-flags which refer to memtestG80 test types and are used in do_memtest
- * to specify which tests to run. */
-enum memtest_G80_test_types {
- MOVING_INVERSIONS_10 = 0x1,
- MOVING_INVERSIONS_RAND = 0x2,
- WALKING_8BIT_M86 = 0x4,
- WALKING_0_8BIT = 0x8,
- WALKING_1_8BIT = 0x10,
- WALKING_0_32BIT = 0x20,
- WALKING_1_32BIT = 0x40,
- RANDOM_BLOCKS = 0x80,
- MOD_20_32BIT = 0x100,
- LOGIC_1_ITER = 0x200,
- LOGIC_4_ITER = 0x400,
- LOGIC_1_ITER_SHMEM = 0x800,
- LOGIC_4_ITER_SHMEM = 0x1000
-};
-
-
/*!
* \brief Runs GPU sanity checks.
*
return 0;
}
-
-/*!
- * \brief Runs a set of memory tests specified by the given bit-flags.
- * Tries to allocate and do the test on \p megs Mb memory or
- * the greatest amount that can be allocated (>10Mb).
- * In case if an error is detected it stops without finishing the remaining
- * steps/iterations and returns greater then zero value.
- * In case of other errors (e.g. kernel launch errors, device querying errors)
- * -1 is returned.
- *
- * \param[in] which_tests variable with bit-flags of the requested tests
- * \param[in] megs amount of memory that will be tested in MB
- * \param[in] iter number of iterations
- * \returns 0 if no error was detected, otherwise >0
+#ifdef HAVE_NVML
+/* TODO: We should actually be using md_print_warn in md_logging.c,
+ * but we can't include mpi.h in CUDA code.
*/
-static int do_memtest(unsigned int which_tests, int megs, int iter)
+static void md_print_info(FILE *fplog,
+ const char *fmt, ...)
{
- memtestState tester;
- int i;
- uint err_count; //, err_iter;
+ va_list ap;
- // no parameter check as this fn won't be called externally
-
- // let's try to allocate the mem
- while (!tester.allocate(megs) && (megs - 10 > 0))
+ if (fplog != NULL)
{
- megs -= 10; tester.deallocate();
- }
+ /* We should only print to stderr on the master node,
+ * in most cases fplog is only set on the master node, so this works.
+ */
+ va_start(ap, fmt);
+ vfprintf(stderr, fmt, ap);
+ va_end(ap);
- if (megs <= 10)
- {
- fprintf(stderr, "Unable to allocate GPU memory!\n");
- return -1;
+ va_start(ap, fmt);
+ vfprintf(fplog, fmt, ap);
+ va_end(ap);
}
+}
+#endif /*HAVE_NVML*/
- // clear the first 18 bits
- which_tests &= 0x3FFF;
- for (i = 0; i < iter; i++)
+/* TODO: We should actually be using md_print_warn in md_logging.c,
+ * but we can't include mpi.h in CUDA code.
+ * This is replicated from nbnxn_cuda_data_mgmt.cu.
+ */
+static void md_print_warn(FILE *fplog,
+ const char *fmt, ...)
+{
+ va_list ap;
+
+ if (fplog != NULL)
{
- // Moving Inversions (ones and zeros)
- if ((MOVING_INVERSIONS_10 & which_tests) == MOVING_INVERSIONS_10)
- {
- tester.gpuMovingInversionsOnesZeros(err_count);
- if (err_count > 0)
- {
- return MOVING_INVERSIONS_10;
- }
- }
- // Moving Inversions (random)
- if ((MOVING_INVERSIONS_RAND & which_tests) == MOVING_INVERSIONS_RAND)
- {
- tester.gpuMovingInversionsRandom(err_count);
- if (err_count > 0)
- {
- return MOVING_INVERSIONS_RAND;
- }
- }
- // Memtest86 Walking 8-bit
- if ((WALKING_8BIT_M86 & which_tests) == WALKING_8BIT_M86)
- {
- for (uint shift = 0; shift < 8; shift++)
- {
- tester.gpuWalking8BitM86(err_count, shift);
- if (err_count > 0)
- {
- return WALKING_8BIT_M86;
- }
- }
- }
- // True Walking zeros (8-bit)
- if ((WALKING_0_8BIT & which_tests) == WALKING_0_8BIT)
- {
- for (uint shift = 0; shift < 8; shift++)
- {
- tester.gpuWalking8Bit(err_count, false, shift);
- if (err_count > 0)
- {
- return WALKING_0_8BIT;
- }
- }
- }
- // True Walking ones (8-bit)
- if ((WALKING_1_8BIT & which_tests) == WALKING_1_8BIT)
- {
- for (uint shift = 0; shift < 8; shift++)
- {
- tester.gpuWalking8Bit(err_count, true, shift);
- if (err_count > 0)
- {
- return WALKING_1_8BIT;
- }
- }
- }
- // Memtest86 Walking zeros (32-bit)
- if ((WALKING_0_32BIT & which_tests) == WALKING_0_32BIT)
- {
- for (uint shift = 0; shift < 32; shift++)
- {
- tester.gpuWalking32Bit(err_count, false, shift);
- if (err_count > 0)
- {
- return WALKING_0_32BIT;
- }
- }
- }
- // Memtest86 Walking ones (32-bit)
- if ((WALKING_1_32BIT & which_tests) == WALKING_1_32BIT)
- {
- for (uint shift = 0; shift < 32; shift++)
- {
- tester.gpuWalking32Bit(err_count, true, shift);
- if (err_count > 0)
- {
- return WALKING_1_32BIT;
- }
- }
- }
- // Random blocks
- if ((RANDOM_BLOCKS & which_tests) == RANDOM_BLOCKS)
- {
- tester.gpuRandomBlocks(err_count, rand());
- if (err_count > 0)
- {
- return RANDOM_BLOCKS;
- }
+ /* We should only print to stderr on the master node,
+ * in most cases fplog is only set on the master node, so this works.
+ */
+ va_start(ap, fmt);
+ fprintf(stderr, "\n");
+ vfprintf(stderr, fmt, ap);
+ fprintf(stderr, "\n");
+ va_end(ap);
- }
+ va_start(ap, fmt);
+ fprintf(fplog, "\n");
+ vfprintf(fplog, fmt, ap);
+ fprintf(fplog, "\n");
+ va_end(ap);
+ }
+}
- // Memtest86 Modulo-20
- if ((MOD_20_32BIT & which_tests) == MOD_20_32BIT)
- {
- for (uint shift = 0; shift < 20; shift++)
- {
- tester.gpuModuloX(err_count, shift, rand(), 20, 2);
- if (err_count > 0)
- {
- return MOD_20_32BIT;
- }
- }
- }
- // Logic (one iteration)
- if ((LOGIC_1_ITER & which_tests) == LOGIC_1_ITER)
+#ifdef HAVE_NVML
+/*! \brief Determines and adds the NVML device ID to the passed \cuda_dev.
+ *
+ * Determines and adds the NVML device ID to the passed \cuda_dev. This is done by
+ * matching PCI-E information from \cuda_dev with the available NVML devices.
+ *
+ * \param[in,out] cuda_dev CUDA device information to enrich with NVML device info
+ * \returns true if \cuda_dev could be enriched with matching NVML device information.
+ */
+static bool addNVMLDeviceId(cuda_dev_info* cuda_dev)
+{
+ nvmlReturn_t nvml_stat = NVML_SUCCESS;
+ nvmlDevice_t nvml_device_id;
+ unsigned int nvml_device_count = 0;
+ cuda_dev->nvml_initialized = false;
+ nvml_stat = nvmlDeviceGetCount ( &nvml_device_count );
+ HANDLE_NVML_RET_ERR( nvml_stat, "nvmlDeviceGetCount failed" );
+ for (unsigned int nvml_device_idx = 0; nvml_stat == NVML_SUCCESS && nvml_device_idx < nvml_device_count; ++nvml_device_idx)
+ {
+ nvml_stat = nvmlDeviceGetHandleByIndex ( nvml_device_idx, &nvml_device_id );
+ HANDLE_NVML_RET_ERR( nvml_stat, "nvmlDeviceGetHandleByIndex failed" );
+ if (nvml_stat != NVML_SUCCESS)
{
- tester.gpuShortLCG0(err_count, 1);
- if (err_count > 0)
- {
- return LOGIC_1_ITER;
- }
+ break;
}
- // Logic (4 iterations)
- if ((LOGIC_4_ITER & which_tests) == LOGIC_4_ITER)
- {
- tester.gpuShortLCG0(err_count, 4);
- if (err_count > 0)
- {
- return LOGIC_4_ITER;
- }
- }
- // Logic (shared memory, one iteration)
- if ((LOGIC_1_ITER_SHMEM & which_tests) == LOGIC_1_ITER_SHMEM)
+ nvmlPciInfo_t nvml_pci_info;
+ nvml_stat = nvmlDeviceGetPciInfo ( nvml_device_id, &nvml_pci_info );
+ HANDLE_NVML_RET_ERR( nvml_stat, "nvmlDeviceGetPciInfo failed" );
+ if (nvml_stat != NVML_SUCCESS)
{
- tester.gpuShortLCG0Shmem(err_count, 1);
- if (err_count > 0)
- {
- return LOGIC_1_ITER_SHMEM;
- }
+ break;
}
- // Logic (shared-memory, 4 iterations)
- if ((LOGIC_4_ITER_SHMEM & which_tests) == LOGIC_4_ITER_SHMEM)
+ if (static_cast<unsigned int>(cuda_dev->prop.pciBusID) == nvml_pci_info.bus &&
+ static_cast<unsigned int>(cuda_dev->prop.pciDeviceID) == nvml_pci_info.device &&
+ static_cast<unsigned int>(cuda_dev->prop.pciDomainID) == nvml_pci_info.domain)
{
- tester.gpuShortLCG0Shmem(err_count, 4);
- if (err_count > 0)
- {
- return LOGIC_4_ITER_SHMEM;
- }
+ cuda_dev->nvml_initialized = true;
+ cuda_dev->nvml_device_id = nvml_device_id;
+ break;
}
}
-
- tester.deallocate();
- return err_count;
+ return cuda_dev->nvml_initialized;
}
+#endif /*HAVE_NVML*/
-/*! \brief Runs a quick memory test and returns 0 in case if no error is detected.
- * If an error is detected it stops before completing the test and returns a
- * value greater then 0. In case of other errors (e.g. kernel launch errors,
- * device querying errors) -1 is returned.
+/*! \brief Tries to set application clocks for the GPU with the given index.
+ *
+ * The variable \gpuid is the index of the GPU in the gpu_info.cuda_dev array
+ * to handle the application clocks for. Application clocks are set to the
+ * max supported value to increase performance if application clock permissions
+ * allow this. For future GPU architectures a more sophisticated scheme might be
+ * required.
*
- * \param[in] dev_id the device id of the GPU or -1 if the device has already been selected
- * \returns 0 if no error was detected, otherwise >0
+ * \param[out] fplog log file to write to
+ * \param[in] gpuid index of the GPU to set application clocks for
+ * \param[in] gpu_info GPU info of all detected devices in the system.
+ * \returns true if no error occurs during application clocks handling.
*/
-int do_quick_memtest(int dev_id)
+static gmx_bool init_gpu_application_clocks(FILE gmx_unused *fplog, int gmx_unused gpuid, const gmx_gpu_info_t gmx_unused *gpu_info)
{
- cudaDeviceProp dev_prop;
- int devmem, res, time = 0;
-
- if (debug)
+#ifndef HAVE_NVML
+ if ( (gpu_info->cuda_dev[gpuid].prop.major * 10 + gpu_info->cuda_dev[gpuid].prop.minor) >= 35 &&
+ (0 == gmx_wcmatch( "*Tesla*", gpu_info->cuda_dev[gpuid].prop.name )))
{
- time = getTimeMilliseconds();
+ //TODO: Maybe need to think about something more user friendly here.
+ md_print_warn( fplog, "Could not set GPU clocks to the optimal value because application clocks handling not possible for %s due to missing NVML support.\n", gpu_info->cuda_dev[gpuid].prop.name );
}
-
- if (do_sanity_checks(dev_id, &dev_prop) != 0)
+ return true;
+#else /* HAVE_NVML defined */
+ nvmlReturn_t nvml_stat = NVML_SUCCESS;
+ char *env;
+ if (!( (gpu_info->cuda_dev[gpuid].prop.major * 10 + gpu_info->cuda_dev[gpuid].prop.minor) >= 35 &&
+ (0 == gmx_wcmatch( "*Tesla*", gpu_info->cuda_dev[gpuid].prop.name ))))
{
- // something went wrong
- return -1;
+ return true;
}
-
- if (debug)
+ //TODO: GMX_GPU_APPLICATION_CLOCKS is currently only used to enable/disable setting of application clocks
+ // this variable can be later used to give a user more fine grained control.
+ env = getenv("GMX_GPU_APPLICATION_CLOCKS");
+ if (env != NULL && ( strcmp( env, "0") == 0 ||
+ gmx_strcasecmp( env, "OFF") == 0 ||
+ gmx_strcasecmp( env, "DISABLE") == 0 ))
{
- devmem = dev_prop.totalGlobalMem/(1024*1024); // in MiB
- fprintf(debug, ">> Running QUICK memtests on %d MiB (out of total %d MiB), %d iterations\n",
- QUICK_MEM, devmem, QUICK_ITER);
+ return true;
}
-
- res = do_memtest(QUICK_TESTS, QUICK_MEM, QUICK_ITER);
-
- if (debug)
+ nvml_stat = nvmlInit();
+ HANDLE_NVML_RET_ERR( nvml_stat, "nvmlInit failed." );
+ if (nvml_stat != NVML_SUCCESS)
{
- fprintf(debug, "Q-RES = %d\n", res);
- fprintf(debug, "Q-runtime: %d ms\n", getTimeMilliseconds() - time);
+ return false;
}
-
- /* destroy context only if we created it */
- if (dev_id != -1)
+ if (!addNVMLDeviceId( &(gpu_info->cuda_dev[gpuid])))
{
- cudaThreadExit();
+ return false;
}
- return res;
-}
-
-/*! \brief Runs a full memory test and returns 0 in case if no error is detected.
- * If an error is detected it stops before completing the test and returns a
- * value greater then 0. In case of other errors (e.g. kernel launch errors,
- * device querying errors) -1 is returned.
- *
- * \param[in] dev_id the device id of the GPU or -1 if the device has already been selected
- * \returns 0 if no error was detected, otherwise >0
- */
-
-int do_full_memtest(int dev_id)
-{
- cudaDeviceProp dev_prop;
- int devmem, res, time = 0;
-
- if (debug)
+ //get current application clocks setting
+ unsigned int app_sm_clock = 0;
+ unsigned int app_mem_clock = 0;
+ nvml_stat = nvmlDeviceGetApplicationsClock ( gpu_info->cuda_dev[gpuid].nvml_device_id, NVML_CLOCK_SM, &app_sm_clock );
+ if (NVML_ERROR_NOT_SUPPORTED == nvml_stat)
{
- time = getTimeMilliseconds();
+ return false;
}
+ HANDLE_NVML_RET_ERR( nvml_stat, "nvmlDeviceGetApplicationsClock failed" );
+ nvml_stat = nvmlDeviceGetApplicationsClock ( gpu_info->cuda_dev[gpuid].nvml_device_id, NVML_CLOCK_MEM, &app_mem_clock );
+ HANDLE_NVML_RET_ERR( nvml_stat, "nvmlDeviceGetApplicationsClock failed" );
+ //get max application clocks
+ unsigned int max_sm_clock = 0;
+ unsigned int max_mem_clock = 0;
+ nvml_stat = nvmlDeviceGetMaxClockInfo ( gpu_info->cuda_dev[gpuid].nvml_device_id, NVML_CLOCK_SM, &max_sm_clock );
+ HANDLE_NVML_RET_ERR( nvml_stat, "nvmlDeviceGetMaxClockInfo failed" );
+ nvml_stat = nvmlDeviceGetMaxClockInfo ( gpu_info->cuda_dev[gpuid].nvml_device_id, NVML_CLOCK_MEM, &max_mem_clock );
+ HANDLE_NVML_RET_ERR( nvml_stat, "nvmlDeviceGetMaxClockInfo failed" );
- if (do_sanity_checks(dev_id, &dev_prop) != 0)
- {
- // something went wrong
- return -1;
- }
+ gpu_info->cuda_dev[gpuid].nvml_is_restricted = NVML_FEATURE_ENABLED;
+ gpu_info->cuda_dev[gpuid].nvml_ap_clocks_changed = false;
- devmem = dev_prop.totalGlobalMem/(1024*1024); // in MiB
+ nvml_stat = nvmlDeviceGetAPIRestriction ( gpu_info->cuda_dev[gpuid].nvml_device_id, NVML_RESTRICTED_API_SET_APPLICATION_CLOCKS, &(gpu_info->cuda_dev[gpuid].nvml_is_restricted) );
+ HANDLE_NVML_RET_ERR( nvml_stat, "nvmlDeviceGetAPIRestriction failed" );
- if (debug)
+ //TODO: Need to distinguish between different type of GPUs might be necessary in the future, e.g. if max application clocks should not be used
+ // for certain GPUs.
+ if (nvml_stat == NVML_SUCCESS && app_sm_clock < max_sm_clock && gpu_info->cuda_dev[gpuid].nvml_is_restricted == NVML_FEATURE_DISABLED)
{
- fprintf(debug, ">> Running FULL memtests on %d MiB (out of total %d MiB), %d iterations\n",
- devmem, devmem, FULL_ITER);
+ //TODO: Maybe need to think about something more user friendly here.
+ md_print_info( fplog, "Changing GPU clocks by setting application clocks for %s to (%d,%d)\n", gpu_info->cuda_dev[gpuid].prop.name, max_mem_clock, max_sm_clock);
+ nvml_stat = nvmlDeviceSetApplicationsClocks ( gpu_info->cuda_dev[gpuid].nvml_device_id, max_mem_clock, max_sm_clock );
+ HANDLE_NVML_RET_ERR( nvml_stat, "nvmlDeviceGetApplicationsClock failed" );
+ gpu_info->cuda_dev[gpuid].nvml_ap_clocks_changed = true;
}
-
- /* do all test on the entire memory */
- res = do_memtest(FULL_TESTS, devmem, FULL_ITER);
-
- if (debug)
+ else if (nvml_stat == NVML_SUCCESS && app_sm_clock < max_sm_clock)
{
- fprintf(debug, "F-RES = %d\n", res);
- fprintf(debug, "F-runtime: %d ms\n", getTimeMilliseconds() - time);
+ //TODO: Maybe need to think about something more user friendly here.
+ md_print_warn( fplog, "Not possible to change GPU clocks to optimal value because of insufficient permissions to set application clocks for %s. Current values are (%d,%d). Max values are (%d,%d)\nUse sudo nvidia-smi -acp UNRESTRICTED or contact your admin to change application clock permissions.\n", gpu_info->cuda_dev[gpuid].prop.name, app_mem_clock, app_sm_clock, max_mem_clock, max_sm_clock);
}
-
- /* destroy context only if we created it */
- if (dev_id != -1)
+ else if (nvml_stat == NVML_SUCCESS && app_sm_clock == max_sm_clock)
{
- cudaThreadExit();
+ //TODO: This should probably be integrated into the GPU Properties table.
+ md_print_info( fplog, "Application clocks (GPU clocks) for %s are (%d,%d)\n", gpu_info->cuda_dev[gpuid].prop.name, app_mem_clock, app_sm_clock);
}
- return res;
+ else
+ {
+ //TODO: Maybe need to think about something more user friendly here.
+ md_print_warn( fplog, "Not possible to change GPU clocks to optimal value because application clocks handling failed with NVML error (%d): %s.\n", nvml_stat, nvmlErrorString(nvml_stat));
+ }
+ return (nvml_stat == NVML_SUCCESS);
+#endif /*HAVE_NVML*/
}
-/*! \brief Runs a time constrained memory test and returns 0 in case if no error is detected.
- * If an error is detected it stops before completing the test and returns a value greater
- * than zero. In case of other errors (e.g. kernel launch errors, device querying errors) -1
- * is returned. Note, that test iterations are not interrupted therefor the total runtime of
- * the test will always be multipple of one iteration's runtime.
+/*! \brief Resets application clocks if changed and cleans up NVML for the passed \cuda_dev.
*
- * \param[in] dev_id the device id of the GPU or -1 if the device has laredy been selected
- * \param[in] time_constr the time limit of the testing
- * \returns 0 if no error was detected, otherwise >0
+ * \param[in] cuda_dev CUDA device information
*/
-int do_timed_memtest(int dev_id, int time_constr)
+static gmx_bool reset_gpu_application_clocks(const cuda_dev_info gmx_unused * cuda_dev)
{
- cudaDeviceProp dev_prop;
- int devmem, res = 0, time = 0, startt;
-
- if (debug)
- {
- time = getTimeMilliseconds();
- }
-
- time_constr *= 1000; /* convert to ms for convenience */
- startt = getTimeMilliseconds();
-
- if (do_sanity_checks(dev_id, &dev_prop) != 0)
- {
- // something went wrong
- return -1;
- }
-
- devmem = dev_prop.totalGlobalMem/(1024*1024); // in MiB
-
- if (debug)
- {
- fprintf(debug, ">> Running time constrained memtests on %d MiB (out of total %d MiB), time limit of %d s \n",
- devmem, devmem, time_constr);
- }
-
- /* do the TIMED_TESTS set, one step at a time on the entire memory
- that can be allocated, and stop when the given time is exceeded */
- while ( ((int)getTimeMilliseconds() - startt) < time_constr)
- {
- res = do_memtest(TIMED_TESTS, devmem, 1);
- if (res != 0)
- {
- break;
- }
- }
-
- if (debug)
- {
- fprintf(debug, "T-RES = %d\n", res);
- fprintf(debug, "T-runtime: %d ms\n", getTimeMilliseconds() - time);
- }
-
- /* destroy context only if we created it */
- if (dev_id != -1)
- {
- cudaThreadExit();
- }
- return res;
+#ifndef HAVE_NVML
+ GMX_UNUSED_VALUE(cuda_dev);
+ return true;
+#else
+ nvmlReturn_t nvml_stat = NVML_SUCCESS;
+ if (cuda_dev &&
+ cuda_dev->nvml_is_restricted == NVML_FEATURE_DISABLED &&
+ cuda_dev->nvml_ap_clocks_changed)
+ {
+ nvml_stat = nvmlDeviceResetApplicationsClocks( cuda_dev->nvml_device_id );
+ HANDLE_NVML_RET_ERR( nvml_stat, "nvmlDeviceResetApplicationsClocks failed" );
+ }
+ nvml_stat = nvmlShutdown();
+ HANDLE_NVML_RET_ERR( nvml_stat, "nvmlShutdown failed" );
+ return (nvml_stat == NVML_SUCCESS);
+#endif /*HAVE_NVML*/
}
+
/*! \brief Initializes the GPU with the given index.
*
* The varible \mygpu is the index of the GPU to initialize in the
* gpu_info.cuda_dev array.
*
+ * \param[out] fplog log file to write to
* \param[in] mygpu index of the GPU to initialize
* \param[out] result_str the message related to the error that occurred
* during the initialization (if there was any).
* \param[in] gpu_opt options for using the GPUs in gpu_info
* \returns true if no error occurs during initialization.
*/
-gmx_bool init_gpu(int mygpu, char *result_str,
+gmx_bool init_gpu(FILE gmx_unused *fplog, int mygpu, char *result_str,
const gmx_gpu_info_t *gpu_info,
const gmx_gpu_opt_t *gpu_opt)
{
fprintf(stderr, "Initialized GPU ID #%d: %s\n", gpuid, gpu_info->cuda_dev[gpuid].prop.name);
}
+ //Ignoring return value as NVML errors should be treated not critical.
+ if (stat == cudaSuccess)
+ {
+ init_gpu_application_clocks(fplog, gpuid, gpu_info);
+ }
return (stat == cudaSuccess);
}
* The context is explicitly destroyed and therefore all data uploaded to the GPU
* is lost. This should only be called when none of this data is required anymore.
*
+ * \param[in] mygpu index of the GPU clean up for
* \param[out] result_str the message related to the error that occurred
* during the initialization (if there was any).
+ * \param[in] gpu_info GPU info of all detected devices in the system.
+ * \param[in] gpu_opt options for using the GPUs in gpu_info
* \returns true if no error occurs during the freeing.
*/
-gmx_bool free_gpu(char *result_str)
+gmx_bool free_gpu(
+ int gmx_unused mygpu, char *result_str,
+ const gmx_gpu_info_t gmx_unused *gpu_info,
+ const gmx_gpu_opt_t gmx_unused *gpu_opt
+ )
{
- cudaError_t stat;
+ cudaError_t stat;
+ gmx_bool reset_gpu_application_clocks_status = true;
+ int gpuid;
assert(result_str);
fprintf(stderr, "Cleaning up context on GPU ID #%d\n", gpuid);
}
+ gpuid = gpu_opt ? gpu_opt->cuda_dev_use[mygpu] : -1;
+ if (gpuid != -1)
+ {
+ reset_gpu_application_clocks_status = reset_gpu_application_clocks( &(gpu_info->cuda_dev[gpuid]) );
+ }
#if CUDA_VERSION < 4000
stat = cudaThreadExit();
#else
stat = cudaDeviceReset();
#endif
strncpy(result_str, cudaGetErrorString(stat), STRLEN);
-
- return (stat == cudaSuccess);
+ return (stat == cudaSuccess) && reset_gpu_application_clocks_status;
}
/*! \brief Returns true if the gpu characterized by the device properties is
}
}
- gpu_opt->ncuda_dev_use = ncompat;
- snew(gpu_opt->cuda_dev_use, ncompat);
- memcpy(gpu_opt->cuda_dev_use, compat, ncompat*sizeof(*compat));
+ gpu_opt->ncuda_dev_compatible = ncompat;
+ snew(gpu_opt->cuda_dev_compatible, ncompat);
+ memcpy(gpu_opt->cuda_dev_compatible, compat, ncompat*sizeof(*compat));
sfree(compat);
}
#ifndef _GPU_UTILS_H_
#define _GPU_UTILS_H_
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "config.h"
-#include "types/simple.h"
-#include "types/hw_info.h"
+#include "gromacs/legacyheaders/types/hw_info.h"
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef GMX_GPU
#define FUNC_TERM_INT ;
+#define FUNC_TERM_SIZE_T ;
#define FUNC_TERM_VOID ;
#define FUNC_QUALIFIER
#else
#define FUNC_TERM_INT {return -1; }
+#define FUNC_TERM_SIZE_T {return 0; }
#define FUNC_TERM_VOID {}
#define FUNC_QUALIFIER static
#endif
extern "C" {
#endif
-FUNC_QUALIFIER
-int do_quick_memtest(int gmx_unused dev_id) FUNC_TERM_INT
-
-FUNC_QUALIFIER
-int do_full_memtest(int gmx_unused dev_id) FUNC_TERM_INT
-
-FUNC_QUALIFIER
-int do_timed_memtest(int gmx_unused dev_id, int gmx_unused time_limit) FUNC_TERM_INT
-
FUNC_QUALIFIER
int detect_cuda_gpus(gmx_gpu_info_t gmx_unused *gpu_info, char gmx_unused *err_str) FUNC_TERM_INT
void free_gpu_info(const gmx_gpu_info_t gmx_unused *gpu_info) FUNC_TERM_VOID
FUNC_QUALIFIER
-gmx_bool init_gpu(int gmx_unused mygpu, char gmx_unused *result_str,
+gmx_bool init_gpu(FILE gmx_unused *fplog, int gmx_unused mygpu, char gmx_unused *result_str,
const gmx_gpu_info_t gmx_unused *gpu_info,
const gmx_gpu_opt_t gmx_unused *gpu_opt) FUNC_TERM_INT
FUNC_QUALIFIER
-gmx_bool free_gpu(char gmx_unused *result_str) FUNC_TERM_INT
+gmx_bool free_gpu(int gmx_unused mygpu, char gmx_unused *result_str,
+ const gmx_gpu_info_t gmx_unused *gpu_info,
+ const gmx_gpu_opt_t gmx_unused *gpu_opt) FUNC_TERM_INT
/*! \brief Returns the device ID of the GPU currently in use.*/
FUNC_QUALIFIER
void get_gpu_device_info_string(char gmx_unused *s, const gmx_gpu_info_t gmx_unused *gpu_info, int gmx_unused index) FUNC_TERM_VOID
FUNC_QUALIFIER
-size_t sizeof_cuda_dev_info(void) FUNC_TERM_INT
+size_t sizeof_cuda_dev_info(void) FUNC_TERM_SIZE_T
#ifdef __cplusplus
}
+++ /dev/null
-/*
- * memtestG80_core.cu
- * MemtestG80 core memory test functions and OOP interface to tester.
- *
- * Author: Imran Haque, 2009
- * Copyright 2009, Stanford University
- *
- * This file is licensed under the terms of the LGPL. Please see
- * the COPYING file in the accompanying source distribution for
- * full license terms.
- *
- */
-
- /*
- * CUDA grid layout: Linear in blocks and threads.
- * Intended usage = 1k blocks, 512 t/blk, with N words (iterations) per thread
- * -> 2*N MiB tested per grid
- * thread address at iteration i = base + blockIdx.x * N * blockDim.x + i*blockDim.x + threadIdx.x
- *
- */
-
-// Naming convention: gpuXXX and cpuXXX functions are user-accessible; deviceXXX functions are internal
-// gpuXXX functions execute a particular test on a block of GPU memory
-// cpuXXX " " " " " " " " " CPU "
-
-#define THREAD_ADDRESS(base,N,i) (base + blockIdx.x * N * blockDim.x + i * blockDim.x + threadIdx.x)
-#define THREAD_OFFSET(N,i) (blockIdx.x * N * blockDim.x + i * blockDim.x + threadIdx.x)
-#define BITSDIFF(x,y) __popc((x) ^ (y))
-
-
-#include "memtestG80_core.h"
-
-#include <stdio.h>
-
-
-
-
-void memtestState::deallocate() {
- if (allocated) {
- cudaFree(devTestMem);
- cudaFree(devTempMem);
- free(hostTempMem);
- devTestMem = NULL;
- devTempMem = NULL;
- hostTempMem = NULL;
- allocated = false;
- }
- initTime = 0;
- }
-
-uint memtestState::allocate(uint mbToTest) {
- deallocate();
-
- initTime = getTimeMilliseconds();
-
- // Round up to nearest 2MiB
- if (mbToTest % 2) mbToTest++;
-
- megsToTest = mbToTest;
- loopIters = megsToTest/2;
-
- if (megsToTest == 0) return 0;
-
- try {
- if (cudaMalloc((void**)&devTestMem,megsToTest*1048576UL) != cudaSuccess) throw 1;
- if (cudaMalloc((void**)&devTempMem,sizeof(uint)*nBlocks) != cudaSuccess) throw 2;
- if ( (hostTempMem = (uint*)malloc(sizeof(uint)*nBlocks)) == NULL) throw 3;
- } catch (...) {
- // Clear CUDA error flag for outside world
- cudaGetLastError();
- if (devTempMem) {
- cudaFree(devTempMem);
- devTempMem = NULL;
- }
- if (devTestMem) {
- cudaFree(devTestMem);
- devTestMem = NULL;
- }
- if (hostTempMem) {
- free(hostTempMem);
- hostTempMem = NULL;
- }
- return 0;
- }
- allocated = true;
- return megsToTest;
- }
-bool memtestState::gpuMemoryBandwidth(double& bandwidth,uint mbToTest,uint iters) {
- if (!allocated || megsToTest < 2*mbToTest) return false;
- bandwidth = ::gpuMemoryBandwidth(devTestMem,devTestMem+mbToTest*1048576/4,mbToTest,iters);
- return cudaGetLastError() == cudaSuccess;
-}
-bool memtestState::gpuWriteConstant(const uint constant) const {
- if (!allocated) return false;
- ::gpuWriteConstant(nBlocks,nThreads,devTestMem,loopIters,constant);
- return cudaGetLastError() == cudaSuccess;
-}
-
-bool memtestState::gpuVerifyConstant(uint& errorCount,const uint constant) const {
- if (!allocated) return false;
- errorCount = ::gpuVerifyConstant(nBlocks,nThreads,devTestMem,loopIters,constant,devTempMem,hostTempMem);
- return ((cudaGetLastError() == cudaSuccess) && (errorCount != 0xFFFFFFFF) && (errorCount != 0xFFFFFFFE));
-}
-
-bool memtestState::gpuShortLCG0(uint& errorCount,const uint repeats) const {
- if (!allocated) return false;
- errorCount = ::gpuShortLCG0(nBlocks,nThreads,devTestMem,loopIters,repeats,lcgPeriod,devTempMem,hostTempMem);
- return ((cudaGetLastError() == cudaSuccess) && (errorCount != 0xFFFFFFFF) && (errorCount != 0xFFFFFFFE));
-}
-bool memtestState::gpuShortLCG0Shmem(uint& errorCount,const uint repeats) const {
- if (!allocated) return false;
- errorCount = ::gpuShortLCG0Shmem(nBlocks,nThreads,devTestMem,loopIters,repeats,lcgPeriod,devTempMem,hostTempMem);
- return ((cudaGetLastError() == cudaSuccess) && (errorCount != 0xFFFFFFFF) && (errorCount != 0xFFFFFFFE));
-}
-bool memtestState::gpuMovingInversionsOnesZeros(uint& errorCount) const {
- if (!allocated) return false;
- errorCount = ::gpuMovingInversionsOnesZeros(nBlocks,nThreads,devTestMem,loopIters,devTempMem,hostTempMem);
- return ((cudaGetLastError() == cudaSuccess) && (errorCount != 0xFFFFFFFF) && (errorCount != 0xFFFFFFFE));
-}
-bool memtestState::gpuWalking8BitM86(uint& errorCount,const uint shift) const {
- if (!allocated) return false;
- errorCount = ::gpuWalking8BitM86(nBlocks,nThreads,devTestMem,loopIters,shift,devTempMem,hostTempMem);
- return ((cudaGetLastError() == cudaSuccess) && (errorCount != 0xFFFFFFFF) && (errorCount != 0xFFFFFFFE));
-}
-bool memtestState::gpuWalking8Bit(uint& errorCount,const bool ones,const uint shift) const {
- if (!allocated) return false;
- errorCount = ::gpuWalking8Bit(nBlocks,nThreads,devTestMem,loopIters,ones,shift,devTempMem,hostTempMem);
- return ((cudaGetLastError() == cudaSuccess) && (errorCount != 0xFFFFFFFF) && (errorCount != 0xFFFFFFFE));
-}
-bool memtestState::gpuMovingInversionsRandom(uint& errorCount) const {
- if (!allocated) return false;
- errorCount = ::gpuMovingInversionsRandom(nBlocks,nThreads,devTestMem,loopIters,devTempMem,hostTempMem);
- return ((cudaGetLastError() == cudaSuccess) && (errorCount != 0xFFFFFFFF) && (errorCount != 0xFFFFFFFE));
-}
-bool memtestState::gpuWalking32Bit(uint& errorCount,const bool ones,const uint shift) const {
- if (!allocated) return false;
- errorCount = ::gpuWalking32Bit(nBlocks,nThreads,devTestMem,loopIters,ones,shift,devTempMem,hostTempMem);
- return ((cudaGetLastError() == cudaSuccess) && (errorCount != 0xFFFFFFFF) && (errorCount != 0xFFFFFFFE));
-}
-bool memtestState::gpuRandomBlocks(uint& errorCount,const uint seed) const {
- if (!allocated) return false;
- errorCount = ::gpuRandomBlocks(nBlocks,nThreads,devTestMem,loopIters,seed,devTempMem,hostTempMem);
- return ((cudaGetLastError() == cudaSuccess) && (errorCount != 0xFFFFFFFF) && (errorCount != 0xFFFFFFFE));
-}
-bool memtestState::gpuModuloX(uint& errorCount,const uint shift,const uint pattern,const uint modulus,const uint overwriteIters) const {
- if (!allocated) return false;
- errorCount = ::gpuModuloX(nBlocks,nThreads,devTestMem,loopIters,shift,pattern,modulus,overwriteIters,devTempMem,hostTempMem);
- return ((cudaGetLastError() == cudaSuccess) && (errorCount != 0xFFFFFFFF) && (errorCount != 0xFFFFFFFE));
-}
-
-
-
-__global__ void deviceWriteConstant(uint* base, uint N, const uint constant);
-__global__ void deviceVerifyConstant(uint* base,uint N,const uint constant,uint* blockErrorCount);
-__global__ void deviceShortLCG0(uint* base,uint N,uint repeats,const int period);
-__global__ void deviceShortLCG0Shmem(uint* base,uint N,uint repeats,const int period);
-__global__ void deviceWriteRandomBlocks(uint* base,uint N,int seed);
-__global__ void deviceVerifyRandomBlocks(uint* base,uint N,int seed,uint* blockErrorCount);
-__global__ void deviceWriteWalking32Bit(uint* base,uint N,bool ones,uint shift);
-__global__ void deviceVerifyWalking32Bit(uint* base,uint N,bool ones,uint shift,uint* blockErrorCount);
-__global__ void deviceWritePairedConstants(uint* base,uint N,uint pattern0,uint pattern1);
-__global__ void deviceVerifyPairedConstants(uint* base,uint N,uint pattern0,uint pattern1,uint* blockErrorCount);
-__global__ void deviceWritePairedModulo(uint* base,const uint N,const uint shift,const uint pattern1,const uint pattern2,const uint modulus,const uint iters);
-__global__ void deviceVerifyPairedModulo(uint* base,uint N,const uint shift,const uint pattern1,const uint modulus,uint* blockErrorCount);
-
-
-// Utility function to measure memory bandwidth
-__host__ double gpuMemoryBandwidth(uint* src,uint* dst,uint mbToTest,uint iters) {
- uint start = getTimeMilliseconds();
- for (uint i = 0; i < iters; i++) {
- cudaMemcpy(dst,src,mbToTest*1048576,cudaMemcpyDeviceToDevice);
- }
- //D-to-D memory copies are non-blocking, so sync to get correct timing
- cudaThreadSynchronize();
- //SOFTWAIT();
- uint end = getTimeMilliseconds();
-
- // Calculate bandwidth in MiB/s
- // Multiply by 2 since we are reading and writing to the same memory
- double bw = 2.0*((double)mbToTest*iters)/((end-start)/1000.0);
- return bw;
-}
-
-// Utility functions to write/verify pure constants in memory, CPU/GPU {{{
-__host__ void gpuWriteConstant(const uint nBlocks,const uint nThreads,uint* base,uint N,const uint constant) { //{{{
- deviceWriteConstant<<<nBlocks,nThreads>>>(base,N,constant);
-}
-
-__global__ void deviceWriteConstant(uint* base, uint N, const uint constant) {
- for (uint i = 0 ; i < N; i++) {
- *(THREAD_ADDRESS(base,N,i)) = constant;
- }
-}
-//}}}
-__host__ uint gpuVerifyConstant(const uint nBlocks,const uint nThreads,uint* base,uint N,const uint constant,uint* blockErrorCount,uint* errorCounts) { //{{{
- // Given device arrays base (tested memory) and blockErrorCount (nBlocks uints in length of temp space)
-
- deviceVerifyConstant<<<nBlocks,nThreads,sizeof(uint)*nThreads>>>(base,N,constant,blockErrorCount);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
-
- cudaMemcpy(errorCounts,blockErrorCount,sizeof(uint)*nBlocks,cudaMemcpyDeviceToHost);
-
- // Sum-reduce block error counts on the host - it's only order of 1k numbers.
- uint totalErrors = 0;
- for (uint i = 0; i < nBlocks; i++) {
- totalErrors += errorCounts[i];
- }
- return totalErrors;
-}
-
-__global__ void deviceVerifyConstant(uint* base,uint N,const uint constant,uint* blockErrorCount) {
- // Verifies memory at base to make sure it has a constant pattern
- // Sums number of errors found in block and stores error count into blockErrorCount[blockIdx.x]
- // Sum-reduce this array afterwards to get total error count over tested region
- // Uses 4*blockDim.x bytes of shared memory
-
- extern __shared__ uint threadErrorCount[];
- threadErrorCount[threadIdx.x] = 0;
-
- for (uint i = 0; i < N; i++) {
- //if ( *(THREAD_ADDRESS(base,N,i)) != constant ) threadErrorCount[threadIdx.x]++;
- threadErrorCount[threadIdx.x] += BITSDIFF(*(THREAD_ADDRESS(base,N,i)),constant);
- }
- // Parallel-reduce error counts over threads in block
- for (uint stride = blockDim.x>>1; stride > 0; stride >>= 1) {
- __syncthreads();
- if (threadIdx.x < stride)
- threadErrorCount[threadIdx.x] += threadErrorCount[threadIdx.x + stride];
- }
- __syncthreads();
-
- if (threadIdx.x == 0)
- blockErrorCount[blockIdx.x] = threadErrorCount[0];
-
- return;
-}
-//}}}
-
- __host__ void cpuWriteConstant(const uint nBlocks,const uint nThreads,uint* base,uint N,const uint constant) { //{{{
- dim3 blockDim(nThreads,0,0);
- dim3 threadIdx(0,0,0);
- dim3 blockIdx(0,0,0);
- for (blockIdx.x = 0; blockIdx.x < nBlocks; blockIdx.x++) {
- for (uint i = 0; i < N; i++) {
- for (threadIdx.x = 0; threadIdx.x < blockDim.x; threadIdx.x++) {
- *(THREAD_ADDRESS(base,N,i)) = constant;
- }
- }
- }
-}
-//}}}
-__host__ uint cpuVerifyConstant(const uint nBlocks,const uint nThreads,uint* base,uint N,const uint constant) { //{{{
- dim3 blockDim(nThreads,0,0);
- dim3 threadIdx(0,0,0);
- dim3 blockIdx(0,0,0);
- uint errorCount = 0;
- for (blockIdx.x = 0; blockIdx.x < nBlocks; blockIdx.x++) {
- for (uint i = 0; i < N; i++) {
- for (threadIdx.x = 0; threadIdx.x < blockDim.x; threadIdx.x++) {
- if (*(THREAD_ADDRESS(base,N,i)) != constant) errorCount++;
- }
- }
- }
- return errorCount;
-}
-//}}}
-//}}}
-
-// Logic test
-// Idea: Run a varying number of iterations (k*N) of a short-period (per=N) LCG that returns to zero (or F's) quickly {{{
-// Store only the result of the last iteration
-// Compare output to the desired constant
-// Compare results between varying k - memory error rate for a given pattern should be constant,
-// so variation should be due to logic errors in loop count
-__host__ uint gpuShortLCG0(const uint nBlocks,const uint nThreads,uint* base,uint N,const uint repeats,const int period,uint* blockErrorCounts,uint* errorCounts) { //{{{
- deviceShortLCG0<<<nBlocks,nThreads>>>(base,N,repeats,period);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
- return gpuVerifyConstant(nBlocks,nThreads,base,N,0,blockErrorCounts,errorCounts);
-} //}}}
-
-__host__ uint gpuShortLCG0Shmem(const uint nBlocks,const uint nThreads,uint* base,uint N,const uint repeats,const int period,uint* blockErrorCounts,uint* errorCounts) { //{{{
- deviceShortLCG0Shmem<<<nBlocks,nThreads,sizeof(uint)*nThreads>>>(base,N,repeats,period);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
- return gpuVerifyConstant(nBlocks,nThreads,base,N,0,blockErrorCounts,errorCounts);
-} //}}}
-
-// Put the LCG loop into a macro so we don't repeat code between versions of logic tester.
-// The paired XOR adds diversity to the instruction stream, and is not reduced to a NOT
-// as a single XOR is (verified with decuda).
-// {{{
-#if defined (LINUX) || defined(OSX)
-#define LCGLOOP(var,repeats,period,a,c) for (uint rep = 0; rep < repeats; rep++) {\
- (var) = ~(var);\
- _Pragma("unroll 1")\
- for (uint iter = 0; iter < period; iter++) {\
- (var) = ~(var);\
- (var) = (a)*(var)+(c);\
- (var) ^= 0xFFFFFFF0;\
- (var) ^= 0xF;\
- }\
- (var) = ~(var);\
-}
-#elif defined (WINDOWS) || defined (WINNV)
-#define LCGLOOP(var,repeats,period,a,c) for (uint rep = 0; rep < repeats; rep++) {\
- (var) = ~(var);\
- __pragma("unroll 1")\
- for (uint iter = 0; iter < period; iter++) {\
- (var) = ~(var);\
- (var) = (a)*(var)+(c);\
- (var) ^= 0xFFFFFFF0;\
- (var) ^= 0xF;\
- }\
- (var) = ~(var);\
-}
-#endif
-//}}}
-
-__global__ void deviceShortLCG0(uint* base,uint N,uint repeats,const int period) { //{{{
- // Pick a different block for different LCG lengths
- // Short periods are useful if LCG goes inside for i in 0..N loop
- int a,c;
- switch (period) {
- case 1024: a = 0x0fbfffff; c = 0x3bf75696; break;
- case 512: a = 0x61c8647f; c = 0x2b3e0000; break;
- case 256: a = 0x7161ac7f; c = 0x43840000; break;
- case 128: a = 0x0432b47f; c = 0x1ce80000; break;
- case 2048: a = 0x763fffff; c = 0x4769466f; break;
- default: a = 0; c = 0; break;
- }
-
- uint value = 0;
- LCGLOOP(value,repeats,period,a,c)
-
- for (uint i = 0 ; i < N; i++) {
- *(THREAD_ADDRESS(base,N,i)) = value;
- }
-} //}}}
-// _shmem version uses shared memory to store inter-iteration values
-// is more sensitive to shared memory errors from (eg) shader overclocking
-__global__ void deviceShortLCG0Shmem(uint* base,uint N,uint repeats,const int period) { //{{{
- // Pick a different block for different LCG lengths
- // Short periods are useful if LCG goes inside for i in 0..N loop
- int a,c;
- extern __shared__ uint shmem[];
- switch (period) {
- case 1024: a = 0x0fbfffff; c = 0x3bf75696; break;
- case 512: a = 0x61c8647f; c = 0x2b3e0000; break;
- case 256: a = 0x7161ac7f; c = 0x43840000; break;
- case 128: a = 0x0432b47f; c = 0x1ce80000; break;
- case 2048: a = 0x763fffff; c = 0x4769466f; break;
- default: a = 0; c = 0; break;
- }
- shmem[threadIdx.x] = 0;
- LCGLOOP(shmem[threadIdx.x],repeats,period,a,c)
-
- for (uint i = 0 ; i < N; i++) {
- *(THREAD_ADDRESS(base,N,i)) = shmem[threadIdx.x];
-
- }
-} //}}} //}}}
-
-
-// Memtest86 Test 2: tseq=0,4
-__host__ uint gpuMovingInversionsOnesZeros(const uint nBlocks,const uint nThreads,uint* base,uint N,uint* blockErrorCounts,uint* errorCounts) { //{{{
-
- uint errorCount;
- gpuWriteConstant(nBlocks,nThreads,base,N,0xFFFFFFFF);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
-
- errorCount = gpuVerifyConstant(nBlocks,nThreads,base,N,0xFFFFFFFF,blockErrorCounts,errorCounts);
- CHECK_LAUNCH_ERROR();
-
- gpuWriteConstant(nBlocks,nThreads,base,N,0x0);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
-
- errorCount += gpuVerifyConstant(nBlocks,nThreads,base,N,0x0,blockErrorCounts,errorCounts);
- CHECK_LAUNCH_ERROR();
- return errorCount;
-} //}}}
-
-// Memtest86 Test 3: tseq=1
-__host__ uint gpuWalking8BitM86(const uint nBlocks,const uint nThreads,uint* base,uint N,uint shift,uint* blockErrorCounts,uint* errorCounts) { //{{{
- // Performs the Memtest86 variation on the walking 8-bit pattern, where the same shifted pattern is
- // written into each 32-bit word in memory, verified, and its complement written and verified
- shift &= 0x7;
- uint pattern = 1 << shift;
- pattern = pattern | (pattern << 8) | (pattern << 16) | (pattern << 24);
-
- uint errorCount;
- gpuWriteConstant(nBlocks,nThreads,base,N,pattern);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
-
- errorCount = gpuVerifyConstant(nBlocks,nThreads,base,N,pattern,blockErrorCounts,errorCounts);
- CHECK_LAUNCH_ERROR();
-
- pattern = ~pattern;
- gpuWriteConstant(nBlocks,nThreads,base,N,pattern);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
-
- errorCount += gpuVerifyConstant(nBlocks,nThreads,base,N,pattern,blockErrorCounts,errorCounts);
- CHECK_LAUNCH_ERROR();
- return errorCount;
-} //}}}
-__host__ uint cpuWalking8BitM86(const uint nBlocks,const uint nThreads,uint* base,uint N,uint shift) { //{{{
- // Performs the Memtest86 variation on the walking 8-bit pattern, where the same shifted pattern is
- // written into each 32-bit word in memory, verified, and its complement written and verified
- shift &= 0x7;
- uint pattern = 1 << shift;
- pattern = pattern | (pattern << 8) | (pattern << 16) | (pattern << 24);
-
- uint errorCount;
- cpuWriteConstant(nBlocks,nThreads,base,N,pattern);
- errorCount = cpuVerifyConstant(nBlocks,nThreads,base,N,pattern);
-
- pattern = ~pattern;
- cpuWriteConstant(nBlocks,nThreads,base,N,pattern);
- errorCount += cpuVerifyConstant(nBlocks,nThreads,base,N,pattern);
-
- return errorCount;
-} //}}}
-__host__ uint gpuWalking8Bit(const uint nBlocks,const uint nThreads,uint* base,uint N,bool ones,uint shift,uint* blockErrorCount,uint* errorCounts) { //{{{
- // Implements one iteration of true walking 8-bit ones/zeros test
- uint patterns[2]={0x0,0x0};
-
- // Build the walking-ones paired pattern of 8-bits with the given shift
- shift &= 0x7;
- uint bits = 0x1 << shift;
- for (uint i = 0; i < 4; i++) {
- patterns[0] = (patterns[0] << 8) | bits;
- bits = (bits == 0x80) ? 0x01 : bits<<1;
- }
- for (uint i = 0; i < 4; i++) {
- patterns[1] = (patterns[1] << 8) | bits;
- bits = (bits == 0x80) ? 0x01 : bits<<1;
- }
-
- if (!ones) {
- patterns[0] = ~patterns[0];
- patterns[1] = ~patterns[1];
- }
-
- //printf("Host Patterns: %08x %08x\n",patterns[0],patterns[1]);
- deviceWritePairedConstants<<<nBlocks,nThreads>>>(base,N,patterns[0],patterns[1]);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
- //cudaMemcpy(errorCounts,base,sizeof(uint)*nBlocks,cudaMemcpyDeviceToHost);
- //printf("First few words in tested RAM: %08x %08x %08x %08x %08x %08x\n",errorCounts[0],errorCounts[1],errorCounts[2],errorCounts[3],errorCounts[4],errorCounts[5]);
- // Given device arrays base (tested memory) and blockErrorCount (nBlocks uints in length of temp space)
- deviceVerifyPairedConstants<<<nBlocks,nThreads,sizeof(uint)*nThreads>>>(base,N,patterns[0],patterns[1],blockErrorCount);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
- //if (cudaGetLastError() != cudaSuccess) {
- // return 0xFFFFFFFF; // -1
- //}
- //uint errorCounts[nBlocks];
- cudaMemcpy(errorCounts,blockErrorCount,sizeof(uint)*nBlocks,cudaMemcpyDeviceToHost);
-
- // Sum-reduce block error counts on the host - it's only order of 1k numbers.
- uint totalErrors = 0;
- for (uint i = 0; i < nBlocks; i++) {
- totalErrors += errorCounts[i];
- }
- return totalErrors;
-}
-
-__global__ void deviceWritePairedConstants(uint* base,uint N,uint pattern0,uint pattern1) {
- // Writes paired constants to memory, such that each offset that is X mod 2 receives patterns[X]
- // Used for true walking-ones/zeros 8-bit test
- //if (threadIdx.x == 0)
- // printf("Device Patterns Block %u: %08x %08x\n",blockIdx.x,patterns[0],patterns[1]);
- const uint pattern = (threadIdx.x & 0x1) ? pattern1 : pattern0;
- //const uint pattern = patterns[threadIdx.x & 0x1];
- for (uint i = 0 ; i < N; i++) {
- *(THREAD_ADDRESS(base,N,i)) = pattern;
- //*(base+blockIdx.x*N*blockDim.x + i*blockDim.x + threadIdx.x) = 0;
- }
-
-}
-
-__global__ void deviceVerifyPairedConstants(uint* base,uint N,uint pattern0,uint pattern1,uint* blockErrorCount) {
- // Verifies memory at base to make sure it has a correct paired-constant pattern
- // Sums number of errors found in block and stores error count into blockErrorCount[blockIdx.x]
- // Sum-reduce this array afterwards to get total error count over tested region
- // Uses 4*blockDim.x bytes of shared memory
-
- extern __shared__ uint threadErrorCount[];
- threadErrorCount[threadIdx.x] = 0;
- //const uint pattern = patterns[threadIdx.x & 0x1];
- const uint pattern = (threadIdx.x & 0x1) ? pattern1 : pattern0;
-
- for (uint i = 0; i < N; i++) {
- //if ( *(THREAD_ADDRESS(base,N,i)) != pattern ) threadErrorCount[threadIdx.x]++;
- threadErrorCount[threadIdx.x] += BITSDIFF(*(THREAD_ADDRESS(base,N,i)),pattern);
- }
- // Parallel-reduce error counts over threads in block
- for (uint stride = blockDim.x>>1; stride > 0; stride >>= 1) {
- __syncthreads();
- if (threadIdx.x < stride)
- threadErrorCount[threadIdx.x] += threadErrorCount[threadIdx.x + stride];
- }
- __syncthreads();
-
- if (threadIdx.x == 0)
- blockErrorCount[blockIdx.x] = threadErrorCount[0];
-
- return;
-}
-//}}}
-
-// Memtest86 Test 4: tseq=10
-__host__ uint gpuMovingInversionsRandom(const uint nBlocks,const uint nThreads,uint* base,uint N,uint* blockErrorCounts,uint* errorCounts) { //{{{
-
- uint errorCount;
-
- uint pattern = (uint)rand();
- gpuWriteConstant(nBlocks,nThreads,base,N,pattern);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
-
- errorCount = gpuVerifyConstant(nBlocks,nThreads,base,N,pattern,blockErrorCounts,errorCounts);
- CHECK_LAUNCH_ERROR();
-
- pattern = ~pattern;
- gpuWriteConstant(nBlocks,nThreads,base,N,pattern);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
-
- errorCount += gpuVerifyConstant(nBlocks,nThreads,base,N,pattern,blockErrorCounts,errorCounts);
- CHECK_LAUNCH_ERROR();
- return errorCount;
-} //}}}
-
-// Memtest86 Test 6: tseq=2
-__host__ uint gpuWalking32Bit(const uint nBlocks,const uint nThreads,uint* base,uint N,bool ones,uint shift,uint* blockErrorCount,uint* errorCounts) { //{{{
- // Given device arrays base (tested memory) and blockErrorCount (nBlocks uints in length of temp space)
- // Does one iteration of the walking-{ones/zeros} 32-bit test paralleling Memtest
- // With the starting pattern 1<<shift
- // NUMBER OF THREADS SHOULD BE A MULTIPLE OF 32
-
- deviceWriteWalking32Bit<<<nBlocks,nThreads>>>(base,N,ones,shift);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
-
- deviceVerifyWalking32Bit<<<nBlocks,nThreads,sizeof(uint)*nThreads>>>(base,N,ones,shift,blockErrorCount);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
-
- cudaMemcpy(errorCounts,blockErrorCount,sizeof(uint)*nBlocks,cudaMemcpyDeviceToHost);
-
- // Sum-reduce block error counts on the host - it's only order of 1k numbers.
- uint totalErrors = 0;
- for (uint i = 0; i < nBlocks; i++) {
- totalErrors += errorCounts[i];
- }
- return totalErrors;
-
-}
-
-__global__ void deviceWriteWalking32Bit(uint* base,uint N,bool ones,uint shift) {
- // Writes one iteration of the walking-{ones/zeros} 32-bit pattern to gpu memory
-
- // Want to write in a 1 << (offset from base + shift % 32)
- // Since thread indices are aligned with base, this reduces to
- // 1 << ((threadIdx.x+shift) & 0x1f)
- // With conditional inversion for walking zeros
- uint pattern = 1 << ((threadIdx.x + shift) & 0x1f);
- pattern = ones ? pattern : ~pattern;
-
- for (uint i = 0; i < N; i++) {
- *(THREAD_ADDRESS(base,N,i)) = pattern;
- }
-}
-
-__global__ void deviceVerifyWalking32Bit(uint* base,uint N,bool ones,uint shift,uint* blockErrorCount) {
- // Verifies memory at base to make sure it has a constant pattern
- // Sums number of errors found in block and stores error count into blockErrorCount[blockIdx.x]
- // Sum-reduce this array afterwards to get total error count over tested region
- // Uses 4*blockDim.x bytes of shared memory
-
- extern __shared__ uint threadErrorCount[];
- threadErrorCount[threadIdx.x] = 0;
-
- uint pattern = 1 << ((threadIdx.x + shift) & 0x1f);
- pattern = ones ? pattern : ~pattern;
-
- for (uint i = 0; i < N; i++) {
- //if ( *(THREAD_ADDRESS(base,N,i)) != pattern ) threadErrorCount[threadIdx.x]++;
- threadErrorCount[threadIdx.x] += BITSDIFF(*(THREAD_ADDRESS(base,N,i)),pattern);
- }
- // Parallel-reduce error counts over threads in block
- for (uint stride = blockDim.x>>1; stride > 0; stride >>= 1) {
- __syncthreads();
- if (threadIdx.x < stride)
- threadErrorCount[threadIdx.x] += threadErrorCount[threadIdx.x + stride];
- }
- __syncthreads();
-
- if (threadIdx.x == 0)
- blockErrorCount[blockIdx.x] = threadErrorCount[0];
-
- return;
-}
-//}}}
-
-// Memtest86 Test 7: tseq=9
-__host__ uint gpuRandomBlocks(const uint nBlocks,const uint nThreads,uint* base,uint N,uint seed,uint* blockErrorCount,uint* errorCounts) { //{{{ {{{
- // Writes random numbers into memory and verifies pattern
- //uint errorCounts[nBlocks];
-
- deviceWriteRandomBlocks<<<nBlocks,nThreads,4*nThreads>>>(base,N,seed);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
-
- //cudaMemcpy(errorCounts,base,sizeof(uint)*nBlocks,cudaMemcpyDeviceToHost);
- //printf("First few words in tested RAM: %08x %08x %08x %08x %08x %08x\n",errorCounts[0],errorCounts[1],errorCounts[2],errorCounts[3],errorCounts[4],errorCounts[5]);
-
- deviceVerifyRandomBlocks<<<nBlocks,nThreads,12*nThreads>>>(base,N,seed,blockErrorCount);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
-
-
- cudaMemcpy(errorCounts,blockErrorCount,sizeof(uint)*nBlocks,cudaMemcpyDeviceToHost);
-
- // Sum-reduce block error counts on the host - it's only order of 1k numbers.
- uint totalErrors = 0;
- for (uint i = 0; i < nBlocks; i++) {
- totalErrors += errorCounts[i];
- }
- return totalErrors;
-}
-//}}}
-//
-// Math functions modulo the Mersenne prime 2^31 -1 {{{
-__device__ void deviceMul3131 (uint v1, uint v2,uint& LO, uint& HI)
-{
- // Given v1, v2 < 2^31
- // Emulate a 31-bit integer multiply by doing instead a 32-bit multiply into LO and HI
- // And shifting bits around to make it look right.
- LO = v1*v2;
- HI = __umulhi(v1,v2);
- HI <<= 1;
- HI |= (LO & 0x80000000) >> 31;
- LO &= 0x7FFFFFFF;
-
-}
-
-__device__ uint deviceModMP31(uint LO,uint HI) {
- // Modulo a 62-bit number HI<<31 + LO, mod 2^31-1
- // Encyclopedia of Cryptography and Security By Henk C. A. van Tilborg
- // page 381, Mersenne Primes
- uint sum = LO+HI;
- if (sum >= 0x80000000) {
- // If a+b > 2^31, then high bit will be set
- return sum - 0x80000000 + 1;
- } else {
- return sum;
- }
-}
-__device__ uint deviceMulMP31(uint a,uint b) {
- // Multiplies a pair of 31-bit integers a and b mod the Mersenne prime 2^31-1
- // Takes result through a 62-bit intermediate
- uint LO,HI;
- deviceMul3131(a,b,LO,HI);
- return deviceModMP31(LO,HI);
-}
-
-__device__ uint deviceExpoModMP31(uint base,uint exponent) {
- uint result = 1;
- while (exponent > 0) {
- if (exponent & 1) {
- result = deviceMulMP31(result,base);
- }
- exponent >>= 1;
- base = deviceMulMP31(base,base);
- }
- return result;
-}
-//}}}
-// deviceRan0p: Parallelized closed-form version of NR's ran0 {{{
-__device__ uint deviceRan0p(int seed,int n) { //
- uint an = deviceExpoModMP31(16807,n+1);
- return deviceMulMP31(an,seed);
-}
-//}}}
-// deviceIrbit2: random bit generation, from NR {{{
-__device__ int deviceIrbit2(uint& seed) {
- const uint IB1 = 1;
- const uint IB2 = 2;
- const uint IB5 = 16;
- const uint IB18 = 131072;
- const uint MASK = IB1+IB2+IB5;
- if (seed & IB18) {
- seed = ((seed ^ MASK) << 1) | IB1;
- return 1;
- } else {
- seed <<= 1;
- return 0;
- }
-}
-//}}}
-__global__ void deviceWriteRandomBlocks(uint* base,uint N,int seed) { //{{{
- // Requires 4*nThreads bytes of shared memory
- extern __shared__ uint randomBlock[];
-
- // Make sure seed is not zero.
- if (seed == 0) seed = 123459876+blockIdx.x;
- uint bitSeed = deviceRan0p(seed + threadIdx.x,threadIdx.x);
-
- for (uint i=0; i < N; i++) {
- // Generate a block of random numbers in parallel using closed-form expression for ran0
- // OR in a random bit because Ran0 will never have the high bit set
- randomBlock[threadIdx.x] = deviceRan0p(seed,threadIdx.x) | (deviceIrbit2(bitSeed) << 31);
- __syncthreads();
-
- // Set the seed for the next round to the last number calculated in this round
- seed = randomBlock[blockDim.x-1];
-
- // Blit shmem block out to global memory
- *(THREAD_ADDRESS(base,N,i)) = randomBlock[threadIdx.x];
- }
-}
-//}}}
-__global__ void deviceVerifyRandomBlocks(uint* base,uint N,int seed,uint* blockErrorCount) { //{{{
- // Verifies memory at base to make sure it has a correct random pattern given the seed
- // Sums number of errors found in block and stores error count into blockErrorCount[blockIdx.x]
- // Sum-reduce this array afterwards to get total error count over tested region
- // Uses 12*blockDim.x bytes of shared memory
-
- extern __shared__ uint shmem[];
- uint* threadErrorCount = shmem;
- uint* randomBlock = shmem + blockDim.x;
- // Put these into shmem to cut register count
- uint* bitSeeds = randomBlock + blockDim.x;
-
- threadErrorCount[threadIdx.x] = 0;
-
- // Make sure seed is not zero.
- if (seed == 0) seed = 123459876+blockIdx.x;
- //uint bitSeed = deviceRan0p(seed + threadIdx.x,threadIdx.x);
- bitSeeds[threadIdx.x] = deviceRan0p(seed + threadIdx.x,threadIdx.x);
-
- for (uint i = 0; i < N; i++) {
- // Generate a block of random numbers in parallel using closed-form expression for ran0
- // OR in a random bit because Ran0 will never have the high bit set
- //randomBlock[threadIdx.x] = deviceRan0p(seed,threadIdx.x) | (deviceIrbit2(bitSeed) << 31);
- randomBlock[threadIdx.x] = deviceRan0p(seed,threadIdx.x) | (deviceIrbit2(bitSeeds[threadIdx.x]) << 31);
- __syncthreads();
-
- // Set the seed for the next round to the last number calculated in this round
- seed = randomBlock[blockDim.x-1];
-
- //if ( randomBlock[threadIdx.x] != *(THREAD_ADDRESS(base,N,i))) threadErrorCount[threadIdx.x]++;
- threadErrorCount[threadIdx.x] += BITSDIFF(*(THREAD_ADDRESS(base,N,i)),randomBlock[threadIdx.x]);
-
- }
-
- // Parallel-reduce error counts over threads in block
- for (uint stride = blockDim.x>>1; stride > 0; stride >>= 1) {
- __syncthreads();
- if (threadIdx.x < stride)
- threadErrorCount[threadIdx.x] += threadErrorCount[threadIdx.x + stride];
- }
- __syncthreads();
-
- if (threadIdx.x == 0)
- blockErrorCount[blockIdx.x] = threadErrorCount[0];
-
- return;
-}
-//}}}
-//}}}
-
-// Memtest86 Test 8: tseq=3 (M86 uses modulus = 20)
-__host__ uint gpuModuloX(const uint nBlocks,const uint nThreads,uint* base,const uint N,uint shift,uint pattern1,const uint modulus,const uint iters,
- uint* blockErrorCount,uint* errorCounts) { //{{{
- // Given device arrays base (tested memory) and blockErrorCount (nBlocks uints in length of temp space)
- // Given a shift, modulus, pattern to test and number of overwrite iterations
- // Performs Modulo-X test on memory
-
- //uint errorCounts[nBlocks];
- uint totalErrors = 0;
- shift %= modulus;
-
- // Test both the given pattern and its inverse
- for (uint i = 0; i < 2; i++, pattern1 = ~pattern1) {
- deviceWritePairedModulo<<<nBlocks,nThreads>>>(base,N,shift,pattern1,~pattern1,modulus,iters);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
-
- deviceVerifyPairedModulo<<<nBlocks,nThreads,sizeof(uint)*nThreads>>>(base,N,shift,pattern1,modulus,blockErrorCount);
- CHECK_LAUNCH_ERROR();
- SOFTWAIT();
- CHECK_LAUNCH_ERROR();
-
- cudaMemcpy(errorCounts,blockErrorCount,sizeof(uint)*nBlocks,cudaMemcpyDeviceToHost);
-
- // Sum-reduce block error counts on the host - it's only order of 1k numbers.
- for (uint i = 0; i < nBlocks; i++) {
- totalErrors += errorCounts[i];
- }
- }
- return totalErrors;
-}
-
-__global__ void deviceWritePairedModulo(uint* base,const uint N,const uint shift,const uint pattern1,const uint pattern2,const uint modulus,const uint iters) {
- // First writes pattern1 into every offset that is 0 mod modulus
- // Next (iters times) writes ~pattern1 into every other address
- uint offset;
- for (uint i = 0 ; i < N; i++) {
- offset = THREAD_OFFSET(N,i);
- if ((offset % modulus) == shift) *(base+offset) = pattern1;
- }
- __syncthreads();
- for (uint j = 0; j < iters; j++) {
- for (uint i = 0 ; i < N; i++) {
- offset = THREAD_OFFSET(N,i);
- if ((offset % modulus) != shift) *(base+offset) = pattern2;
- }
- }
-}
-__global__ void deviceVerifyPairedModulo(uint* base,uint N,const uint shift,const uint pattern1,const uint modulus,uint* blockErrorCount) {
- // Verifies that memory at each (offset mod modulus == shift) stores pattern1
- // Sums number of errors found in block and stores error count into blockErrorCount[blockIdx.x]
- // Sum-reduce this array afterwards to get total error count over tested region
- // Uses 4*blockDim.x bytes of shared memory
-
- extern __shared__ uint threadErrorCount[];
- threadErrorCount[threadIdx.x] = 0;
- uint offset;
-
- for (uint i = 0; i < N; i++) {
- offset = THREAD_OFFSET(N,i);
- //if (((offset % modulus) == shift) && (*(base+offset) != pattern1)) threadErrorCount[threadIdx.x]++;
- if ((offset % modulus) == shift) threadErrorCount[threadIdx.x] += BITSDIFF(*(base+offset),pattern1);
- }
- // Parallel-reduce error counts over threads in block
- for (uint stride = blockDim.x>>1; stride > 0; stride >>= 1) {
- __syncthreads();
- if (threadIdx.x < stride)
- threadErrorCount[threadIdx.x] += threadErrorCount[threadIdx.x + stride];
- }
- __syncthreads();
-
- if (threadIdx.x == 0)
- blockErrorCount[blockIdx.x] = threadErrorCount[0];
-
- return;
-}
-//}}}
+++ /dev/null
-/*
- * memtestG80_core.h
- * Public API for core memory test functions for MemtestG80
- * Includes functional and OO interfaces to GPU test functions.
- *
- * Author: Imran Haque, 2009
- * Copyright 2009, Stanford University
- *
- * This file is licensed under the terms of the LGPL. Please see
- * the COPYING file in the accompanying source distribution for
- * full license terms.
- *
- */
-#ifndef _MEMTESTG80_CORE_H_
-#define _MEMTESTG80_CORE_H_
-
-#if defined (WINDOWS) || defined (WINNV)
- #include <windows.h>
-inline unsigned int getTimeMilliseconds(void)
-{
- return GetTickCount();
-}
- #include <windows.h>
- #define SLEEPMS(x) Sleep(x)
-#elif defined (LINUX) || defined (OSX)
- #include <sys/time.h>
-inline unsigned int getTimeMilliseconds(void)
-{
- struct timeval tv;
- gettimeofday(&tv, NULL);
- return tv.tv_sec*1000 + tv.tv_usec/1000;
-}
- #include <unistd.h>
- #define SLEEPMS(x) usleep(x*1000)
-#else
- #error Must #define LINUX, WINDOWS, WINNV, or OSX
-#endif
-
-// By default the driver will spinwait when blocked on a kernel call
-// Use the SOFTWAIT macro to replace this with a thread sleep and occasional poll
-// limit expresses the max time we're willing to stay in the sleep loop - default = 15sec
-inline int _pollStatus(unsigned length = 1, unsigned limit = 15000)
-{
- //while (cudaStreamQuery(0) != cudaSuccess) {SLEEPMS(length);}
- unsigned startTime = getTimeMilliseconds();
- while (cudaStreamQuery(0) == cudaErrorNotReady)
- {
- if ((getTimeMilliseconds() - startTime) > limit)
- {
- return -1;
- }
- SLEEPMS(length);
- }
- return 0;
-}
-#define SOFTWAIT() if (_pollStatus() != 0) {return 0xFFFFFFFE; } // -2
-#define SOFTWAIT_LIM(lim) if (_pollStatus(1, lim) != 0) {return 0xFFFFFFFE; } // -2
-//#define SOFTWAIT()
-//#define SOFTWAIT(delay) if (_pollStatus(delay) != 0) return -2;
-//#define SOFTWAIT(delay,limit) if (_pollStatus(delay,limit) != 0) return -2;
-//#define SOFTWAIT() while (cudaStreamQuery(0) != cudaSuccess) {SLEEPMS(1);}
-//#define SOFTWAIT(x) while (cudaStreamQuery(0) != cudaSuccess) {SLEEPMS(x);}
-//#define SOFTWAIT()
-
-// Use this macro to check for kernel errors
-#define CHECK_LAUNCH_ERROR() if (cudaGetLastError() != cudaSuccess) {return 0xFFFFFFFF; /* -1 */}
-
-
-typedef unsigned int uint;
-
-// OO interface to MemtestG80 functions
-class memtestState
-{
- protected:
- const uint nBlocks;
- const uint nThreads;
- uint loopIters;
- uint megsToTest;
- int lcgPeriod;
- uint * devTestMem;
- uint * devTempMem;
- uint * hostTempMem;
- bool allocated;
- public:
- uint initTime;
- memtestState() : nBlocks(1024), nThreads(512), loopIters(0), megsToTest(0), allocated(false), devTestMem(NULL), devTempMem(NULL), hostTempMem(NULL), initTime(0), lcgPeriod(1024) {};
- ~memtestState() {deallocate(); }
-
- uint allocate(uint mbToTest);
- void deallocate();
- bool isAllocated() const {return allocated; }
- uint size() const {return megsToTest; }
- void setLCGPeriod(int period) {lcgPeriod = period; }
- int getLCGPeriod() const {return lcgPeriod; }
-
- bool gpuMemoryBandwidth(double &bandwidth, uint mbToTest, uint iters = 5);
- bool gpuWriteConstant(const uint constant) const;
- bool gpuVerifyConstant(uint &errorCount, const uint constant) const;
- bool gpuShortLCG0(uint &errorCount, const uint repeats) const;
- bool gpuShortLCG0Shmem(uint &errorCount, const uint repeats) const;
- bool gpuMovingInversionsOnesZeros(uint &errorCount) const;
- bool gpuWalking8BitM86(uint &errorCount, const uint shift) const;
- bool gpuWalking8Bit(uint &errorCount, const bool ones, const uint shift) const;
- bool gpuMovingInversionsRandom(uint &errorCount) const;
- bool gpuWalking32Bit(uint &errorCount, const bool ones, const uint shift) const;
- bool gpuRandomBlocks(uint &errorCount, const uint seed) const;
- bool gpuModuloX(uint &errorCount, const uint shift, const uint pattern, const uint modulus, const uint overwriteIters) const;
-};
-
-// Utility functions
-__host__ double gpuMemoryBandwidth(uint* src, uint* dst, uint mbToTest, uint iters);
-__host__ void gpuWriteConstant(const uint nBlocks, const uint nThreads, uint* base, uint N, const uint constant);
-__host__ uint gpuVerifyConstant(const uint nBlocks, const uint nThreads, uint* base, uint N, const uint constant, uint* blockErrorCount, uint* errorCounts);
-
-__host__ void cpuWriteConstant(const uint nBlocks, const uint nThreads, uint* base, uint N, const uint constant);
-__host__ uint cpuVerifyConstant(const uint nBlocks, const uint nThreads, uint* base, uint N, const uint constant);
-
-// Logic tests
-__host__ uint gpuShortLCG0(const uint nBlocks, const uint nThreads, uint* base, uint N, const uint repeats, const int period, uint* blockErrorCounts, uint* errorCounts);
-__host__ uint gpuShortLCG0Shmem(const uint nBlocks, const uint nThreads, uint* base, uint N, const uint repeats, const int period, uint* blockErrorCounts, uint* errorCounts);
-
-// Memtest86 Test 2: tseq=0,4
-__host__ uint gpuMovingInversionsOnesZeros(const uint nBlocks, const uint nThreads, uint* base, uint N, uint* blockErrorCounts, uint* errorCounts);
-
-// Memtest86 Test 3: tseq=1
-__host__ uint gpuWalking8BitM86(const uint nBlocks, const uint nThreads, uint* base, uint N, uint shift, uint* blockErrorCounts, uint* errorCounts);
-__host__ uint cpuWalking8BitM86(const uint nBlocks, const uint nThreads, uint* base, uint N, uint shift);
-__host__ uint gpuWalking8Bit(const uint nBlocks, const uint nThreads, uint* base, uint N, bool ones, uint shift, uint* blockErrorCount, uint* errorCounts);
-
-// Memtest86 Test 4: tseq=10
-__host__ uint gpuMovingInversionsRandom(const uint nBlocks, const uint nThreads, uint* base, uint N, uint* blockErrorCounts, uint* errorCounts);
-
-// Memtest86 Test 6: tseq=2
-__host__ uint gpuWalking32Bit(const uint nBlocks, const uint nThreads, uint* base, uint N, bool ones, uint shift, uint* blockErrorCount, uint* errorCounts);
-//
-// Memtest86 Test 7: tseq=9
-__host__ uint gpuRandomBlocks(const uint nBlocks, const uint nThreads, uint* base, uint N, uint seed, uint* blockErrorCount, uint* errorCounts);
-
-// Memtest86 Test 8: tseq=3 (M86 uses modulus = 20)
-__host__ uint gpuModuloX(const uint nBlocks, const uint nThreads, uint* base, const uint N, uint shift, uint pattern1, const uint modulus, const uint iters, uint* blockErrorCount, uint* errorCounts);
-
-#endif
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-
-#include "typedefs.h"
-#include "bondf.h"
-#include "disre.h"
-#include "orires.h"
-#include "genborn.h"
+#include "gmxpre.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/listed-forces/bonded.h"
#define def_bonded(str, lstr, nra, nrpa, nrpb, ind, func) \
{str, lstr, (nra), (nrpa), (nrpb), IF_BOND, (ind), (func)}
#define def_nofc(str, lstr) \
{str, lstr, 0, 0, 0, IF_NULL, -1, unimplemented}
-/* this MUST correspond to the enum in include/types/idef.h */
+/* this MUST correspond to the enum in src/gromacs/topology/idef.h */
const t_interaction_function interaction_function[F_NRE] =
{
def_bond ("BONDS", "Bond", 2, 2, 2, eNR_BONDS, bonds ),
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "gromacs/legacyheaders/inputrec.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "inputrec.h"
-#include "gmx_fatal.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/fatalerror.h"
/* The minimum number of integration steps required for reasonably accurate
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/main.h"
+
+#include "config.h"
+#include <limits.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include <limits.h>
-#include <time.h>
-
-#ifdef HAVE_SYS_TIME_H
-#include <sys/time.h>
-#endif
-#include "gromacs/utility/smalloc.h"
-#include "types/commrec.h"
-#include "gmx_fatal.h"
-#include "network.h"
-#include "main.h"
-#include "macros.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/filenm.h"
#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/utility/cstringutil.h"
-#include "copyrite.h"
-
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/snprintf.h"
+#include "gromacs/utility/sysinfo.h"
/* The source code in this file should be thread-safe.
Please keep it that way. */
-
-#ifdef HAVE_UNISTD_H
-#include <unistd.h>
-#endif
-
-#ifdef GMX_NATIVE_WINDOWS
-#include <process.h>
-#endif
-
#define BUFSIZE 1024
-
static void par_fn(char *base, int ftp, const t_commrec *cr,
gmx_bool bAppendSimId, gmx_bool bAppendNodeId,
char buf[], int bufsize)
strcat(buf, ".");
/* Add extension again */
- strcat(buf, (ftp == efTPX) ? "tpr" : (ftp == efEDR) ? "edr" : ftp2ext(ftp));
+ strcat(buf, (ftp == efTPR) ? "tpr" : (ftp == efEDR) ? "edr" : ftp2ext(ftp));
if (debug)
{
fprintf(debug, "rank %d par_fn '%s'\n", cr->nodeid, buf);
}
-int gmx_gethostname(char *name, size_t len)
-{
- if (len < 8)
- {
- gmx_incons("gmx_gethostname called with len<8");
- }
-#if defined(HAVE_UNISTD_H) && !defined(__native_client__) && !defined(__MINGW32__)
- if (gethostname(name, len-1) != 0)
- {
- strncpy(name, "unknown", 8);
- return -1;
- }
- return 0;
-#else
- strncpy(name, "unknown", 8);
- return -1;
-#endif
-}
-
-
-void gmx_log_open(const char *lognm, const t_commrec *cr, gmx_bool bMasterOnly,
+void gmx_log_open(const char *lognm, const t_commrec *cr,
gmx_bool bAppendFiles, FILE** fplog)
{
- int len, pid;
- char buf[256], host[256];
- time_t t;
+ int pid;
+ char host[256];
char timebuf[STRLEN];
FILE *fp = *fplog;
- char *tmpnm;
debug_gmx();
- /* Communicate the filename for logfile */
- if (cr->nnodes > 1 && !bMasterOnly
-#ifdef GMX_THREAD_MPI
- /* With thread MPI the non-master log files are opened later
- * when the files names are already known on all nodes.
- */
- && FALSE
-#endif
- )
- {
- if (MASTER(cr))
- {
- len = strlen(lognm) + 1;
- }
- gmx_bcast(sizeof(len), &len, cr);
- if (!MASTER(cr))
- {
- snew(tmpnm, len+8);
- }
- else
- {
- tmpnm = gmx_strdup(lognm);
- }
- gmx_bcast(len*sizeof(*tmpnm), tmpnm, cr);
- }
- else
+ if (!bAppendFiles)
{
- tmpnm = gmx_strdup(lognm);
+ fp = gmx_fio_fopen(lognm, bAppendFiles ? "a+" : "w+" );
}
- debug_gmx();
-
- if (!bMasterOnly && !MASTER(cr))
- {
- /* Since log always ends with '.log' let's use this info */
- par_fn(tmpnm, efLOG, cr, FALSE, !bMasterOnly, buf, 255);
- fp = gmx_fio_fopen(buf, bAppendFiles ? "a+" : "w+" );
- }
- else if (!bAppendFiles)
- {
- fp = gmx_fio_fopen(tmpnm, bAppendFiles ? "a+" : "w+" );
- }
-
- sfree(tmpnm);
-
gmx_fatal_set_log_file(fp);
/* Get some machine parameters */
gmx_gethostname(host, 256);
-
- time(&t);
-
-#ifndef NO_GETPID
-# ifdef GMX_NATIVE_WINDOWS
- pid = _getpid();
-# else
- pid = getpid();
-# endif
-#else
- pid = 0;
-#endif
+ pid = gmx_getpid();
+ gmx_format_current_time(timebuf, STRLEN);
if (bAppendFiles)
{
);
}
- gmx_ctime_r(&t, timebuf, STRLEN);
-
fprintf(fp,
"Log file opened on %s"
"Host: %s pid: %d rank ID: %d number of ranks: %d\n",
* at the actual file name
*/
if (is_output(&fnm[i]) ||
- fnm[i].ftp == efTPX || fnm[i].ftp == efCPT ||
+ fnm[i].ftp == efTPR || fnm[i].ftp == efCPT ||
strcmp(fnm[i].opt, "-rerun") == 0)
{
ftp = fn2ftp(fnm[i].fns[0]);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/md_logging.h"
-#include <stdio.h>
#include <stdarg.h>
-#include "types/commrec.h"
-#include "md_logging.h"
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/types/commrec.h"
void md_print_info(const t_commrec *cr, FILE *fplog,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "typedefs.h"
-#include "names.h"
+#include "gromacs/legacyheaders/names.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
/* note: these arrays should correspond to enums in include/types/enums.h */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/network.h"
+
+#include "config.h"
-#include <string.h>
-#include "gmx_fatal.h"
-#include "main.h"
-#include "gromacs/utility/smalloc.h"
-#include "types/commrec.h"
-#include "network.h"
-#include "copyrite.h"
#include <ctype.h>
-#include "macros.h"
-#include "gromacs/utility/cstringutil.h"
+#include <stdarg.h>
+#include <stdlib.h>
+#include <string.h>
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxmpi.h"
-
+#include "gromacs/utility/smalloc.h"
/* The source code in this file should be thread-safe.
Please keep it that way. */
-gmx_bool gmx_mpi_initialized(void)
-{
- int n;
-#ifndef GMX_MPI
- return 0;
-#else
- MPI_Initialized(&n);
-
- return n;
-#endif
-}
-
void gmx_fill_commrec_from_mpi(t_commrec gmx_unused *cr)
{
#ifndef GMX_MPI
#endif
}
-int gmx_node_num(void)
-{
-#ifndef GMX_MPI
- return 1;
-#else
- int i;
- (void) MPI_Comm_size(MPI_COMM_WORLD, &i);
- return i;
-#endif
-}
-
-int gmx_node_rank(void)
-{
-#ifndef GMX_MPI
- return 0;
-#else
- int i;
- (void) MPI_Comm_rank(MPI_COMM_WORLD, &i);
- return i;
-#endif
-}
-
-static int mpi_hostname_hash(void)
-{
- int hash_int;
-
-#ifndef GMX_LIB_MPI
- /* We have a single physical node */
- hash_int = 0;
-#else
- int resultlen;
- char mpi_hostname[MPI_MAX_PROCESSOR_NAME];
-
- /* This procedure can only differentiate nodes with different names.
- * Architectures where different physical nodes have identical names,
- * such as IBM Blue Gene, should use an architecture specific solution.
- */
- MPI_Get_processor_name(mpi_hostname, &resultlen);
-
- /* The string hash function returns an unsigned int. We cast to an int.
- * Negative numbers are converted to positive by setting the sign bit to 0.
- * This makes the hash one bit smaller.
- * A 63-bit hash (with 64-bit int) should be enough for unique node hashes,
- * even on a million node machine. 31 bits might not be enough though!
- */
- hash_int =
- (int)gmx_string_fullhash_func(mpi_hostname, gmx_string_hash_init);
- if (hash_int < 0)
- {
- hash_int -= INT_MIN;
- }
-#endif
-
- return hash_int;
-}
-
-#if defined GMX_LIB_MPI && defined GMX_TARGET_BGQ
-
-#ifdef __clang__
-/* IBM's declaration of this function in
- * /bgsys/drivers/V1R2M2/ppc64/spi/include/kernel/process.h
- * erroneously fails to specify __INLINE__, despite
- * /bgsys/drivers/V1R2M2/ppc64/spi/include/kernel/cnk/process_impl.h
- * specifiying __INLINE__, so bgclang thinks they are different enough
- * to complain about. */
-static uint64_t Kernel_GetJobID();
-#endif
-
-#include <spi/include/kernel/location.h>
-
-static int bgq_nodenum(void)
-{
- int hostnum;
- Personality_t personality;
- Kernel_GetPersonality(&personality, sizeof(personality));
- /* Each MPI rank has a unique coordinate in a 6-dimensional space
- (A,B,C,D,E,T), with dimensions A-E corresponding to different
- physical nodes, and T within each node. Each node has sixteen
- physical cores, each of which can have up to four hardware
- threads, so 0 <= T <= 63 (but the maximum value of T depends on
- the confituration of ranks and OpenMP threads per
- node). However, T is irrelevant for computing a suitable return
- value for gmx_hostname_num().
- */
- hostnum = personality.Network_Config.Acoord;
- hostnum *= personality.Network_Config.Bnodes;
- hostnum += personality.Network_Config.Bcoord;
- hostnum *= personality.Network_Config.Cnodes;
- hostnum += personality.Network_Config.Ccoord;
- hostnum *= personality.Network_Config.Dnodes;
- hostnum += personality.Network_Config.Dcoord;
- hostnum *= personality.Network_Config.Enodes;
- hostnum += personality.Network_Config.Ecoord;
-
- if (debug)
- {
- fprintf(debug,
- "Torus ID A: %d / %d B: %d / %d C: %d / %d D: %d / %d E: %d / %d\nNode ID T: %d / %d core: %d / %d hardware thread: %d / %d\n",
- personality.Network_Config.Acoord,
- personality.Network_Config.Anodes,
- personality.Network_Config.Bcoord,
- personality.Network_Config.Bnodes,
- personality.Network_Config.Ccoord,
- personality.Network_Config.Cnodes,
- personality.Network_Config.Dcoord,
- personality.Network_Config.Dnodes,
- personality.Network_Config.Ecoord,
- personality.Network_Config.Enodes,
- Kernel_ProcessorCoreID(),
- 16,
- Kernel_ProcessorID(),
- 64,
- Kernel_ProcessorThreadID(),
- 4);
- }
- return hostnum;
-}
-#endif
-
-int gmx_physicalnode_id_hash(void)
-{
- int hash;
-
-#ifndef GMX_MPI
- hash = 0;
-#else
-#ifdef GMX_THREAD_MPI
- /* thread-MPI currently puts the thread number in the process name,
- * we might want to change this, as this is inconsistent with what
- * most MPI implementations would do when running on a single node.
- */
- hash = 0;
-#else
-#ifdef GMX_TARGET_BGQ
- hash = bgq_nodenum();
-#else
- hash = mpi_hostname_hash();
-#endif
-#endif
-#endif
-
- if (debug)
- {
- fprintf(debug, "In gmx_physicalnode_id_hash: hash %d\n", hash);
- }
-
- return hash;
-}
-
void gmx_setup_nodecomm(FILE gmx_unused *fplog, t_commrec *cr)
{
gmx_nodecomm_t *nc;
#endif
}
-void gmx_abort(int gmx_unused noderank, int gmx_unused nnodes, int gmx_unused errorno)
-{
-#ifndef GMX_MPI
- gmx_call("gmx_abort");
-#else
-#ifdef GMX_THREAD_MPI
- fprintf(stderr, "Halting program %s\n", ShortProgram());
- gmx_thanx(stderr);
- exit(1);
-#else
- if (nnodes > 1)
- {
- fprintf(stderr, "Halting parallel program %s on CPU %d out of %d\n",
- ShortProgram(), noderank, nnodes);
- }
- else
- {
- fprintf(stderr, "Halting program %s\n", ShortProgram());
- }
-
- gmx_thanx(stderr);
- MPI_Abort(MPI_COMM_WORLD, errorno);
- exit(1);
-#endif
-#endif
-}
-
void gmx_bcast(int gmx_unused nbytes, void gmx_unused *b, const t_commrec gmx_unused *cr)
{
#ifndef GMX_MPI
#endif
#endif
}
+
+gmx_bool gmx_fexist_master(const char *fname, t_commrec *cr)
+{
+ gmx_bool bExist;
+
+ if (SIMMASTER(cr))
+ {
+ bExist = gmx_fexist(fname);
+ }
+ if (PAR(cr))
+ {
+ gmx_bcast(sizeof(bExist), &bExist, cr);
+ }
+ return bExist;
+}
+
+void gmx_fatal_collective(int f_errno, const char *file, int line,
+ const t_commrec *cr, gmx_domdec_t *dd,
+ const char *fmt, ...)
+{
+ va_list ap;
+ gmx_bool bMaster, bFinalize;
+#ifdef GMX_MPI
+ int result;
+ /* Check if we are calling on all processes in MPI_COMM_WORLD */
+ if (cr != NULL)
+ {
+ MPI_Comm_compare(cr->mpi_comm_mysim, MPI_COMM_WORLD, &result);
+ }
+ else
+ {
+ MPI_Comm_compare(dd->mpi_comm_all, MPI_COMM_WORLD, &result);
+ }
+ /* Any result except MPI_UNEQUAL allows us to call MPI_Finalize */
+ bFinalize = (result != MPI_UNEQUAL);
+#else
+ bFinalize = TRUE;
+#endif
+ bMaster = (cr != NULL && MASTER(cr)) || (dd != NULL && DDMASTER(dd));
+
+ va_start(ap, fmt);
+ gmx_fatal_mpi_va(f_errno, file, line, bMaster, bFinalize, fmt, ap);
+ va_end(ap);
+}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <math.h>
-
-#include "vec.h"
-#include "typedefs.h"
-#include "nonbonded.h"
-#include "nb_kernel.h"
-#include "nrnb.h"
-#include "macros.h"
#include "nb_free_energy.h"
-#include "gmx_fatal.h"
+#include <math.h>
+
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
void
gmx_nb_free_energy_kernel(const t_nblist * gmx_restrict nlist,
int ewitab;
real ewrt, eweps, ewtabscale, ewtabhalfspace, sh_ewald;
+ const real onetwelfth = 1.0/12.0;
+ const real onesixth = 1.0/6.0;
+ const real zero = 0.0;
+ const real half = 0.5;
+ const real one = 1.0;
+ const real two = 2.0;
+ const real six = 6.0;
+ const real fourtyeight = 48.0;
+
sh_ewald = fr->ic->sh_ewald;
ewtab = fr->ic->tabq_coul_FDV0;
ewtabscale = fr->ic->tabq_scale;
- ewtabhalfspace = 0.5/ewtabscale;
+ ewtabhalfspace = half/ewtabscale;
tab_ewald_F_lj = fr->ic->tabq_vdw_F;
tab_ewald_V_lj = fr->ic->tabq_vdw_V;
bDoPotential = kernel_data->flags & GMX_NONBONDED_DO_POTENTIAL;
rcoulomb = fr->rcoulomb;
- sh_ewald = fr->ic->sh_ewald;
rvdw = fr->rvdw;
sh_invrc6 = fr->ic->sh_invrc6;
sh_lj_ewald = fr->ic->sh_lj_ewald;
dvdl_vdw = 0;
/* Lambda factor for state A, 1-lambda*/
- LFC[STATE_A] = 1.0 - lambda_coul;
- LFV[STATE_A] = 1.0 - lambda_vdw;
+ LFC[STATE_A] = one - lambda_coul;
+ LFV[STATE_A] = one - lambda_vdw;
/* Lambda factor for state B, lambda*/
LFC[STATE_B] = lambda_coul;
r = 0;
}
- if (sc_r_power == 6.0)
+ if (sc_r_power == six)
{
rpm2 = rsq*rsq; /* r4 */
rp = rpm2*rsq; /* r6 */
}
- else if (sc_r_power == 48.0)
+ else if (sc_r_power == fourtyeight)
{
rp = rsq*rsq*rsq; /* r6 */
rp = rp*rp; /* r12 */
if ((c6[i] > 0) && (c12[i] > 0))
{
/* c12 is stored scaled with 12.0 and c6 is scaled with 6.0 - correct for this */
- sigma6[i] = 0.5*c12[i]/c6[i];
+ sigma6[i] = half*c12[i]/c6[i];
sigma2[i] = pow(sigma6[i], 1.0/3.0);
/* should be able to get rid of this ^^^ internal pow call eventually. Will require agreement on
what data to store externally. Can't be fixed without larger scale changes, so not 4.6 */
sigma6[i] = sigma6_def;
sigma2[i] = sigma2_def;
}
- if (sc_r_power == 6.0)
+ if (sc_r_power == six)
{
sigma_pow[i] = sigma6[i];
sigma_powm2[i] = sigma6[i]/sigma2[i];
}
- else if (sc_r_power == 48.0)
+ else if (sc_r_power == fourtyeight)
{
sigma_pow[i] = sigma6[i]*sigma6[i]; /* sigma^12 */
sigma_pow[i] = sigma_pow[i]*sigma_pow[i]; /* sigma^24 */
if ( (qq[i] != 0) || (c6[i] != 0) || (c12[i] != 0) )
{
/* this section has to be inside the loop because of the dependence on sigma_pow */
- rpinvC = 1.0/(alpha_coul_eff*lfac_coul[i]*sigma_pow[i]+rp);
- rinvC = pow(rpinvC, 1.0/sc_r_power);
- rC = 1.0/rinvC;
+ rpinvC = one/(alpha_coul_eff*lfac_coul[i]*sigma_pow[i]+rp);
+ rinvC = pow(rpinvC, one/sc_r_power);
+ rC = one/rinvC;
- rpinvV = 1.0/(alpha_vdw_eff*lfac_vdw[i]*sigma_pow[i]+rp);
- rinvV = pow(rpinvV, 1.0/sc_r_power);
- rV = 1.0/rinvV;
+ rpinvV = one/(alpha_vdw_eff*lfac_vdw[i]*sigma_pow[i]+rp);
+ rinvV = pow(rpinvV, one/sc_r_power);
+ rV = one/rinvV;
if (do_tab)
{
case GMX_NBKERNEL_ELEC_REACTIONFIELD:
/* reaction-field */
Vcoul[i] = qq[i]*(rinvC + krf*rC*rC-crf);
- FscalC[i] = qq[i]*(rinvC - 2.0*krf*rC*rC);
+ FscalC[i] = qq[i]*(rinvC - two*krf*rC*rC);
break;
case GMX_NBKERNEL_ELEC_CUBICSPLINETABLE:
Heps2 = eps2C*VFtab[nnn+3];
Fp = F+Geps+Heps2;
VV = Y+epsC*Fp;
- FF = Fp+Geps+2.0*Heps2;
+ FF = Fp+Geps+two*Heps2;
Vcoul[i] = qq[i]*VV;
FscalC[i] = -qq[i]*tabscale*FF*rC;
break;
break;
case GMX_NBKERNEL_ELEC_NONE:
- FscalC[i] = 0.0;
- Vcoul[i] = 0.0;
+ FscalC[i] = zero;
+ Vcoul[i] = zero;
break;
default:
if (fr->coulomb_modifier == eintmodPOTSWITCH)
{
d = rC-fr->rcoulomb_switch;
- d = (d > 0.0) ? d : 0.0;
+ d = (d > zero) ? d : zero;
d2 = d*d;
- sw = 1.0+d2*d*(elec_swV3+d*(elec_swV4+d*elec_swV5));
+ sw = one+d2*d*(elec_swV3+d*(elec_swV4+d*elec_swV5));
dsw = d2*(elec_swF2+d*(elec_swF3+d*elec_swF4));
FscalC[i] = FscalC[i]*sw - rC*Vcoul[i]*dsw;
Vcoul[i] *= sw;
- FscalC[i] = (rC < rcoulomb) ? FscalC[i] : 0.0;
- Vcoul[i] = (rC < rcoulomb) ? Vcoul[i] : 0.0;
+ FscalC[i] = (rC < rcoulomb) ? FscalC[i] : zero;
+ Vcoul[i] = (rC < rcoulomb) ? Vcoul[i] : zero;
}
}
{
case GMX_NBKERNEL_VDW_LENNARDJONES:
/* cutoff LJ */
- if (sc_r_power == 6.0)
+ if (sc_r_power == six)
{
rinv6 = rpinvV;
}
Vvdw6 = c6[i]*rinv6;
Vvdw12 = c12[i]*rinv6*rinv6;
- Vvdw[i] = ( (Vvdw12 - c12[i]*sh_invrc6*sh_invrc6)*(1.0/12.0)
- - (Vvdw6 - c6[i]*sh_invrc6)*(1.0/6.0));
+ Vvdw[i] = ( (Vvdw12 - c12[i]*sh_invrc6*sh_invrc6)*onetwelfth
+ - (Vvdw6 - c6[i]*sh_invrc6)*onesixth);
FscalV[i] = Vvdw12 - Vvdw6;
break;
Heps2 = eps2V*VFtab[nnn+3];
Fp = F+Geps+Heps2;
VV = Y+epsV*Fp;
- FF = Fp+Geps+2.0*Heps2;
+ FF = Fp+Geps+two*Heps2;
Vvdw[i] += c6[i]*VV;
FscalV[i] -= c6[i]*tabscale*FF*rV;
Heps2 = eps2V*VFtab[nnn+7];
Fp = F+Geps+Heps2;
VV = Y+epsV*Fp;
- FF = Fp+Geps+2.0*Heps2;
+ FF = Fp+Geps+two*Heps2;
Vvdw[i] += c12[i]*VV;
FscalV[i] -= c12[i]*tabscale*FF*rV;
break;
case GMX_NBKERNEL_VDW_LJEWALD:
- if (sc_r_power == 6.0)
+ if (sc_r_power == six)
{
rinv6 = rpinvV;
}
Vvdw6 = c6[i]*rinv6;
Vvdw12 = c12[i]*rinv6*rinv6;
- Vvdw[i] = ( (Vvdw12 - c12[i]*sh_invrc6*sh_invrc6)*(1.0/12.0)
- - (Vvdw6 - c6[i]*sh_invrc6 - c6grid*sh_lj_ewald)*(1.0/6.0));
+ Vvdw[i] = ( (Vvdw12 - c12[i]*sh_invrc6*sh_invrc6)*onetwelfth
+ - (Vvdw6 - c6[i]*sh_invrc6 - c6grid*sh_lj_ewald)*onesixth);
FscalV[i] = Vvdw12 - Vvdw6;
}
else
/* Normal LJ-PME */
ewcljrsq = ewclj2*rV*rV;
exponent = exp(-ewcljrsq);
- poly = exponent*(1.0 + ewcljrsq + ewcljrsq*ewcljrsq*0.5);
- vvdw_disp = (c6[i]-c6grid*(1.0-poly))*rinv6;
+ poly = exponent*(one + ewcljrsq + ewcljrsq*ewcljrsq*half);
+ vvdw_disp = (c6[i]-c6grid*(one-poly))*rinv6;
vvdw_rep = c12[i]*rinv6*rinv6;
- FscalV[i] = vvdw_rep - vvdw_disp - c6grid*(1.0/6.0)*exponent*ewclj6;
- Vvdw[i] = (vvdw_rep - c12[i]*sh_invrc6*sh_invrc6)/12.0 - (vvdw_disp - c6[i]*sh_invrc6 - c6grid*sh_lj_ewald)/6.0;
+ FscalV[i] = vvdw_rep - vvdw_disp - c6grid*onesixth*exponent*ewclj6;
+ Vvdw[i] = (vvdw_rep - c12[i]*sh_invrc6*sh_invrc6)*onetwelfth - (vvdw_disp - c6[i]*sh_invrc6 - c6grid*sh_lj_ewald)/six;
}
break;
case GMX_NBKERNEL_VDW_NONE:
- Vvdw[i] = 0.0;
- FscalV[i] = 0.0;
+ Vvdw[i] = zero;
+ FscalV[i] = zero;
break;
default:
if (fr->vdw_modifier == eintmodPOTSWITCH)
{
d = rV-fr->rvdw_switch;
- d = (d > 0.0) ? d : 0.0;
+ d = (d > zero) ? d : zero;
d2 = d*d;
- sw = 1.0+d2*d*(vdw_swV3+d*(vdw_swV4+d*vdw_swV5));
+ sw = one+d2*d*(vdw_swV3+d*(vdw_swV4+d*vdw_swV5));
dsw = d2*(vdw_swF2+d*(vdw_swF3+d*vdw_swF4));
FscalV[i] = FscalV[i]*sw - rV*Vvdw[i]*dsw;
Vvdw[i] *= sw;
- FscalV[i] = (rV < rvdw) ? FscalV[i] : 0.0;
- Vvdw[i] = (rV < rvdw) ? Vvdw[i] : 0.0;
+ FscalV[i] = (rV < rvdw) ? FscalV[i] : zero;
+ Vvdw[i] = (rV < rvdw) ? Vvdw[i] : zero;
}
}
* As there is no singularity, there is no need for soft-core.
*/
VV = krf*rsq - crf;
- FF = -2.0*krf;
+ FF = -two*krf;
if (ii == jnr)
{
- VV *= 0.5;
+ VV *= half;
}
for (i = 0; i < NSTATES; i++)
* scheme, and corresponds to a self-interaction that will
* occur twice. Scale it down by 50% to only include it once.
*/
- v_lr *= 0.5;
+ v_lr *= half;
}
for (i = 0; i < NSTATES; i++)
/* TODO: Currently the Ewald LJ table does not contain
* the factor 1/6, we should add this.
*/
- FF = f_lr*rinv/6.0;
- VV = (tab_ewald_V_lj[ri] - ewtabhalfspace*frac*(tab_ewald_F_lj[ri] + f_lr))/6.0;
+ FF = f_lr*rinv/six;
+ VV = (tab_ewald_V_lj[ri] - ewtabhalfspace*frac*(tab_ewald_F_lj[ri] + f_lr))/six;
if (ii == jnr)
{
* scheme, and corresponds to a self-interaction that will
* occur twice. Scale it down by 50% to only include it once.
*/
- VV *= 0.5;
+ VV *= half;
}
for (i = 0; i < NSTATES; i++)
#pragma omp atomic
inc_nrnb(nrnb, eNR_NBKERNEL_FREE_ENERGY, nlist->nri*12 + nlist->jindex[n]*150);
}
-
-real
-nb_free_energy_evaluate_single(real r2, real sc_r_power, real alpha_coul, real alpha_vdw,
- real tabscale, real *vftab,
- real qqA, real c6A, real c12A, real qqB, real c6B, real c12B,
- real LFC[2], real LFV[2], real DLF[2],
- real lfac_coul[2], real lfac_vdw[2], real dlfac_coul[2], real dlfac_vdw[2],
- real sigma6_def, real sigma6_min, real sigma2_def, real sigma2_min,
- real *velectot, real *vvdwtot, real *dvdl)
-{
- real r, rp, rpm2, rtab, eps, eps2, Y, F, Geps, Heps2, Fp, VV, FF, fscal;
- real qq[2], c6[2], c12[2], sigma6[2], sigma2[2], sigma_pow[2], sigma_powm2[2];
- real alpha_coul_eff, alpha_vdw_eff, dvdl_coul, dvdl_vdw;
- real rpinv, r_coul, r_vdw, velecsum, vvdwsum;
- real fscal_vdw[2], fscal_elec[2];
- real velec[2], vvdw[2];
- int i, ntab;
-
- qq[0] = qqA;
- qq[1] = qqB;
- c6[0] = c6A;
- c6[1] = c6B;
- c12[0] = c12A;
- c12[1] = c12B;
-
- if (sc_r_power == 6.0)
- {
- rpm2 = r2*r2; /* r4 */
- rp = rpm2*r2; /* r6 */
- }
- else if (sc_r_power == 48.0)
- {
- rp = r2*r2*r2; /* r6 */
- rp = rp*rp; /* r12 */
- rp = rp*rp; /* r24 */
- rp = rp*rp; /* r48 */
- rpm2 = rp/r2; /* r46 */
- }
- else
- {
- rp = pow(r2, 0.5*sc_r_power); /* not currently supported as input, but can handle it */
- rpm2 = rp/r2;
- }
-
- /* Loop over state A(0) and B(1) */
- for (i = 0; i < 2; i++)
- {
- if ((c6[i] > 0) && (c12[i] > 0))
- {
- /* The c6 & c12 coefficients now contain the constants 6.0 and 12.0, respectively.
- * Correct for this by multiplying with (1/12.0)/(1/6.0)=6.0/12.0=0.5.
- */
- sigma6[i] = 0.5*c12[i]/c6[i];
- sigma2[i] = pow(0.5*c12[i]/c6[i], 1.0/3.0);
- /* should be able to get rid of this ^^^ internal pow call eventually. Will require agreement on
- what data to store externally. Can't be fixed without larger scale changes, so not 5.0 */
- if (sigma6[i] < sigma6_min) /* for disappearing coul and vdw with soft core at the same time */
- {
- sigma6[i] = sigma6_min;
- sigma2[i] = sigma2_min;
- }
- }
- else
- {
- sigma6[i] = sigma6_def;
- sigma2[i] = sigma2_def;
- }
- if (sc_r_power == 6.0)
- {
- sigma_pow[i] = sigma6[i];
- sigma_powm2[i] = sigma6[i]/sigma2[i];
- }
- else if (sc_r_power == 48.0)
- {
- sigma_pow[i] = sigma6[i]*sigma6[i]; /* sigma^12 */
- sigma_pow[i] = sigma_pow[i]*sigma_pow[i]; /* sigma^24 */
- sigma_pow[i] = sigma_pow[i]*sigma_pow[i]; /* sigma^48 */
- sigma_powm2[i] = sigma_pow[i]/sigma2[i];
- }
- else
- { /* not really supported as input, but in here for testing the general case*/
- sigma_pow[i] = pow(sigma2[i], sc_r_power/2);
- sigma_powm2[i] = sigma_pow[i]/(sigma2[i]);
- }
- }
-
- /* only use softcore if one of the states has a zero endstate - softcore is for avoiding infinities!*/
- if ((c12[0] > 0) && (c12[1] > 0))
- {
- alpha_vdw_eff = 0;
- alpha_coul_eff = 0;
- }
- else
- {
- alpha_vdw_eff = alpha_vdw;
- alpha_coul_eff = alpha_coul;
- }
-
- /* Loop over A and B states again */
- for (i = 0; i < 2; i++)
- {
- fscal_elec[i] = 0;
- fscal_vdw[i] = 0;
- velec[i] = 0;
- vvdw[i] = 0;
-
- /* Only spend time on A or B state if it is non-zero */
- if ( (qq[i] != 0) || (c6[i] != 0) || (c12[i] != 0) )
- {
- /* Coulomb */
- rpinv = 1.0/(alpha_coul_eff*lfac_coul[i]*sigma_pow[i]+rp);
- r_coul = pow(rpinv, -1.0/sc_r_power);
-
- /* Electrostatics table lookup data */
- rtab = r_coul*tabscale;
- ntab = rtab;
- eps = rtab-ntab;
- eps2 = eps*eps;
- ntab = 12*ntab;
- /* Electrostatics */
- Y = vftab[ntab];
- F = vftab[ntab+1];
- Geps = eps*vftab[ntab+2];
- Heps2 = eps2*vftab[ntab+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- velec[i] = qq[i]*VV;
- fscal_elec[i] = -qq[i]*FF*r_coul*rpinv*tabscale;
-
- /* Vdw */
- rpinv = 1.0/(alpha_vdw_eff*lfac_vdw[i]*sigma_pow[i]+rp);
- r_vdw = pow(rpinv, -1.0/sc_r_power);
- /* Vdw table lookup data */
- rtab = r_vdw*tabscale;
- ntab = rtab;
- eps = rtab-ntab;
- eps2 = eps*eps;
- ntab = 12*ntab;
- /* Dispersion */
- Y = vftab[ntab+4];
- F = vftab[ntab+5];
- Geps = eps*vftab[ntab+6];
- Heps2 = eps2*vftab[ntab+7];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vvdw[i] = c6[i]*VV;
- fscal_vdw[i] = -c6[i]*FF;
-
- /* Repulsion */
- Y = vftab[ntab+8];
- F = vftab[ntab+9];
- Geps = eps*vftab[ntab+10];
- Heps2 = eps2*vftab[ntab+11];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vvdw[i] += c12[i]*VV;
- fscal_vdw[i] -= c12[i]*FF;
- fscal_vdw[i] *= r_vdw*rpinv*tabscale;
- }
- }
- /* Now we have velec[i], vvdw[i], and fscal[i] for both states */
- /* Assemble A and B states */
- velecsum = 0;
- vvdwsum = 0;
- dvdl_coul = 0;
- dvdl_vdw = 0;
- fscal = 0;
- for (i = 0; i < 2; i++)
- {
- velecsum += LFC[i]*velec[i];
- vvdwsum += LFV[i]*vvdw[i];
-
- fscal += (LFC[i]*fscal_elec[i]+LFV[i]*fscal_vdw[i])*rpm2;
-
- dvdl_coul += velec[i]*DLF[i] + LFC[i]*alpha_coul_eff*dlfac_coul[i]*fscal_elec[i]*sigma_pow[i];
- dvdl_vdw += vvdw[i]*DLF[i] + LFV[i]*alpha_vdw_eff*dlfac_vdw[i]*fscal_vdw[i]*sigma_pow[i];
- }
-
- dvdl[efptCOUL] += dvdl_coul;
- dvdl[efptVDW] += dvdl_vdw;
-
- *velectot = velecsum;
- *vvdwtot = vvdwsum;
-
- return fscal;
-}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _nb_free_energy_h_
#define _nb_free_energy_h_
-#include "nb_kernel.h"
-#include "typedefs.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/typedefs.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
void
-gmx_nb_free_energy_kernel(const t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
- const t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb);
+ gmx_nb_free_energy_kernel(const t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ const t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb);
-real
- nb_free_energy_evaluate_single(real r2, real sc_r_power, real alpha_coul,
- real alpha_vdw, real tabscale, real *vftab,
- real qqA, real c6A, real c12A, real qqB,
- real c6B, real c12B, real LFC[2], real LFV[2], real DLF[2],
- real lfac_coul[2], real lfac_vdw[2], real dlfac_coul[2],
- real dlfac_vdw[2], real sigma6_def, real sigma6_min,
- real sigma2_def, real sigma2_min,
- real *velectot, real *vvdwtot, real *dvdl);
+#ifdef __cplusplus
+}
+#endif
#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <math.h>
-
-#include "types/simple.h"
-#include "vec.h"
-#include "typedefs.h"
#include "nb_generic.h"
-#include "nrnb.h"
-#include "gmx_fatal.h"
+#include <math.h>
-#include "nonbonded.h"
-#include "nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
void
gmx_nb_generic_kernel(t_nblist * nlist,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _nb_generic_h_
#define _nb_generic_h_
-#include "nb_kernel.h"
-#include "types/simple.h"
-#include "typedefs.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
void
gmx_nb_generic_kernel(t_nblist * nlist,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <math.h>
-
-#include "types/simple.h"
-#include "vec.h"
-#include "typedefs.h"
#include "nb_generic_adress.h"
-#include "nrnb.h"
-#include "gmx_fatal.h"
+#include <math.h>
-#include "nonbonded.h"
-#include "nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
#define ALMOST_ZERO 1e-30
#define ALMOST_ONE 1-(1e-30)
*
* Copyright (c) 2009 Christoph Junghans, Brad Lambeth.
* Copyright (c) 2011 Christoph Junghans, Sebastian Fritsch.
- * Copyright (c) 2011,2012, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _nb_generic_adress_h_
#define _nb_generic_adress_h_
-#include "nb_kernel.h"
-#include "types/simple.h"
-#include "typedefs.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
void
gmx_nb_generic_adress_kernel(t_nblist * nlist,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <math.h>
-
-#include "types/simple.h"
-#include "vec.h"
-#include "typedefs.h"
#include "nb_generic_cg.h"
-#include "nonbonded.h"
-#include "nb_kernel.h"
-#include "nrnb.h"
-#include "gmx_fatal.h"
+#include <math.h>
+
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
void
gmx_nb_generic_cg_kernel(t_nblist * nlist,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _nb_generic_cg_h_
#define _nb_generic_cg_h_
-#include "types/simple.h"
-#include "typedefs.h"
-#include "nb_kernel.h"
-#include "nrnb.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
void
gmx_nb_generic_cg_kernel(t_nblist * nlist,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "nb_kernel.h"
#include <stdio.h>
#include <string.h>
-#include "nb_kernel.h"
-#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* Static data structures to find kernels */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _nb_kernel_h_
#define _nb_kernel_h_
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-
#ifdef __cplusplus
extern "C" {
#endif
#endif
-#include "types/simple.h"
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
/* Structure to collect kernel data not available in forcerec or mdatoms structures.
* This is only used inside the nonbonded module.
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
fpdecl = open('nb_kernel_' + Arch + '.c','w')
fpdecl.write( FileHeader )
-fpdecl.write( '#ifndef nb_kernel_' + Arch + '_h\n' )
-fpdecl.write( '#define nb_kernel_' + Arch + '_h\n\n' )
+fpdecl.write( '#include "gmxpre.h"\n\n' )
fpdecl.write( '#include "../nb_kernel.h"\n\n' )
for KernelElec in ElectrostaticsList:
fpdecl.write( kerneldecl[-1] + '\n' )
fpdecl.write( '};\n\n' )
fpdecl.write( 'int\n' )
-fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
-fpdecl.write( '#endif\n')
+fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n')
fpdecl.close()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#error This file must be processed with the Gromacs pre-preprocessor
/* #endif */
/* #if INCLUDE_HEADER */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/* #endif */
#define ALMOST_ZERO 1e-30
#define _kernelutil_x86_avx_128_fma_double_h_
#include <math.h>
+
#include <immintrin.h>
#ifdef _MSC_VER
# include <intrin.h>
# include <x86intrin.h>
#endif
+#include "config.h"
+
#define gmx_mm_castsi128_pd _mm_castsi128_pd
#define gmx_mm_extract_epi32 _mm_extract_epi32
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013')
+FileHeader = create_copyright_header('2012,2013,2014')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
fpdecl = open('nb_kernel_' + Arch + '.c','w')
fpdecl.write( FileHeader )
-fpdecl.write( '#ifndef nb_kernel_' + Arch + '_h\n' )
-fpdecl.write( '#define nb_kernel_' + Arch + '_h\n\n' )
+fpdecl.write( '#include "gmxpre.h"\n\n' )
fpdecl.write( '#include "../nb_kernel.h"\n\n' )
for KernelElec in ElectrostaticsList:
fpdecl.write( kerneldecl[-1] + '\n' )
fpdecl.write( '};\n\n' )
fpdecl.write( 'int\n' )
-fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
-fpdecl.write( '#endif\n')
+fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n')
fpdecl.close()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
*/
-#ifndef nb_kernel_avx_128_fma_double_h
-#define nb_kernel_avx_128_fma_double_h
+#include "gmxpre.h"
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_avx_128_fma_double;
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_avx_128_fma_double;
int
kernellist_avx_128_fma_double_size = sizeof(kernellist_avx_128_fma_double)/sizeof(kernellist_avx_128_fma_double[0]);
-
-#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef nb_kernel_avx_128_fma_double_h
#define nb_kernel_avx_128_fma_double_h
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
/* List of kernels for this architecture with metadata about them */
#error This file must be processed with the Gromacs pre-preprocessor
/* #endif */
/* #if INCLUDE_HEADER */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_double.h"
#include "kernelutil_x86_avx_128_fma_double.h"
#ifndef _kernelutil_x86_avx_128_fma_single_h_
#define _kernelutil_x86_avx_128_fma_single_h_
+#include "config.h"
#include <math.h>
+
#include <immintrin.h>
#ifdef _MSC_VER
# include <intrin.h>
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013')
+FileHeader = create_copyright_header('2012,2013,2014')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
fpdecl = open('nb_kernel_' + Arch + '.c','w')
fpdecl.write( FileHeader )
-fpdecl.write( '#ifndef nb_kernel_' + Arch + '_h\n' )
-fpdecl.write( '#define nb_kernel_' + Arch + '_h\n\n' )
+fpdecl.write( '#include "gmxpre.h"\n\n' )
fpdecl.write( '#include "../nb_kernel.h"\n\n' )
for KernelElec in ElectrostaticsList:
fpdecl.write( kerneldecl[-1] + '\n' )
fpdecl.write( '};\n\n' )
fpdecl.write( 'int\n' )
-fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
-fpdecl.write( '#endif\n')
+fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n')
fpdecl.close()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
/*
* Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
*/
-#ifndef nb_kernel_avx_128_fma_single_h
-#define nb_kernel_avx_128_fma_single_h
+#include "gmxpre.h"
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_avx_128_fma_single;
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_avx_128_fma_single;
int
kernellist_avx_128_fma_single_size = sizeof(kernellist_avx_128_fma_single)/sizeof(kernellist_avx_128_fma_single[0]);
-
-#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef nb_kernel_avx_128_fma_single_h
#define nb_kernel_avx_128_fma_single_h
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
/* List of kernels for this architecture with metadata about them */
#error This file must be processed with the Gromacs pre-preprocessor
/* #endif */
/* #if INCLUDE_HEADER */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_128_fma_single.h"
#include "kernelutil_x86_avx_128_fma_single.h"
#ifndef _kernelutil_x86_avx_256_double_h_
#define _kernelutil_x86_avx_256_double_h_
+#include "config.h"
+
#define gmx_mm_castsi128_ps(a) _mm_castsi128_ps(a)
#define _GMX_MM_BLEND256D(b3, b2, b1, b0) (((b3) << 3) | ((b2) << 2) | ((b1) << 1) | ((b0)))
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013')
+FileHeader = create_copyright_header('2012,2013,2014')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
fpdecl = open('nb_kernel_' + Arch + '.c','w')
fpdecl.write( FileHeader )
-fpdecl.write( '#ifndef nb_kernel_' + Arch + '_h\n' )
-fpdecl.write( '#define nb_kernel_' + Arch + '_h\n\n' )
+fpdecl.write( '#include "gmxpre.h"\n\n' )
fpdecl.write( '#include "../nb_kernel.h"\n\n' )
for KernelElec in ElectrostaticsList:
fpdecl.write( kerneldecl[-1] + '\n' )
fpdecl.write( '};\n\n' )
fpdecl.write( 'int\n' )
-fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
-fpdecl.write( '#endif\n')
+fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n')
fpdecl.close()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
/*
* Note: this file was generated by the GROMACS avx_256_double kernel generator.
*/
-#ifndef nb_kernel_avx_256_double_h
-#define nb_kernel_avx_256_double_h
+#include "gmxpre.h"
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_avx_256_double;
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_avx_256_double;
int
kernellist_avx_256_double_size = sizeof(kernellist_avx_256_double)/sizeof(kernellist_avx_256_double[0]);
-
-#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef nb_kernel_avx_256_double_h
#define nb_kernel_avx_256_double_h
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
/* List of kernels for this architecture with metadata about them */
#error This file must be processed with the Gromacs pre-preprocessor
/* #endif */
/* #if INCLUDE_HEADER */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_double.h"
#include "kernelutil_x86_avx_256_double.h"
#ifndef _kernelutil_x86_avx_256_single_h_
#define _kernelutil_x86_avx_256_single_h_
+#include "config.h"
+
#define gmx_mm_castsi128_ps(a) _mm_castsi128_ps(a)
static gmx_inline __m256 gmx_simdcall
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013')
+FileHeader = create_copyright_header('2012,2013,2014')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
fpdecl = open('nb_kernel_' + Arch + '.c','w')
fpdecl.write( FileHeader )
-fpdecl.write( '#ifndef nb_kernel_' + Arch + '_h\n' )
-fpdecl.write( '#define nb_kernel_' + Arch + '_h\n\n' )
+fpdecl.write( '#include "gmxpre.h"\n\n' )
fpdecl.write( '#include "../nb_kernel.h"\n\n' )
for KernelElec in ElectrostaticsList:
fpdecl.write( kerneldecl[-1] + '\n' )
fpdecl.write( '};\n\n' )
fpdecl.write( 'int\n' )
-fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
-fpdecl.write( '#endif\n')
+fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n')
fpdecl.close()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
/*
* Note: this file was generated by the GROMACS avx_256_single kernel generator.
*/
-#ifndef nb_kernel_avx_256_single_h
-#define nb_kernel_avx_256_single_h
+#include "gmxpre.h"
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_avx_256_single;
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_avx_256_single;
int
kernellist_avx_256_single_size = sizeof(kernellist_avx_256_single)/sizeof(kernellist_avx_256_single[0]);
-
-#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef nb_kernel_avx_256_single_h
#define nb_kernel_avx_256_single_h
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
/* List of kernels for this architecture with metadata about them */
#error This file must be processed with the Gromacs pre-preprocessor
/* #endif */
/* #if INCLUDE_HEADER */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_avx_256_single.h"
#include "kernelutil_x86_avx_256_single.h"
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013')
+FileHeader = create_copyright_header('2012,2013,2014')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
fpdecl = open('nb_kernel_' + Arch + '.c','w')
fpdecl.write( FileHeader )
-fpdecl.write( '#ifndef nb_kernel_' + Arch + '_h\n' )
-fpdecl.write( '#define nb_kernel_' + Arch + '_h\n\n' )
+fpdecl.write( '#include "gmxpre.h"\n\n' )
fpdecl.write( '#include "../nb_kernel.h"\n\n' )
for KernelElec in ElectrostaticsList:
fpdecl.write( kerneldecl[-1] + '\n' )
fpdecl.write( '};\n\n' )
fpdecl.write( 'int\n' )
-fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
-fpdecl.write( '#endif\n')
+fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n')
fpdecl.close()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwBham_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwBham_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwBham_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwBham_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwBham_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwBham_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwBham_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwBham_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwBham_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwBham_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_VF_c
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_VF_c
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_VF_c
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_VF_c
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_VF_c
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwNone_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwNone_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwNone_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwNone_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwNone_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwNone_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwNone_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwNone_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwNone_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwBham_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwBham_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwBham_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwBham_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwBham_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwCSTab_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwCSTab_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwCSTab_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwCSTab_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwCSTab_GeomW4W4_VF_c
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_c
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_c
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJEw_GeomW3W3_VF_c
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJEw_GeomW4P1_VF_c
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJEw_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJ_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJ_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJ_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJ_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJ_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwNone_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwNone_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwNone_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwNone_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwNone_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwBham_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwBham_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_c
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_VF_c
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwLJSh_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwLJSw_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwNone_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwNone_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwNone_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwNone_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwNone_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwBham_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwBham_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwBham_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwBham_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwBham_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwCSTab_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwCSTab_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwCSTab_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomW4W4_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwNone_GeomP1P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwNone_GeomW3P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwNone_GeomW3W3_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwNone_GeomW4P1_VF_c
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/*
* Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwNone_GeomW4W4_VF_c
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <math.h>
+#include "nb_kernel_allvsall.h"
-#include "types/simple.h"
+#include "config.h"
-#include "vec.h"
-#include "gromacs/utility/smalloc.h"
+#include <math.h>
-#include "nb_kernel_allvsall.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
typedef struct
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _NB_KERNEL_ALLVSALL_H
#define _NB_KERNEL_ALLVSALL_H
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "config.h"
-#include "types/simple.h"
-#include "typedefs.h"
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
void
nb_kernel_allvsall(t_nblist * nlist,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <math.h>
+#include "nb_kernel_allvsallgb.h"
-#include "types/simple.h"
+#include "config.h"
-#include "vec.h"
-#include "gromacs/utility/smalloc.h"
+#include <math.h>
-#include "nb_kernel_allvsallgb.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
typedef struct
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _NB_KERNEL_ALLVSALLGB_H
#define _NB_KERNEL_ALLVSALLGB_H
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "config.h"
-#include "types/simple.h"
-#include "typedefs.h"
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
void
nb_kernel_allvsallgb(t_nblist * nlist,
/*
* Note: this file was generated by the GROMACS c kernel generator.
*/
-#ifndef nb_kernel_c_h
-#define nb_kernel_c_h
+#include "gmxpre.h"
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_c;
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_c;
int
kernellist_c_size = sizeof(kernellist_c)/sizeof(kernellist_c[0]);
-
-#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef nb_kernel_c_h
#define nb_kernel_c_h
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
/* List of kernels for this architecture with metadata about them */
#error This file must be processed with the Gromacs pre-preprocessor
/* #endif */
/* #if INCLUDE_HEADER */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
/* #endif */
/* ## List of variables set by the generating script: */
fpdecl = open('nb_kernel_' + Arch + '.c','w')
fpdecl.write( FileHeader )
-fpdecl.write( '#ifndef nb_kernel_' + Arch + '_h\n' )
-fpdecl.write( '#define nb_kernel_' + Arch + '_h\n\n' )
+fpdecl.write( '#include "gmxpre.h"\n\n' )
fpdecl.write( '#include "../nb_kernel.h"\n\n' )
for KernelElec in ElectrostaticsList:
fpdecl.write( kerneldecl[-1] + '\n' )
fpdecl.write( '};\n\n' )
fpdecl.write( 'int\n' )
-fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
-fpdecl.write( '#endif\n')
+fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n')
fpdecl.close()
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/*
* Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
*/
-#ifndef nb_kernel_sparc64_hpc_ace_double_h
-#define nb_kernel_sparc64_hpc_ace_double_h
+#include "gmxpre.h"
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_sparc64_hpc_ace_double;
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_sparc64_hpc_ace_double;
int
kernellist_sparc64_hpc_ace_double_size = sizeof(kernellist_sparc64_hpc_ace_double)/sizeof(kernellist_sparc64_hpc_ace_double[0]);
-
-#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef nb_kernel_sparc64_hpc_ace_double_h
#define nb_kernel_sparc64_hpc_ace_double_h
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
/* List of kernels for this architecture with metadata about them */
#error This file must be processed with the Gromacs pre-preprocessor
/* #endif */
/* #if INCLUDE_HEADER */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "kernelutil_sparc64_hpc_ace_double.h"
/* #endif */
#ifndef _kernelutil_x86_sse2_double_h_
#define _kernelutil_x86_sse2_double_h_
-#include <math.h>
-
+#include "config.h"
+#include <math.h>
#include <stdio.h>
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013')
+FileHeader = create_copyright_header('2012,2013,2014')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
fpdecl = open('nb_kernel_' + Arch + '.c','w')
fpdecl.write( FileHeader )
-fpdecl.write( '#ifndef nb_kernel_' + Arch + '_h\n' )
-fpdecl.write( '#define nb_kernel_' + Arch + '_h\n\n' )
+fpdecl.write( '#include "gmxpre.h"\n\n' )
fpdecl.write( '#include "../nb_kernel.h"\n\n' )
for KernelElec in ElectrostaticsList:
fpdecl.write( kerneldecl[-1] + '\n' )
fpdecl.write( '};\n\n' )
fpdecl.write( 'int\n' )
-fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
-fpdecl.write( '#endif\n')
+fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n')
fpdecl.close()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/*
* Note: this file was generated by the GROMACS sse2_double kernel generator.
*/
-#ifndef nb_kernel_sse2_double_h
-#define nb_kernel_sse2_double_h
+#include "gmxpre.h"
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_sse2_double;
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_sse2_double;
int
kernellist_sse2_double_size = sizeof(kernellist_sse2_double)/sizeof(kernellist_sse2_double[0]);
-
-#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef nb_kernel_sse2_double_h
#define nb_kernel_sse2_double_h
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
/* List of kernels for this architecture with metadata about them */
#error This file must be processed with the Gromacs pre-preprocessor
/* #endif */
/* #if INCLUDE_HEADER */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_double.h"
#include "kernelutil_x86_sse2_double.h"
/* We require SSE2 now! */
+#include "config.h"
+
#include <math.h>
#define gmx_mm_castsi128_ps _mm_castsi128_ps
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013')
+FileHeader = create_copyright_header('2012,2013,2014')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
fpdecl = open('nb_kernel_' + Arch + '.c','w')
fpdecl.write( FileHeader )
-fpdecl.write( '#ifndef nb_kernel_' + Arch + '_h\n' )
-fpdecl.write( '#define nb_kernel_' + Arch + '_h\n\n' )
+fpdecl.write( '#include "gmxpre.h"\n\n' )
fpdecl.write( '#include "../nb_kernel.h"\n\n' )
for KernelElec in ElectrostaticsList:
fpdecl.write( kerneldecl[-1] + '\n' )
fpdecl.write( '};\n\n' )
fpdecl.write( 'int\n' )
-fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
-fpdecl.write( '#endif\n')
+fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n')
fpdecl.close()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
/*
* Note: this file was generated by the GROMACS sse2_single kernel generator.
*/
-#ifndef nb_kernel_sse2_single_h
-#define nb_kernel_sse2_single_h
+#include "gmxpre.h"
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_sse2_single;
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_sse2_single;
int
kernellist_sse2_single_size = sizeof(kernellist_sse2_single)/sizeof(kernellist_sse2_single[0]);
-
-#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef nb_kernel_sse2_single_h
#define nb_kernel_sse2_single_h
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
/* List of kernels for this architecture with metadata about them */
#error This file must be processed with the Gromacs pre-preprocessor
/* #endif */
/* #if INCLUDE_HEADER */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse2_single.h"
#include "kernelutil_x86_sse2_single.h"
#ifndef _kernelutil_x86_sse4_1_double_h_
#define _kernelutil_x86_sse4_1_double_h_
-#include <math.h>
+#include "config.h"
+#include <math.h>
#include <stdio.h>
#define gmx_mm_extract_epi32(x, imm) _mm_extract_epi32((x), (imm))
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013')
+FileHeader = create_copyright_header('2012,2013,2014')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
fpdecl = open('nb_kernel_' + Arch + '.c','w')
fpdecl.write( FileHeader )
-fpdecl.write( '#ifndef nb_kernel_' + Arch + '_h\n' )
-fpdecl.write( '#define nb_kernel_' + Arch + '_h\n\n' )
+fpdecl.write( '#include "gmxpre.h"\n\n' )
fpdecl.write( '#include "../nb_kernel.h"\n\n' )
for KernelElec in ElectrostaticsList:
fpdecl.write( kerneldecl[-1] + '\n' )
fpdecl.write( '};\n\n' )
fpdecl.write( 'int\n' )
-fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
-fpdecl.write( '#endif\n')
+fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n')
fpdecl.close()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
/*
* Note: this file was generated by the GROMACS sse4_1_double kernel generator.
*/
-#ifndef nb_kernel_sse4_1_double_h
-#define nb_kernel_sse4_1_double_h
+#include "gmxpre.h"
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_sse4_1_double;
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_sse4_1_double;
int
kernellist_sse4_1_double_size = sizeof(kernellist_sse4_1_double)/sizeof(kernellist_sse4_1_double[0]);
-
-#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef nb_kernel_sse4_1_double_h
#define nb_kernel_sse4_1_double_h
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
/* List of kernels for this architecture with metadata about them */
#error This file must be processed with the Gromacs pre-preprocessor
/* #endif */
/* #if INCLUDE_HEADER */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_double.h"
#include "kernelutil_x86_sse4_1_double.h"
#ifndef _kernelutil_x86_sse4_1_single_h_
#define _kernelutil_x86_sse4_1_single_h_
+#include "config.h"
+
#include <math.h>
#undef gmx_restrict
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013')
+FileHeader = create_copyright_header('2012,2013,2014')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
fpdecl = open('nb_kernel_' + Arch + '.c','w')
fpdecl.write( FileHeader )
-fpdecl.write( '#ifndef nb_kernel_' + Arch + '_h\n' )
-fpdecl.write( '#define nb_kernel_' + Arch + '_h\n\n' )
+fpdecl.write( '#include "gmxpre.h"\n\n' )
fpdecl.write( '#include "../nb_kernel.h"\n\n' )
for KernelElec in ElectrostaticsList:
fpdecl.write( kerneldecl[-1] + '\n' )
fpdecl.write( '};\n\n' )
fpdecl.write( 'int\n' )
-fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
-fpdecl.write( '#endif\n')
+fpdecl.write( ' kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n')
fpdecl.close()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
/*
* Note: this file was generated by the GROMACS sse4_1_single kernel generator.
*/
-#ifndef nb_kernel_sse4_1_single_h
-#define nb_kernel_sse4_1_single_h
+#include "gmxpre.h"
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_VF_sse4_1_single;
nb_kernel_t nb_kernel_ElecNone_VdwLJEw_GeomP1P1_F_sse4_1_single;
int
kernellist_sse4_1_single_size = sizeof(kernellist_sse4_1_single)/sizeof(kernellist_sse4_1_single[0]);
-
-#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef nb_kernel_sse4_1_single_h
#define nb_kernel_sse4_1_single_h
-#include "../nb_kernel.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
/* List of kernels for this architecture with metadata about them */
#error This file must be processed with the Gromacs pre-preprocessor
/* #endif */
/* #if INCLUDE_HEADER */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include "../nb_kernel.h"
-#include "types/simple.h"
-#include "vec.h"
-#include "nrnb.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/nrnb.h"
#include "gromacs/simd/math_x86_sse4_1_single.h"
#include "kernelutil_x86_sse4_1_single.h"
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/nonbonded.h"
+
+#include "config.h"
#include <stdio.h>
#include <stdlib.h>
#include "thread_mpi/threads.h"
-#include "typedefs.h"
-#include "txtdump.h"
-#include "gromacs/utility/smalloc.h"
-#include "ns.h"
-#include "vec.h"
+#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
+#include "gromacs/gmxlib/nonbonded/nb_generic.h"
+#include "gromacs/gmxlib/nonbonded/nb_generic_adress.h"
+#include "gromacs/gmxlib/nonbonded/nb_generic_cg.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/listed-forces/bonded.h"
#include "gromacs/math/utilities.h"
-#include "macros.h"
-#include "gromacs/utility/cstringutil.h"
-#include "force.h"
-#include "names.h"
-#include "main.h"
-#include "xvgr.h"
-#include "gmx_fatal.h"
-#include "physics.h"
-#include "force.h"
-#include "bondf.h"
-#include "nrnb.h"
-#include "nonbonded.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/simd/simd.h"
-
-#include "nb_kernel.h"
-#include "nb_free_energy.h"
-#include "nb_generic.h"
-#include "nb_generic_cg.h"
-#include "nb_generic_adress.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* Different default (c) and SIMD instructions interaction-specific kernels */
-#include "nb_kernel_c/nb_kernel_c.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.h"
#if (defined GMX_SIMD_X86_SSE2) && !(defined GMX_DOUBLE)
-# include "nb_kernel_sse2_single/nb_kernel_sse2_single.h"
+# include "gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.h"
#endif
#if (defined GMX_SIMD_X86_SSE4_1) && !(defined GMX_DOUBLE)
-# include "nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h"
+# include "gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h"
#endif
#if (defined GMX_SIMD_X86_AVX_128_FMA) && !(defined GMX_DOUBLE)
-# include "nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h"
+# include "gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h"
#endif
#if (defined GMX_SIMD_X86_AVX_256_OR_HIGHER) && !(defined GMX_DOUBLE)
-# include "nb_kernel_avx_256_single/nb_kernel_avx_256_single.h"
+# include "gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.h"
#endif
#if (defined GMX_SIMD_X86_SSE2 && defined GMX_DOUBLE)
-# include "nb_kernel_sse2_double/nb_kernel_sse2_double.h"
+# include "gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.h"
#endif
#if (defined GMX_SIMD_X86_SSE4_1 && defined GMX_DOUBLE)
-# include "nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h"
+# include "gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h"
#endif
#if (defined GMX_SIMD_X86_AVX_128_FMA && defined GMX_DOUBLE)
-# include "nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h"
+# include "gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h"
#endif
#if (defined GMX_SIMD_X86_AVX_256_OR_HIGHER && defined GMX_DOUBLE)
-# include "nb_kernel_avx_256_double/nb_kernel_avx_256_double.h"
+# include "gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.h"
#endif
#if (defined GMX_SIMD_SPARC64_HPC_ACE && defined GMX_DOUBLE)
-# include "nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h"
+# include "gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h"
#endif
nlist = nblists->nlist_sr;
f = f_shortrange;
}
- else if (range == 1)
+ else
{
/* Long-range */
if (!(flags & GMX_NONBONDED_DO_LR))
}
}
}
-
-static void
-nb_listed_warning_rlimit(const rvec *x, int ai, int aj, int * global_atom_index, real r, real rlimit)
-{
- gmx_warning("Listed nonbonded interaction between particles %d and %d\n"
- "at distance %.3f which is larger than the table limit %.3f nm.\n\n"
- "This is likely either a 1,4 interaction, or a listed interaction inside\n"
- "a smaller molecule you are decoupling during a free energy calculation.\n"
- "Since interactions at distances beyond the table cannot be computed,\n"
- "they are skipped until they are inside the table limit again. You will\n"
- "only see this message once, even if it occurs for several interactions.\n\n"
- "IMPORTANT: This should not happen in a stable simulation, so there is\n"
- "probably something wrong with your system. Only change the table-extension\n"
- "distance in the mdp file if you are really sure that is the reason.\n",
- glatnr(global_atom_index, ai), glatnr(global_atom_index, aj), r, rlimit);
-
- if (debug)
- {
- fprintf(debug,
- "%8f %8f %8f\n%8f %8f %8f\n1-4 (%d,%d) interaction not within cut-off! r=%g. Ignored\n",
- x[ai][XX], x[ai][YY], x[ai][ZZ], x[aj][XX], x[aj][YY], x[aj][ZZ],
- glatnr(global_atom_index, ai), glatnr(global_atom_index, aj), r);
- }
-}
-
-
-
-/* This might logically belong better in the nb_generic.c module, but it is only
- * used in do_nonbonded_listed(), and we want it to be inlined there to avoid an
- * extra functional call for every single pair listed in the topology.
- */
-static real
-nb_evaluate_single(real r2, real tabscale, real *vftab,
- real qq, real c6, real c12, real *velec, real *vvdw)
-{
- real rinv, r, rtab, eps, eps2, Y, F, Geps, Heps2, Fp, VVe, FFe, VVd, FFd, VVr, FFr, fscal;
- int ntab;
-
- /* Do the tabulated interactions - first table lookup */
- rinv = gmx_invsqrt(r2);
- r = r2*rinv;
- rtab = r*tabscale;
- ntab = rtab;
- eps = rtab-ntab;
- eps2 = eps*eps;
- ntab = 12*ntab;
- /* Electrostatics */
- Y = vftab[ntab];
- F = vftab[ntab+1];
- Geps = eps*vftab[ntab+2];
- Heps2 = eps2*vftab[ntab+3];
- Fp = F+Geps+Heps2;
- VVe = Y+eps*Fp;
- FFe = Fp+Geps+2.0*Heps2;
- /* Dispersion */
- Y = vftab[ntab+4];
- F = vftab[ntab+5];
- Geps = eps*vftab[ntab+6];
- Heps2 = eps2*vftab[ntab+7];
- Fp = F+Geps+Heps2;
- VVd = Y+eps*Fp;
- FFd = Fp+Geps+2.0*Heps2;
- /* Repulsion */
- Y = vftab[ntab+8];
- F = vftab[ntab+9];
- Geps = eps*vftab[ntab+10];
- Heps2 = eps2*vftab[ntab+11];
- Fp = F+Geps+Heps2;
- VVr = Y+eps*Fp;
- FFr = Fp+Geps+2.0*Heps2;
-
- *velec = qq*VVe;
- *vvdw = c6*VVd+c12*VVr;
-
- fscal = -(qq*FFe+c6*FFd+c12*FFr)*tabscale*rinv;
-
- return fscal;
-}
-
-
-real
-do_nonbonded_listed(int ftype, int nbonds,
- const t_iatom iatoms[], const t_iparams iparams[],
- const rvec x[], rvec f[], rvec fshift[],
- const t_pbc *pbc, const t_graph *g,
- real *lambda, real *dvdl,
- const t_mdatoms *md,
- const t_forcerec *fr, gmx_grppairener_t *grppener,
- int *global_atom_index)
-{
- int ielec, ivdw;
- real qq, c6, c12;
- rvec dx;
- ivec dt;
- int i, j, itype, ai, aj, gid;
- int fshift_index;
- real r2, rinv;
- real fscal, velec, vvdw;
- real * energygrp_elec;
- real * energygrp_vdw;
- static gmx_bool warned_rlimit = FALSE;
- /* Free energy stuff */
- gmx_bool bFreeEnergy;
- real LFC[2], LFV[2], DLF[2], lfac_coul[2], lfac_vdw[2], dlfac_coul[2], dlfac_vdw[2];
- real qqB, c6B, c12B, sigma2_def, sigma2_min;
-
-
- switch (ftype)
- {
- case F_LJ14:
- case F_LJC14_Q:
- energygrp_elec = grppener->ener[egCOUL14];
- energygrp_vdw = grppener->ener[egLJ14];
- break;
- case F_LJC_PAIRS_NB:
- energygrp_elec = grppener->ener[egCOULSR];
- energygrp_vdw = grppener->ener[egLJSR];
- break;
- default:
- energygrp_elec = NULL; /* Keep compiler happy */
- energygrp_vdw = NULL; /* Keep compiler happy */
- gmx_fatal(FARGS, "Unknown function type %d in do_nonbonded14", ftype);
- break;
- }
-
- if (fr->efep != efepNO)
- {
- /* Lambda factor for state A=1-lambda and B=lambda */
- LFC[0] = 1.0 - lambda[efptCOUL];
- LFV[0] = 1.0 - lambda[efptVDW];
- LFC[1] = lambda[efptCOUL];
- LFV[1] = lambda[efptVDW];
-
- /*derivative of the lambda factor for state A and B */
- DLF[0] = -1;
- DLF[1] = 1;
-
- /* precalculate */
- sigma2_def = pow(fr->sc_sigma6_def, 1.0/3.0);
- sigma2_min = pow(fr->sc_sigma6_min, 1.0/3.0);
-
- for (i = 0; i < 2; i++)
- {
- lfac_coul[i] = (fr->sc_power == 2 ? (1-LFC[i])*(1-LFC[i]) : (1-LFC[i]));
- dlfac_coul[i] = DLF[i]*fr->sc_power/fr->sc_r_power*(fr->sc_power == 2 ? (1-LFC[i]) : 1);
- lfac_vdw[i] = (fr->sc_power == 2 ? (1-LFV[i])*(1-LFV[i]) : (1-LFV[i]));
- dlfac_vdw[i] = DLF[i]*fr->sc_power/fr->sc_r_power*(fr->sc_power == 2 ? (1-LFV[i]) : 1);
- }
- }
- else
- {
- sigma2_min = sigma2_def = 0;
- }
-
- bFreeEnergy = FALSE;
- for (i = 0; (i < nbonds); )
- {
- itype = iatoms[i++];
- ai = iatoms[i++];
- aj = iatoms[i++];
- gid = GID(md->cENER[ai], md->cENER[aj], md->nenergrp);
-
- /* Get parameters */
- switch (ftype)
- {
- case F_LJ14:
- bFreeEnergy =
- (fr->efep != efepNO &&
- ((md->nPerturbed && (md->bPerturbed[ai] || md->bPerturbed[aj])) ||
- iparams[itype].lj14.c6A != iparams[itype].lj14.c6B ||
- iparams[itype].lj14.c12A != iparams[itype].lj14.c12B));
- qq = md->chargeA[ai]*md->chargeA[aj]*fr->epsfac*fr->fudgeQQ;
- c6 = iparams[itype].lj14.c6A;
- c12 = iparams[itype].lj14.c12A;
- break;
- case F_LJC14_Q:
- qq = iparams[itype].ljc14.qi*iparams[itype].ljc14.qj*fr->epsfac*iparams[itype].ljc14.fqq;
- c6 = iparams[itype].ljc14.c6;
- c12 = iparams[itype].ljc14.c12;
- break;
- case F_LJC_PAIRS_NB:
- qq = iparams[itype].ljcnb.qi*iparams[itype].ljcnb.qj*fr->epsfac;
- c6 = iparams[itype].ljcnb.c6;
- c12 = iparams[itype].ljcnb.c12;
- break;
- default:
- /* Cannot happen since we called gmx_fatal() above in this case */
- qq = c6 = c12 = 0; /* Keep compiler happy */
- break;
- }
-
- /* To save flops in the optimized kernels, c6/c12 have 6.0/12.0 derivative prefactors
- * included in the general nfbp array now. This means the tables are scaled down by the
- * same factor, so when we use the original c6/c12 parameters from iparams[] they must
- * be scaled up.
- */
- c6 *= 6.0;
- c12 *= 12.0;
-
- /* Do we need to apply full periodic boundary conditions? */
- if (fr->bMolPBC == TRUE)
- {
- fshift_index = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
- }
- else
- {
- fshift_index = CENTRAL;
- rvec_sub(x[ai], x[aj], dx);
- }
- r2 = norm2(dx);
-
- if (r2 >= fr->tab14.r*fr->tab14.r)
- {
- if (warned_rlimit == FALSE)
- {
- nb_listed_warning_rlimit(x, ai, aj, global_atom_index, sqrt(r2), fr->tab14.r);
- warned_rlimit = TRUE;
- }
- continue;
- }
-
- if (bFreeEnergy)
- {
- /* Currently free energy is only supported for F_LJ14, so no need to check for that if we got here */
- qqB = md->chargeB[ai]*md->chargeB[aj]*fr->epsfac*fr->fudgeQQ;
- c6B = iparams[itype].lj14.c6B*6.0;
- c12B = iparams[itype].lj14.c12B*12.0;
-
- fscal = nb_free_energy_evaluate_single(r2, fr->sc_r_power, fr->sc_alphacoul, fr->sc_alphavdw,
- fr->tab14.scale, fr->tab14.data, qq, c6, c12, qqB, c6B, c12B,
- LFC, LFV, DLF, lfac_coul, lfac_vdw, dlfac_coul, dlfac_vdw,
- fr->sc_sigma6_def, fr->sc_sigma6_min, sigma2_def, sigma2_min, &velec, &vvdw, dvdl);
- }
- else
- {
- /* Evaluate tabulated interaction without free energy */
- fscal = nb_evaluate_single(r2, fr->tab14.scale, fr->tab14.data, qq, c6, c12, &velec, &vvdw);
- }
-
- energygrp_elec[gid] += velec;
- energygrp_vdw[gid] += vvdw;
- svmul(fscal, dx, dx);
-
- /* Add the forces */
- rvec_inc(f[ai], dx);
- rvec_dec(f[aj], dx);
-
- if (g)
- {
- /* Correct the shift forces using the graph */
- ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
- fshift_index = IVEC2IS(dt);
- }
- if (fshift_index != CENTRAL)
- {
- rvec_inc(fshift[fshift_index], dx);
- rvec_dec(fshift[CENTRAL], dx);
- }
- }
- return 0.0;
-}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/nrnb.h"
+#include <stdlib.h>
#include <string.h>
-#include "types/commrec.h"
-#include "sysstuff.h"
-#include "names.h"
-#include "macros.h"
-#include "nrnb.h"
-#include "main.h"
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/utility/smalloc.h"
typedef struct {
}
void print_perf(FILE *out, double time_per_thread, double time_per_node,
- gmx_int64_t nsteps, real delta_t,
+ gmx_int64_t nsteps, double delta_t,
double nbfs, double mflop)
{
- real wallclocktime;
+ double wallclocktime;
fprintf(out, "\n");
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "oenv.h"
+#include "gmxpre.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/oenv.h"
-#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
struct output_env
{
view = FALSE;
xvg_format = exvgNONE;
verbosity = 0;
- debug_level = 0;
}
const gmx::ProgramContextInterface &programContext;
xvg_format_t xvg_format;
/* The level of verbosity for this program */
int verbosity;
- /* the debug level */
- int debug_level;
};
/* The source code in this file should be thread-safe.
void output_env_init(output_env_t *oenvp,
const gmx::ProgramContextInterface &context,
time_unit_t tmu, gmx_bool view, xvg_format_t xvg_format,
- int verbosity, int debug_level)
+ int verbosity)
{
try
{
oenv->view = view;
oenv->xvg_format = xvg_format;
oenv->verbosity = verbosity;
- oenv->debug_level = debug_level;
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
return oenv->verbosity;
}
-int output_env_get_debug_level(const output_env_t oenv)
-{
- return oenv->debug_level;
-}
-
const char *output_env_get_time_unit(const output_env_t oenv)
{
return time_units_str[oenv->time_unit];
return oenv->xvg_format;
}
-const char *output_env_get_program_name(const output_env_t oenv)
-{
- const char *programName = NULL;
-
- try
- {
- programName = oenv->programContext.fullBinaryPath();
- }
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
-
- return programName;
-}
-
-const char *output_env_get_short_program_name(const output_env_t oenv)
+const char *output_env_get_program_display_name(const output_env_t oenv)
{
- const char *programName = NULL;
+ const char *displayName = NULL;
try
{
- // TODO: Use the display name once it doesn't break anything.
- programName = oenv->programContext.programName();
+ displayName = oenv->programContext.displayName();
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
- return programName;
+ return displayName;
}
-const char *output_env_get_cmd_line(const output_env_t oenv)
+const gmx::ProgramContextInterface &
+output_env_get_program_context(const output_env_t oenv)
{
- const char *commandLine = NULL;
-
- try
- {
- commandLine = oenv->programContext.commandLine();
- }
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
-
- return commandLine;
+ return oenv->programContext;
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "types/commrec.h"
-#include "network.h"
-#include "orires.h"
-#include "main.h"
-#include "copyrite.h"
-#include "pbc.h"
-#include "mtop_util.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/linearalgebra/nrjac.h"
#include "gromacs/math/do_fit.h"
-#include "gmx_fatal.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
void init_orires(FILE *fplog, const gmx_mtop_t *mtop,
rvec xref[],
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/rbin.h"
-#include "typedefs.h"
-#include "main.h"
-#include "network.h"
-#include "rbin.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/utility/smalloc.h"
t_bin *mk_bin(void)
}
/* Copy pointer */
rbuf = b->rbuf+b->nreal;
+
+#if (__ICC == 1500 || __ICL == 1500) && defined __MIC__
+#pragma novector /* Work-around for incorrect vectorization */
+#endif
for (i = 0; (i < nr); i++)
{
rbuf[i] = r[i];
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/readinp.h"
#include <stdio.h>
#include <stdlib.h>
-#include "typedefs.h"
+
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/warninp.h"
#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/qsort_threadsafe.h"
#include "gromacs/utility/smalloc.h"
-#include "readinp.h"
-#include "macros.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "names.h"
-#include "warninp.h"
-#include "gmx_fatal.h"
t_inpfile *read_inpfile(const char *fn, int *ninp,
warninp_t wi)
inp[nin-1].count = 0;
inp[nin-1].bObsolete = FALSE;
inp[nin-1].bSet = FALSE;
- inp[nin-1].name = strdup(lbuf);
- inp[nin-1].value = strdup(rbuf);
+ inp[nin-1].name = gmx_strdup(lbuf);
+ inp[nin-1].value = gmx_strdup(rbuf);
}
else
{
{
/* override */
sfree(inp[found_index].value);
- inp[found_index].value = strdup(rbuf);
+ inp[found_index].value = gmx_strdup(rbuf);
sprintf(warn_buf,
"Overriding existing parameter \"%s\" with value \"%s\"\n",
lbuf, rbuf);
inp[i].count = mm++;
}
}
- qsort(inp, ninp, (size_t)sizeof(inp[0]), inp_comp);
+ gmx_qsort(inp, ninp, (size_t)sizeof(inp[0]), inp_comp);
}
void write_inpfile(const char *fn, int ninp, t_inpfile inp[], gmx_bool bHaltOnUnknown,
fprintf(stderr, "Replacing old mdp entry '%s' by '%s'\n",
inp[i].name, new_entry);
sfree(inp[i].name);
- inp[i].name = strdup(new_entry);
+ inp[i].name = gmx_strdup(new_entry);
}
else
{
notfound = TRUE;
i = (*ninp)++;
srenew(*inp, (*ninp));
- (*inp)[i].name = strdup(name);
+ (*inp)[i].name = gmx_strdup(name);
(*inp)[i].bSet = TRUE;
}
(*inp)[i].count = (*inp)[0].inp_count++;
if (ii == -1)
{
sprintf(buf, "%d", def);
- (*inp)[(*ninp)-1].value = strdup(buf);
+ (*inp)[(*ninp)-1].value = gmx_strdup(buf);
return def;
}
if (ii == -1)
{
sprintf(buf, "%"GMX_PRId64, def);
- (*inp)[(*ninp)-1].value = strdup(buf);
+ (*inp)[(*ninp)-1].value = gmx_strdup(buf);
return def;
}
if (ii == -1)
{
sprintf(buf, "%g", def);
- (*inp)[(*ninp)-1].value = strdup(buf);
+ (*inp)[(*ninp)-1].value = gmx_strdup(buf);
return def;
}
if (def)
{
sprintf(buf, "%s", def);
- (*inp)[(*ninp)-1].value = strdup(buf);
+ (*inp)[(*ninp)-1].value = gmx_strdup(buf);
}
else
{
if (ii == -1)
{
- (*inp)[(*ninp)-1].value = strdup(defs[0]);
+ (*inp)[(*ninp)-1].value = gmx_strdup(defs[0]);
return 0;
}
fprintf(stderr, "%s\n", buf);
}
- (*inp)[ii].value = strdup(defs[0]);
+ (*inp)[ii].value = gmx_strdup(defs[0]);
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/sighandler.h"
+
+#include "config.h"
-#include "typedefs.h"
-#include "gmx_fatal.h"
-#include "sighandler.h"
+#include <stdlib.h>
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/fatalerror.h"
const char *gmx_stop_cond_name[] =
{
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "splitter.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gromacs/legacyheaders/splitter.h"
#include <assert.h>
+#include <stdlib.h>
#include <string.h>
-#include "macros.h"
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "mshift.h"
-#include "gmx_fatal.h"
typedef struct {
int atom, sid;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
/* This file is completely threadsafe - please keep it that way! */
+#include "gromacs/legacyheaders/txtdump.h"
+
#include <stdio.h>
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "names.h"
-#include "txtdump.h"
-#include "vec.h"
-#include "macros.h"
-
-#include "gmx_fatal.h"
+#include <stdlib.h>
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
int pr_indent(FILE *fp, int n)
j++;
for (k = 0; k < interaction_function[ftype].nratoms; k++)
{
- (void) fprintf(fp, " %u", *(iatoms++));
+ (void) fprintf(fp, " %d", *(iatoms++));
}
(void) fprintf(fp, "\n");
i += 1+interaction_function[ftype].nratoms;
for (i = 0; i <= block->nr; i++)
{
(void) pr_indent(fp, indent+INDENT);
- (void) fprintf(fp, "%s->index[%d]=%u\n",
+ (void) fprintf(fp, "%s->index[%d]=%d\n",
title, bShowNumbers ? i : -1, block->index[i]);
}
for (i = 0; i < block->nra; i++)
{
(void) pr_indent(fp, indent+INDENT);
- (void) fprintf(fp, "%s->a[%d]=%u\n",
+ (void) fprintf(fp, "%s->a[%d]=%d\n",
title, bShowNumbers ? i : -1, block->a[i]);
}
}
(void) fprintf(fp, "\n");
size = pr_indent(fp, indent+INDENT);
}
- size += fprintf(fp, "%u", block->a[j]);
+ size += fprintf(fp, "%d", block->a[j]);
}
(void) fprintf(fp, "}\n");
start = end;
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "thread_mpi/threads.h"
+#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "symtab.h"
-#include "vec.h"
-#include "pbc.h"
-#include "macros.h"
#include <string.h>
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/random/random.h"
+#include "gromacs/utility/smalloc.h"
/* The source code in this file should be thread-safe.
Please keep it that way. */
-
-
-static gmx_bool bOverAllocDD = FALSE;
-static tMPI_Thread_mutex_t over_alloc_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
-
-
-void set_over_alloc_dd(gmx_bool set)
-{
- tMPI_Thread_mutex_lock(&over_alloc_mutex);
- /* we just make sure that we don't set this at the same time.
- We don't worry too much about reading this rarely-set variable */
- bOverAllocDD = set;
- tMPI_Thread_mutex_unlock(&over_alloc_mutex);
-}
-
-int over_alloc_dd(int n)
-{
- if (bOverAllocDD)
- {
- return OVER_ALLOC_FAC*n + 100;
- }
- else
- {
- return n;
- }
-}
-
int gmx_int64_to_int(gmx_int64_t step, const char *warn)
{
int i;
return i;
}
-char *gmx_step_str(gmx_int64_t i, char *buf)
-{
- sprintf(buf, "%"GMX_PRId64, i);
-
- return buf;
-}
-
-void init_block(t_block *block)
-{
- int i;
-
- block->nr = 0;
- block->nalloc_index = 1;
- snew(block->index, block->nalloc_index);
- block->index[0] = 0;
-}
-
-void init_blocka(t_blocka *block)
-{
- int i;
-
- block->nr = 0;
- block->nra = 0;
- block->nalloc_index = 1;
- snew(block->index, block->nalloc_index);
- block->index[0] = 0;
- block->nalloc_a = 0;
- block->a = NULL;
-}
-
-void init_atom(t_atoms *at)
-{
- int i;
-
- at->nr = 0;
- at->nres = 0;
- at->atom = NULL;
- at->resinfo = NULL;
- at->atomname = NULL;
- at->atomtype = NULL;
- at->atomtypeB = NULL;
- at->pdbinfo = NULL;
-}
-
-void init_atomtypes(t_atomtypes *at)
-{
- at->nr = 0;
- at->radius = NULL;
- at->vol = NULL;
- at->atomnumber = NULL;
- at->gb_radius = NULL;
- at->S_hct = NULL;
-}
-
-void init_groups(gmx_groups_t *groups)
-{
- int g;
-
- groups->ngrpname = 0;
- groups->grpname = NULL;
- for (g = 0; (g < egcNR); g++)
- {
- groups->grps[g].nm_ind = NULL;
- groups->ngrpnr[g] = 0;
- groups->grpnr[g] = NULL;
- }
-
-}
-
-void init_mtop(gmx_mtop_t *mtop)
-{
- mtop->name = NULL;
- mtop->nmoltype = 0;
- mtop->moltype = NULL;
- mtop->nmolblock = 0;
- mtop->molblock = NULL;
- mtop->maxres_renum = 0;
- mtop->maxresnr = -1;
- init_groups(&mtop->groups);
- init_block(&mtop->mols);
- open_symtab(&mtop->symtab);
-}
-
-void init_top(t_topology *top)
-{
- int i;
-
- top->name = NULL;
- init_atom (&(top->atoms));
- init_atomtypes(&(top->atomtypes));
- init_block(&top->cgs);
- init_block(&top->mols);
- init_blocka(&top->excls);
- open_symtab(&top->symtab);
-}
-
void init_inputrec(t_inputrec *ir)
{
memset(ir, 0, (size_t)sizeof(*ir));
snew(ir->simtempvals, 1);
}
-void stupid_fill_block(t_block *grp, int natom, gmx_bool bOneIndexGroup)
-{
- int i;
-
- if (bOneIndexGroup)
- {
- grp->nalloc_index = 2;
- snew(grp->index, grp->nalloc_index);
- grp->index[0] = 0;
- grp->index[1] = natom;
- grp->nr = 1;
- }
- else
- {
- grp->nalloc_index = natom+1;
- snew(grp->index, grp->nalloc_index);
- snew(grp->index, natom+1);
- for (i = 0; (i <= natom); i++)
- {
- grp->index[i] = i;
- }
- grp->nr = natom;
- }
-}
-
-void stupid_fill_blocka(t_blocka *grp, int natom)
-{
- int i;
-
- grp->nalloc_a = natom;
- snew(grp->a, grp->nalloc_a);
- for (i = 0; (i < natom); i++)
- {
- grp->a[i] = i;
- }
- grp->nra = natom;
-
- grp->nalloc_index = natom + 1;
- snew(grp->index, grp->nalloc_index);
- for (i = 0; (i <= natom); i++)
- {
- grp->index[i] = i;
- }
- grp->nr = natom;
-}
-
-void copy_blocka(const t_blocka *src, t_blocka *dest)
-{
- int i;
-
- dest->nr = src->nr;
- dest->nalloc_index = dest->nr + 1;
- snew(dest->index, dest->nalloc_index);
- for (i = 0; i < dest->nr+1; i++)
- {
- dest->index[i] = src->index[i];
- }
- dest->nra = src->nra;
- dest->nalloc_a = dest->nra + 1;
- snew(dest->a, dest->nalloc_a);
- for (i = 0; i < dest->nra+1; i++)
- {
- dest->a[i] = src->a[i];
- }
-}
-
-void done_block(t_block *block)
-{
- block->nr = 0;
- sfree(block->index);
- block->nalloc_index = 0;
-}
-
-void done_blocka(t_blocka *block)
-{
- block->nr = 0;
- block->nra = 0;
- sfree(block->index);
- sfree(block->a);
- block->index = NULL;
- block->a = NULL;
- block->nalloc_index = 0;
- block->nalloc_a = 0;
-}
-
-void done_atom (t_atoms *at)
-{
- at->nr = 0;
- at->nres = 0;
- sfree(at->atom);
- sfree(at->resinfo);
- sfree(at->atomname);
- sfree(at->atomtype);
- sfree(at->atomtypeB);
- if (at->pdbinfo)
- {
- sfree(at->pdbinfo);
- }
-}
-
-void done_atomtypes(t_atomtypes *atype)
-{
- atype->nr = 0;
- sfree(atype->radius);
- sfree(atype->vol);
- sfree(atype->surftens);
- sfree(atype->atomnumber);
- sfree(atype->gb_radius);
- sfree(atype->S_hct);
-}
-
-void done_moltype(gmx_moltype_t *molt)
-{
- int f;
-
- done_atom(&molt->atoms);
- done_block(&molt->cgs);
- done_blocka(&molt->excls);
-
- for (f = 0; f < F_NRE; f++)
- {
- sfree(molt->ilist[f].iatoms);
- molt->ilist[f].nalloc = 0;
- }
-}
-
-void done_molblock(gmx_molblock_t *molb)
-{
- if (molb->nposres_xA > 0)
- {
- molb->nposres_xA = 0;
- free(molb->posres_xA);
- }
- if (molb->nposres_xB > 0)
- {
- molb->nposres_xB = 0;
- free(molb->posres_xB);
- }
-}
-
-void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab)
-{
- int i;
-
- if (bDoneSymtab)
- {
- done_symtab(&mtop->symtab);
- }
-
- sfree(mtop->ffparams.functype);
- sfree(mtop->ffparams.iparams);
-
- for (i = 0; i < mtop->nmoltype; i++)
- {
- done_moltype(&mtop->moltype[i]);
- }
- sfree(mtop->moltype);
- for (i = 0; i < mtop->nmolblock; i++)
- {
- done_molblock(&mtop->molblock[i]);
- }
- sfree(mtop->molblock);
- done_block(&mtop->mols);
-}
-
-void done_top(t_topology *top)
-{
- int f;
-
- sfree(top->idef.functype);
- sfree(top->idef.iparams);
- for (f = 0; f < F_NRE; ++f)
- {
- sfree(top->idef.il[f].iatoms);
- top->idef.il[f].iatoms = NULL;
- top->idef.il[f].nalloc = 0;
- }
-
- done_atom (&(top->atoms));
-
- /* For GB */
- done_atomtypes(&(top->atomtypes));
-
- done_symtab(&(top->symtab));
- done_block(&(top->cgs));
- done_block(&(top->mols));
- done_blocka(&(top->excls));
-}
-
static void done_pull_group(t_pull_group *pgrp)
{
if (pgrp->nat > 0)
}
}
-void add_t_atoms(t_atoms *atoms, int natom_extra, int nres_extra)
-{
- int i;
-
- if (natom_extra > 0)
- {
- srenew(atoms->atomname, atoms->nr+natom_extra);
- srenew(atoms->atom, atoms->nr+natom_extra);
- if (NULL != atoms->pdbinfo)
- {
- srenew(atoms->pdbinfo, atoms->nr+natom_extra);
- }
- if (NULL != atoms->atomtype)
- {
- srenew(atoms->atomtype, atoms->nr+natom_extra);
- }
- if (NULL != atoms->atomtypeB)
- {
- srenew(atoms->atomtypeB, atoms->nr+natom_extra);
- }
- for (i = atoms->nr; (i < atoms->nr+natom_extra); i++)
- {
- atoms->atomname[i] = NULL;
- memset(&atoms->atom[i], 0, sizeof(atoms->atom[i]));
- if (NULL != atoms->pdbinfo)
- {
- memset(&atoms->pdbinfo[i], 0, sizeof(atoms->pdbinfo[i]));
- }
- if (NULL != atoms->atomtype)
- {
- atoms->atomtype[i] = NULL;
- }
- if (NULL != atoms->atomtypeB)
- {
- atoms->atomtypeB[i] = NULL;
- }
- }
- atoms->nr += natom_extra;
- }
- if (nres_extra > 0)
- {
- srenew(atoms->resinfo, atoms->nres+nres_extra);
- for (i = atoms->nres; (i < atoms->nres+nres_extra); i++)
- {
- memset(&atoms->resinfo[i], 0, sizeof(atoms->resinfo[i]));
- }
- atoms->nres += nres_extra;
- }
-}
-
-void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo)
-{
- atoms->nr = natoms;
- atoms->nres = 0;
- snew(atoms->atomname, natoms);
- atoms->atomtype = NULL;
- atoms->atomtypeB = NULL;
- snew(atoms->resinfo, natoms);
- snew(atoms->atom, natoms);
- if (bPdbinfo)
- {
- snew(atoms->pdbinfo, natoms);
- }
- else
- {
- atoms->pdbinfo = NULL;
- }
-}
-
-t_atoms *copy_t_atoms(t_atoms *src)
-{
- t_atoms *dst;
- int i;
-
- snew(dst, 1);
- init_t_atoms(dst, src->nr, (NULL != src->pdbinfo));
- dst->nr = src->nr;
- if (NULL != src->atomname)
- {
- snew(dst->atomname, src->nr);
- }
- if (NULL != src->atomtype)
- {
- snew(dst->atomtype, src->nr);
- }
- if (NULL != src->atomtypeB)
- {
- snew(dst->atomtypeB, src->nr);
- }
- for (i = 0; (i < src->nr); i++)
- {
- dst->atom[i] = src->atom[i];
- if (NULL != src->pdbinfo)
- {
- dst->pdbinfo[i] = src->pdbinfo[i];
- }
- if (NULL != src->atomname)
- {
- dst->atomname[i] = src->atomname[i];
- }
- if (NULL != src->atomtype)
- {
- dst->atomtype[i] = src->atomtype[i];
- }
- if (NULL != src->atomtypeB)
- {
- dst->atomtypeB[i] = src->atomtypeB[i];
- }
- }
- dst->nres = src->nres;
- for (i = 0; (i < src->nres); i++)
- {
- dst->resinfo[i] = src->resinfo[i];
- }
- return dst;
-}
-
-void t_atoms_set_resinfo(t_atoms *atoms, int atom_ind, t_symtab *symtab,
- const char *resname, int resnr, unsigned char ic,
- int chainnum, char chainid)
-{
- t_resinfo *ri;
-
- ri = &atoms->resinfo[atoms->atom[atom_ind].resind];
- ri->name = put_symtab(symtab, resname);
- ri->rtp = NULL;
- ri->nr = resnr;
- ri->ic = ic;
- ri->chainnum = chainnum;
- ri->chainid = chainid;
-}
-
-void free_t_atoms(t_atoms *atoms, gmx_bool bFreeNames)
-{
- int i;
-
- if (bFreeNames && atoms->atomname != NULL)
- {
- for (i = 0; i < atoms->nr; i++)
- {
- if (atoms->atomname[i] != NULL)
- {
- sfree(*atoms->atomname[i]);
- *atoms->atomname[i] = NULL;
- }
- }
- }
- if (bFreeNames && atoms->resinfo != NULL)
- {
- for (i = 0; i < atoms->nres; i++)
- {
- if (atoms->resinfo[i].name != NULL)
- {
- sfree(*atoms->resinfo[i].name);
- *atoms->resinfo[i].name = NULL;
- }
- }
- }
- if (bFreeNames && atoms->atomtype != NULL)
- {
- for (i = 0; i < atoms->nr; i++)
- {
- if (atoms->atomtype[i] != NULL)
- {
- sfree(*atoms->atomtype[i]);
- *atoms->atomtype[i] = NULL;
- }
- }
- }
- if (bFreeNames && atoms->atomtypeB != NULL)
- {
- for (i = 0; i < atoms->nr; i++)
- {
- if (atoms->atomtypeB[i] != NULL)
- {
- sfree(*atoms->atomtypeB[i]);
- *atoms->atomtypeB[i] = NULL;
- }
- }
- }
- sfree(atoms->atomname);
- sfree(atoms->atomtype);
- sfree(atoms->atomtypeB);
- sfree(atoms->resinfo);
- sfree(atoms->atom);
- sfree(atoms->pdbinfo);
- atoms->nr = 0;
- atoms->nres = 0;
- atoms->atomname = NULL;
- atoms->atomtype = NULL;
- atoms->atomtypeB = NULL;
- atoms->resinfo = NULL;
- atoms->atom = NULL;
- atoms->pdbinfo = NULL;
-}
-
real max_cutoff(real cutoff1, real cutoff2)
{
if (cutoff1 == 0 || cutoff2 == 0)
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "gromacs/legacyheaders/viewit.h"
+
+#include <stdlib.h>
#include <string.h>
-#include "oenv.h"
-#include "viewit.h"
-#include "gromacs/utility/cstringutil.h"
#include "gromacs/fileio/filenm.h"
-#include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
static const int can_view_ftp[] = {
0,
"ghostview", "display", NULL, "xterm -e rasmol"
};
-int can_view(int ftp)
+static int can_view(int ftp)
{
int i;
{
sprintf(buf, "%s %s %s &", cmd, opts ? opts : "", fn);
fprintf(stderr, "Executing '%s'\n", buf);
-#ifdef GMX_NO_SYSTEM
- printf("Warning-- No calls to system(3) supported on this platform.");
- printf("Warning-- Skipping execution of 'system(\"%s\")'.", buf);
-#else
if (0 != system(buf) )
{
gmx_fatal(FARGS, "Failed executing command: %s", buf);
}
-#endif
}
}
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/warninp.h"
#include <string.h>
-#include "gromacs/utility/smalloc.h"
-#include "copyrite.h"
+#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
-#include "warninp.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
typedef struct warninp {
gmx_bool bAllowWarnings;
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <string.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "grompp-impl.h"
-#include "macros.h"
-#include "toputil.h"
-#include "hackblock.h"
+
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static void clear_atom_list(int i0, atom_id a[])
{
#ifndef GMX_GMXPREPROCESS_ADD_PAR_H
#define GMX_GMXPREPROCESS_ADD_PAR_H
-#include "typedefs.h"
-#include "pdb2top.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C"
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "addconf.h"
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <stdlib.h>
-#include <string.h>
-#include "vec.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "types/commrec.h"
-#include "force.h"
-#include "names.h"
-#include "nsgrid.h"
-#include "mdatoms.h"
-#include "nrnb.h"
-#include "ns.h"
-#include "mtop_util.h"
-#include "chargegroup.h"
-
-static real box_margin;
-
-static real max_dist(rvec *x, real *r, int start, int end)
-{
- real maxd;
- int i, j;
-
- maxd = 0;
- for (i = start; i < end; i++)
- {
- for (j = i+1; j < end; j++)
- {
- maxd = max(maxd, sqrt(distance2(x[i], x[j]))+0.5*(r[i]+r[j]));
- }
- }
-
- return 0.5*maxd;
-}
-
-static gmx_bool outside_box_minus_margin2(rvec x, matrix box)
-{
- return ( (x[XX] < 2*box_margin) || (x[XX] > box[XX][XX]-2*box_margin) ||
- (x[YY] < 2*box_margin) || (x[YY] > box[YY][YY]-2*box_margin) ||
- (x[ZZ] < 2*box_margin) || (x[ZZ] > box[ZZ][ZZ]-2*box_margin) );
-}
-
-static gmx_bool outside_box_plus_margin(rvec x, matrix box)
-{
- return ( (x[XX] < -box_margin) || (x[XX] > box[XX][XX]+box_margin) ||
- (x[YY] < -box_margin) || (x[YY] > box[YY][YY]+box_margin) ||
- (x[ZZ] < -box_margin) || (x[ZZ] > box[ZZ][ZZ]+box_margin) );
-}
-
-static int mark_res(int at, gmx_bool *mark, int natoms, t_atom *atom, int *nmark)
-{
- int resind;
-
- resind = atom[at].resind;
- while ( (at > 0) && (resind == atom[at-1].resind) )
- {
- at--;
- }
- while ( (at < natoms) && (resind == atom[at].resind) )
- {
- if (!mark[at])
- {
- mark[at] = TRUE;
- (*nmark)++;
- }
- at++;
- }
-
- return at;
-}
-
-static real find_max_real(int n, real radius[])
-{
- int i;
- real rmax;
-
- rmax = 0;
- if (n > 0)
- {
- rmax = radius[0];
- for (i = 1; (i < n); i++)
- {
- rmax = max(rmax, radius[i]);
- }
- }
- return rmax;
-}
-
-static void combine_atoms(t_atoms *ap, t_atoms *as,
- rvec xp[], rvec *vp, rvec xs[], rvec *vs,
- t_atoms **a_comb, rvec **x_comb, rvec **v_comb)
-{
- t_atoms *ac;
- rvec *xc, *vc = NULL;
- int i, j, natot, res0;
-
- /* Total number of atoms */
- natot = ap->nr+as->nr;
-
- snew(ac, 1);
- init_t_atoms(ac, natot, FALSE);
-
- snew(xc, natot);
- if (vp && vs)
- {
- snew(vc, natot);
- }
-
- /* Fill the new structures */
- for (i = j = 0; (i < ap->nr); i++, j++)
- {
- copy_rvec(xp[i], xc[j]);
- if (vc)
- {
- copy_rvec(vp[i], vc[j]);
- }
- memcpy(&(ac->atom[j]), &(ap->atom[i]), sizeof(ap->atom[i]));
- ac->atom[j].type = 0;
- }
- res0 = ap->nres;
- for (i = 0; (i < as->nr); i++, j++)
- {
- copy_rvec(xs[i], xc[j]);
- if (vc)
- {
- copy_rvec(vs[i], vc[j]);
- }
- memcpy(&(ac->atom[j]), &(as->atom[i]), sizeof(as->atom[i]));
- ac->atom[j].type = 0;
- ac->atom[j].resind += res0;
- }
- ac->nr = j;
- ac->nres = ac->atom[j-1].resind+1;
- /* Fill all elements to prevent uninitialized memory */
- for (i = 0; i < ac->nr; i++)
- {
- ac->atom[i].m = 1;
- ac->atom[i].q = 0;
- ac->atom[i].mB = 1;
- ac->atom[i].qB = 0;
- ac->atom[i].type = 0;
- ac->atom[i].typeB = 0;
- ac->atom[i].ptype = eptAtom;
- }
-
- /* Return values */
- *a_comb = ac;
- *x_comb = xc;
- *v_comb = vc;
-}
-
-static t_forcerec *fr = NULL;
-
-static void do_nsgrid(FILE *fp, gmx_bool bVerbose,
- matrix box, rvec x[], t_atoms *atoms, real rlong,
- const output_env_t oenv)
-{
- gmx_mtop_t *mtop;
- gmx_localtop_t *top;
- t_mdatoms *md;
- t_block *cgs;
- t_inputrec *ir;
- t_nrnb nrnb;
- t_commrec *cr;
- int *cg_index;
- gmx_moltype_t *molt;
- gmx_ffparams_t *ffp;
- ivec *nFreeze;
- int i, m, natoms;
- rvec box_size;
- real *lambda, *dvdl;
-
- natoms = atoms->nr;
-
- /* Charge group index */
- snew(cg_index, natoms);
- for (i = 0; (i < natoms); i++)
- {
- cg_index[i] = i;
- }
-
- /* Topology needs charge groups and exclusions */
- snew(mtop, 1);
- init_mtop(mtop);
- mtop->natoms = natoms;
- /* Make one moltype that contains the whol system */
- mtop->nmoltype = 1;
- snew(mtop->moltype, mtop->nmoltype);
- molt = &mtop->moltype[0];
- molt->name = mtop->name;
- molt->atoms = *atoms;
- stupid_fill_block(&molt->cgs, mtop->natoms, FALSE);
- stupid_fill_blocka(&molt->excls, natoms);
- /* Make one molblock for the whole system */
- mtop->nmolblock = 1;
- snew(mtop->molblock, mtop->nmolblock);
- mtop->molblock[0].type = 0;
- mtop->molblock[0].nmol = 1;
- mtop->molblock[0].natoms_mol = natoms;
- /* Initialize a single energy group */
- mtop->groups.grps[egcENER].nr = 1;
- mtop->groups.ngrpnr[egcENER] = 0;
- mtop->groups.grpnr[egcENER] = NULL;
-
- ffp = &mtop->ffparams;
-
- ffp->ntypes = 1;
- ffp->atnr = 1;
- ffp->reppow = 12;
- snew(ffp->functype, 1);
- snew(ffp->iparams, 1);
- ffp->iparams[0].lj.c6 = 1;
- ffp->iparams[0].lj.c12 = 1;
-
- /* inputrec structure */
- snew(ir, 1);
- ir->cutoff_scheme = ecutsGROUP;
- ir->coulomb_modifier = eintmodNONE;
- ir->vdw_modifier = eintmodNONE;
- ir->coulombtype = eelCUT;
- ir->vdwtype = evdwCUT;
- ir->ns_type = ensGRID;
- snew(ir->opts.egp_flags, 1);
-
- top = gmx_mtop_generate_local_top(mtop, ir);
-
- /* Some nasty shortcuts */
- cgs = &(top->cgs);
-
- /* mdatoms structure */
- snew(nFreeze, 2);
- snew(md, 1);
- md = init_mdatoms(fp, mtop, FALSE);
- atoms2md(mtop, ir, 0, NULL, mtop->natoms, md);
- sfree(nFreeze);
-
- /* forcerec structure */
- if (fr == NULL)
- {
- fr = mk_forcerec();
- }
- snew(cr, 1);
- cr->nnodes = 1;
- /* cr->nthreads = 1; */
-
- /* ir->rlist = ir->rcoulomb = ir->rvdw = rlong;
- printf("Neighborsearching with a cut-off of %g\n",rlong);
- init_forcerec(stdout,fr,ir,top,cr,md,box,FALSE,NULL,NULL,NULL,TRUE);*/
- fr->cg0 = 0;
- fr->hcg = top->cgs.nr;
- fr->nWatMol = 0;
-
- /* Prepare for neighboursearching */
- init_nrnb(&nrnb);
-
- /* Init things dependent on parameters */
- ir->rlistlong = ir->rlist = ir->rcoulomb = ir->rvdw = rlong;
- /* create free energy data to avoid NULLs */
- snew(ir->fepvals, 1);
- printf("Neighborsearching with a cut-off of %g\n", rlong);
- init_forcerec(stdout, oenv, fr, NULL, ir, mtop, cr, box,
- NULL, NULL, NULL, NULL, NULL, TRUE, -1);
- if (debug)
- {
- pr_forcerec(debug, fr);
- }
-
- /* Calculate new stuff dependent on coords and box */
- for (m = 0; (m < DIM); m++)
- {
- box_size[m] = box[m][m];
- }
- calc_shifts(box, fr->shift_vec);
- put_charge_groups_in_box(fp, 0, cgs->nr, fr->ePBC, box, cgs, x, fr->cg_cm);
-
- /* Do the actual neighboursearching */
- snew(lambda, efptNR);
- snew(dvdl, efptNR);
- init_neighbor_list(fp, fr, md->homenr);
- search_neighbours(fp, fr, box, top,
- &mtop->groups, cr, &nrnb, md, TRUE, FALSE);
-
- if (debug)
- {
- dump_nblist(debug, cr, fr, 0);
- }
-
- if (bVerbose)
- {
- fprintf(stderr, "Successfully made neighbourlist\n");
- }
-}
-
-static gmx_bool bXor(gmx_bool b1, gmx_bool b2)
-{
- return (b1 && !b2) || (b2 && !b1);
-}
-
-void add_conf(t_atoms *atoms, rvec **x, rvec **v, real **r, gmx_bool bSrenew,
- int ePBC, matrix box, gmx_bool bInsert,
- t_atoms *atoms_solvt, rvec *x_solvt, rvec *v_solvt, real *r_solvt,
- gmx_bool bVerbose, real rshell, int max_sol, const output_env_t oenv)
-{
- t_nblist *nlist;
- t_atoms *atoms_all;
- real max_vdw, *r_prot, *r_all, n2, r2, ib1, ib2;
- int natoms_prot, natoms_solvt;
- int i, j, jj, m, j0, j1, jjj, jnres, jnr, inr, iprot, is1, is2;
- int prev, resnr, nresadd, d, k, ncells, maxincell;
- int dx0, dx1, dy0, dy1, dz0, dz1;
- int ntest, nremove, nkeep;
- rvec dx, xi, xj, xpp, *x_all, *v_all;
- gmx_bool *remove, *keep;
- int bSolSol;
-
- natoms_prot = atoms->nr;
- natoms_solvt = atoms_solvt->nr;
- if (natoms_solvt <= 0)
- {
- fprintf(stderr, "WARNING: Nothing to add\n");
- return;
- }
-
- if (ePBC == epbcSCREW)
- {
- gmx_fatal(FARGS, "Sorry, %s pbc is not yet supported", epbc_names[ePBC]);
- }
-
- if (bVerbose)
- {
- fprintf(stderr, "Calculating Overlap...\n");
- }
-
- /* Set margin around box edges to largest solvent dimension.
- * The maximum distance between atoms in a solvent molecule should
- * be calculated. At the moment a fudge factor of 3 is used.
- */
- r_prot = *r;
- box_margin = 3*find_max_real(natoms_solvt, r_solvt);
- max_vdw = max(3*find_max_real(natoms_prot, r_prot), box_margin);
- fprintf(stderr, "box_margin = %g\n", box_margin);
-
- snew(remove, natoms_solvt);
-
- nremove = 0;
- if (!bInsert)
- {
- for (i = 0; i < atoms_solvt->nr; i++)
- {
- if (outside_box_plus_margin(x_solvt[i], box) )
- {
- i = mark_res(i, remove, atoms_solvt->nr, atoms_solvt->atom, &nremove);
- }
- }
- fprintf(stderr, "Removed %d atoms that were outside the box\n", nremove);
- }
-
- /* Define grid stuff */
- /* Largest VDW radius */
- snew(r_all, natoms_prot+natoms_solvt);
- for (i = j = 0; i < natoms_prot; i++, j++)
- {
- r_all[j] = r_prot[i];
- }
- for (i = 0; i < natoms_solvt; i++, j++)
- {
- r_all[j] = r_solvt[i];
- }
-
- /* Combine arrays */
- combine_atoms(atoms, atoms_solvt, *x, v ? *v : NULL, x_solvt, v_solvt,
- &atoms_all, &x_all, &v_all);
-
- /* Do neighboursearching step */
- do_nsgrid(stdout, bVerbose, box, x_all, atoms_all, max_vdw, oenv);
-
- /* check solvent with solute */
- nlist = &(fr->nblists[0].nlist_sr[eNL_VDW]);
- fprintf(stderr, "nri = %d, nrj = %d\n", nlist->nri, nlist->nrj);
- for (bSolSol = 0; (bSolSol <= (bInsert ? 0 : 1)); bSolSol++)
- {
- ntest = nremove = 0;
- fprintf(stderr, "Checking %s-Solvent overlap:",
- bSolSol ? "Solvent" : "Protein");
- for (i = 0; (i < nlist->nri && nremove < natoms_solvt); i++)
- {
- inr = nlist->iinr[i];
- j0 = nlist->jindex[i];
- j1 = nlist->jindex[i+1];
- rvec_add(x_all[inr], fr->shift_vec[nlist->shift[i]], xi);
-
- for (j = j0; (j < j1 && nremove < natoms_solvt); j++)
- {
- jnr = nlist->jjnr[j];
- if (jnr < 0)
- {
- /* skip padding */
- continue;
- }
- copy_rvec(x_all[jnr], xj);
-
- /* Check solvent-protein and solvent-solvent */
- is1 = inr-natoms_prot;
- is2 = jnr-natoms_prot;
-
- /* Check if at least one of the atoms is a solvent that is not yet
- * listed for removal, and if both are solvent, that they are not in the
- * same residue.
- */
- if ((!bSolSol &&
- bXor((is1 >= 0), (is2 >= 0)) && /* One atom is protein */
- ((is1 < 0) || ((is1 >= 0) && !remove[is1])) &&
- ((is2 < 0) || ((is2 >= 0) && !remove[is2]))) ||
-
- (bSolSol &&
- (is1 >= 0) && (!remove[is1]) && /* is1 is solvent */
- (is2 >= 0) && (!remove[is2]) && /* is2 is solvent */
- (bInsert || /* when inserting also check inside the box */
- (outside_box_minus_margin2(x_solvt[is1], box) && /* is1 on edge */
- outside_box_minus_margin2(x_solvt[is2], box)) /* is2 on edge */
- ) &&
- (atoms_solvt->atom[is1].resind != /* Not the same residue */
- atoms_solvt->atom[is2].resind)))
- {
-
- ntest++;
- rvec_sub(xi, xj, dx);
- n2 = norm2(dx);
- r2 = sqr(r_all[inr]+r_all[jnr]);
- if (n2 < r2)
- {
- if (bInsert)
- {
- nremove = natoms_solvt;
- for (k = 0; k < nremove; k++)
- {
- remove[k] = TRUE;
- }
- }
- /* Need only remove one of the solvents... */
- if (is2 >= 0)
- {
- (void) mark_res(is2, remove, natoms_solvt, atoms_solvt->atom,
- &nremove);
- }
- else if (is1 >= 0)
- {
- (void) mark_res(is1, remove, natoms_solvt, atoms_solvt->atom,
- &nremove);
- }
- else
- {
- fprintf(stderr, "Neither atom is solvent%d %d\n", is1, is2);
- }
- }
- }
- }
- }
- if (!bInsert)
- {
- fprintf(stderr, " tested %d pairs, removed %d atoms.\n", ntest, nremove);
- }
- }
- if (debug)
- {
- for (i = 0; i < natoms_solvt; i++)
- {
- fprintf(debug, "remove[%5d] = %s\n", i, bool_names[remove[i]]);
- }
- }
-
- /* Search again, now with another cut-off */
- if (rshell > 0)
- {
- do_nsgrid(stdout, bVerbose, box, x_all, atoms_all, rshell, oenv);
- nlist = &(fr->nblists[0].nlist_sr[eNL_VDW]);
- fprintf(stderr, "nri = %d, nrj = %d\n", nlist->nri, nlist->nrj);
- nkeep = 0;
- snew(keep, natoms_solvt);
- for (i = 0; i < nlist->nri; i++)
- {
- inr = nlist->iinr[i];
- j0 = nlist->jindex[i];
- j1 = nlist->jindex[i+1];
-
- for (j = j0; j < j1; j++)
- {
- jnr = nlist->jjnr[j];
-
- /* Check solvent-protein and solvent-solvent */
- is1 = inr-natoms_prot;
- is2 = jnr-natoms_prot;
-
- /* Check if at least one of the atoms is a solvent that is not yet
- * listed for removal, and if both are solvent, that they are not in the
- * same residue.
- */
- if (is1 >= 0 && is2 < 0)
- {
- mark_res(is1, keep, natoms_solvt, atoms_solvt->atom, &nkeep);
- }
- else if (is1 < 0 && is2 >= 0)
- {
- mark_res(is2, keep, natoms_solvt, atoms_solvt->atom, &nkeep);
- }
- }
- }
- fprintf(stderr, "Keeping %d solvent atoms after proximity check\n",
- nkeep);
- for (i = 0; i < natoms_solvt; i++)
- {
- remove[i] = remove[i] || !keep[i];
- }
- sfree(keep);
- }
- /* count how many atoms and residues will be added and make space */
- if (bInsert)
- {
- j = atoms_solvt->nr;
- jnres = atoms_solvt->nres;
- }
- else
- {
- j = 0;
- jnres = 0;
- for (i = 0; ((i < atoms_solvt->nr) &&
- ((max_sol == 0) || (jnres < max_sol))); i++)
- {
- if (!remove[i])
- {
- j++;
- if ((i == 0) ||
- (atoms_solvt->atom[i].resind != atoms_solvt->atom[i-1].resind))
- {
- jnres++;
- }
- }
- }
- }
- if (debug)
- {
- fprintf(debug, "Will add %d atoms in %d residues\n", j, jnres);
- }
- if (!bInsert)
- {
- /* Flag the remaing solvent atoms to be removed */
- jjj = atoms_solvt->atom[i-1].resind;
- for (; (i < atoms_solvt->nr); i++)
- {
- if (atoms_solvt->atom[i].resind > jjj)
- {
- remove[i] = TRUE;
- }
- else
- {
- j++;
- }
- }
- }
-
- if (bSrenew)
- {
- srenew(atoms->resinfo, atoms->nres+jnres);
- srenew(atoms->atomname, atoms->nr+j);
- srenew(atoms->atom, atoms->nr+j);
- srenew(*x, atoms->nr+j);
- if (v)
- {
- srenew(*v, atoms->nr+j);
- }
- srenew(*r, atoms->nr+j);
- }
-
- /* add the selected atoms_solvt to atoms */
- if (atoms->nr > 0)
- {
- resnr = atoms->resinfo[atoms->atom[atoms->nr-1].resind].nr;
- }
- else
- {
- resnr = 0;
- }
- prev = -1;
- nresadd = 0;
- for (i = 0; i < atoms_solvt->nr; i++)
- {
- if (!remove[i])
- {
- if (prev == -1 ||
- atoms_solvt->atom[i].resind != atoms_solvt->atom[prev].resind)
- {
- nresadd++;
- atoms->nres++;
- resnr++;
- atoms->resinfo[atoms->nres-1] =
- atoms_solvt->resinfo[atoms_solvt->atom[i].resind];
- atoms->resinfo[atoms->nres-1].nr = resnr;
- /* calculate shift of the solvent molecule using the first atom */
- copy_rvec(x_solvt[i], dx);
- put_atoms_in_box(ePBC, box, 1, &dx);
- rvec_dec(dx, x_solvt[i]);
- }
- atoms->atom[atoms->nr] = atoms_solvt->atom[i];
- atoms->atomname[atoms->nr] = atoms_solvt->atomname[i];
- rvec_add(x_solvt[i], dx, (*x)[atoms->nr]);
- if (v)
- {
- copy_rvec(v_solvt[i], (*v)[atoms->nr]);
- }
- (*r)[atoms->nr] = r_solvt[i];
- atoms->atom[atoms->nr].resind = atoms->nres-1;
- atoms->nr++;
- prev = i;
- }
- }
- if (bSrenew)
- {
- srenew(atoms->resinfo, atoms->nres+nresadd);
- }
-
- if (bVerbose)
- {
- fprintf(stderr, "Added %d molecules\n", nresadd);
- }
-
- sfree(remove);
- done_atom(atoms_all);
- sfree(x_all);
- sfree(v_all);
-}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "calc_verletbuf.h"
#include <assert.h>
+#include <math.h>
+#include <stdlib.h>
#include <sys/types.h>
-#include <math.h>
-#include "typedefs.h"
-#include "physics.h"
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/calculate-ewald-splitting-coefficient.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-#include "vec.h"
-#include "coulomb.h"
-#include "calc_verletbuf.h"
-#include "../mdlib/nbnxn_consts.h"
#ifdef GMX_NBNXN_SIMD
/* The include below sets the SIMD instruction type (precision+width)
for (i = 0; i < il->nr; i += 1+NRAL(ft))
{
const t_iparams *ip;
- real cam[5], inv_mass, coeff, m_aj;
+ real cam[5] = {0}, inv_mass, coeff, m_aj;
int a1, j, aj;
ip = &ffparams->iparams[il->iatoms[i]];
#ifndef GMX_GMXPREPROCESS_CALC_VERLETBUF_H
#define GMX_GMXPREPROCESS_CALC_VERLETBUF_H
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "macros.h"
#include "calch.h"
-#include "gromacs/math/utilities.h"
-#include "vec.h"
-#include "physics.h"
-#include "gmx_fatal.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
#define xAI xa[0]
#define xAJ xa[1]
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_PREPROCESS_CALCH_H
+#define GMX_PREPROCESS_CALCH_H
-#ifndef _calch_h
-#define _calch_h
-
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
}
#endif
-#endif /* _calch_h */
+#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <signal.h>
#include <stdlib.h>
-#include "typedefs.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
static int div_nsteps(int nsteps, int nst)
{
#ifndef GMX_GMXPREPROCESS_COMPUTE_IO_H
#define GMX_GMXPREPROCESS_COMPUTE_IO_H
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "convparm.h"
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
-#include "physics.h"
-#include "vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "gmx_fatal.h"
-#include "topio.h"
-#include "toputil.h"
-#include "convparm.h"
-#include "names.h"
-#include "gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/topio.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static int round_check(real r, int limit, int ftype, const char *name)
{
#ifndef GMX_GMXPREPROCESS_CONVPARM_H
#define GMX_GMXPREPROCESS_CONVPARM_H
-#include "typedefs.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "fflibutil.h"
-#include <stdio.h>
-#include <stdlib.h>
#include <string.h>
-#include <sys/types.h>
-#include <sys/stat.h>
-#include <fcntl.h>
-#include "sysstuff.h"
-#include "network.h"
-#include "gmx_fatal.h"
-#include "gromacs/utility/smalloc.h"
-#ifdef HAVE_UNISTD_H
-#include <unistd.h>
-#endif
+#include <string>
+#include <vector>
-#include "fflibutil.h"
-
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/path.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/datafilefinder.h"
+#include "gromacs/utility/dir_separator.h"
+#include "gromacs/utility/directoryenumerator.h"
#include "gromacs/utility/exceptions.h"
-#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/file.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/path.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
const char *fflib_forcefield_dir_ext()
{
}
}
-static void sort_filenames(int n, char **name, char **name2)
-{
- /* Slow sort, but we usually have tens of names */
- int i, j, f;
- char *tmp;
-
- for (i = 0; i < n-1; i++)
- {
- f = i;
- for (j = i+1; j < n; j++)
- {
- if (strcmp(name[j], name[f]) < 0)
- {
- f = j;
- }
- }
- if (f > i)
- {
- tmp = name[i];
- name[i] = name[f];
- name[f] = tmp;
- if (name2 != NULL)
- {
- tmp = name2[i];
- name2[i] = name2[f];
- name2[f] = tmp;
- }
- }
- }
-}
-
-static int low_fflib_search_file_end(const char *ffdir,
- gmx_bool bAddCWD,
- const char *file_end,
- gmx_bool bFatalError,
- char ***filenames,
- char ***filenames_short)
+int fflib_search_file_end(const char *ffdir,
+ const char *file_end,
+ gmx_bool bFatalError,
+ char ***filenames)
{
- char **fns = NULL, **fns_short = NULL;
- int n = 0;
try
{
- std::vector<std::string> libPaths;
- bool bEnvIsSet = false;
-
- if (ffdir != NULL)
+ std::string ffdirFull(gmx::getLibraryFileFinder().findFile(ffdir));
+ std::vector<std::string> result
+ = gmx::DirectoryEnumerator::enumerateFilesWithExtension(
+ ffdirFull.c_str(), file_end, true);
+ if (result.empty() && bFatalError)
{
- /* Search ffdir in current dir and library dirs */
- libPaths.push_back(gmxlibfn(ffdir));
+ std::string message
+ = gmx::formatString("Could not find any files ending on '%s' "
+ "in the force field directory '%s'",
+ file_end, ffdir);
+ GMX_THROW(gmx::InvalidInputError(message));
}
- else
+ const int count = static_cast<int>(result.size());
+ for (int i = 0; i < count; ++i)
{
- /* GMXLIB can be a path now */
- if (bAddCWD)
- {
- libPaths.push_back(".");
- }
- const char *lib = getenv("GMXLIB");
- if (lib != NULL)
- {
- bEnvIsSet = true;
- gmx::Path::splitPathEnvironment(lib, &libPaths);
- }
- else
- {
- libPaths.push_back(gmx::getProgramContext().defaultLibraryDataPath());
- }
+ result[i] = gmx::Path::join(ffdir, result[i]);
}
-
- const int len_fe = strlen(file_end);
-
- std::vector<std::string>::const_iterator i;
- for (i = libPaths.begin(); i != libPaths.end(); ++i)
+ char **fns;
+ snew(fns, count);
+ for (int i = 0; i < count; ++i)
{
- const char *dir = i->c_str();
- gmx_directory_t dirhandle;
- const int rc = gmx_directory_open(&dirhandle, dir);
- if (rc == 0)
- {
- char nextname[STRLEN];
- int n_thisdir = 0;
- while (gmx_directory_nextfile(dirhandle, nextname, STRLEN-1) == 0)
- {
- nextname[STRLEN-1] = 0;
- if (debug)
- {
- fprintf(debug, "dir '%s' %d file '%s'\n",
- dir, n_thisdir, nextname);
- }
- const int len_name = strlen(nextname);
- /* What about case sensitivity? */
- if (len_name >= len_fe &&
- strcmp(nextname+len_name-len_fe, file_end) == 0)
- {
- char fn_dir[GMX_PATH_MAX];
- /* We have a match */
- srenew(fns, n+1);
- sprintf(fn_dir, "%s%c%s", dir, DIR_SEPARATOR, nextname);
-
- /* Copy the file name, possibly including the path. */
- fns[n] = strdup(fn_dir);
-
- if (ffdir == NULL)
- {
- /* We are searching in a path.
- * Use the relative path when we use share/top
- * from the installation.
- * Add the full path when we use the current
- * working directory of GMXLIB.
- */
- srenew(fns_short, n+1);
- if (strcmp(dir, ".") == 0 || bEnvIsSet)
- {
- fns_short[n] = strdup(fn_dir);
- }
- else
- {
- fns_short[n] = strdup(nextname);
- }
- }
- n++;
- n_thisdir++;
- }
- }
- gmx_directory_close(dirhandle);
-
- sort_filenames(n_thisdir,
- fns+n-n_thisdir,
- fns_short == NULL ? NULL : fns_short+n-n_thisdir);
- }
+ fns[i] = gmx_strdup(result[i].c_str());
}
+ *filenames = fns;
+ return count;
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
-
- if (n == 0 && bFatalError)
- {
- if (ffdir != NULL)
- {
- gmx_fatal(FARGS, "Could not find any files ending on '%s' in the force field directory '%s'", file_end, ffdir);
- }
- else
- {
- gmx_fatal(FARGS, "Could not find any files ending on '%s' in the current directory or the GROMACS library search path", file_end);
- }
- }
-
- *filenames = fns;
- if (ffdir == NULL)
- {
- *filenames_short = fns_short;
- }
-
- return n;
}
-int fflib_search_file_end(const char *ffdir,
- const char *file_end,
- gmx_bool bFatalError,
- char ***filenames)
-{
- return low_fflib_search_file_end(ffdir, FALSE, file_end, bFatalError,
- filenames, NULL);
-}
-
-int fflib_search_file_in_dirend(const char *filename, const char *dirend,
- char ***dirnames)
+std::vector<gmx::DataFileInfo> fflib_enumerate_forcefields()
{
- int nf, i;
- char **f, **f_short;
- int n;
- char **dns;
- gmx_directory_t dirhandle;
- char nextname[STRLEN];
- int rc;
-
- /* Find all files (not only dir's) ending on dirend */
- nf = low_fflib_search_file_end(NULL, TRUE, dirend, FALSE, &f, &f_short);
-
- n = 0;
- dns = NULL;
- for (i = 0; i < nf; i++)
+ const char *const dirend = fflib_forcefield_dir_ext();
+ const char *const filename = fflib_forcefield_itp();
+ std::vector<gmx::DataFileInfo> candidates
+ = gmx::getLibraryFileFinder().enumerateFiles(
+ gmx::DataFileOptions(dirend)
+ .throwIfNotFound(false));
+
+ std::vector<gmx::DataFileInfo> result;
+ for (size_t i = 0; i < candidates.size(); ++i)
{
- rc = gmx_directory_open(&dirhandle, f[i]);
-
- if (rc == 0)
+ std::string testPath(gmx::Path::join(
+ candidates[i].dir, candidates[i].name, filename));
+ // TODO: Consider also checking that the directory can be listed.
+ if (gmx::File::exists(testPath))
{
- while (gmx_directory_nextfile(dirhandle, nextname, STRLEN-1) == 0)
- {
- nextname[STRLEN-1] = 0;
- if (strcmp(nextname, filename) == 0)
- {
- /* We have a match */
- srenew(dns, n+1);
- dns[n] = strdup(f_short[i]);
- n++;
- }
- }
- gmx_directory_close(dirhandle);
+ result.push_back(candidates[i]);
}
- sfree(f[i]);
- sfree(f_short[i]);
}
- sfree(f);
- sfree(f_short);
- *dirnames = dns;
+ // TODO: Consider merging this into enumerateFiles(), such that the error
+ // could also list the directories searched.
+ if (result.empty())
+ {
+ std::string message
+ = gmx::formatString("No force fields found (files with name '%s' "
+ "in subdirectories ending on '%s')",
+ filename, dirend);
+ GMX_THROW(gmx::InvalidInputError(message));
+ }
- return n;
+ return result;
}
gmx_bool fflib_fexist(const char *file)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_GMXPREPROCESS_FFLIBUTIL_H
#define GMX_GMXPREPROCESS_FFLIBUTIL_H
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
#include <stdio.h>
-#include "typedefs.h"
+
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
+#include <vector>
+
+#include "gromacs/utility/datafilefinder.h"
+
+/*! \brief
+ * Enumerates forcefields in the data directories.
+ */
+std::vector<gmx::DataFileInfo> fflib_enumerate_forcefields();
+
extern "C" {
#endif
* Return the number of files and the file names in filenames.
*/
-int fflib_search_file_in_dirend(const char *filename, const char *dirend,
- char ***dirnames);
-/* Search for files with name filename in subdirectories with names
- * ending on dirend.
- * Return the number of files and the directory names in dirnames.
- */
gmx_bool fflib_fexist(const char *file);
/* Check if a file exists in the force field library */
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gen_ad.h"
#include <ctype.h>
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/cstringutil.h"
#include "gromacs/fileio/confio.h"
-#include "vec.h"
-#include "pbc.h"
-#include "toputil.h"
-#include "topio.h"
-#include "gpp_nextnb.h"
-#include "symtab.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "pgutil.h"
-#include "resall.h"
-#include "gen_ad.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/topio.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#define DIHEDRAL_WAS_SET_IN_RTP 0
static gmx_bool was_dihedral_set_in_rtp(t_param *dih)
{
fprintf(debug,
"Something VERY strange is going on in rm2par (gen_ad.c)\n"
- "a[0] %u a[1] %u a[2] %u a[3] %u\n",
+ "a[0] %d a[1] %d a[2] %d a[3] %d\n",
p[i].a[0], p[i].a[1], p[i].a[2], p[i].a[3]);
}
strcpy(p[i].s, "");
#ifndef GMX_GMXPREPROCESS_GEN_AD_H
#define GMX_GMXPREPROCESS_GEN_AD_H
-#include "typedefs.h"
-#include "toputil.h"
-#include "gpp_nextnb.h"
-#include "resall.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gen_maxwell_velocities.h"
#include <math.h>
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
-#include "sysstuff.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/smalloc.h"
-#include "physics.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "gen_maxwell_velocities.h"
-#include "mtop_util.h"
static void low_mspeed(real tempi,
gmx_mtop_t *mtop, rvec v[], gmx_rng_t rng)
if (seed == 0)
{
seed = gmx_rng_make_seed();
- fprintf(stderr, "Using random seed %d for generating velocities\n", seed);
+ fprintf(stderr, "Using random seed %u for generating velocities\n", seed);
}
rng = gmx_rng_init(seed);
#ifndef GMX_MAXWELL_VELOCITIES
#define GMX_MAXWELL_VELOCITIES
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gen_vsite.h"
#include <math.h>
#include <stdio.h>
+#include <stdlib.h>
#include <string.h>
+#include "gromacs/gmxpreprocess/add_par.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/topology/symtab.h"
#include "gromacs/utility/cstringutil.h"
-#include "gen_vsite.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "resall.h"
-#include "add_par.h"
-#include "vec.h"
-#include "toputil.h"
-#include "physics.h"
-#include "index.h"
-#include "names.h"
-#include "gromacs/fileio/futil.h"
-#include "gpp_atomtype.h"
-#include "fflibutil.h"
-#include "macros.h"
-
-#include "gmx_fatal.h"
#define MAXNAME 32
#define OPENDIR '[' /* starting sign for directive */
}
static int get_atype(int atom, t_atoms *at, int nrtp, t_restp rtp[],
- gmx_residuetype_t rt)
+ gmx_residuetype_t *rt)
{
int type;
gmx_bool bNterm;
}
static real get_amass(int atom, t_atoms *at, int nrtp, t_restp rtp[],
- gmx_residuetype_t rt)
+ gmx_residuetype_t *rt)
{
real mass;
gmx_bool bNterm;
char **db;
int nvsiteconf, nvsitetop, cmplength;
gmx_bool isN, planarN, bFound;
- gmx_residuetype_t rt;
+ gmx_residuetype_t*rt;
t_vsiteconf *vsiteconflist;
/* pointer to a list of CH3/NH3/NH2 configuration entries.
{
if (debug)
{
- fprintf(debug, " [%u -> %u]", params->param[i].a[j],
+ fprintf(debug, " [%d -> %d]", params->param[i].a[j],
params->param[i].a[j]-add_shift);
}
params->param[i].a[j] = params->param[i].a[j]-add_shift;
{
if (debug)
{
- fprintf(debug, " [%u -> %d]", params->param[i].a[j],
+ fprintf(debug, " [%d -> %d]", params->param[i].a[j],
o2n[params->param[i].a[j]]);
}
params->param[i].a[j] = o2n[params->param[i].a[j]];
#ifndef GMX_GMXPREPROCESS_GEN_VSITE_H
#define GMX_GMXPREPROCESS_GEN_VSITE_H
-#include "typedefs.h"
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
-#include "hackblock.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C"
/* stuff for pdb2gmx */
void do_vsites(int nrtp, t_restp rtp[], gpp_atomtype_t atype,
- t_atoms *at, t_symtab *symtab, rvec *x[],
+ t_atoms *at, struct t_symtab *symtab, rvec *x[],
t_params plist[], int *dummy_type[], int *cgnr[],
real mHmult, gmx_bool bVSiteAromatics,
const char *ffdir);
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
#include "genconf.h"
-#include "gromacs/math/utilities.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "gromacs/fileio/confio.h"
#include "gromacs/commandline/pargs.h"
-#include "vec.h"
-#include "gromacs/random/random.h"
-#include "gromacs/math/3dview.h"
-#include "txtdump.h"
-#include "readinp.h"
-#include "names.h"
-#include "sortwater.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/trxio.h"
-
-#include "gmx_fatal.h"
+#include "gromacs/gmxpreprocess/sortwater.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/3dtransforms.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/random/random.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static void rand_rot(int natoms, rvec x[], rvec v[], vec4 xrot[], vec4 vrot[],
gmx_rng_t rng, rvec max_rot)
}
fprintf(stderr, "center of geometry: %f, %f, %f\n", xcm[0], xcm[1], xcm[2]);
- translate(-xcm[XX], -xcm[YY], -xcm[ZZ], mt1); /* move c.o.ma to origin */
+ /* move c.o.ma to origin */
+ gmx_mat4_init_translation(-xcm[XX], -xcm[YY], -xcm[ZZ], mt1);
for (m = 0; (m < DIM); m++)
{
phi = M_PI*max_rot[m]*(2*gmx_rng_uniform_real(rng) - 1)/180;
- rotate(m, phi, mr[m]);
+ gmx_mat4_init_rotation(m, phi, mr[m]);
}
- translate(xcm[XX], xcm[YY], xcm[ZZ], mt2);
+ gmx_mat4_init_translation(xcm[XX], xcm[YY], xcm[ZZ], mt2);
- /* For mult_matrix we need to multiply in the opposite order
+ /* For gmx_mat4_mmul() we need to multiply in the opposite order
* compared to normal mathematical notation.
*/
- mult_matrix(mtemp1, mt1, mr[XX]);
- mult_matrix(mtemp2, mr[YY], mr[ZZ]);
- mult_matrix(mtemp3, mtemp1, mtemp2);
- mult_matrix(mxtot, mtemp3, mt2);
- mult_matrix(mvtot, mr[XX], mtemp2);
+ gmx_mat4_mmul(mtemp1, mt1, mr[XX]);
+ gmx_mat4_mmul(mtemp2, mr[YY], mr[ZZ]);
+ gmx_mat4_mmul(mtemp3, mtemp1, mtemp2);
+ gmx_mat4_mmul(mxtot, mtemp3, mt2);
+ gmx_mat4_mmul(mvtot, mr[XX], mtemp2);
for (i = 0; (i < natoms); i++)
{
- m4_op(mxtot, x[i], xrot[i]);
- m4_op(mvtot, v[i], vrot[i]);
+ gmx_mat4_transform_point(mxtot, x[i], xrot[i]);
+ gmx_mat4_transform_point(mvtot, v[i], vrot[i]);
}
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "genhydro.h"
#include <string.h>
#include <time.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
#include "gromacs/fileio/confio.h"
-#include "symtab.h"
-#include "vec.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
-#include "physics.h"
-#include "calch.h"
-#include "genhydro.h"
-#include "h_db.h"
-#include "ter_db.h"
-#include "resall.h"
-#include "pgutil.h"
-#include "network.h"
-#include "macros.h"
+#include "gromacs/gmxpreprocess/calch.h"
+#include "gromacs/gmxpreprocess/h_db.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/ter_db.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void copy_atom(t_atoms *atoms1, int a1, t_atoms *atoms2, int a2)
{
atoms2->atom[a2] = atoms1->atom[a1];
snew(atoms2->atomname[a2], 1);
- *atoms2->atomname[a2] = strdup(*atoms1->atomname[a1]);
+ *atoms2->atomname[a2] = gmx_strdup(*atoms1->atomname[a1]);
}
static atom_id pdbasearch_atom(const char *name, int resind, t_atoms *pdba,
{
if (hb[rnr].name == NULL)
{
- hb[rnr].name = strdup(ahptr->name);
+ hb[rnr].name = gmx_strdup(ahptr->name);
}
merge_hacks(ahptr, &hb[rnr]);
}
{
if ( (*abi)[*nabi + k].oname == NULL)
{
- (*abi)[*nabi + k].nname = strdup(atomname);
+ (*abi)[*nabi + k].nname = gmx_strdup(atomname);
(*abi)[*nabi + k].nname[0] = 'H';
}
}
(*abi)[*nabi + k].oname ? (*abi)[*nabi + k].oname : "");
}
sfree((*abi)[*nabi + k].nname);
- (*abi)[*nabi + k].nname = strdup(hbr->hack[j].nname);
+ (*abi)[*nabi + k].nname = gmx_strdup(hbr->hack[j].nname);
}
if (hbr->hack[j].tp == 10 && k == 2)
ab[i][j].nname);
}
snew(newpdba->atomname[newi], 1);
- *newpdba->atomname[newi] = strdup(ab[i][j].nname);
+ *newpdba->atomname[newi] = gmx_strdup(ab[i][j].nname);
if (ab[i][j].oname != NULL && ab[i][j].atom) /* replace */
{ /* newpdba->atom[newi].m = ab[i][j].atom->m; */
/* newpdba->atom[newi].q = ab[i][j].atom->q; */
#define GMX_GMXPREPROCESS_GENHYDRO_H
#include "gromacs/fileio/pdbio.h"
-#include "hackblock.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
#ifdef __cplusplus
extern "C" {
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <sys/types.h>
+#include "gmxcpp.h"
+
+#include <ctype.h>
+#include <errno.h>
+#include <limits.h>
+#include <math.h>
#include <stdio.h>
#include <stdlib.h>
-#include <math.h>
#include <string.h>
-#include <errno.h>
-#include <limits.h>
-#include <ctype.h>
+#include <sys/types.h>
+
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/dir_separator.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "gmxcpp.h"
typedef struct {
char *name;
{
nincl++;
srenew(incl, nincl);
- incl[nincl-1] = strdup(include);
+ incl[nincl-1] = gmx_strdup(include);
}
}
ndef++;
srenew(defs, ndef);
i = ndef - 1;
- defs[i].name = strdup(name);
+ defs[i].name = gmx_strdup(name);
}
else if (defs[i].def)
{
}
if (value && strlen(value) > 0)
{
- defs[i].def = strdup(value);
+ defs[i].def = gmx_strdup(value);
}
else
{
/* Find the file. First check whether it is in the current directory. */
if (gmx_fexist(filenm))
{
- cpp->fn = strdup(filenm);
+ cpp->fn = gmx_strdup(filenm);
}
else
{
{
cpp->path = cpp->fn;
*ptr = '\0';
- cpp->fn = strdup(ptr+1);
+ cpp->fn = gmx_strdup(ptr+1);
snew(cpp->cwd, STRLEN);
gmx_getcwd(cpp->cwd, STRLEN);
(handle) ? handle->line_nr : -1,
handle->line ? handle->line : "");
- return strdup(buf);
+ return gmx_strdup(buf);
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gpp_atomtype.h"
#include <math.h>
#include <string.h>
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "macros.h"
-#include "topdirs.h"
-#include "toputil.h"
-#include "topdirs.h"
-#include "toputil.h"
-#include "symtab.h"
-#include "gmx_fatal.h"
-#include "txtdump.h"
-#include "gpp_atomtype.h"
typedef struct gpp_atomtype {
int nr; /* The number of atomtypes */
sfree(ga->atomnumber);
ga->nr = 0;
sfree(ga);
- ga = NULL;
}
static int search_atomtypes(gpp_atomtype_t ga, int *n, int typelist[],
#define GMX_GMXPREPROCESS_GPP_ATOMTYPE_H
#include <stdio.h>
-#include "typedefs.h"
-#include "grompp-impl.h"
+
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
void done_atomtype(gpp_atomtype_t at);
/* Free the memory in the structure */
-int set_atomtype(int nt, gpp_atomtype_t at, t_symtab *tab,
+int set_atomtype(int nt, gpp_atomtype_t at, struct t_symtab *tab,
t_atom *a, const char *name, t_param *nb,
int bondatomtype,
real radius, real vol, real surftens, int atomnumber,
real radius, real vol, real surftens,
real gb_radius, real S_hct);
-int add_atomtype(gpp_atomtype_t at, t_symtab *tab,
+int add_atomtype(gpp_atomtype_t at, struct t_symtab *tab,
t_atom *a, const char *name, t_param *nb,
int bondatomtype,
real radius, real vol, real surftens, real atomnumber,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "macros.h"
-#include "symtab.h"
-#include "gromacs/utility/cstringutil.h"
#include "gpp_bond_atomtype.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
+
typedef struct {
int nr; /* The number of atomtypes */
char ***atomname; /* Names of the atomtypes */
#ifndef GMX_GMXPREPROCESS_GPP_BONDATOMTYPE_H
#define GMX_GMXPREPROCESS_GPP_BONDATOMTYPE_H
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
#include <stdio.h>
-#include "typedefs.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
void done_bond_atomtype(t_bond_atomtype *at);
/* Free the memory in the structure */
-void add_bond_atomtype(t_bond_atomtype at, t_symtab *tab,
+void add_bond_atomtype(t_bond_atomtype at, struct t_symtab *tab,
char *name);
/* Add a complete new atom type to an existing atomtype structure */
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gpp_nextnb.h"
-#include "sysstuff.h"
+#include <stdlib.h>
+
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "macros.h"
+
/* #define DEBUG_NNB */
-#include "gpp_nextnb.h"
-#include "gmx_fatal.h"
-#include "toputil.h"
typedef struct {
int ai, aj;
#ifndef GMX_GMXPREPROCESS_GPP_NEXTNB_H
#define GMX_GMXPREPROCESS_GPP_NEXTNB_H
-#include "grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
#ifdef __cplusplus
extern "C" {
#ifndef GMX_GMXPREPROCESS_GROMPP_IMPL_H
#define GMX_GMXPREPROCESS_GROMPP_IMPL_H
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
* non-bonded parameter combinations, which will be copied to t_params.
*/
+#ifndef __cplusplus
+/*
+ * With the macros below you don't
+ * have to use an index if you don't wan't to. You can eg. use
+ * param.C0 instead of param.c[0].
+ * In a similar fashion, you can use param.AI instead of
+ * param.a[0]
+ *
+ * For C++ those should be replaced with member functions.
+ */
+
+#define AI a[0]
+#define AJ a[1]
+#define AK a[2]
+#define AL a[3]
+#define AM a[4]
+
+#define C0 c[0]
+#define C1 c[1]
+#define C2 c[2]
+#endif
+
typedef struct {
atom_id a[MAXATOMLIST]; /* The atom list (eg. bonds: particle */
/* i = a[0] (AI), j = a[1] (AJ)) */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "grompp.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "grompp.h"
-#include <sys/types.h>
-#include <math.h>
-#include <string.h>
+#include <assert.h>
#include <errno.h>
#include <limits.h>
-#include <assert.h>
+#include <math.h>
+#include <string.h>
+
+#include <sys/types.h>
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "readir.h"
-#include "toputil.h"
-#include "topio.h"
-#include "gromacs/fileio/confio.h"
-#include "readir.h"
-#include "symtab.h"
-#include "names.h"
-#include "grompp-impl.h"
-#include "gromacs/random/random.h"
-#include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
-#include "vec.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/commandline/pargs.h"
-#include "splitter.h"
-#include "gromacs/gmxpreprocess/sortwater.h"
-#include "convparm.h"
-#include "gmx_fatal.h"
-#include "warninp.h"
-#include "index.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/trxio.h"
-#include "vsite_parm.h"
-#include "txtdump.h"
-#include "calcgrid.h"
-#include "add_par.h"
-#include "gromacs/fileio/enxio.h"
-#include "perf_est.h"
-#include "compute_io.h"
-#include "gpp_atomtype.h"
-#include "mtop_util.h"
-#include "genborn.h"
-#include "calc_verletbuf.h"
-#include "tomorse.h"
+#include "gromacs/gmxpreprocess/add_par.h"
+#include "gromacs/gmxpreprocess/calc_verletbuf.h"
+#include "gromacs/gmxpreprocess/compute_io.h"
+#include "gromacs/gmxpreprocess/convparm.h"
+#include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/gmxpreprocess/sortwater.h"
+#include "gromacs/gmxpreprocess/tomorse.h"
+#include "gromacs/gmxpreprocess/topio.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/gmxpreprocess/vsite_parm.h"
#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/calcgrid.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/perf_est.h"
+#include "gromacs/legacyheaders/splitter.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/random/random.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
-
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/snprintf.h"
static int rm_interactions(int ifunc, int nrmols, t_molinfo mols[])
{
}
}
+/* TODO Decide whether this function can be consolidated with
+ * gmx_mtop_ftype_count */
static gmx_bool nint_ftype(gmx_mtop_t *mtop, t_molinfo *mi, int ftype)
{
int nint, mb;
nmismatch, (nmismatch == 1) ? "" : "s", topfile, confin);
warning(wi, buf);
}
+
+ /* Do more checks, mostly related to constraints */
if (bVerbose)
{
fprintf(stderr, "double-checking input for internal consistency...\n");
}
- double_check(ir, state->box, nint_ftype(sys, molinfo, F_CONSTR), wi);
+ {
+ int bHasNormalConstraints = 0 < (nint_ftype(sys, molinfo, F_CONSTR) +
+ nint_ftype(sys, molinfo, F_CONSTRNC));
+ int bHasAnyConstraints = bHasNormalConstraints || 0 < nint_ftype(sys, molinfo, F_SETTLE);
+ double_check(ir, state->box,
+ bHasNormalConstraints,
+ bHasAnyConstraints,
+ wi);
+ }
}
if (bGenVel)
{ efNDX, NULL, NULL, ffOPTRD },
{ efTOP, NULL, NULL, ffREAD },
{ efTOP, "-pp", "processed", ffOPTWR },
- { efTPX, "-o", NULL, ffWRITE },
+ { efTPR, "-o", NULL, ffWRITE },
{ efTRN, "-t", NULL, ffOPTRD },
{ efEDR, "-e", NULL, ffOPTRD },
/* This group is needed by the VMD viewer as the start configuration for IMD sessions: */
}
done_warning(wi, FARGS);
- write_tpx_state(ftp2fn(efTPX, NFILE, fnm), ir, &state, sys);
+ write_tpx_state(ftp2fn(efTPR, NFILE, fnm), ir, &state, sys);
/* Output IMD group, if bIMD is TRUE */
write_IMDgroup_to_file(ir->bIMD, ir, &state, sys, NFILE, fnm);
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "h_db.h"
+
+#include <stdlib.h>
#include <string.h>
+
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/utility/cstringutil.h"
-#include "sysstuff.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
-#include "symtab.h"
-#include "h_db.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "fflibutil.h"
-#include "gmx_fatal.h"
-#include "macros.h"
/* Number of control atoms for each 'add' type.
*
}
for (i = 0; (i < hack->nctl); i++)
{
- hack->a[i] = strdup(a[i]);
+ hack->a[i] = gmx_strdup(a[i]);
}
for (; i < 4; i++)
{
hack->a[i] = NULL;
}
hack->oname = NULL;
- hack->nname = strdup(hn);
+ hack->nname = gmx_strdup(hn);
hack->atom = NULL;
hack->cgnr = NOTSET;
hack->bXSet = FALSE;
}
srenew(aah, nah+1);
clear_t_hackblock(&aah[nah]);
- aah[nah].name = strdup(buf);
- aah[nah].filebase = strdup(filebase);
+ aah[nah].name = gmx_strdup(buf);
+ aah[nah].filebase = gmx_strdup(filebase);
if (sscanf(line+n, "%d", &nab) == 1)
{
#ifndef GMX_GMXPREPROCESS_H_DB_H
#define GMX_GMXPREPROCESS_H_DB_H
-#include "sysstuff.h"
-#include "hackblock.h"
+#include <stdio.h>
+
+#include "gromacs/gmxpreprocess/hackblock.h"
#ifdef __cplusplus
extern "C" {
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <string.h>
#include "hackblock.h"
+
+#include <string.h>
+
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "macros.h"
-#include "names.h"
/* these MUST correspond to the enum in hackblock.h */
const char *btsNames[ebtsNR] = { "bonds", "angles", "dihedrals", "impropers", "exclusions", "cmap" };
free_t_bondeds(&(*rtp)[i].rb[j]);
}
}
- free(*rtp);
+ sfree(*rtp);
}
void free_t_hack(int nh, t_hack **h)
}
}
-#define safe_strdup(str) ((str != NULL) ? strdup(str) : NULL)
+#define safe_strdup(str) ((str != NULL) ? gmx_strdup(str) : NULL)
static void copy_t_rbonded(t_rbonded *s, t_rbonded *d)
{
#ifndef GMX_GMXPREPROCESS_HACKBLOCK_H
#define GMX_GMXPREPROCESS_HACKBLOCK_H
-#include "typedefs.h"
-#include "../fileio/pdbio.h"
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/topology/symtab.h"
#ifdef __cplusplus
extern "C" {
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <stdio.h>
#include <string.h>
-#include "typedefs.h"
+
#include "gromacs/fileio/pdbio.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "physics.h"
-#include "toputil.h"
-#include "pdb2top.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/block.h"
#include "gromacs/utility/cstringutil.h"
-#include "macros.h"
-
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static int in_strings(char *key, int nstr, const char **str)
{
}
snew(pdba->resinfo[hisind].rtp, 1);
- *pdba->resinfo[hisind].rtp = strdup(hh[type]);
+ *pdba->resinfo[hisind].rtp = gmx_strdup(hh[type]);
}
}
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "insert-molecules.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "insert-molecules.h"
+#include <algorithm>
+#include <string>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/math/utilities.h"
+#include "gromacs/commandline/cmdlineoptionsmodule.h"
#include "gromacs/fileio/confio.h"
-#include "macros.h"
-#include "gromacs/random/random.h"
-#include "gromacs/fileio/futil.h"
-#include "atomprop.h"
-#include "names.h"
-#include "vec.h"
-#include "gmx_fatal.h"
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxlib/conformation-utilities.h"
-#include "addconf.h"
-#include "read-conformation.h"
-#include "pbc.h"
-#include "xvgr.h"
-
-static gmx_bool in_box(t_pbc *pbc, rvec x)
-{
- rvec box_center, dx;
- int shift;
-
- /* pbc_dx_aiuc only works correctly with the rectangular box center */
- calc_box_center(ecenterRECT, pbc->box, box_center);
+#include "gromacs/gmxpreprocess/read-conformation.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/options.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/random/random.h"
+#include "gromacs/selection/nbsearch.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
- shift = pbc_dx_aiuc(pbc, x, box_center, dx);
+/* enum for random rotations of inserted solutes */
+enum {
+ en_rotXYZ, en_rotZ, en_rotNone
+};
- return (shift == CENTRAL);
+static void center_molecule(int atomCount, rvec x[])
+{
+ rvec center;
+ clear_rvec(center);
+ for (int i = 0; i < atomCount; ++i)
+ {
+ rvec_inc(center, x[i]);
+ }
+ svmul(1.0/atomCount, center, center);
+ for (int i = 0; i < atomCount; ++i)
+ {
+ rvec_dec(x[i], center);
+ }
}
-/* This is a (maybe) slow workaround to avoid the neighbor searching in addconf.c, which
- * leaks memory (May 2012). The function could be deleted as soon as the memory leaks
- * there are fixed.
- * However, when inserting a small molecule in a system containing not too many atoms,
- * allPairsDistOk is probably even faster than the other code.
- */
-static gmx_bool
-allPairsDistOk(t_atoms *atoms, rvec *x, real *exclusionDistances,
- int ePBC, matrix box,
- t_atoms *atoms_insrt, rvec *x_n, real *exclusionDistances_insrt)
+static void generate_trial_conf(int atomCount, const rvec xin[],
+ const rvec offset, int enum_rot, gmx_rng_t rng,
+ rvec xout[])
{
- int i, j;
- rvec dx;
- real n2, r2;
- t_pbc pbc;
+ for (int i = 0; i < atomCount; ++i)
+ {
+ copy_rvec(xin[i], xout[i]);
+ }
+ real alfa = 0.0, beta = 0.0, gamma = 0.0;
+ switch (enum_rot)
+ {
+ case en_rotXYZ:
+ alfa = 2*M_PI * gmx_rng_uniform_real(rng);
+ beta = 2*M_PI * gmx_rng_uniform_real(rng);
+ gamma = 2*M_PI * gmx_rng_uniform_real(rng);
+ break;
+ case en_rotZ:
+ alfa = beta = 0.;
+ gamma = 2*M_PI * gmx_rng_uniform_real(rng);
+ break;
+ case en_rotNone:
+ alfa = beta = gamma = 0.;
+ break;
+ }
+ if (enum_rot == en_rotXYZ || (enum_rot == en_rotZ))
+ {
+ rotate_conf(atomCount, xout, NULL, alfa, beta, gamma);
+ }
+ for (int i = 0; i < atomCount; ++i)
+ {
+ rvec_inc(xout[i], offset);
+ }
+}
- set_pbc(&pbc, ePBC, box);
- for (i = 0; i < atoms->nr; i++)
+static bool is_insertion_allowed(gmx::AnalysisNeighborhoodSearch *search,
+ const real *exclusionDistances,
+ int atomCount, const rvec *x,
+ const real *exclusionDistances_insrt)
+{
+ gmx::AnalysisNeighborhoodPositions pos(x, atomCount);
+ gmx::AnalysisNeighborhoodPairSearch pairSearch = search->startPairSearch(pos);
+ gmx::AnalysisNeighborhoodPair pair;
+ while (pairSearch.findNextPair(&pair))
{
- for (j = 0; j < atoms_insrt->nr; j++)
+ const real r1 = exclusionDistances[pair.refIndex()];
+ const real r2 = exclusionDistances_insrt[pair.testIndex()];
+ if (pair.distance2() < sqr(r1 + r2))
{
- pbc_dx(&pbc, x[i], x_n[j], dx);
- n2 = norm2(dx);
- r2 = sqr(exclusionDistances[i]+exclusionDistances_insrt[j]);
- if (n2 < r2)
- {
- return FALSE;
- }
+ return false;
}
}
- return TRUE;
+ return true;
}
-/* enum for random rotations of inserted solutes */
-enum {
- en_rot, en_rotXYZ, en_rotZ, en_rotNone, en_NR
-};
+static void merge_atoms_noalloc(t_atoms *atoms, const t_atoms *atoms_add)
+{
+ int resnr = 0;
+ if (atoms->nr > 0)
+ {
+ resnr = atoms->resinfo[atoms->atom[atoms->nr-1].resind].nr;
+ }
+ int prevResInd = -1;
+ for (int i = 0; i < atoms_add->nr; ++i)
+ {
+ if (atoms_add->atom[i].resind != prevResInd)
+ {
+ prevResInd = atoms_add->atom[i].resind;
+ ++resnr;
+ atoms->resinfo[atoms->nres] = atoms_add->resinfo[prevResInd];
+ atoms->resinfo[atoms->nres].nr = resnr;
+ ++atoms->nres;
+ }
+ atoms->atom[atoms->nr] = atoms_add->atom[i];
+ atoms->atomname[atoms->nr] = atoms_add->atomname[i];
+ atoms->atom[atoms->nr].resind = atoms->nres-1;
+ ++atoms->nr;
+ }
+}
-static char *insert_mols(const char *mol_insrt, int nmol_insrt, int ntry, int seed,
- t_atoms *atoms, rvec **x, real **exclusionDistances, int ePBC, matrix box,
- gmx_atomprop_t aps,
- real defaultDistance, real scaleFactor, real rshell,
- const output_env_t oenv,
- const char* posfn, const rvec deltaR, int enum_rot,
- gmx_bool bCheckAllPairDist)
+static void insert_mols(int nmol_insrt, int ntry, int seed,
+ real defaultDistance, real scaleFactor,
+ t_atoms *atoms, rvec **x,
+ const t_atoms *atoms_insrt, const rvec *x_insrt,
+ int ePBC, matrix box,
+ const std::string &posfn, const rvec deltaR, int enum_rot)
{
t_pbc pbc;
- static char *title_insrt;
- t_atoms atoms_insrt;
- rvec *x_insrt, *x_n;
- real *exclusionDistances_insrt;
- int ePBC_insrt;
- matrix box_insrt;
- int i, mol, onr, ncol;
- real alfa = 0., beta = 0., gamma = 0.;
- rvec offset_x;
- int trial;
- double **rpos;
- gmx_rng_t rng;
-
- rng = gmx_rng_init(seed);
- set_pbc(&pbc, ePBC, box);
+ rvec *x_n;
+
+ fprintf(stderr, "Initialising inter-atomic distances...\n");
+ gmx_atomprop_t aps = gmx_atomprop_init();
+ real *exclusionDistances
+ = makeExclusionDistances(atoms, aps, defaultDistance, scaleFactor);
+ real *exclusionDistances_insrt
+ = makeExclusionDistances(atoms_insrt, aps, defaultDistance, scaleFactor);
+ gmx_atomprop_destroy(aps);
- /* read number of atoms of insert molecules */
+ const real maxInsertRadius
+ = *std::max_element(exclusionDistances_insrt,
+ exclusionDistances_insrt + atoms_insrt->nr);
+ real maxRadius = maxInsertRadius;
+ if (atoms->nr > 0)
{
- int natoms;
- get_stx_coordnum(mol_insrt, &natoms);
- if (natoms == 0)
- {
- gmx_fatal(FARGS, "No molecule in %s, please check your input\n", mol_insrt);
- }
- init_t_atoms(&atoms_insrt, natoms, FALSE);
+ const real maxExistingRadius
+ = *std::max_element(exclusionDistances,
+ exclusionDistances + atoms->nr);
+ maxRadius = std::max(maxInsertRadius, maxExistingRadius);
}
- /* allocate memory for atom coordinates of insert molecules */
- snew(x_insrt, atoms_insrt.nr);
- snew(atoms_insrt.resinfo, atoms_insrt.nr);
- snew(atoms_insrt.atomname, atoms_insrt.nr);
- snew(atoms_insrt.atom, atoms_insrt.nr);
- atoms_insrt.pdbinfo = NULL;
- snew(x_n, atoms_insrt.nr);
- snew(title_insrt, STRLEN);
-
- /* read residue number, residue names, atomnames, coordinates etc. */
- fprintf(stderr, "Reading molecule configuration \n");
- read_stx_conf(mol_insrt, title_insrt, &atoms_insrt, x_insrt, NULL,
- &ePBC_insrt, box_insrt);
- fprintf(stderr, "%s\nContaining %d atoms in %d residue\n",
- title_insrt, atoms_insrt.nr, atoms_insrt.nres);
- srenew(atoms_insrt.resinfo, atoms_insrt.nres);
-
- /* initialise distance arrays for inserted molecules */
- exclusionDistances_insrt = makeExclusionDistances(&atoms_insrt, aps, defaultDistance, scaleFactor);
+
+ // TODO: Make all of this exception-safe.
+ gmx::AnalysisNeighborhood nb;
+ nb.setCutoff(maxInsertRadius + maxRadius);
+
+ gmx_rng_t rng = gmx_rng_init(seed);
+ set_pbc(&pbc, ePBC, box);
+
+ snew(x_n, atoms_insrt->nr);
/* With -ip, take nmol_insrt from file posfn */
- if (posfn != NULL)
+ double **rpos = NULL;
+ if (!posfn.empty())
{
- nmol_insrt = read_xvg(posfn, &rpos, &ncol);
+ int ncol;
+ nmol_insrt = read_xvg(posfn.c_str(), &rpos, &ncol);
if (ncol != 3)
{
- gmx_fatal(FARGS, "Expected 3 columns (x/y/z coordinates) in file %s\n", ncol, posfn);
+ gmx_fatal(FARGS, "Expected 3 columns (x/y/z coordinates) in file %s\n",
+ posfn.c_str());
}
- fprintf(stderr, "Read %d positions from file %s\n\n", nmol_insrt, posfn);
+ fprintf(stderr, "Read %d positions from file %s\n\n",
+ nmol_insrt, posfn.c_str());
}
- srenew(atoms->resinfo, (atoms->nres+nmol_insrt*atoms_insrt.nres));
- srenew(atoms->atomname, (atoms->nr+atoms_insrt.nr*nmol_insrt));
- srenew(atoms->atom, (atoms->nr+atoms_insrt.nr*nmol_insrt));
- srenew(*x, (atoms->nr+atoms_insrt.nr*nmol_insrt));
- srenew(*exclusionDistances, (atoms->nr+atoms_insrt.nr*nmol_insrt));
+ {
+ const int finalAtomCount = atoms->nr + nmol_insrt * atoms_insrt->nr;
+ const int finalResidueCount = atoms->nres + nmol_insrt * atoms_insrt->nres;
+ srenew(atoms->resinfo, finalResidueCount);
+ srenew(atoms->atomname, finalAtomCount);
+ srenew(atoms->atom, finalAtomCount);
+ srenew(*x, finalAtomCount);
+ srenew(exclusionDistances, finalAtomCount);
+ }
- trial = mol = 0;
+ int mol = 0;
+ int trial = 0;
+ int firstTrial = 0;
+ int failed = 0;
while ((mol < nmol_insrt) && (trial < ntry*nmol_insrt))
{
- fprintf(stderr, "\rTry %d", trial++);
- for (i = 0; (i < atoms_insrt.nr); i++)
- {
- copy_rvec(x_insrt[i], x_n[i]);
- }
- switch (enum_rot)
- {
- case en_rotXYZ:
- alfa = 2*M_PI * gmx_rng_uniform_real(rng);
- beta = 2*M_PI * gmx_rng_uniform_real(rng);
- gamma = 2*M_PI * gmx_rng_uniform_real(rng);
- break;
- case en_rotZ:
- alfa = beta = 0.;
- gamma = 2*M_PI * gmx_rng_uniform_real(rng);
- break;
- case en_rotNone:
- alfa = beta = gamma = 0.;
- break;
- }
- if (enum_rot == en_rotXYZ || (enum_rot == en_rotZ))
- {
- rotate_conf(atoms_insrt.nr, x_n, NULL, alfa, beta, gamma);
- }
- if (posfn == NULL)
+ rvec offset_x;
+ if (posfn.empty())
{
- /* insert at random positions */
+ // Insert at random positions.
offset_x[XX] = box[XX][XX] * gmx_rng_uniform_real(rng);
offset_x[YY] = box[YY][YY] * gmx_rng_uniform_real(rng);
offset_x[ZZ] = box[ZZ][ZZ] * gmx_rng_uniform_real(rng);
- make_new_box(atoms_insrt.nr, x_n, box_insrt, offset_x, TRUE);
- if (!in_box(&pbc, x_n[0]) || !in_box(&pbc, x_n[atoms_insrt.nr-1]))
- {
- continue;
- }
}
else
{
- /* Insert at positions taken from option -ip file */
+ // Skip a position if ntry trials were not successful.
+ if (trial >= firstTrial + ntry)
+ {
+ fprintf(stderr, " skipped position (%.3f, %.3f, %.3f)\n",
+ rpos[XX][mol], rpos[YY][mol], rpos[ZZ][mol]);
+ ++mol;
+ ++failed;
+ }
+ // Insert at positions taken from option -ip file.
offset_x[XX] = rpos[XX][mol] + deltaR[XX]*(2 * gmx_rng_uniform_real(rng)-1);
offset_x[YY] = rpos[YY][mol] + deltaR[YY]*(2 * gmx_rng_uniform_real(rng)-1);
offset_x[ZZ] = rpos[ZZ][mol] + deltaR[ZZ]*(2 * gmx_rng_uniform_real(rng)-1);
- for (i = 0; i < atoms_insrt.nr; i++)
- {
- rvec_inc(x_n[i], offset_x);
- }
}
-
- onr = atoms->nr;
-
- /* This is a (maybe) slow workaround to avoid too many calls of add_conf, which
- * leaks memory (status May 2012). If the momory leaks in add_conf() are fixed,
- * this check could be removed. Note, however, that allPairsDistOk is probably
- * even faster than add_conf() when inserting a small molecule into a moderately
- * small system.
- */
- if (bCheckAllPairDist && !allPairsDistOk(atoms, *x, *exclusionDistances, ePBC, box, &atoms_insrt, x_n, exclusionDistances_insrt))
+ fprintf(stderr, "\rTry %d", ++trial);
+ generate_trial_conf(atoms_insrt->nr, x_insrt, offset_x, enum_rot, rng,
+ x_n);
+ gmx::AnalysisNeighborhoodPositions pos(*x, atoms->nr);
+ gmx::AnalysisNeighborhoodSearch search = nb.initSearch(&pbc, pos);
+ if (is_insertion_allowed(&search, exclusionDistances, atoms_insrt->nr,
+ x_n, exclusionDistances_insrt))
{
- continue;
- }
-
- add_conf(atoms, x, NULL, exclusionDistances, FALSE, ePBC, box, TRUE,
- &atoms_insrt, x_n, NULL, exclusionDistances_insrt, FALSE, rshell, 0, oenv);
-
- if (atoms->nr == (atoms_insrt.nr+onr))
- {
- mol++;
+ const int firstIndex = atoms->nr;
+ for (int i = 0; i < atoms_insrt->nr; ++i)
+ {
+ copy_rvec(x_n[i], (*x)[firstIndex + i]);
+ exclusionDistances[firstIndex + i] = exclusionDistances_insrt[i];
+ }
+ merge_atoms_noalloc(atoms, atoms_insrt);
+ ++mol;
+ firstTrial = trial;
fprintf(stderr, " success (now %d atoms)!\n", atoms->nr);
}
}
srenew(atoms->atomname, atoms->nr);
srenew(atoms->atom, atoms->nr);
srenew(*x, atoms->nr);
- srenew(*exclusionDistances, atoms->nr);
fprintf(stderr, "\n");
/* print number of molecules added */
- fprintf(stderr, "Added %d molecules (out of %d requested) of %s\n",
- mol, nmol_insrt, *atoms_insrt.resinfo[0].name);
+ fprintf(stderr, "Added %d molecules (out of %d requested)\n",
+ mol - failed, nmol_insrt);
sfree(x_n);
+ sfree(exclusionDistances);
sfree(exclusionDistances_insrt);
- done_atom(&atoms_insrt);
-
- return title_insrt;
+ if (rpos != NULL)
+ {
+ for (int i = 0; i < DIM; ++i)
+ {
+ sfree(rpos[i]);
+ }
+ sfree(rpos);
+ }
}
-int gmx_insert_molecules(int argc, char *argv[])
+namespace gmx
+{
+
+namespace
{
- const char *desc[] = {
+
+class InsertMolecules : public CommandLineOptionsModuleInterface
+{
+ public:
+ InsertMolecules()
+ : bBox_(false), nmolIns_(0), nmolTry_(10), seed_(1997),
+ defaultDistance_(0.105), scaleFactor_(0.57), enumRot_(en_rotXYZ)
+ {
+ clear_rvec(newBox_);
+ clear_rvec(deltaR_);
+ }
+
+ virtual void init(CommandLineModuleSettings * /*settings*/)
+ {
+ }
+
+ virtual void initOptions(Options *options);
+ virtual void optionsFinished(Options *options);
+
+ virtual int run();
+
+ private:
+ std::string inputConfFile_;
+ std::string insertConfFile_;
+ std::string positionFile_;
+ std::string outputConfFile_;
+ rvec newBox_;
+ bool bBox_;
+ int nmolIns_;
+ int nmolTry_;
+ int seed_;
+ real defaultDistance_;
+ real scaleFactor_;
+ rvec deltaR_;
+ int enumRot_;
+};
+
+void InsertMolecules::initOptions(Options *options)
+{
+ const char *const desc[] = {
"[THISMODULE] inserts [TT]-nmol[tt] copies of the system specified in",
"the [TT]-ci[tt] input file. The insertions take place either into",
"vacant space in the solute conformation given with [TT]-f[tt], or",
"[THISMODULE] (e.g. from [gmx-editconf] [TT]-center[tt]).",
"Comments in that file starting with # are ignored. Option [TT]-dr[tt]",
"defines the maximally allowed displacements during insertial trials.",
- "[TT]-try[tt] and [TT]-rot[tt] work as in the default mode (see above).",
- "[PAR]",
- };
-
- const char *bugs[] = {
- "Molecules must be whole in the initial configurations.",
- "Many repeated neighbor searchings with -ci blows up the allocated memory. "
- "Option -allpair avoids this using all-to-all distance checks (slow for large systems)"
+ "[TT]-try[tt] and [TT]-rot[tt] work as in the default mode (see above)."
};
- /* parameter data */
- gmx_bool bProt, bBox;
- const char *conf_prot, *confout;
- real *exclusionDistances = NULL;
- char *title_ins = NULL;
- gmx_atomprop_t aps;
-
- /* protein configuration data */
- char *title = NULL;
- t_atoms *atoms;
- rvec *x = NULL;
- int ePBC = -1;
- matrix box;
-
- t_filenm fnm[] = {
- { efSTX, "-f", "protein", ffOPTRD },
- { efSTX, "-ci", "insert", ffREAD},
- { efDAT, "-ip", "positions", ffOPTRD},
- { efSTO, NULL, NULL, ffWRITE},
- };
-#define NFILE asize(fnm)
-
- static int nmol_ins = 0, nmol_try = 10, seed = 1997, enum_rot;
- static real defaultDistance = 0.105, scaleFactor = 0.57;
- static rvec new_box = {0.0, 0.0, 0.0}, deltaR = {0.0, 0.0, 0.0};
- static gmx_bool bCheckAllPairDist = FALSE;
- output_env_t oenv;
- const char *enum_rot_string[] = {NULL, "xyz", "z", "none", NULL};
- t_pargs pa[] = {
- { "-box", FALSE, etRVEC, {new_box},
- "Box size (in nm)" },
- { "-nmol", FALSE, etINT, {&nmol_ins},
- "Number of extra molecules to insert" },
- { "-try", FALSE, etINT, {&nmol_try},
- "Try inserting [TT]-nmol[tt] times [TT]-try[tt] times" },
- { "-seed", FALSE, etINT, {&seed},
- "Random generator seed"},
- { "-radius", FALSE, etREAL, {&defaultDistance},
- "Default van der Waals distance"},
- { "-scale", FALSE, etREAL, {&scaleFactor},
- "Scale factor to multiply Van der Waals radii from the database in share/gromacs/top/vdwradii.dat. The default value of 0.57 yields density close to 1000 g/l for proteins in water." },
- { "-dr", FALSE, etRVEC, {deltaR},
- "Allowed displacement in x/y/z from positions in [TT]-ip[tt] file" },
- { "-rot", FALSE, etENUM, {enum_rot_string},
- "rotate inserted molecules randomly" },
- { "-allpair", FALSE, etBOOL, {&bCheckAllPairDist},
- "Avoid momory leaks during neighbor searching with option -ci. May be slow for large systems." },
- };
+ options->setDescription(desc);
+
+ // TODO: Replace use of legacyType.
+ options->addOption(FileNameOption("f")
+ .legacyType(efSTX).inputFile()
+ .store(&inputConfFile_)
+ .defaultBasename("protein")
+ .description("Existing configuration to insert into"));
+ options->addOption(FileNameOption("ci")
+ .legacyType(efSTX).inputFile().required()
+ .store(&insertConfFile_)
+ .defaultBasename("insert")
+ .description("Configuration to insert"));
+ options->addOption(FileNameOption("ip")
+ .filetype(eftGenericData).inputFile()
+ .store(&positionFile_)
+ .defaultBasename("positions")
+ .description("Predefined insertion trial positions"));
+ options->addOption(FileNameOption("o")
+ .legacyType(efSTO).outputFile().required()
+ .store(&outputConfFile_)
+ .defaultBasename("out")
+ .description("Output configuration after insertion"));
+
+ options->addOption(RealOption("box").vector()
+ .store(newBox_)
+ .description("Box size (in nm)"));
+ options->addOption(IntegerOption("nmol")
+ .store(&nmolIns_)
+ .description("Number of extra molecules to insert"));
+ options->addOption(IntegerOption("try")
+ .store(&nmolTry_)
+ .description("Try inserting [TT]-nmol[tt] times [TT]-try[tt] times"));
+ options->addOption(IntegerOption("seed")
+ .store(&seed_)
+ .description("Random generator seed"));
+ options->addOption(RealOption("radius")
+ .store(&defaultDistance_)
+ .description("Default van der Waals distance"));
+ options->addOption(RealOption("scale")
+ .store(&scaleFactor_)
+ .description("Scale factor to multiply Van der Waals radii from the database in share/gromacs/top/vdwradii.dat. The default value of 0.57 yields density close to 1000 g/l for proteins in water."));
+ options->addOption(RealOption("dr").vector()
+ .store(deltaR_)
+ .description("Allowed displacement in x/y/z from positions in [TT]-ip[tt] file"));
+ const char *const cRotationEnum[] = {"xyz", "z", "none"};
+ options->addOption(StringOption("rot").enumValue(cRotationEnum)
+ .storeEnumIndex(&enumRot_)
+ .description("Rotate inserted molecules randomly"));
+}
- if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, asize(bugs), bugs, &oenv))
- {
- return 0;
- }
+void InsertMolecules::optionsFinished(Options *options)
+{
+ bBox_ = options->isSet("box");
+}
- bProt = opt2bSet("-f", NFILE, fnm);
- bBox = opt2parg_bSet("-box", asize(pa), pa);
- enum_rot = nenum(enum_rot_string);
+int InsertMolecules::run()
+{
+ const bool bProt = !inputConfFile_.empty();
/* check input */
- const char *insertionMoleculeFileName = opt2fn("-ci", NFILE, fnm);
- if (!gmx_fexist(insertionMoleculeFileName))
- {
- gmx_fatal(FARGS,
- "A molecule conformation to insert is required in -ci. %s was not found!",
- insertionMoleculeFileName);
- }
- if (nmol_ins <= 0 && !opt2bSet("-ip", NFILE, fnm))
+ if (nmolIns_ <= 0 && positionFile_.empty())
{
gmx_fatal(FARGS, "Either -nmol must be larger than 0, "
"or positions must be given with -ip");
}
- if (!bProt && !bBox)
+ if (!bProt && !bBox_)
{
gmx_fatal(FARGS, "When no solute (-f) is specified, "
"a box size (-box) must be specified");
}
- aps = gmx_atomprop_init();
-
+ char *title = NULL;
+ t_atoms *atoms;
+ rvec *x = NULL;
+ matrix box;
+ int ePBC = -1;
snew(atoms, 1);
init_t_atoms(atoms, 0, FALSE);
if (bProt)
{
/* Generate a solute configuration */
- conf_prot = opt2fn("-f", NFILE, fnm);
- title = readConformation(conf_prot, atoms, &x, NULL,
- &ePBC, box);
- exclusionDistances = makeExclusionDistances(atoms, aps, defaultDistance, scaleFactor);
+ title = readConformation(inputConfFile_.c_str(), atoms, &x, NULL,
+ &ePBC, box, "solute");
if (atoms->nr == 0)
{
- fprintf(stderr, "Note: no atoms in %s\n", conf_prot);
- bProt = FALSE;
+ fprintf(stderr, "Note: no atoms in %s\n", inputConfFile_.c_str());
+ sfree(title);
+ title = NULL;
}
}
- if (bBox)
+ if (bBox_)
{
ePBC = epbcXYZ;
clear_mat(box);
- box[XX][XX] = new_box[XX];
- box[YY][YY] = new_box[YY];
- box[ZZ][ZZ] = new_box[ZZ];
+ box[XX][XX] = newBox_[XX];
+ box[YY][YY] = newBox_[YY];
+ box[ZZ][ZZ] = newBox_[ZZ];
}
if (det(box) == 0)
{
"or give explicit -box command line option");
}
+ t_atoms *atoms_insrt;
+ rvec *x_insrt = NULL;
+ snew(atoms_insrt, 1);
+ init_t_atoms(atoms_insrt, 0, FALSE);
+ {
+ int ePBC_dummy;
+ matrix box_dummy;
+ char *title_ins
+ = readConformation(insertConfFile_.c_str(), atoms_insrt, &x_insrt,
+ NULL, &ePBC_dummy, box_dummy, "molecule");
+ if (atoms_insrt->nr == 0)
+ {
+ gmx_fatal(FARGS, "No molecule in %s, please check your input",
+ insertConfFile_.c_str());
+ }
+ if (title == NULL)
+ {
+ title = title_ins;
+ }
+ else
+ {
+ sfree(title_ins);
+ }
+ if (positionFile_.empty())
+ {
+ center_molecule(atoms_insrt->nr, x_insrt);
+ }
+ }
+
/* add nmol_ins molecules of atoms_ins
in random orientation at random place */
- title_ins = insert_mols(insertionMoleculeFileName, nmol_ins, nmol_try, seed,
- atoms, &x, &exclusionDistances, ePBC, box, aps,
- defaultDistance, scaleFactor, 0,
- oenv, opt2fn_null("-ip", NFILE, fnm), deltaR, enum_rot,
- bCheckAllPairDist);
+ insert_mols(nmolIns_, nmolTry_, seed_, defaultDistance_, scaleFactor_,
+ atoms, &x, atoms_insrt, x_insrt,
+ ePBC, box, positionFile_, deltaR_, enumRot_);
/* write new configuration to file confout */
- confout = ftp2fn(efSTO, NFILE, fnm);
- fprintf(stderr, "Writing generated configuration to %s\n", confout);
- if (bProt)
- {
- write_sto_conf(confout, title, atoms, x, NULL, ePBC, box);
- /* print box sizes and box type to stderr */
- fprintf(stderr, "%s\n", title);
- }
- else
- {
- write_sto_conf(confout, title_ins, atoms, x, NULL, ePBC, box);
- }
+ fprintf(stderr, "Writing generated configuration to %s\n",
+ outputConfFile_.c_str());
+ write_sto_conf(outputConfFile_.c_str(), title, atoms, x, NULL, ePBC, box);
/* print size of generated configuration */
fprintf(stderr, "\nOutput configuration contains %d atoms in %d residues\n",
atoms->nr, atoms->nres);
- gmx_atomprop_destroy(aps);
- sfree(exclusionDistances);
sfree(x);
+ sfree(x_insrt);
done_atom(atoms);
+ done_atom(atoms_insrt);
sfree(atoms);
+ sfree(atoms_insrt);
+ sfree(title);
return 0;
}
+
+} // namespace
+
+const char InsertMoleculesInfo::name[] = "insert-molecules";
+const char InsertMoleculesInfo::shortDescription[] =
+ "Insert molecules into existing vacancies";
+CommandLineOptionsModuleInterface *InsertMoleculesInfo::create()
+{
+ return new InsertMolecules();
+}
+
+} // namespace gmx
#ifndef GMX_GMXPREPROCESS_INSERT_MOLECULES_H
#define GMX_GMXPREPROCESS_INSERT_MOLECULES_H
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
+namespace gmx
+{
-int gmx_insert_molecules(int argc, char *argv[]);
+class CommandLineOptionsModuleInterface;
-#ifdef __cplusplus
-}
-#endif
+class InsertMoleculesInfo
+{
+ public:
+ static const char name[];
+ static const char shortDescription[];
+ static CommandLineOptionsModuleInterface *create();
+};
+
+} // namespace gmx
#endif
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "nm2type.h"
#include <string.h>
+#include "gromacs/fileio/confio.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/gmxpreprocess/toppush.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
#include "gromacs/math/utilities.h"
-#include "macros.h"
-#include "bondf.h"
+#include "gromacs/math/vec.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "gromacs/fileio/confio.h"
-#include "physics.h"
-#include "vec.h"
-#include "gromacs/math/3dview.h"
-#include "txtdump.h"
-#include "readinp.h"
-#include "names.h"
-#include "toppush.h"
-#include "pdb2top.h"
-#include "gpp_nextnb.h"
-#include "gpp_atomtype.h"
-#include "fflibutil.h"
-
-#include "nm2type.h"
-
-#include "gmx_fatal.h"
static void rd_nm2type_file(const char *fn, int *nnm, t_nm2type **nmp)
{
{
gmx_fatal(FARGS, "Error on line %d of %s", line, libfilename);
}
- newbuf[i] = strdup(nbbuf);
+ newbuf[i] = gmx_strdup(nbbuf);
strcat(format, "%*s%*s");
}
}
{
newbuf = NULL;
}
- nm2t[nnnm].elem = strdup(elem);
- nm2t[nnnm].type = strdup(type);
+ nm2t[nnnm].elem = gmx_strdup(elem);
+ nm2t[nnnm].type = gmx_strdup(type);
nm2t[nnnm].q = qq;
nm2t[nnnm].m = mm;
nm2t[nnnm].nbonds = nb;
}
}
-int nm2type(int nnm, t_nm2type nm2t[], t_symtab *tab, t_atoms *atoms,
+int nm2type(int nnm, t_nm2type nm2t[], struct t_symtab *tab, t_atoms *atoms,
gpp_atomtype_t atype, int *nbonds, t_params *bonds)
{
int cur = 0;
#include <stdio.h>
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/topology/atoms.h"
+
#ifdef __cplusplus
extern "C" {
#endif
void dump_nm2type(FILE *fp, int nnm, t_nm2type nm2t[]);
/* Dump the database for debugging. Can be reread by the program */
-int nm2type(int nnm, t_nm2type nm2t[], t_symtab *tab, t_atoms *atoms,
+int nm2type(int nnm, t_nm2type nm2t[], struct t_symtab *tab, t_atoms *atoms,
gpp_atomtype_t atype, int *nbonds, t_params *bond);
/* Try to determine the atomtype (force field dependent) for the atoms
* with help of the bond list
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "pdb2gmx.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "pdb2gmx.h"
#include <ctype.h>
+#include <stdlib.h>
#include <string.h>
#include <time.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/utility/smalloc.h"
-#include "copyrite.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/confio.h"
-#include "symtab.h"
-#include "vec.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/pdbio.h"
-#include "toputil.h"
-#include "h_db.h"
-#include "physics.h"
-#include "pgutil.h"
-#include "calch.h"
-#include "resall.h"
-#include "pdb2top.h"
-#include "ter_db.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
-#include "genhydro.h"
-#include "readinp.h"
-#include "atomprop.h"
-#include "index.h"
-#include "fflibutil.h"
-#include "macros.h"
-
#include "gromacs/fileio/strdb.h"
-
-#include "hizzie.h"
-#include "specbond.h"
-#include "xlate.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/genhydro.h"
+#include "gromacs/gmxpreprocess/h_db.h"
+#include "gromacs/gmxpreprocess/hizzie.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/specbond.h"
+#include "gromacs/gmxpreprocess/ter_db.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/gmxpreprocess/xlate.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/dir_separator.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
char gmx[6];
static int read_pdball(const char *inf, const char *outf, char *title,
t_atoms *atoms, rvec **x,
int *ePBC, matrix box, gmx_bool bRemoveH,
- t_symtab *symtab, gmx_residuetype_t rt, const char *watres,
+ t_symtab *symtab, gmx_residuetype_t *rt, const char *watres,
gmx_atomprop_t aps, gmx_bool bVerbose)
/* Read a pdb file. (containing proteins) */
{
return pdba->nr;
}
-void find_nc_ter(t_atoms *pdba, int r0, int r1, int *r_start, int *r_end, gmx_residuetype_t rt)
+void find_nc_ter(t_atoms *pdba, int r0, int r1, int *r_start, int *r_end,
+ gmx_residuetype_t *rt)
{
int i;
const char *p_startrestype;
t_hackblock *ah;
t_symtab symtab;
gpp_atomtype_t atype;
- gmx_residuetype_t rt;
+ gmx_residuetype_t*rt;
const char *top_fn;
char fn[256], itp_fn[STRLEN], posre_fn[STRLEN], buf_fn[STRLEN];
char molname[STRLEN], title[STRLEN], quote[STRLEN];
chains[i].pdba->atom[j] = pdba_all.atom[pdb_ch[si].start+j];
snew(chains[i].pdba->atomname[j], 1);
*chains[i].pdba->atomname[j] =
- strdup(*pdba_all.atomname[pdb_ch[si].start+j]);
+ gmx_strdup(*pdba_all.atomname[pdb_ch[si].start+j]);
chains[i].pdba->pdbinfo[j] = pdba_all.pdbinfo[pdb_ch[si].start+j];
copy_rvec(pdbx[pdb_ch[si].start+j], chains[i].x[j]);
}
{
chains[i].pdba->resinfo[j] = pdba_all.resinfo[k+j];
snew(chains[i].pdba->resinfo[j].name, 1);
- *chains[i].pdba->resinfo[j].name = strdup(*pdba_all.resinfo[k+j].name);
+ *chains[i].pdba->resinfo[j].name = gmx_strdup(*pdba_all.resinfo[k+j].name);
/* make all chain identifiers equal to that of the chain */
chains[i].pdba->resinfo[j].chainid = pdb_ch[si].chainid;
}
nincl++;
srenew(incls, nincl);
- incls[nincl-1] = strdup(itp_fn);
+ incls[nincl-1] = gmx_strdup(itp_fn);
itp_file = gmx_fio_fopen(itp_fn, "w");
}
else
srenew(mols, nmol+1);
if (cc->bAllWat)
{
- mols[nmol].name = strdup("SOL");
+ mols[nmol].name = gmx_strdup("SOL");
mols[nmol].nr = pdba->nres;
}
else
{
- mols[nmol].name = strdup(molname);
+ mols[nmol].name = gmx_strdup(molname);
mols[nmol].nr = 1;
}
nmol++;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "pdb2top.h"
-#include <stdio.h>
-#include <math.h>
#include <ctype.h>
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
-#include "vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "symtab.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
-#include "pdb2top.h"
-#include "gpp_nextnb.h"
-#include "topdirs.h"
-#include "toputil.h"
-#include "h_db.h"
-#include "pgutil.h"
-#include "resall.h"
-#include "topio.h"
-#include "gromacs/utility/cstringutil.h"
-#include "physics.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gen_ad.h"
-#include "gromacs/fileio/filenm.h"
-#include "index.h"
-#include "gen_vsite.h"
-#include "add_par.h"
-#include "toputil.h"
-#include "fflibutil.h"
-#include "copyrite.h"
+#include <algorithm>
+#include <string>
+#include <vector>
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/strdb.h"
+#include "gromacs/gmxpreprocess/add_par.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/gen_ad.h"
+#include "gromacs/gmxpreprocess/gen_vsite.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/h_db.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/topio.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/dir_separator.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/file.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/path.h"
#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
/* this must correspond to enum in pdb2top.h */
const char *hh[ehisNR] = { "HISD", "HISE", "HISH", "HIS1" };
return (fabs(x-ix) < tol);
}
-static void swap_strings(char **s, int i, int j)
-{
- char *tmp;
-
- tmp = s[i];
- s[i] = s[j];
- s[j] = tmp;
-}
-
-void
-choose_ff(const char *ffsel,
- char *forcefield, int ff_maxlen,
- char *ffdir, int ffdir_maxlen)
+static void
+choose_ff_impl(const char *ffsel,
+ char *forcefield, int ff_maxlen,
+ char *ffdir, int ffdir_maxlen)
{
- int nff;
- char **ffdirs, **ffs, **ffs_dir, *ptr;
- int i, j, sel, cwdsel, nfound;
- char buf[STRLEN], **desc;
- FILE *fp;
- char *pret;
-
- nff = fflib_search_file_in_dirend(fflib_forcefield_itp(),
- fflib_forcefield_dir_ext(),
- &ffdirs);
-
- if (nff == 0)
- {
- gmx_fatal(FARGS, "No force fields found (files with name '%s' in subdirectories ending on '%s')",
- fflib_forcefield_itp(), fflib_forcefield_dir_ext());
- }
+ std::vector<gmx::DataFileInfo> ffdirs = fflib_enumerate_forcefields();
+ const int nff = static_cast<int>(ffdirs.size());
/* Replace with unix path separators */
if (DIR_SEPARATOR != '/')
{
- for (i = 0; i < nff; i++)
+ for (int i = 0; i < nff; ++i)
{
- while ( (ptr = strchr(ffdirs[i], DIR_SEPARATOR)) != NULL)
- {
- *ptr = '/';
- }
+ std::replace(ffdirs[i].dir.begin(), ffdirs[i].dir.end(), DIR_SEPARATOR, '/');
}
}
/* Store the force field names in ffs */
- snew(ffs, nff);
- snew(ffs_dir, nff);
- for (i = 0; i < nff; i++)
+ std::vector<std::string> ffs;
+ ffs.reserve(ffdirs.size());
+ for (int i = 0; i < nff; ++i)
{
- /* Remove the path from the ffdir name - use our unix standard here! */
- ptr = strrchr(ffdirs[i], '/');
- if (ptr == NULL)
- {
- ffs[i] = strdup(ffdirs[i]);
- ffs_dir[i] = low_gmxlibfn(ffdirs[i], FALSE, FALSE);
- if (ffs_dir[i] == NULL)
- {
- gmx_fatal(FARGS, "Can no longer find file '%s'", ffdirs[i]);
- }
- }
- else
- {
- ffs[i] = strdup(ptr+1);
- ffs_dir[i] = strdup(ffdirs[i]);
- }
- ffs_dir[i][strlen(ffs_dir[i])-strlen(ffs[i])-1] = '\0';
- /* Remove the extension from the ffdir name */
- ffs[i][strlen(ffs[i])-strlen(fflib_forcefield_dir_ext())] = '\0';
+ ffs.push_back(gmx::stripSuffixIfPresent(ffdirs[i].name,
+ fflib_forcefield_dir_ext()));
}
+ int sel;
if (ffsel != NULL)
{
- sel = -1;
- cwdsel = -1;
- nfound = 0;
- for (i = 0; i < nff; i++)
+ sel = -1;
+ int cwdsel = -1;
+ int nfound = 0;
+ for (int i = 0; i < nff; ++i)
{
- if (strcmp(ffs[i], ffsel) == 0)
+ if (ffs[i] == ffsel)
{
/* Matching ff name */
sel = i;
nfound++;
- if (strncmp(ffs_dir[i], ".", 1) == 0)
+ if (ffdirs[i].dir == ".")
{
cwdsel = i;
}
}
else
{
- gmx_fatal(FARGS,
- "Force field '%s' occurs in %d places, but not in the current directory.\n"
- "Run without the -ff switch and select the force field interactively.", ffsel, nfound);
+ std::string message = gmx::formatString(
+ "Force field '%s' occurs in %d places, but not in "
+ "the current directory.\n"
+ "Run without the -ff switch and select the force "
+ "field interactively.", ffsel, nfound);
+ GMX_THROW(gmx::InconsistentInputError(message));
}
}
else if (nfound == 0)
{
- gmx_fatal(FARGS, "Could not find force field '%s' in current directory, install tree or GMXDATA path.", ffsel);
+ std::string message = gmx::formatString(
+ "Could not find force field '%s' in current directory, "
+ "install tree or GMXLIB path.", ffsel);
+ GMX_THROW(gmx::InconsistentInputError(message));
}
}
else if (nff > 1)
{
- snew(desc, nff);
- for (i = 0; (i < nff); i++)
+ std::vector<std::string> desc;
+ desc.reserve(ffdirs.size());
+ for (int i = 0; i < nff; ++i)
{
- sprintf(buf, "%s%c%s%s%c%s",
- ffs_dir[i], DIR_SEPARATOR,
- ffs[i], fflib_forcefield_dir_ext(), DIR_SEPARATOR,
- fflib_forcefield_doc());
- if (gmx_fexist(buf))
+ std::string docFileName(
+ gmx::Path::join(ffdirs[i].dir, ffdirs[i].name,
+ fflib_forcefield_doc()));
+ // TODO: Just try to open the file with a method that does not
+ // throw/bail out with a fatal error instead of multiple checks.
+ if (gmx::File::exists(docFileName))
{
+ // TODO: Use a C++ API without such an intermediate/fixed-length buffer.
+ char buf[STRLEN];
/* We don't use fflib_open, because we don't want printf's */
- fp = gmx_ffopen(buf, "r");
- snew(desc[i], STRLEN);
- get_a_line(fp, desc[i], STRLEN);
+ FILE *fp = gmx_ffopen(docFileName.c_str(), "r");
+ get_a_line(fp, buf, STRLEN);
gmx_ffclose(fp);
+ desc.push_back(buf);
}
else
{
- desc[i] = strdup(ffs[i]);
+ desc.push_back(ffs[i]);
}
}
/* Order force fields from the same dir alphabetically
* and put deprecated force fields at the end.
*/
- for (i = 0; (i < nff); i++)
+ for (int i = 0; i < nff; ++i)
{
- for (j = i+1; (j < nff); j++)
+ for (int j = i + 1; j < nff; ++j)
{
- if (strcmp(ffs_dir[i], ffs_dir[j]) == 0 &&
+ if (ffdirs[i].dir == ffdirs[j].dir &&
((desc[i][0] == '[' && desc[j][0] != '[') ||
((desc[i][0] == '[' || desc[j][0] != '[') &&
- gmx_strcasecmp(desc[i], desc[j]) > 0)))
+ gmx_strcasecmp(desc[i].c_str(), desc[j].c_str()) > 0)))
{
- swap_strings(ffdirs, i, j);
- swap_strings(ffs, i, j);
- swap_strings(desc, i, j);
+ std::swap(ffdirs[i].name, ffdirs[j].name);
+ std::swap(ffs[i], ffs[j]);
+ std::swap(desc[i], desc[j]);
}
}
}
printf("\nSelect the Force Field:\n");
- for (i = 0; (i < nff); i++)
+ for (int i = 0; i < nff; ++i)
{
- if (i == 0 || strcmp(ffs_dir[i-1], ffs_dir[i]) != 0)
+ if (i == 0 || ffdirs[i-1].dir != ffdirs[i].dir)
{
- if (strcmp(ffs_dir[i], ".") == 0)
+ if (ffdirs[i].dir == ".")
{
printf("From current directory:\n");
}
else
{
- printf("From '%s':\n", ffs_dir[i]);
+ printf("From '%s':\n", ffdirs[i].dir.c_str());
}
}
- printf("%2d: %s\n", i+1, desc[i]);
- sfree(desc[i]);
+ printf("%2d: %s\n", i+1, desc[i].c_str());
}
- sfree(desc);
sel = -1;
+ // TODO: Add a C++ API for this.
+ char buf[STRLEN];
+ char *pret;
do
{
pret = fgets(buf, STRLEN, stdin);
* This check assumes that the order of ffs matches the order
* in which fflib_open searches ff library files.
*/
- for (i = 0; i < sel; i++)
+ for (int i = 0; i < sel; i++)
{
- if (strcmp(ffs[i], ffs[sel]) == 0)
+ if (ffs[i] == ffs[sel])
{
- gmx_fatal(FARGS, "Can only select the first of multiple force field entries with directory name '%s%s' in the list. If you want to use the next entry, run pdb2gmx in a different directory or rename or move the force field directory present in the current working directory.",
- ffs[sel], fflib_forcefield_dir_ext());
+ std::string message = gmx::formatString(
+ "Can only select the first of multiple force "
+ "field entries with directory name '%s%s' in "
+ "the list. If you want to use the next entry, "
+ "run pdb2gmx in a different directory, set GMXLIB "
+ "to point to the desired force field first, and/or "
+ "rename or move the force field directory present "
+ "in the current working directory.",
+ ffs[sel].c_str(), fflib_forcefield_dir_ext());
+ GMX_THROW(gmx::NotImplementedError(message));
}
}
}
sel = 0;
}
- if (strlen(ffs[sel]) >= (size_t)ff_maxlen)
+ if (ffs[sel].length() >= static_cast<size_t>(ff_maxlen))
{
- gmx_fatal(FARGS, "Length of force field name (%d) >= maxlen (%d)",
- strlen(ffs[sel]), ff_maxlen);
+ std::string message = gmx::formatString(
+ "Length of force field name (%d) >= maxlen (%d)",
+ static_cast<int>(ffs[sel].length()), ff_maxlen);
+ GMX_THROW(gmx::InvalidInputError(message));
}
- strcpy(forcefield, ffs[sel]);
+ strcpy(forcefield, ffs[sel].c_str());
- if (strlen(ffdirs[sel]) >= (size_t)ffdir_maxlen)
+ std::string ffpath;
+ if (ffdirs[sel].bFromDefaultDir)
{
- gmx_fatal(FARGS, "Length of force field dir (%d) >= maxlen (%d)",
- strlen(ffdirs[sel]), ffdir_maxlen);
+ ffpath = ffdirs[sel].name;
}
- strcpy(ffdir, ffdirs[sel]);
+ else
+ {
+ ffpath = gmx::Path::join(ffdirs[sel].dir, ffdirs[sel].name);
+ }
+ if (ffpath.length() >= static_cast<size_t>(ffdir_maxlen))
+ {
+ std::string message = gmx::formatString(
+ "Length of force field dir (%d) >= maxlen (%d)",
+ static_cast<int>(ffpath.length()), ffdir_maxlen);
+ GMX_THROW(gmx::InvalidInputError(message));
+ }
+ strcpy(ffdir, ffpath.c_str());
+}
- for (i = 0; (i < nff); i++)
+void
+choose_ff(const char *ffsel,
+ char *forcefield, int ff_maxlen,
+ char *ffdir, int ffdir_maxlen)
+{
+ try
{
- sfree(ffdirs[i]);
- sfree(ffs[i]);
- sfree(ffs_dir[i]);
+ choose_ff_impl(ffsel, forcefield, ff_maxlen, ffdir, ffdir_maxlen);
}
- sfree(ffdirs);
- sfree(ffs);
- sfree(ffs_dir);
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
void choose_watermodel(const char *wmsel, const char *ffdir,
}
else if (strcmp(wmsel, "select") != 0)
{
- *watermodel = strdup(wmsel);
+ *watermodel = gmx_strdup(wmsel);
return;
}
}
else
{
- *watermodel = strdup(model[sel]);
+ *watermodel = gmx_strdup(model[sel]);
}
for (i = 0; i < nwm; i++)
}
static int name2type(t_atoms *at, int **cgnr,
- t_restp restp[], gmx_residuetype_t rt)
+ t_restp restp[], gmx_residuetype_t *rt)
{
int i, j, prevresind, resind, i0, prevcg, cg, curcg;
char *name;
}
snew( restp->atomname[at_start+1+k], 1);
restp->atom [at_start+1+k] = *hack->atom;
- *restp->atomname[at_start+1+k] = strdup(buf);
+ *restp->atomname[at_start+1+k] = gmx_strdup(buf);
if (hack->cgnr != NOTSET)
{
restp->cgnr [at_start+1+k] = hack->cgnr;
}
snew( (*restp)[i].atomname[l], 1);
(*restp)[i].atom[l] = *(*hb)[i].hack[j].atom;
- *(*restp)[i].atomname[l] = strdup((*hb)[i].hack[j].nname);
+ *(*restp)[i].atomname[l] = gmx_strdup((*hb)[i].hack[j].nname);
if ( (*hb)[i].hack[j].cgnr != NOTSET)
{
(*restp)[i].cgnr [l] = (*hb)[i].hack[j].cgnr;
}
/* Rename the atom in pdba */
snew(pdba->atomname[atind], 1);
- *pdba->atomname[atind] = strdup(newnm);
+ *pdba->atomname[atind] = gmx_strdup(newnm);
}
else if (hbr->hack[j].oname != NULL && hbr->hack[j].nname == NULL &&
gmx_strcasecmp(oldnm, hbr->hack[j].oname) == 0)
int *vsite_type;
int i, nmissat;
int bts[ebtsNR];
- gmx_residuetype_t rt;
+ gmx_residuetype_t*rt;
init_plist(plist);
gmx_residuetype_init(&rt);
#ifndef GMX_GMXPREPROCESS_PDB2TOP_H
#define GMX_GMXPREPROCESS_PDB2TOP_H
-#include "typedefs.h"
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
-#include "toputil.h"
-#include "hackblock.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C"
void pdb2top(FILE *top_file, char *posre_fn, char *molname,
t_atoms *atoms, rvec **x,
- gpp_atomtype_t atype, t_symtab *tab,
+ gpp_atomtype_t atype, struct t_symtab *tab,
int nrtp, t_restp rtp[],
t_restp *restp, t_hackblock *hb,
gmx_bool bAllowMissing,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include "gromacs/utility/cstringutil.h"
+#include "gmxpre.h"
+
#include "pgutil.h"
+
#include <string.h>
-#include "gmx_fatal.h"
+
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/snprintf.h"
#define BUFSIZE 1024
static void atom_not_found(int fatal_errno, const char *file, int line,
#ifndef GMX_GMXPREPROCESS_PGUTIL_H
#define GMX_GMXPREPROCESS_PGUTIL_H
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C"
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "protonate.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "protonate.h"
#include <math.h>
-#include "gromacs/utility/cstringutil.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
+
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
-#include "genhydro.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "index.h"
-#include "vec.h"
-#include "hackblock.h"
-
-#include "gmx_fatal.h"
+#include "gromacs/gmxpreprocess/genhydro.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
int gmx_protonate(int argc, char *argv[])
{
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
#include "read-conformation.h"
#include "gromacs/fileio/confio.h"
-#include "atomprop.h"
-#include "types/simple.h"
-#include "types/atoms.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
real *makeExclusionDistances(const t_atoms *a, gmx_atomprop_t aps,
snew(exclusionDistances, a->nr);
/* initialise arrays with distances usually based on van der Waals
radii */
- fprintf(stderr, "Initialising inter-atomic distances...\n");
for (i = 0; (i < a->nr); i++)
{
if (!gmx_atomprop_query(aps, epropVDW,
}
char *readConformation(const char *confin, t_atoms *atoms, rvec **x, rvec **v,
- int *ePBC, matrix box)
+ int *ePBC, matrix box, const char *statusTitle)
{
char *title;
int natoms;
init_t_atoms(atoms, natoms, FALSE);
/* read residue number, residue names, atomnames, coordinates etc. */
- fprintf(stderr, "Reading solute configuration%s\n", v ? " and velocities" : "");
+ fprintf(stderr, "Reading %s configuration%s\n", statusTitle, v ? " and velocities" : "");
read_stx_conf(confin, title, atoms, *x, v ? *v : NULL, ePBC, box);
fprintf(stderr, "%s\nContaining %d atoms in %d residues\n",
title, atoms->nr, atoms->nres);
#ifndef GMX_GMXPREPROCESS_READ_CONFORMATION_H
#define GMX_GMXPREPROCESS_READ_CONFORMATION_H
-#include "types/simple.h"
-#include "types/atoms.h"
-#include "atomprop.h"
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct gmx_atomprop;
+struct t_atoms;
+
/*! \brief Allocate and fill an array of inter-atomic half distances
*
* These are either scaled VDW radii taken from vdwradii.dat, or the
* default value. Used directly and indirectly by solvate and
* insert-molecules for deciding whether molecules clash. The return
* pointer should be freed by the caller. */
-real *makeExclusionDistances(const t_atoms *a, gmx_atomprop_t aps,
+real *makeExclusionDistances(const struct t_atoms *a, struct gmx_atomprop *aps,
real defaultDistance, real scaleFactor);
/*! \brief Read a conformation from a file, allocate and fill data structures.
* Used by solvate and insert-molecules. The returned pointers *x and
* *v should be freed by the caller. atoms should have its destructor
* called. */
-char *readConformation(const char *confin, t_atoms *atoms, rvec **x, rvec **v,
- int *ePBC, matrix box);
+char *readConformation(const char *confin, struct t_atoms *atoms, rvec **x, rvec **v,
+ int *ePBC, matrix box, const char *statusTitle);
#ifdef __cplusplus
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
+#include <stdlib.h>
#include <string.h>
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/names.h"
#include "gromacs/utility/cstringutil.h"
-#include "readir.h"
-#include "names.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
#define MAXPTR 254
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "readir.h"
#include <ctype.h>
-#include <stdlib.h>
#include <limits.h>
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "physics.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-#include "index.h"
-#include "symtab.h"
+#include <stdlib.h>
+
+#include "gromacs/gmxpreprocess/calc_verletbuf.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/inputrec.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/symtab.h"
#include "gromacs/utility/cstringutil.h"
-#include "readinp.h"
-#include "warninp.h"
-#include "readir.h"
-#include "toputil.h"
-#include "index.h"
-#include "network.h"
-#include "vec.h"
-#include "pbc.h"
-#include "mtop_util.h"
-#include "chargegroup.h"
-#include "inputrec.h"
-#include "calc_verletbuf.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#define MAXPTR 254
#define NOGID 255
}
else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
{
- simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*((exp(temperature_lambdas[i])-1)/(exp(1.0)-1));
+ simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*(gmx_expm1(temperature_lambdas[i])/gmx_expm1(1.0));
}
else
{
{
warning_error(wi, "rlist should be >= 0");
}
+ sprintf(err_buf, "nstlist can not be smaller than 0. (If you were trying to use the heuristic neighbour-list update scheme for efficient buffering for improved energy conservation, please use the Verlet cut-off scheme instead.)");
+ CHECK(ir->nstlist < 0);
process_interaction_modifier(ir, &ir->coulomb_modifier);
process_interaction_modifier(ir, &ir->vdw_modifier);
{
warning_error(wi, "rlistlong can not be shorter than rlist");
}
- if (IR_TWINRANGE(*ir) && ir->nstlist <= 0)
+ if (IR_TWINRANGE(*ir) && ir->nstlist == 0)
{
- warning_error(wi, "Can not have nstlist<=0 with twin-range interactions");
+ warning_error(wi, "Can not have nstlist == 0 with twin-range interactions");
}
}
(ir->ePBC != epbcNONE) ||
(ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
- if (ir->nstlist < 0)
- {
- warning_error(wi, "Can not have heuristic neighborlist updates without cut-off");
- }
if (ir->nstlist > 0)
{
warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
if (ir->cutoff_scheme == ecutsGROUP)
{
if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
- (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)) &&
- ir->nstlist != 1)
+ (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)))
{
warning_note(wi, "With exact cut-offs, rlist should be "
"larger than rcoulomb and rvdw, so that there "
warning_note(wi, "You have selected user tables with dispersion correction, the dispersion will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction between rvdw_switch and rvdw will not be double counted). Make sure that you really want dispersion correction to -C6/r^6.");
}
- if (ir->nstlist == -1)
- {
- sprintf(err_buf, "With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
- CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
- }
- sprintf(err_buf, "nstlist can not be smaller than -1");
- CHECK(ir->nstlist < -1);
-
if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
&& ir->rvdw != 0)
{
int np = 0;
char *copy0, *copy;
- copy0 = strdup(str);
+ copy0 = gmx_strdup(str);
copy = copy0;
ltrim(copy);
while (*copy != '\0')
}
for (i = 0; i < ir->nwall; i++)
{
- opts->wall_atomtype[i] = strdup(names[i]);
+ opts->wall_atomtype[i] = gmx_strdup(names[i]);
}
if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
{
if (ir->efep != efepNO)
{
- opts->couple_moltype = strdup(is->couple_moltype);
+ opts->couple_moltype = gmx_strdup(is->couple_moltype);
if (opts->couple_lam0 == opts->couple_lam1)
{
warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
double a, phi;
int i;
- t = strdup(s);
+ t = gmx_strdup(s);
trim(t);
cosine->n = 0;
void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
{
- int ig = -1, i;
+ int ig, i;
ig = search_string(IMDgname, grps->nr, gnames);
case efbposresSPHERE:
AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
break;
+ case efbposresCYLINDERX:
+ AbsRef[YY] = AbsRef[ZZ] = 1;
+ break;
+ case efbposresCYLINDERY:
+ AbsRef[XX] = AbsRef[ZZ] = 1;
+ break;
case efbposresCYLINDER:
+ /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
+ case efbposresCYLINDERZ:
AbsRef[XX] = AbsRef[YY] = 1;
break;
case efbposresX: /* d=XX */
check_disre(sys);
}
-void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr, warninp_t wi)
+void double_check(t_inputrec *ir, matrix box,
+ gmx_bool bHasNormalConstraints,
+ gmx_bool bHasAnyConstraints,
+ warninp_t wi)
{
real min_size;
gmx_bool bTWIN;
warning_error(wi, ptr);
}
- if (bConstr && ir->eConstrAlg == econtSHAKE)
+ if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
{
if (ir->shake_tol <= 0.0)
{
}
}
- if ( (ir->eConstrAlg == econtLINCS) && bConstr)
+ if ( (ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
{
/* If we have Lincs constraints: */
if (ir->eI == eiMD && ir->etc == etcNO &&
}
}
- if (bConstr && ir->epc == epcMTTK)
+ if (bHasAnyConstraints && ir->epc == epcMTTK)
{
- warning_note(wi, "MTTK with constraints is deprecated, and will be removed in GROMACS 5.1");
+ warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
}
if (ir->LincsWarnAngle > 90.0)
#ifndef GMX_GMXPREPROCESS_READIR_H
#define GMX_GMXPREPROCESS_READIR_H
-#include "typedefs.h"
-#include "readinp.h"
-#include "grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
int search_string(const char *s, int ng, char *gn[]);
/* Returns the index of string s in the index groups */
-void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr,
+void double_check(t_inputrec *ir, matrix box,
+ gmx_bool bHasNormalConstraints,
+ gmx_bool bHasAnyConstraints,
warninp_t wi);
/* Do more checks */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <string.h>
#include <stdlib.h>
+#include <string.h>
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
#include "gromacs/utility/cstringutil.h"
-#include "sysstuff.h"
-#include "princ.h"
-#include "gromacs/fileio/futil.h"
-#include "vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-#include "index.h"
-#include "symtab.h"
-#include "readinp.h"
-#include "readir.h"
-#include "mdatoms.h"
-#include "pbc.h"
-#include "gromacs/pulling/pull.h"
static char pulldim[STRLEN];
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "readir.h"
-#include "names.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/trnio.h"
-#include "txtdump.h"
-
-#include "gmx_fatal.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static char *RotStr = {"Enforced rotation:"};
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "resall.h"
#include <ctype.h>
+#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
+#include "gromacs/fileio/strdb.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/topology/symtab.h"
#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "symtab.h"
-#include "macros.h"
-#include "resall.h"
-#include "pgutil.h"
-#include "fflibutil.h"
-
-#include "gromacs/fileio/strdb.h"
gpp_atomtype_t read_atype(const char *ffdir, t_symtab *tab)
{
{
if (sscanf(line+n, "%s%n", str, &ni) == 1)
{
- rtp->rb[bt].b[rtp->rb[bt].nb].a[j] = strdup(str);
+ rtp->rb[bt].b[rtp->rb[bt].nb].a[j] = gmx_strdup(str);
}
else
{
n++;
}
rtrim(line+n);
- rtp->rb[bt].b[rtp->rb[bt].nb].s = strdup(line+n);
+ rtp->rb[bt].b[rtp->rb[bt].nb].s = gmx_strdup(line+n);
rtp->rb[bt].nb++;
}
/* give back unused memory */
{
gmx_fatal(FARGS, "in .rtp file at line:\n%s\n", line);
}
- rrtp[nrtp].resname = strdup(header);
- rrtp[nrtp].filebase = strdup(filebase);
+ rrtp[nrtp].resname = gmx_strdup(header);
+ rrtp[nrtp].filebase = gmx_strdup(filebase);
get_a_line(in, line, STRLEN);
bError = FALSE;
#ifndef GMX_GMXPREPROCESS_RESALL_H
#define GMX_GMXPREPROCESS_RESALL_H
-#include "typedefs.h"
-#include "hackblock.h"
-#include "gpp_atomtype.h"
-#include "grompp-impl.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
* Generates a fatal error when rtpname is not found.
*/
-gpp_atomtype_t read_atype(const char *ffdir, t_symtab *tab);
+gpp_atomtype_t read_atype(const char *ffdir, struct t_symtab *tab);
/* read atom type database(s) */
void read_resall(char *resdb, int *nrtp, t_restp **rtp,
- gpp_atomtype_t atype, t_symtab *tab,
+ gpp_atomtype_t atype, struct t_symtab *tab,
gmx_bool bAllowOverrideRTP);
/* read rtp database, append to the existing database */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "solvate.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "solvate.h"
#include <string.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/confio.h"
-#include "macros.h"
-#include "gromacs/fileio/futil.h"
-#include "atomprop.h"
-#include "names.h"
-#include "vec.h"
-#include "gmx_fatal.h"
+#include <algorithm>
+
#include "gromacs/commandline/pargs.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
-#include "addconf.h"
-#include "read-conformation.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/pdbio.h"
-#include "pbc.h"
-
-#ifdef DEBUG
-static void print_stat(rvec *x, int natoms, matrix box)
-{
- int i, m;
- rvec xmin, xmax;
- for (m = 0; (m < DIM); m++)
- {
- xmin[m] = x[0][m];
- xmax[m] = x[0][m];
- }
- for (i = 0; (i < natoms); i++)
- {
- for (m = 0; m < DIM; m++)
- {
- xmin[m] = min(xmin[m], x[i][m]);
- xmax[m] = max(xmax[m], x[i][m]);
- }
- }
- for (m = 0; (m < DIM); m++)
- {
- fprintf(stderr, "DIM %d XMIN %8.3f XMAX %8.3f BOX %8.3f\n",
- m, xmin[m], xmax[m], box[m][m]);
- }
-}
-#endif
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/gmxpreprocess/read-conformation.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/selection/nbsearch.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/atomsbuilder.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
char *name;
if ( (i == 0) || (atoms->atom[i].resind != atoms->atom[i-1].resind) )
{
/* see if this was a molecule type we haven't had yet: */
- moltp = NOTSET;
- for (j = 0; (j < nrmoltypes) && (moltp == NOTSET); j++)
+ moltp = -1;
+ for (j = 0; (j < nrmoltypes) && (moltp == -1); j++)
{
- if (strcmp(*(atoms->resinfo[atoms->atom[i].resind].name),
- moltypes[j].name) == 0)
+ /* cppcheck-suppress nullPointer
+ * moltypes is guaranteed to be allocated because otherwise
+ * nrmoltypes is 0. */
+ if (strcmp(*(atoms->resinfo[atoms->atom[i].resind].name), moltypes[j].name) == 0)
{
moltp = j;
}
}
- if (moltp == NOTSET)
+ if (moltp == -1)
{
moltp = nrmoltypes;
nrmoltypes++;
}
}
-/* Make a new configuration by adding boxes*/
-static void make_new_conformation(t_atoms *atoms, rvec *x, rvec *v, real *r, matrix box, ivec n_box)
+/*! \brief
+ * Generates a solvent configuration of desired size by stacking solvent boxes.
+ *
+ * \param[in,out] atoms Solvent atoms.
+ * \param[in,out] x Solvent positions.
+ * \param[in,out] v Solvent velocities (`*v` can be NULL).
+ * \param[in,out] r Solvent exclusion radii.
+ * \param[in] box Initial solvent box.
+ * \param[in] boxTarget Target box size.
+ *
+ * The solvent box of desired size is created by stacking the initial box in
+ * the smallest k*l*m array that covers the box, and then removing any residue
+ * where all atoms are outside the target box (with a small margin).
+ * This function does not remove overlap between solvent atoms across the
+ * edges.
+ *
+ * Note that the input configuration should be in the rectangular unit cell and
+ * have whole residues.
+ */
+static void replicateSolventBox(t_atoms *atoms, rvec **x, rvec **v, real **r,
+ const matrix box, const matrix boxTarget)
{
- int i, ix, iy, iz, m, j, imol, offset;
- rvec delta;
- int nmol;
+ // Calculate the box multiplication factors.
+ ivec n_box;
+ int nmol = 1;
+ for (int i = 0; i < DIM; ++i)
+ {
+ n_box[i] = 1;
+ while (n_box[i] * box[i][i] < boxTarget[i][i])
+ {
+ n_box[i]++;
+ }
+ nmol *= n_box[i];
+ }
+ fprintf(stderr, "Will generate new solvent configuration of %dx%dx%d boxes\n",
+ n_box[XX], n_box[YY], n_box[ZZ]);
+
+ // Create arrays for storing the generated system (cannot be done in-place
+ // in case the target box is smaller than the original in one dimension,
+ // but not in all).
+ t_atoms newAtoms;
+ init_t_atoms(&newAtoms, 0, FALSE);
+ gmx::AtomsBuilder builder(&newAtoms);
+ builder.reserve(atoms->nr * nmol, atoms->nres * nmol);
+ rvec *newX;
+ rvec *newV = NULL;
+ real *newR;
+ snew(newX, atoms->nr * nmol);
+ snew(newR, atoms->nr * nmol);
+ if (*v)
+ {
+ snew(newV, atoms->nr * nmol);
+ }
- nmol = n_box[XX]*n_box[YY]*n_box[ZZ];
+ const real maxRadius = *std::max_element(*r, *r + atoms->nr);
+ rvec boxWithMargin;
+ for (int i = 0; i < DIM; ++i)
+ {
+ // The code below is only interested about the box diagonal.
+ boxWithMargin[i] = boxTarget[i][i] + 3*maxRadius;
+ }
- /*print message*/
- fprintf(stderr, "Generating configuration\n");
- imol = 0;
- for (ix = 0; (ix < n_box[XX]); ix++)
+ for (int ix = 0; ix < n_box[XX]; ++ix)
{
+ rvec delta;
delta[XX] = ix*box[XX][XX];
- for (iy = 0; (iy < n_box[YY]); iy++)
+ for (int iy = 0; iy < n_box[YY]; ++iy)
{
delta[YY] = iy*box[YY][YY];
- for (iz = 0; (iz < n_box[ZZ]); iz++)
+ for (int iz = 0; iz < n_box[ZZ]; ++iz)
{
delta[ZZ] = iz*box[ZZ][ZZ];
- offset = imol*atoms->nr;
- for (i = 0; (i < atoms->nr); i++)
+ bool bKeepResidue = false;
+ for (int i = 0; i < atoms->nr; ++i)
{
- for (m = 0; (m < DIM); m++)
+ const int newIndex = builder.currentAtomCount();
+ bool bKeepAtom = true;
+ for (int m = 0; m < DIM; ++m)
{
- x[offset+i][m] = delta[m]+x[i][m];
+ const real newCoord = delta[m] + (*x)[i][m];
+ bKeepAtom = bKeepAtom && (newCoord < boxWithMargin[m]);
+ newX[newIndex][m] = newCoord;
}
- if (v)
+ bKeepResidue = bKeepResidue || bKeepAtom;
+ if (newV)
{
- for (m = 0; (m < DIM); m++)
+ copy_rvec((*v)[i], newV[newIndex]);
+ }
+ newR[newIndex] = (*r)[i];
+ builder.addAtom(*atoms, i);
+ if (i == atoms->nr - 1
+ || atoms->atom[i+1].resind != atoms->atom[i].resind)
+ {
+ if (bKeepResidue)
+ {
+ builder.finishResidue(atoms->resinfo[atoms->atom[i].resind]);
+ }
+ else
{
- v[offset+i][m] = v[i][m];
+ builder.discardCurrentResidue();
}
+ // Reset state for the next residue.
+ bKeepResidue = false;
}
- r[offset+i] = r[i];
}
- imol++;
}
}
}
- for (i = 1; (i < nmol); i++)
+ sfree(atoms->atom);
+ sfree(atoms->atomname);
+ sfree(atoms->resinfo);
+ atoms->nr = newAtoms.nr;
+ atoms->nres = newAtoms.nres;
+ atoms->atom = newAtoms.atom;
+ atoms->atomname = newAtoms.atomname;
+ atoms->resinfo = newAtoms.resinfo;
+ sfree(*x);
+ sfree(*v);
+ sfree(*r);
+ *x = newX;
+ *v = newV;
+ *r = newR;
+ fprintf(stderr, "Solvent box contains %d atoms in %d residues\n",
+ atoms->nr, atoms->nres);
+}
+
+/*! \brief
+ * Removes overlap of solvent atoms across the edges.
+ *
+ * \param[in,out] atoms Solvent atoms.
+ * \param[in,out] x Solvent positions.
+ * \param[in,out] v Solvent velocities (can be NULL).
+ * \param[in,out] r Solvent exclusion radii.
+ * \param[in] pbc PBC information.
+ *
+ * Solvent residues that lay on the edges that do not touch the origin are
+ * removed if they overlap with other solvent atoms across the PBC.
+ * This is done in this way as the assumption is that the input solvent
+ * configuration is already equilibrated, and so does not contain any
+ * undesirable overlap. The only overlap that should be removed is caused by
+ * cutting the box in half in replicateSolventBox() and leaving a margin of
+ * solvent outside those box edges; these atoms can then overlap with those on
+ * the opposite box edge in a way that is not part of the pre-equilibrated
+ * configuration.
+ */
+static void removeSolventBoxOverlap(t_atoms *atoms, rvec *x, rvec *v, real *r,
+ const t_pbc &pbc)
+{
+ gmx::AtomsRemover remover(*atoms);
+
+ // TODO: We could limit the amount of pairs searched significantly,
+ // since we are only interested in pairs where the positions are on
+ // opposite edges.
+ const real maxRadius = *std::max_element(r, r + atoms->nr);
+ gmx::AnalysisNeighborhood nb;
+ nb.setCutoff(2*maxRadius);
+ gmx::AnalysisNeighborhoodPositions pos(x, atoms->nr);
+ gmx::AnalysisNeighborhoodSearch search = nb.initSearch(&pbc, pos);
+ gmx::AnalysisNeighborhoodPairSearch pairSearch = search.startPairSearch(pos);
+ gmx::AnalysisNeighborhoodPair pair;
+ while (pairSearch.findNextPair(&pair))
{
- int offs = i*atoms->nr;
- int offsres = i*atoms->nres;
- for (j = 0; (j < atoms->nr); j++)
+ const int i1 = pair.refIndex();
+ const int i2 = pair.testIndex();
+ if (remover.isMarked(i2))
+ {
+ pairSearch.skipRemainingPairsForTestPosition();
+ continue;
+ }
+ if (remover.isMarked(i1) || atoms->atom[i1].resind == atoms->atom[i2].resind)
{
- atoms->atomname[offs+j] = atoms->atomname[j];
- atoms->atom[offs+j].resind = atoms->atom[j].resind + offsres;
- atoms->resinfo[atoms->atom[offs+j].resind] =
- atoms->resinfo[atoms->atom[j].resind];
- atoms->resinfo[atoms->atom[offs+j].resind].nr += offsres;
+ continue;
}
+ if (pair.distance2() < sqr(r[i1] + r[i2]))
+ {
+ rvec dx;
+ rvec_sub(x[i2], x[i1], dx);
+ bool bCandidate1 = false, bCandidate2 = false;
+ // To satisfy Clang static analyzer.
+ GMX_ASSERT(pbc.ndim_ePBC <= DIM, "Too many periodic dimensions");
+ for (int d = 0; d < pbc.ndim_ePBC; ++d)
+ {
+ // If the distance in some dimension is larger than the
+ // cutoff, then it means that the distance has been computed
+ // over the PBC. Mark the position with a larger coordinate
+ // for potential removal.
+ if (dx[d] > maxRadius)
+ {
+ bCandidate2 = true;
+ }
+ else if (dx[d] < -maxRadius)
+ {
+ bCandidate1 = true;
+ }
+ }
+ // Only mark one of the positions for removal if both were
+ // candidates.
+ if (bCandidate2 && (!bCandidate1 || i2 > i1))
+ {
+ remover.markResidue(*atoms, i2, true);
+ pairSearch.skipRemainingPairsForTestPosition();
+ }
+ else if (bCandidate1)
+ {
+ remover.markResidue(*atoms, i1, true);
+ }
+ }
+ }
+
+ remover.removeMarkedVectors(x);
+ if (v != NULL)
+ {
+ remover.removeMarkedVectors(v);
+ }
+ remover.removeMarkedValues(r);
+ const int originalAtomCount = atoms->nr;
+ remover.removeMarkedAtoms(atoms);
+ fprintf(stderr, "Removed %d solvent atoms due to solvent-solvent overlap\n",
+ originalAtomCount - atoms->nr);
+}
+
+/*! \brief
+ * Removes solvent molecules that overlap with the solute, and optionally also
+ * those that are outside a given shell radius from the solute.
+ *
+ * \param[in,out] atoms Solvent atoms.
+ * \param[in,out] x Solvent positions.
+ * \param[in,out] v Solvent velocities (can be NULL).
+ * \param[in,out] r Solvent exclusion radii.
+ * \param[in] pbc PBC information.
+ * \param[in] soluteAtomCount Number of solute atoms.
+ * \param[in] x_solute Solute positions.
+ * \param[in] r_solute Solute exclusion radii.
+ * \param[in] rshell If >0, only keep solvent atoms within a shell of
+ * this size from the solute.
+ */
+static void removeSoluteOverlap(t_atoms *atoms, rvec *x, rvec *v, real *r,
+ const t_pbc &pbc, int soluteAtomCount,
+ const rvec *x_solute, const real *r_solute,
+ real rshell)
+{
+ const real maxRadius1
+ = *std::max_element(r, r + atoms->nr);
+ const real maxRadius2
+ = *std::max_element(r_solute, r_solute + soluteAtomCount);
+
+ gmx::AtomsRemover remover(*atoms);
+ // If rshell is >0, the neighborhood search looks at all pairs
+ // within rshell, and unmarks those that are within the cutoff.
+ // This line marks everything, so that solvent outside rshell remains
+ // marked after the loop.
+ // Without rshell, the neighborhood search only marks the overlapping
+ // solvent atoms, and all others are left alone.
+ if (rshell > 0.0)
+ {
+ remover.markAll();
+ }
+
+ gmx::AnalysisNeighborhood nb;
+ nb.setCutoff(std::max(maxRadius1 + maxRadius2, rshell));
+ gmx::AnalysisNeighborhoodPositions posSolute(x_solute, soluteAtomCount);
+ gmx::AnalysisNeighborhoodSearch search = nb.initSearch(&pbc, posSolute);
+ gmx::AnalysisNeighborhoodPositions pos(x, atoms->nr);
+ gmx::AnalysisNeighborhoodPairSearch pairSearch = search.startPairSearch(pos);
+ gmx::AnalysisNeighborhoodPair pair;
+ while (pairSearch.findNextPair(&pair))
+ {
+ if (remover.isMarked(pair.testIndex()))
+ {
+ pairSearch.skipRemainingPairsForTestPosition();
+ continue;
+ }
+ const real r1 = r_solute[pair.refIndex()];
+ const real r2 = r[pair.testIndex()];
+ const bool bRemove = (pair.distance2() < sqr(r1 + r2));
+ remover.markResidue(*atoms, pair.testIndex(), bRemove);
}
- atoms->nr *= nmol;
- atoms->nres *= nmol;
- for (i = 0; i < DIM; i++)
+
+ remover.removeMarkedVectors(x);
+ if (v != NULL)
+ {
+ remover.removeMarkedVectors(v);
+ }
+ remover.removeMarkedValues(r);
+ const int originalAtomCount = atoms->nr;
+ remover.removeMarkedAtoms(atoms);
+ fprintf(stderr, "Removed %d solvent atoms due to solute-solvent overlap\n",
+ originalAtomCount - atoms->nr);
+}
+
+/*! \brief
+ * Removes a given number of solvent residues.
+ *
+ * \param[in,out] atoms Solvent atoms.
+ * \param[in,out] x Solvent positions.
+ * \param[in,out] v Solvent velocities (can be NULL).
+ * \param[in] numberToRemove Number of residues to remove.
+ *
+ * This function is called last in the process of creating the solvent box,
+ * so it does not operate on the exclusion radii, as no code after this needs
+ * them.
+ */
+static void removeExtraSolventMolecules(t_atoms *atoms, rvec *x, rvec *v,
+ int numberToRemove)
+{
+ gmx::AtomsRemover remover(*atoms);
+ // TODO: It might be nicer to remove a random set of residues, but
+ // in practice this should give a roughly uniform spatial distribution.
+ const int stride = atoms->nr / numberToRemove;
+ for (int i = 0; i < numberToRemove; ++i)
{
- for (j = 0; j < DIM; j++)
+ int atomIndex = (i+1)*stride - 1;
+ while (remover.isMarked(atomIndex))
{
- box[j][i] *= n_box[j];
+ ++atomIndex;
+ if (atomIndex == atoms->nr)
+ {
+ atomIndex = 0;
+ }
}
+ remover.markResidue(*atoms, atomIndex, true);
+ }
+ remover.removeMarkedVectors(x);
+ if (v != NULL)
+ {
+ remover.removeMarkedVectors(v);
}
+ remover.removeMarkedAtoms(atoms);
}
-static void add_solv(const char *fn, t_atoms *atoms, rvec **x, rvec **v, real **exclusionDistances,
- int ePBC, matrix box,
- gmx_atomprop_t aps,
- real defaultDistance, real scaleFactor, int *atoms_added,
- int *residues_added, real rshell, int max_sol,
- const output_env_t oenv)
+static void add_solv(const char *fn, t_atoms *atoms, rvec **x, rvec **v,
+ int ePBC, matrix box, gmx_atomprop_t aps,
+ real defaultDistance, real scaleFactor,
+ real rshell, int max_sol)
{
- int i, nmol;
- ivec n_box;
- char filename[STRLEN];
- char title_solvt[STRLEN];
t_atoms *atoms_solvt;
rvec *x_solvt, *v_solvt = NULL;
- real *exclusionDistances_solvt;
int ePBC_solvt;
matrix box_solvt;
- int onr, onres;
- char *lfn;
- lfn = gmxlibfn(fn);
- strncpy(filename, lfn, STRLEN);
- sfree(lfn);
+ char *filename = gmxlibfn(fn);
+ snew(atoms_solvt, 1);
+ char *title_solvt
+ = readConformation(filename, atoms_solvt, &x_solvt, &v_solvt,
+ &ePBC_solvt, box_solvt, "solvent");
+ sfree(title_solvt);
+ if (0 == atoms_solvt->nr)
{
- int natoms;
- get_stx_coordnum(filename, &natoms);
- if (0 == natoms)
- {
- gmx_fatal(FARGS, "No solvent in %s, please check your input\n", filename);
- }
- snew(atoms_solvt, 1);
- init_t_atoms(atoms_solvt, natoms, FALSE);
- }
- snew(x_solvt, atoms_solvt->nr);
- if (v)
- {
- snew(v_solvt, atoms_solvt->nr);
- }
- snew(exclusionDistances_solvt, atoms_solvt->nr);
- snew(atoms_solvt->resinfo, atoms_solvt->nr);
- snew(atoms_solvt->atomname, atoms_solvt->nr);
- snew(atoms_solvt->atom, atoms_solvt->nr);
- atoms_solvt->pdbinfo = NULL;
- fprintf(stderr, "Reading solvent configuration%s\n",
- v_solvt ? " and velocities" : "");
- read_stx_conf(filename, title_solvt, atoms_solvt, x_solvt, v_solvt,
- &ePBC_solvt, box_solvt);
- fprintf(stderr, "\"%s\"\n", title_solvt);
- fprintf(stderr, "solvent configuration contains %d atoms in %d residues\n",
- atoms_solvt->nr, atoms_solvt->nres);
+ gmx_fatal(FARGS, "No solvent in %s, please check your input\n", filename);
+ }
+ sfree(filename);
fprintf(stderr, "\n");
/* apply pbc for solvent configuration for whole molecules */
rm_res_pbc(atoms_solvt, x_solvt, box_solvt);
/* initialise distance arrays for solvent configuration */
- exclusionDistances_solvt = makeExclusionDistances(atoms_solvt, aps, defaultDistance, scaleFactor);
+ fprintf(stderr, "Initialising inter-atomic distances...\n");
+ real *exclusionDistances
+ = makeExclusionDistances(atoms, aps, defaultDistance, scaleFactor);
+ real *exclusionDistances_solvt
+ = makeExclusionDistances(atoms_solvt, aps, defaultDistance, scaleFactor);
- /* calculate the box multiplication factors n_box[0...DIM] */
- nmol = 1;
- for (i = 0; (i < DIM); i++)
+ /* generate a new solvent configuration */
+ fprintf(stderr, "Generating solvent configuration\n");
+ t_pbc pbc;
+ set_pbc(&pbc, ePBC, box);
+ replicateSolventBox(atoms_solvt, &x_solvt, &v_solvt, &exclusionDistances_solvt,
+ box_solvt, box);
+ if (ePBC != epbcNONE)
{
- n_box[i] = 1;
- while (n_box[i]*box_solvt[i][i] < box[i][i])
- {
- n_box[i]++;
- }
- nmol *= n_box[i];
+ removeSolventBoxOverlap(atoms_solvt, x_solvt, v_solvt, exclusionDistances_solvt, pbc);
}
- fprintf(stderr, "Will generate new solvent configuration of %dx%dx%d boxes\n",
- n_box[XX], n_box[YY], n_box[ZZ]);
-
- /* realloc atoms_solvt for the new solvent configuration */
- srenew(atoms_solvt->resinfo, atoms_solvt->nres*nmol);
- srenew(atoms_solvt->atomname, atoms_solvt->nr*nmol);
- srenew(atoms_solvt->atom, atoms_solvt->nr*nmol);
- srenew(x_solvt, atoms_solvt->nr*nmol);
- if (v_solvt)
+ if (atoms->nr > 0)
{
- srenew(v_solvt, atoms_solvt->nr*nmol);
+ removeSoluteOverlap(atoms_solvt, x_solvt, v_solvt, exclusionDistances_solvt, pbc,
+ atoms->nr, *x, exclusionDistances, rshell);
}
- srenew(exclusionDistances_solvt, atoms_solvt->nr*nmol);
-
- /* generate a new solvent configuration */
- make_new_conformation(atoms_solvt, x_solvt, v_solvt, exclusionDistances_solvt, box_solvt, n_box);
-#ifdef DEBUG
- print_stat(x_solvt, atoms_solvt->nr, box_solvt);
-#endif
+ if (max_sol > 0 && atoms_solvt->nres > max_sol)
+ {
+ const int numberToRemove = atoms_solvt->nres - max_sol;
+ removeExtraSolventMolecules(atoms_solvt, x_solvt, v_solvt, numberToRemove);
+ }
-#ifdef DEBUG
- print_stat(x_solvt, atoms_solvt->nr, box_solvt);
-#endif
/* Sort the solvent mixture, not the protein... */
sort_molecule(&atoms_solvt, x_solvt, v_solvt, exclusionDistances_solvt);
- /* add the two configurations */
- onr = atoms->nr;
- onres = atoms->nres;
- add_conf(atoms, x, v, exclusionDistances, TRUE, ePBC, box, FALSE,
- atoms_solvt, x_solvt, v_solvt, exclusionDistances_solvt, TRUE, rshell, max_sol, oenv);
- *atoms_added = atoms->nr-onr;
- *residues_added = atoms->nres-onres;
+ // Merge the two configurations.
+ srenew(*x, atoms->nr + atoms_solvt->nr);
+ if (v != NULL)
+ {
+ srenew(*v, atoms->nr + atoms_solvt->nr);
+ }
+ for (int i = 0; i < atoms_solvt->nr; ++i)
+ {
+ const int index = atoms->nr + i;
+ copy_rvec(x_solvt[i], (*x)[index]);
+ if (v != NULL)
+ {
+ copy_rvec(v_solvt[i], (*v)[index]);
+ }
+ }
+ {
+ gmx::AtomsBuilder builder(atoms);
+ builder.mergeAtoms(*atoms_solvt);
+ }
+ fprintf(stderr, "Generated solvent containing %d atoms in %d residues\n",
+ atoms_solvt->nr, atoms_solvt->nres);
sfree(x_solvt);
+ sfree(v_solvt);
+ sfree(exclusionDistances);
sfree(exclusionDistances_solvt);
done_atom(atoms_solvt);
sfree(atoms_solvt);
-
- fprintf(stderr, "Generated solvent containing %d atoms in %d residues\n",
- *atoms_added, *residues_added);
}
static void update_top(t_atoms *atoms, matrix box, int NFILE, t_filenm fnm[],
"into the box. This can create a void that can cause problems later.",
"Choose your volume wisely.[PAR]",
- "The program can optionally rotate the solute molecule to align the",
- "longest molecule axis along a box edge. This way the amount of solvent",
- "molecules necessary is reduced.",
- "It should be kept in mind that this only works for",
- "short simulations, as e.g. an alpha-helical peptide in solution can ",
- "rotate over 90 degrees, within 500 ps. In general it is therefore ",
- "better to make a more or less cubic box.[PAR]",
-
"Setting [TT]-shell[tt] larger than zero will place a layer of water of",
"the specified thickness (nm) around the solute. Hint: it is a good",
"idea to put the protein in the center of a box first (using [gmx-editconf]).",
/* parameter data */
gmx_bool bProt, bBox;
const char *conf_prot, *confout;
- real *exclusionDistances = NULL;
gmx_atomprop_t aps;
/* protein configuration data */
int ePBC = -1;
matrix box;
- /* other data types */
- int atoms_added, residues_added;
-
t_filenm fnm[] = {
{ efSTX, "-cp", "protein", ffOPTRD },
{ efSTX, "-cs", "spc216", ffLIBRD},
"Keep velocities from input solute and solvent" },
};
- if (!parse_common_args(&argc, argv, PCA_BE_NICE, NFILE, fnm, asize(pa), pa,
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
/* Generate a solute configuration */
conf_prot = opt2fn("-cp", NFILE, fnm);
title = readConformation(conf_prot, atoms, &x,
- bReadV ? &v : NULL, &ePBC, box);
- exclusionDistances = makeExclusionDistances(atoms, aps, defaultDistance, scaleFactor);
-
+ bReadV ? &v : NULL, &ePBC, box, "solute");
if (bReadV && !v)
{
fprintf(stderr, "Note: no velocities found\n");
"or give explicit -box command line option");
}
- add_solv(solventFileName, atoms, &x, v ? &v : NULL, &exclusionDistances, ePBC, box,
- aps, defaultDistance, scaleFactor, &atoms_added, &residues_added, r_shell, max_sol,
- oenv);
+ add_solv(solventFileName, atoms, &x, v ? &v : NULL, ePBC, box,
+ aps, defaultDistance, scaleFactor, r_shell, max_sol);
/* write new configuration 1 to file confout */
confout = ftp2fn(efSTO, NFILE, fnm);
if (bProt)
{
write_sto_conf(confout, title, atoms, x, v, ePBC, box);
- /* print box sizes and box type to stderr */
- fprintf(stderr, "%s\n", title);
}
else
{
update_top(atoms, box, NFILE, fnm, aps);
gmx_atomprop_destroy(aps);
- sfree(exclusionDistances);
sfree(x);
sfree(v);
done_atom(atoms);
sfree(atoms);
+ sfree(title);
+ output_env_done(oenv);
+ done_filenms(NFILE, fnm);
return 0;
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "typedefs.h"
+#include "sortwater.h"
+
+#include <stdlib.h>
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "sortwater.h"
static rvec *xptr, box_1;
static int nwat;
#ifndef _sortwater_h
#define _sortwater_h
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/random/random.h"
#ifdef __cplusplus
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "specbond.h"
#include <ctype.h>
#include <math.h>
#include <string.h>
-#include "typedefs.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/strdb.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
-#include "specbond.h"
-#include "pdb2top.h"
-#include "vec.h"
-#include "macros.h"
gmx_bool yesno(void)
{
}
else
{
- sb[n].res1 = strdup(r1buf);
- sb[n].res2 = strdup(r2buf);
- sb[n].newres1 = strdup(nr1buf);
- sb[n].newres2 = strdup(nr2buf);
- sb[n].atom1 = strdup(a1buf);
- sb[n].atom2 = strdup(a2buf);
+ sb[n].res1 = gmx_strdup(r1buf);
+ sb[n].res2 = gmx_strdup(r2buf);
+ sb[n].newres1 = gmx_strdup(nr1buf);
+ sb[n].newres2 = gmx_strdup(nr2buf);
+ sb[n].atom1 = gmx_strdup(a1buf);
+ sb[n].atom2 = gmx_strdup(a2buf);
sb[n].nbond1 = nb1;
sb[n].nbond2 = nb2;
sb[n].length = length;
}
/* this used to free *resname, which messes up the symtab! */
snew(pdba->resinfo[resind].rtp, 1);
- *pdba->resinfo[resind].rtp = strdup(newres);
+ *pdba->resinfo[resind].rtp = gmx_strdup(newres);
}
int mk_specbonds(t_atoms *pdba, rvec x[], gmx_bool bInteractive,
/* Store the residue numbers in the bonds array */
bonds[nbonds].res1 = specp[i];
bonds[nbonds].res2 = specp[j];
- bonds[nbonds].a1 = strdup(*pdba->atomname[ai]);
- bonds[nbonds].a2 = strdup(*pdba->atomname[aj]);
+ bonds[nbonds].a1 = gmx_strdup(*pdba->atomname[ai]);
+ bonds[nbonds].a2 = gmx_strdup(*pdba->atomname[aj]);
/* rename residues */
if (bSwap)
{
#ifndef GMX_GMXPREPROCESS_SPECBOND_H
#define GMX_GMXPREPROCESS_SPECBOND_H
-#include "pdb2top.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "ter_db.h"
#include <ctype.h>
#include <string.h>
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "symtab.h"
-#include "gromacs/fileio/futil.h"
-#include "resall.h"
-#include "h_db.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
-#include "ter_db.h"
-#include "toputil.h"
#include "gromacs/fileio/gmxfio.h"
-#include "fflibutil.h"
-
#include "gromacs/fileio/strdb.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/h_db.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
/* use bonded types definitions in hackblock.h */
#define ekwRepl ebtsNR+1
{
if (nr == 4)
{
- *nname = strdup(buf[i++]);
+ *nname = gmx_strdup(buf[i++]);
}
else
{
srenew(tb, maxnb);
}
clear_t_hackblock(&tb[nb]);
- tb[nb].name = strdup(header);
- tb[nb].filebase = strdup(filebase);
+ tb[nb].name = gmx_strdup(header);
+ tb[nb].filebase = gmx_strdup(filebase);
}
}
else
gmx_fatal(FARGS, "Reading Termini Database '%s': "
"expected atom name on line\n%s", fn, line);
}
- tb[nb].hack[nh].oname = strdup(buf);
+ tb[nb].hack[nh].oname = gmx_strdup(buf);
/* we only replace or delete one atom at a time */
tb[nb].hack[nh].nr = 1;
}
{
if (tb[nb].hack[nh].oname != NULL)
{
- tb[nb].hack[nh].nname = strdup(tb[nb].hack[nh].oname);
+ tb[nb].hack[nh].nname = gmx_strdup(tb[nb].hack[nh].oname);
}
else
{
{
if (sscanf(line+n, "%s%n", buf, &ni) == 1)
{
- tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = strdup(buf);
+ tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = gmx_strdup(buf);
}
else
{
}
strcpy(buf, "");
sscanf(line+n, "%s", buf);
- tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].s = strdup(buf);
+ tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].s = gmx_strdup(buf);
tb[nb].rb[kwnr].nb++;
}
else
#ifndef GMX_GMXPREPROCESS_TER_DB_H
#define GMX_GMXPREPROCESS_TER_DB_H
-#include "sysstuff.h"
-#include "hackblock.h"
-#include "grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
#ifdef __cplusplus
extern "C" {
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-set(testname "PreprocessingTests")
-set(exename "preprocessing-tools-test")
-
-gmx_build_unit_test(
- ${testname}
- ${exename}
- # files with code for test fixtures
- solvate.cpp
- insert-molecules.cpp
- )
-gmx_register_integration_test(
- ${testname}
- ${exename}
- )
+gmx_add_unit_test(GmxPreprocessTests gmxpreprocess-test
+ solvate.cpp
+ insert-molecules.cpp
+ )
* Tests for insertion of molecules.
*
* \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
*/
+#include "gmxpre.h"
+
+#include "gromacs/gmxpreprocess/insert-molecules.h"
-#include "../insert-molecules.h"
-#include "testutils/integrationtests.h"
#include "testutils/cmdlinetest.h"
-#include "gromacs/fileio/futil.h"
+#include "testutils/refdata.h"
namespace
{
-//! Helper typedef
-typedef int (*CMainFunction)(int argc, char *argv[]);
+using gmx::test::CommandLine;
-//! Test fixture for insert-molecules
-class InsertMoleculesTest : public gmx::test::IntegrationTestFixture
+class InsertMoleculesTest : public gmx::test::CommandLineTestBase
{
public:
- //! Constructor
InsertMoleculesTest()
- : ciFileName(fileManager_.getInputFilePath("x.gro")),
- outputFileName(fileManager_.getTemporaryFilePath("out.gro")),
- theFunction(gmx_insert_molecules)
{
- caller.append("insert-molecules");
- caller.addOption("-o", outputFileName);
+ setOutputFile("-o", "out.gro");
}
- public:
- //! Name of file to use for -ci
- std::string ciFileName;
- //! Name of output file to use for -o
- std::string outputFileName;
- //! Helper object for managing the call to gmx_insert_molecules
- gmx::test::CommandLine caller;
- //! Points to the function to be tested
- CMainFunction theFunction;
+ void runTest(const CommandLine &args)
+ {
+ CommandLine &cmdline = commandLine();
+ cmdline.merge(args);
+
+ gmx::test::TestReferenceChecker rootChecker(this->rootChecker());
+ rootChecker.checkString(args.toString(), "CommandLine");
+
+ ASSERT_EQ(0, gmx::test::CommandLineTestHelper::runModule(
+ &gmx::InsertMoleculesInfo::create, &cmdline));
+
+ checkOutputFiles();
+ }
};
-TEST_F(InsertMoleculesTest, f_ci_Works)
+TEST_F(InsertMoleculesTest, InsertsMoleculesIntoExistingConfiguration)
{
- caller.addOption("-f", fileManager_.getInputFilePath("spc-and-methanol.gro"));
- caller.addOption("-nmol", "1");
- caller.addOption("-ci", ciFileName);
-
- ASSERT_EQ(0, theFunction(caller.argc(), caller.argv()));
+ const char *const cmdline[] = {
+ "insert-molecules", "-nmol", "1"
+ };
+ setInputFile("-f", "spc-and-methanol.gro");
+ setInputFile("-ci", "x2.gro");
+ runTest(CommandLine(cmdline));
}
-TEST_F(InsertMoleculesTest, box_ci_Works)
+TEST_F(InsertMoleculesTest, InsertsMoleculesIntoEmptyBox)
{
- caller.addOption("-box", "4");
- caller.addOption("-nmol", "5");
- caller.addOption("-ci", ciFileName);
-
- ASSERT_EQ(0, theFunction(caller.argc(), caller.argv()));
+ const char *const cmdline[] = {
+ "insert-molecules", "-box", "4", "-nmol", "5"
+ };
+ setInputFile("-ci", "x2.gro");
+ runTest(CommandLine(cmdline));
}
-TEST_F(InsertMoleculesTest, f_box_ci_Works)
+TEST_F(InsertMoleculesTest, InsertsMoleculesIntoEnlargedBox)
{
- caller.addOption("-f", fileManager_.getInputFilePath("spc-and-methanol.gro"));
- caller.addOption("-box", "4");
- caller.addOption("-nmol", "2");
- caller.addOption("-ci", ciFileName);
-
- ASSERT_EQ(0, theFunction(caller.argc(), caller.argv()));
+ const char *const cmdline[] = {
+ "insert-molecules", "-box", "4", "-nmol", "2"
+ };
+ setInputFile("-f", "spc-and-methanol.gro");
+ setInputFile("-ci", "x.gro");
+ runTest(CommandLine(cmdline));
}
-// TODO Someone who knows what -ip is good for should write something
-// to test it
+TEST_F(InsertMoleculesTest, InsertsMoleculesIntoFixedPositions)
+{
+ const char *const cmdline[] = {
+ "insert-molecules", "-box", "4"
+ };
+ const char *const positions[] = {
+ "0.0 0.0 0.0",
+ "1.0 2.0 3.0",
+ "0.99 2.01 3.0",
+ "2.0 1.0 2.0"
+ };
+ setInputFile("-ci", "x0.gro");
+ setInputFileContents("-ip", "dat", positions);
+ runTest(CommandLine(cmdline));
+}
} // namespace
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">insert-molecules -box 4 -nmol 5</String>
+ <OutputFiles Name="Files">
+ <String Name="-o"><![CDATA[
+test two-residue molecule for insertion
+ 10
+ 1X X1 1 3.071 2.691 0.351
+ 2Y Y1 2 3.098 2.610 0.247
+ 3X X1 3 3.891 3.308 3.910
+ 4Y Y1 4 3.910 3.371 4.028
+ 5X X1 5 2.401 2.975 2.308
+ 6Y Y1 6 2.489 3.059 2.248
+ 7X X1 7 3.193 2.571 3.486
+ 8Y Y1 8 3.102 2.666 3.516
+ 9X X1 9 3.937 1.138 0.823
+ 10Y Y1 10 3.845 1.125 0.921
+ 4.00000 4.00000 4.00000
+]]></String>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">insert-molecules -box 4 -nmol 2</String>
+ <OutputFiles Name="Files">
+ <String Name="-o"><![CDATA[
+Test system for solvate/insert-molecules
+ 10
+ 1MeOH Me1 1 1.970 1.460 1.209
+ 1MeOH O2 2 1.978 1.415 1.082
+ 1MeOH H3 3 1.905 1.460 1.030
+ 2SOL OW 4 1.555 1.511 0.703
+ 2SOL HW1 5 1.498 1.495 0.784
+ 2SOL HW2 6 1.496 1.521 0.623
+ 3X X1 7 3.071 2.691 0.351
+ 3X X2 8 3.098 2.610 0.247
+ 4X X1 9 3.891 3.308 3.910
+ 4X X2 10 3.910 3.371 4.028
+ 4.00000 4.00000 4.00000
+]]></String>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">insert-molecules -nmol 1</String>
+ <OutputFiles Name="Files">
+ <String Name="-o"><![CDATA[
+Test system for solvate/insert-molecules
+ 8
+ 1MeOH Me1 1 1.970 1.460 1.209
+ 1MeOH O2 2 1.978 1.415 1.082
+ 1MeOH H3 3 1.905 1.460 1.030
+ 2SOL OW 4 1.555 1.511 0.703
+ 2SOL HW1 5 1.498 1.495 0.784
+ 2SOL HW2 6 1.496 1.521 0.623
+ 3X X1 7 2.308 2.035 0.277
+ 4Y Y1 8 2.335 1.954 0.173
+ 3.01000 3.01000 3.01000
+]]></String>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">insert-molecules -box 4</String>
+ <OutputFiles Name="Files">
+ <String Name="-o"><![CDATA[
+test molecule for insertion at origin
+ 6
+ 1X X1 1 0.000 0.000 0.000
+ 1X X2 2 0.027 -0.081 -0.104
+ 2X X1 3 1.000 2.000 3.000
+ 2X X2 4 1.019 2.063 3.118
+ 3X X1 5 2.000 1.000 2.000
+ 3X X2 6 1.893 1.048 1.933
+ 4.00000 4.00000 4.00000
+]]></String>
+ </OutputFiles>
+</ReferenceData>
* Tests for solvation.
*
* \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
*/
-#include "../solvate.h"
-#include "testutils/integrationtests.h"
+#include "gmxpre.h"
+
+#include "gromacs/gmxpreprocess/solvate.h"
+
+#include "gromacs/utility/futil.h"
+
#include "testutils/cmdlinetest.h"
-#include "gromacs/fileio/futil.h"
+#include "testutils/testfilemanager.h"
namespace
{
-//! Helper typedef
-typedef int (*CMainFunction)(int argc, char *argv[]);
+using gmx::test::CommandLine;
-//! Test fixture for gmx solvate
-class SolvateTest : public gmx::test::IntegrationTestFixture
+class SolvateTest : public gmx::test::CommandLineTestBase
{
public:
- //! Constructor
SolvateTest()
- : cpFileName(fileManager_.getInputFilePath("spc-and-methanol.gro")),
- topFileName(fileManager_.getInputFilePath("spc-and-methanol.top")),
- outputFileName(fileManager_.getTemporaryFilePath("out.gro")),
- theFunction(gmx_solvate)
{
- caller.append("solvate");
- caller.addOption("-o", outputFileName);
+ setOutputFile("-o", "out.gro");
}
- public:
- //! Name of file to use for -cp
- std::string cpFileName;
- //! Name of input file to use for -p (if used)
- std::string topFileName;
- //! Name of output file to use for -o
- std::string outputFileName;
- //! Helper object for managing the call to gmx_solvate
- gmx::test::CommandLine caller;
- //! Points to the function to be tested
- CMainFunction theFunction;
+ void runTest(const CommandLine &args)
+ {
+ CommandLine &cmdline = commandLine();
+ cmdline.merge(args);
+
+ ASSERT_EQ(0, gmx_solvate(cmdline.argc(), cmdline.argv()));
+ }
};
TEST_F(SolvateTest, cs_box_Works)
{
- caller.append("-cs"); // use default solvent box
- caller.addOption("-box", "1.1");
-
- ASSERT_EQ(0, theFunction(caller.argc(), caller.argv()));
+ // use default solvent box (-cs without argument)
+ const char *const cmdline[] = {
+ "solvate", "-cs", "-box", "1.1"
+ };
+ runTest(CommandLine(cmdline));
}
TEST_F(SolvateTest, cs_cp_Works)
{
- caller.append("-cs"); // use default solvent box
- caller.addOption("-cp", cpFileName);
-
- ASSERT_EQ(0, theFunction(caller.argc(), caller.argv()));
+ // use default solvent box (-cs without argument)
+ const char *const cmdline[] = {
+ "solvate", "-cs"
+ };
+ setInputFile("-cp", "spc-and-methanol.gro");
+ runTest(CommandLine(cmdline));
}
TEST_F(SolvateTest, cs_cp_p_Works)
{
- caller.append("-cs"); // use default solvent box
- caller.addOption("-cp", cpFileName);
+ // use default solvent box (-cs without argument)
+ const char *const cmdline[] = {
+ "solvate", "-cs"
+ };
+ setInputFile("-cp", "spc-and-methanol.gro");
- std::string modifiableTopFileName = fileManager_.getTemporaryFilePath(".top");
+ // TODO: Consider adding a convenience method for this.
+ std::string topFileName = fileManager().getInputFilePath("spc-and-methanol.top");
+ std::string modifiableTopFileName = fileManager().getTemporaryFilePath(".top");
gmx_file_copy(topFileName.c_str(), modifiableTopFileName.c_str(), true);
- caller.addOption("-p", modifiableTopFileName);
+ commandLine().addOption("-p", modifiableTopFileName);
- ASSERT_EQ(0, theFunction(caller.argc(), caller.argv()));
+ runTest(CommandLine(cmdline));
}
} // namespace
-
+Test system for solvate/insert-molecules
6
1MeOH Me1 1 1.970 1.460 1.209 -0.8587 -0.1344 -0.0643
1MeOH O2 2 1.978 1.415 1.082 0.0623 -0.1787 0.0036
--- /dev/null
+test molecule for insertion at origin
+ 2
+ 1X X1 1 0.000 0.000 0.000
+ 1X X2 2 0.008 -0.045 -0.127
+ 3.01000 3.01000 3.01000
--- /dev/null
+test two-residue molecule for insertion
+ 2
+ 1X X1 1 1.970 1.460 1.209 -0.8587 -0.1344 -0.0643
+ 2Y Y1 2 1.978 1.415 1.082 0.0623 -0.1787 0.0036
+ 3.01000 3.01000 3.01000
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "tomorse.h"
#include <ctype.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
-#include "typedefs.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/utility/cstringutil.h"
-#include "grompp-impl.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "toputil.h"
-#include "gmx_fatal.h"
-#include "gpp_atomtype.h"
-#include "macros.h"
-
-#include "tomorse.h"
typedef struct {
char *ai, *aj;
srenew(t2m, maxn2m);
}
/* Copy the values */
- t2m[n2m].ai = strdup(ai);
- t2m[n2m].aj = strdup(aj);
+ t2m[n2m].ai = gmx_strdup(ai);
+ t2m[n2m].aj = gmx_strdup(aj);
t2m[n2m].e_diss = e_diss;
/* Increment counter */
n2m++;
#ifndef GMX_GMXPREPROCESS_TOMORSE_H
#define GMX_GMXPREPROCESS_TOMORSE_H
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
#include <stdio.h>
-#include "typedefs.h"
+
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "topdirs.h"
-#include <stdio.h>
#include <stdarg.h>
+#include <stdio.h>
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
-#include "topdirs.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* Must correspond to the directive enum in grompp-impl.h */
static const char *directive_names[d_maxdir+1] = {
#ifndef GMX_GMXPREPROCESS_TOPDIRS_H
#define GMX_GMXPREPROCESS_TOPDIRS_H
-#include "grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "topio.h"
+
+#include <assert.h>
+#include <ctype.h>
+#include <errno.h>
#include <math.h>
-#include <sys/types.h>
#include <stdio.h>
+#include <stdlib.h>
#include <string.h>
-#include <errno.h>
-#include <ctype.h>
-#include <assert.h>
-#include "gromacs/fileio/futil.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
+#include <sys/types.h>
+
#include "gromacs/fileio/gmxfio.h"
-#include "txtdump.h"
-#include "physics.h"
-#include "macros.h"
-#include "names.h"
-#include "gromacs/utility/cstringutil.h"
-#include "symtab.h"
-#include "gmx_fatal.h"
-#include "warninp.h"
-#include "vsite_parm.h"
-
-#include "grompp-impl.h"
-#include "toputil.h"
-#include "toppush.h"
-#include "topdirs.h"
-#include "gpp_nextnb.h"
-#include "topio.h"
-#include "topshake.h"
-#include "gmxcpp.h"
-#include "gpp_bond_atomtype.h"
-#include "genborn.h"
+#include "gromacs/gmxpreprocess/gmxcpp.h"
+#include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/toppush.h"
+#include "gromacs/gmxpreprocess/topshake.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/gmxpreprocess/vsite_parm.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define OPENDIR '[' /* starting sign for directive */
#define CLOSEDIR ']' /* ending sign for directive */
else
{
srenew(cppopts, ++ncppopts);
- cppopts[ncppopts-1] = strdup(buf);
+ cppopts[ncppopts-1] = gmx_strdup(buf);
}
sfree(buf);
ptr = rptr;
set_warning_line(wi, cpp_cur_file(&handle), cpp_cur_linenr(&handle));
- pline = strdup(line);
+ pline = gmx_strdup(line);
/* Strip trailing '\' from pline, if it exists */
sl = strlen(pline);
/* Since we depend on the '\' being present to continue to read, we copy line
* to a tmp string, strip the '\' from that string, and cat it to pline
*/
- tmp_line = strdup(line);
+ tmp_line = gmx_strdup(line);
sl = strlen(tmp_line);
if ((sl > 0) && (tmp_line[sl-1] == CONTINUE))
* without the brackets into dirstr, then
* skip spaces and tabs on either side of directive
*/
- dirstr = strdup((pline+1));
+ dirstr = gmx_strdup((pline+1));
if ((dummy2 = strchr (dirstr, CLOSEDIR)) != NULL)
{
(*dummy2) = 0;
break;
}
default:
- fprintf (stderr, "case: %d\n", d);
+ fprintf (stderr, "case: %d\n", (int)d);
gmx_incons("unknown directive");
}
}
j = 0;
while (j < molt->ilist[i].nr)
{
- bexcl = FALSE;
a1 = molt->ilist[i].iatoms[j+1];
a2 = molt->ilist[i].iatoms[j+2];
bexcl = ((bQMMM[a1] && bQMMM[a2]) ||
#ifndef GMX_GMXPREPROCESS_TOPIO_H
#define GMX_GMXPREPROCESS_TOPIO_H
-#include "typedefs.h"
-#include "readir.h"
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
const char *topppfile,
t_gromppopts *opts,
gmx_bool bZero,
- t_symtab *symtab,
+ struct t_symtab *symtab,
t_params plist[],
int *combination_rule,
double *repulsion_power,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "toppush.h"
+
+#include <assert.h>
#include <ctype.h>
#include <math.h>
-#include <assert.h>
-
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
+#include <stdlib.h>
+
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/topology/symtab.h"
#include "gromacs/utility/cstringutil.h"
-#include "names.h"
-#include "toputil.h"
-#include "toppush.h"
-#include "topdirs.h"
-#include "readir.h"
-#include "symtab.h"
-#include "gmx_fatal.h"
-#include "warninp.h"
-#include "gpp_atomtype.h"
-#include "gpp_bond_atomtype.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
void generate_nbparams(int comb, int ftype, t_params *plist, gpp_atomtype_t atype,
warninp_t wi)
gmx_fatal(FARGS, "Invalid particle type %s on line %s",
ptype, line);
}
+ /* cppcheck-suppress arrayIndexOutOfBounds #6329 */
pt = xl[j].ptype;
if (debug)
{
#ifndef GMX_GMXPREPROCESS_TOPPUSH_H
#define GMX_GMXPREPROCESS_TOPPUSH_H
-#include "typedefs.h"
-#include "toputil.h"
-#include "gpp_atomtype.h"
-#include "gpp_bond_atomtype.h"
-#include "warninp.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/warninp.h"
#ifdef __cplusplus
extern "C" {
gpp_atomtype_t atype,
warninp_t wi);
-void push_at (t_symtab *symtab, gpp_atomtype_t at,
+void push_at (struct t_symtab *symtab, gpp_atomtype_t at,
t_bond_atomtype bat, char *line, int nb_funct,
t_nbparam ***nbparam, t_nbparam ***pair,
warninp_t wi);
char *line,
warninp_t wi);
-void push_atom(t_symtab *symtab,
- t_block *cgs,
- t_atoms *at,
- gpp_atomtype_t atype,
- char *line,
- int *lastcg,
- warninp_t wi);
+void push_atom(struct t_symtab *symtab,
+ t_block *cgs,
+ t_atoms *at,
+ gpp_atomtype_t atype,
+ char *line,
+ int *lastcg,
+ warninp_t wi);
void push_bond(directive d, t_params bondtype[], t_params bond[],
t_atoms *at, gpp_atomtype_t atype, char *line,
int *whichmol, int *nrcopies,
warninp_t wi);
-void push_molt(t_symtab *symtab, int *nmol, t_molinfo **mol, char *line,
+void push_molt(struct t_symtab *symtab, int *nmol, t_molinfo **mol, char *line,
warninp_t wi);
void init_block2(t_block2 *b2, int natom);
void b2_to_b(t_block2 *b2, t_blocka *b);
-int add_atomtype_decoupled(t_symtab *symtab, gpp_atomtype_t at,
+int add_atomtype_decoupled(struct t_symtab *symtab, gpp_atomtype_t at,
t_nbparam ***nbparam, t_nbparam ***pair);
/* Add an atom type with all parameters set to zero (no interactions).
* Returns the atom type number.
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "topshake.h"
#include <ctype.h>
#include <math.h>
-#include "sysstuff.h"
-#include "physics.h"
-#include "macros.h"
-#include "readir.h"
-#include "typedefs.h"
-#include "topshake.h"
-#include "toppush.h"
-#include "toputil.h"
-#include "topdirs.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/toppush.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
static void copy_bond (t_params *pr, int to, int from)
/* copies an entry in a bond list to another position.
#ifndef GMX_GMXPREPROCESS_TOPSHAKE_H
#define GMX_GMXPREPROCESS_TOPSHAKE_H
-#include "topio.h"
+#include "gromacs/gmxpreprocess/topio.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "toputil.h"
#include <assert.h>
#include <math.h>
#include <string.h>
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "macros.h"
-#include "topdirs.h"
-#include "toputil.h"
-#include "symtab.h"
-#include "gmx_fatal.h"
-#include "gpp_atomtype.h"
/* UTILITIES */
#ifndef GMX_GMXPREPROCESS_TOPUTIL_H
#define GMX_GMXPREPROCESS_TOPUTIL_H
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "vsite_parm.h"
-#include <stdio.h>
-#include <math.h>
#include <assert.h>
+#include <math.h>
+#include <stdio.h>
#include <string.h>
-#include "vsite_parm.h"
-#include "gromacs/utility/smalloc.h"
-#include "resall.h"
-#include "add_par.h"
-#include "vec.h"
-#include "toputil.h"
-#include "physics.h"
-#include "index.h"
-#include "names.h"
-#include "gmx_fatal.h"
+
+#include "gromacs/gmxpreprocess/add_par.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
#include "gromacs/utility/cstringutil.h"
-#include "physics.h"
-#include "macros.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
t_iatom a[4];
fprintf(fp, "bonds:");
for (i = 0; i < nrbond; i++)
{
- fprintf(fp, " %u-%u (%g)",
+ fprintf(fp, " %d-%d (%g)",
bonds[i].AI+1, bonds[i].AJ+1, bonds[i].c);
}
fprintf(fp, "\n");
fprintf(fp, "angles:");
for (i = 0; i < nrang; i++)
{
- fprintf(fp, " %u-%u-%u (%g)",
+ fprintf(fp, " %d-%d-%d (%g)",
angles[i].AI+1, angles[i].AJ+1,
angles[i].AK+1, angles[i].c);
}
fprintf(fp, "idihs:");
for (i = 0; i < nridih; i++)
{
- fprintf(fp, " %u-%u-%u-%u (%g)",
+ fprintf(fp, " %d-%d-%d-%d (%g)",
idihs[i].AI+1, idihs[i].AJ+1,
idihs[i].AK+1, idihs[i].AL+1, idihs[i].c);
}
int i;
for (i = 0; i < 4; i++)
{
- fprintf(debug, "atom %u type %s ",
+ fprintf(debug, "atom %d type %s ",
param->a[i]+1,
get_atomtype_name_AB(&at->atom[param->a[i]], atype));
}
if (debug)
{
- fprintf(debug, "params for vsite3 %u: %g %g\n",
+ fprintf(debug, "params for vsite3 %d: %g %g\n",
param->AI+1, param->C0, param->C1);
}
if (debug)
{
- fprintf(debug, "params for vsite3fd %u: %g %g\n",
+ fprintf(debug, "params for vsite3fd %d: %g %g\n",
param->AI+1, param->C0, param->C1);
}
return bError;
if (debug)
{
- fprintf(debug, "params for vsite3fad %u: %g %g\n",
+ fprintf(debug, "params for vsite3fad %d: %g %g\n",
param->AI+1, param->C0, param->C1);
}
return bError;
int i;
for (i = 0; i < 4; i++)
{
- fprintf(debug, "atom %u type %s ",
+ fprintf(debug, "atom %d type %s ",
param->a[i]+1, get_atomtype_name_AB(&at->atom[param->a[i]], atype));
}
fprintf(debug, "\n");
}
if (debug)
{
- fprintf(debug, "params for vsite3out %u: %g %g %g\n",
+ fprintf(debug, "params for vsite3out %d: %g %g %g\n",
param->AI+1, param->C0, param->C1, param->C2);
}
return bError;
param->C2 = -bij;
if (debug)
{
- fprintf(debug, "params for vsite4fd %u: %g %g %g\n",
+ fprintf(debug, "params for vsite4fd %d: %g %g %g\n",
param->AI+1, param->C0, param->C1, param->C2);
}
}
if (debug)
{
- fprintf(debug, "params for vsite4fdn %u: %g %g %g\n",
+ fprintf(debug, "params for vsite4fdn %d: %g %g %g\n",
param->AI+1, param->C0, param->C1, param->C2);
}
}
if (debug)
{
fprintf(debug, "Found %d bonds, %d angles and %d idihs "
- "for virtual site %u (%s)\n", nrbond, nrang, nridih,
+ "for virtual site %d (%s)\n", nrbond, nrang, nridih,
plist[ftype].param[i].AI+1,
interaction_function[ftype].longname);
print_bad(debug, nrbond, bonds, nrang, angles, nridih, idihs);
atom = ps->param[i].a[k];
if (vsite_type[atom] != NOTSET)
{
- fprintf(stderr, "ERROR: Cannot have constraint (%u-%u) with virtual site (%u)\n",
+ fprintf(stderr, "ERROR: Cannot have constraint (%d-%d) with virtual site (%d)\n",
ps->param[i].AI+1, ps->param[i].AJ+1, atom+1);
n++;
}
nvsite = 0;
if (debug)
{
- fprintf(debug, "constr %u %u:", ps->param[i].AI+1, ps->param[i].AJ+1);
+ fprintf(debug, "constr %d %d:", ps->param[i].AI+1, ps->param[i].AJ+1);
}
for (k = 0; (k < 2) && !bKeep && !bRemove; k++)
{
}
if (debug)
{
- fprintf(debug, "dih w. vsite: %u %u %u %u\n",
+ fprintf(debug, "dih w. vsite: %d %d %d %d\n",
ps->param[i].AI+1, ps->param[i].AJ+1,
ps->param[i].AK+1, ps->param[i].AL+1);
- fprintf(debug, "vsite %u from: %u %u %u\n",
+ fprintf(debug, "vsite %d from: %d %d %d\n",
atom+1, vsiteatoms[0]+1, vsiteatoms[1]+1, vsiteatoms[2]+1);
}
}
bKeep = TRUE;
if (debug)
{
- fprintf(debug, "unused atom in dih: %u\n", atom+1);
+ fprintf(debug, "unused atom in dih: %d\n", atom+1);
}
}
}
#ifndef GMX_GMXPREPROCESS_VSITE_PARM_H
#define GMX_GMXPREPROCESS_VSITE_PARM_H
-#include "typedefs.h"
-#include "grompp-impl.h"
-#include "gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "x2top.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "x2top.h"
#include <assert.h>
-#include "copyrite.h"
-#include "gromacs/math/utilities.h"
-#include "macros.h"
-#include "bondf.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/gmxpreprocess/gen_ad.h"
+#include "gromacs/gmxpreprocess/gpp_nextnb.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/gmxpreprocess/nm2type.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/gmxpreprocess/toppush.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/symtab.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "gromacs/fileio/confio.h"
-#include "physics.h"
-#include "gromacs/commandline/pargs.h"
-#include "vec.h"
-#include "gromacs/math/3dview.h"
-#include "txtdump.h"
-#include "readinp.h"
-#include "names.h"
-#include "toppush.h"
-#include "pdb2top.h"
-#include "gen_ad.h"
-#include "gpp_nextnb.h"
-#include "vec.h"
-#include "atomprop.h"
-#include "hackblock.h"
-#include "nm2type.h"
-
-#include "gmx_fatal.h"
char atp[7] = "HCNOSX";
#define NATP (asize(atp)-1)
bOPLS = (strcmp(forcefield, "oplsaa") == 0);
- mymol.name = strdup(molnm);
+ mymol.name = gmx_strdup(molnm);
mymol.nr = 1;
/* Init parameter lists */
dump_hybridization(debug, atoms, nbonds);
}
close_symtab(&symtab);
- free(mymol.name);
+ sfree(mymol.name);
printf("\nWARNING: topologies generated by %s can not be trusted at face value.\n",
- ShortProgram());
+ output_env_get_program_display_name(oenv));
printf(" Please verify atomtypes and charges by comparison to other\n");
printf(" topologies.\n");
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "xlate.h"
#include <ctype.h>
#include <string.h>
-#include "typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "symtab.h"
-#include "index.h"
-#include "gromacs/fileio/futil.h"
-#include "fflibutil.h"
-#include "hackblock.h"
-#include "gmx_fatal.h"
-#include "xlate.h"
#include "gromacs/fileio/strdb.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
char *filebase;
}
srenew(xl, n+1);
- xl[n].filebase = strdup(filebase);
+ xl[n].filebase = gmx_strdup(filebase);
/* Use wildcards... */
if (strcmp(rbuf, "*") != 0)
{
- xl[n].res = strdup(rbuf);
+ xl[n].res = gmx_strdup(rbuf);
}
else
{
*_ptr = ' ';
}
- xl[n].atom = strdup(abuf);
- xl[n].replace = strdup(repbuf);
+ xl[n].atom = gmx_strdup(abuf);
+ xl[n].replace = gmx_strdup(repbuf);
n++;
}
void rename_atoms(const char *xlfile, const char *ffdir,
t_atoms *atoms, t_symtab *symtab, const t_restp *restp,
- gmx_bool bResname, gmx_residuetype_t rt, gmx_bool bReorderNum,
+ gmx_bool bResname, gmx_residuetype_t *rt, gmx_bool bReorderNum,
gmx_bool bVerbose)
{
FILE *fp;
/* Don't free the old atomname,
* since it might be in the symtab.
*/
- ptr0 = strdup(xlatom[i].replace);
+ ptr0 = gmx_strdup(xlatom[i].replace);
if (bVerbose)
{
printf("Renaming atom '%s' in residue %d %s to '%s'\n",
#ifndef GMX_GMXPREPROCESS_XLATE_H
#define GMX_GMXPREPROCESS_XLATE_H
-#include "index.h"
+#include "gromacs/gmxpreprocess/hackblock.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct gmx_residuetype_t;
+struct t_atoms;
+struct t_symtab;
+
/* If bResname is true renames atoms based on residue names,
* otherwise renames atoms based on rtp entry names.
*/
void rename_atoms(const char *xlfile, const char *ffdir,
- t_atoms *atoms, t_symtab *symtab, const t_restp *restp,
- gmx_bool bResname, gmx_residuetype_t rt, gmx_bool bReorderNum,
+ struct t_atoms *atoms, struct t_symtab *symtab, const t_restp *restp,
+ gmx_bool bResname, struct gmx_residuetype_t *rt, gmx_bool bReorderNum,
gmx_bool bVerbose);
#ifdef __cplusplus
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+set(PACKAGE_VERSION "@GMX_VERSION@")
+
+if ("${PACKAGE_VERSION}" VERSION_LESS "${PACKAGE_FIND_VERSION}")
+ set(PACKAGE_VERSION_COMPATIBLE FALSE)
+else()
+ # TODO: Check that major and minor version match.
+ set(PACKAGE_VERSION_COMPATIBLE TRUE)
+ if ("${PACKAGE_VERSION}" VERSION_EQUAL "${PACKAGE_FIND_VERSION}")
+ set(PACKAGE_VERSION_EXACT TRUE)
+ endif()
+endif()
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+set(_gmx_cmake_dir ${CMAKE_CURRENT_LIST_DIR})
+get_filename_component(_gmx_root_dir "${_gmx_cmake_dir}" PATH)
+get_filename_component(_gmx_root_dir "${_gmx_root_dir}" PATH)
+get_filename_component(_gmx_root_dir "${_gmx_root_dir}" PATH)
+
+# Find the exported targets (file name depends on whether shared or static
+# libraries were built to allow both to coexist in the same prefix), and
+# import them.
+set(_gmx_import_file ${_gmx_cmake_dir}/libgromacs.cmake)
+if (GROMACS_PREFER_STATIC OR NOT EXISTS ${_gmx_import_file})
+ set(_gmx_import_file_static ${_gmx_cmake_dir}/libgromacs_static.cmake)
+ if (EXISTS ${_gmx_import_file_static})
+ set(_gmx_import_file ${_gmx_import_file_static})
+ endif()
+ unset(_gmx_import_file_static)
+endif()
+if (NOT EXISTS ${_gmx_import_file})
+ message(FATAL_ERROR
+ "The GROMACS installation at ${_gmx_root_dir} does not contain "
+ "libgromacs.cmake or libgromacs_static.cmake to define the imported "
+ "targets.")
+endif()
+include(${_gmx_import_file})
+unset(_gmx_import_file)
+
+set(GROMACS_INCLUDE_DIRS)
+set(_include_dirs "@INSTALLED_HEADER_INCLUDE_DIRS@")
+foreach (_dir ${_include_dirs})
+ if (IS_ABSOLUTE ${_dir})
+ list(APPEND GROMACS_INCLUDE_DIRS ${_dir})
+ else()
+ list(APPEND GROMACS_INCLUDE_DIRS ${_gmx_root_dir}/${_dir})
+ endif()
+endforeach()
+set(GROMACS_LIBRARIES libgromacs)
+set(GROMACS_DEFINITIONS @INSTALLED_HEADER_DEFINITIONS@)
+set(GROMACS_IS_DOUBLE @GMX_DOUBLE@)
+if (DEFINED GROMACS_SUFFIX AND NOT "${GROMACS_SUFFIX}" STREQUAL "@GMX_LIBS_SUFFIX@")
+ message(FATAL_ERROR "GROMACS_SUFFIX is set inconsistently, expected '@GMX_LIBS_SUFFIX@'")
+endif()
+set(GROMACS_SUFFIX "@GMX_LIBS_SUFFIX@")
+set(GROMACS_CXX_COMPILER "@GROMACS_CXX_COMPILER@")
+set(GROMACS_CXX_COMPILER_ID "@CMAKE_CXX_COMPILER_ID@")
+set(GROMACS_CXX_COMPILER_VERSION "@CMAKE_CXX_COMPILER_VERSION@")
+
+# Produce a message, since find_package() prints nothing on success.
+include(FindPackageMessage)
+# The version info is set by CMake when it determines whether this file
+# is suitable (by calling the version file, which sets PACKAGE_VERSION).
+# TODO: Make also the full version string available from somewhere.
+set(_gmx_info "${GROMACS_VERSION}")
+if (GROMACS_SUFFIX)
+ set(_gmx_info "${_gmx_info} (suffix: ${GROMACS_SUFFIX})")
+endif()
+find_package_message(GROMACS "Found GROMACS: ${_gmx_info}" "${CMAKE_CURRENT_LIST_FILE}")
+
+unset(_gmx_cmake_dir)
+unset(_gmx_root_dir)
+unset(_gmx_info)
+
+#####################################################################
+# Macros for use in calling code
+
+# This does not work as a function if called as gromacs_check_double(GMX_DOUBLE)
+# (i.e., with the parameter value equal to the formal parameter name) because
+# of scoping rules.
+macro (gromacs_check_double GMX_DOUBLE)
+ if (${GMX_DOUBLE} AND NOT GROMACS_IS_DOUBLE)
+ message(FATAL_ERROR
+ "The found GROMACS installation is compiled in mixed precision, "
+ "but double-precision compilation was requested with ${GMX_DOUBLE}=${${GMX_DOUBLE}}")
+ elseif (NOT ${GMX_DOUBLE} AND GROMACS_IS_DOUBLE)
+ message(FATAL_ERROR
+ "The found GROMACS installation is compiled in double precision, "
+ "but mixed-precision compilation was requested with ${GMX_DOUBLE}=${${GMX_DOUBLE}}")
+ endif()
+endmacro()
+
+function (gromacs_check_compiler LANG)
+ if (NOT LANG STREQUAL CXX)
+ message(FATAL_ERROR
+ "gromacs_check_compiler(CXX) is currently the only supported call")
+ endif()
+ # Deal with possible symlinks (it is fine if one of the used compilers was
+ # a symlink to another one).
+ get_filename_component(_cmake_compiler_realpath ${CMAKE_${LANG}_COMPILER} REALPATH)
+ if (NOT "${_cmake_compiler_realpath}" STREQUAL "${GROMACS_${LANG}_COMPILER}" OR
+ NOT "${CMAKE_${LANG}_COMPILER_ID}" STREQUAL "${GROMACS_${LANG}_COMPILER_ID}" OR
+ NOT "${CMAKE_${LANG}_COMPILER_VERSION}" STREQUAL "${GROMACS_${LANG}_COMPILER_VERSION}")
+ message(WARNING
+ "You are compiling with a different C++ compiler than what was used "
+ "to compile GROMACS. This may lead to linking or runtime problems. "
+ "GROMACS was compiled with "
+ "${GROMACS_${LANG}_COMPILER_ID} ${GROMACS_${LANG}_COMPILER_VERSION} "
+ "(${GROMACS_${LANG}_COMPILER}).")
+ endif()
+endfunction()
*
* \ingroup module_imd
*/
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "imd.h"
+#include "config.h"
+#include <errno.h>
#include <string.h>
#ifdef GMX_NATIVE_WINDOWS
#include <unistd.h>
#endif
-#include "imd.h"
-#include "imdsocket.h"
-#include "gromacs/utility/smalloc.h"
-#include "network.h"
-#include "mdrun.h"
-#include "sighandler.h"
-#include "gmx_ga2la.h"
-#include "xvgr.h"
-#include "gromacs/mdlib/groupcoord.h"
#include "gromacs/fileio/confio.h"
-#include "mtop_util.h"
-#include "names.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/imd/imdsocket.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/sighandler.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/groupcoord.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
-
-#include "gmx_fatal.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/*! \brief How long shall we wait in seconds until we check for a connection again? */
#define IMDLOOPWAIT 1
#ifndef GMX_IMD_IMD_H
#define GMX_IMD_IMD_H
-#include "typedefs.h"
-#include "../fileio/filenm.h"
+#include "config.h"
+
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/timing/wallcycle.h"
#ifdef GMX_NATIVE_WINDOWS
#include <Windows.h>
* \ingroup module_imd
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "imdsocket.h"
+#include "config.h"
+#include <errno.h>
#include <string.h>
-#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "imdsocket.h"
-#include "imd.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#ifdef GMX_NATIVE_WINDOWS
#ifdef GMX_HAVE_WINSOCK
#endif
#else
/* On UNIX, we can use nice errors from errno.h */
-#include <errno.h>
#include <unistd.h>
#endif
extern int imdsock_bind(IMDSocket *sock, int port)
{
- int ret = -1;
+ int ret;
#ifdef GMX_IMD
/* Try to bind to address and port ...*/
ret = bind(sock->sockfd, (struct sockaddr *) &sock->address, sizeof(sock->address));
+#else
+ ret = -1;
#endif
if (ret)
extern int imd_sock_listen(IMDSocket *sock)
{
- int ret = -1;
+ int ret;
#ifdef GMX_IMD
/* Try to set to listening state */
ret = listen(sock->sockfd, MAXIMDCONNECTIONS);
+#else
+ ret = -1;
#endif
if (ret)
extern IMDSocket* imdsock_accept(IMDSocket *sock)
{
- int ret = -1;
+ int ret;
#ifdef GMX_IMD
socklen_t length;
extern int imdsock_getport(IMDSocket *sock, int *port)
{
- int ret = -1;
+ int ret;
#ifdef GMX_IMD
struct sockaddr_in sin;
socklen_t len;
#ifndef GMX_IMD_IMDSOCKET_H
#define GMX_IMD_IMDSOCKET_H
+#include "config.h"
+
/* Check if we can/should use winsock or standard UNIX sockets. */
#ifdef GMX_NATIVE_WINDOWS
#ifdef GMX_HAVE_WINSOCK
#define GMX_IMD
#endif
#else
-#include <sys/socket.h>
#include <netinet/in.h>
+#include <sys/socket.h>
#define GMX_IMD
#endif
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2009,2010,2012,2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2014, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# the research papers on the package. Check out http://www.gromacs.org.
# includes: Nothing to build, just installation
-file(GLOB ROOT_LEGACY_HEADERS *.h)
-file(GLOB ROOT_LEGACY_HEADERS_PRIVATE thread_mpi.h tmpi.h gmx_hash.h
- gmx_ga2la.h gpu_utils.h pmalloc_cuda.h nbnxn_cuda_data_mgmt.h)
-file(GLOB TYPES_LEGACY_HEADERS types/*.h)
-file(GLOB TYPES_LEGACY_HEADERS_PRIVATE types/commrec.h)
-list(REMOVE_ITEM ROOT_LEGACY_HEADERS ${ROOT_LEGACY_HEADERS_PRIVATE})
-list(REMOVE_ITEM TYPES_LEGACY_HEADERS ${TYPES_LEGACY_HEADERS_PRIVATE})
-gmx_install_headers(legacyheaders ${ROOT_LEGACY_HEADERS})
-gmx_install_headers(legacyheaders/types ${TYPES_LEGACY_HEADERS})
+file(GLOB HEADERS RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.h)
+list(REMOVE_ITEM HEADERS gmx_hash.h gmx_ga2la.h)
+gmx_install_headers(${HEADERS})
+
+add_subdirectory(types)
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef _bondf_h
-#define _bondf_h
-
-
-#include <stdio.h>
-#include "typedefs.h"
-#include "nrnb.h"
-#include "pbc.h"
-#include "genborn.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-int glatnr(int *global_atom_index, int i);
-/* Returns the global topology atom number belonging to local atom index i.
- * This function is intended for writing ascii output
- * and returns atom numbers starting at 1.
- * When global_atom_index=NULL returns i+1.
- */
-
-void calc_bonds(FILE *fplog, const gmx_multisim_t *ms,
- const t_idef *idef,
- rvec x[], history_t *hist,
- rvec f[], t_forcerec *fr,
- const t_pbc *pbc, const t_graph *g,
- gmx_enerdata_t *enerd, t_nrnb *nrnb, real *lambda,
- const t_mdatoms *md,
- t_fcdata *fcd, int *ddgatindex,
- t_atomtypes *atype, gmx_genborn_t *born,
- int force_flags,
- gmx_bool bPrintSepPot, gmx_int64_t step);
-/*
- * The function calc_bonds() calculates all bonded force interactions.
- * The "bonds" are specified as follows:
- * int nbonds
- * the total number of bonded interactions.
- * t_iatom *forceatoms
- * specifies which atoms are involved in a bond of a certain
- * type, see also struct t_idef.
- * t_functype *functype
- * defines for every bonded force type what type of function to
- * use, see also struct t_idef.
- * t_iparams *forceparams
- * defines the parameters for every bond type, see also struct
- * t_idef.
- * real epot[NR_F]
- * total potential energy split up over the function types.
- * int *ddgatindex
- * global atom number indices, should be NULL when not using DD.
- * gmx_bool bPrintSepPot
- * if TRUE print local potential and dVdlambda for each bonded type.
- * int step
- * used with bPrintSepPot
- * return value:
- * the total potential energy (sum over epot).
- */
-
-void calc_bonds_lambda(FILE *fplog,
- const t_idef *idef,
- rvec x[],
- t_forcerec *fr,
- const t_pbc *pbc, const t_graph *g,
- gmx_grppairener_t *grpp, real *epot, t_nrnb *nrnb,
- real *lambda,
- const t_mdatoms *md,
- t_fcdata *fcd, int *global_atom_index);
-/* As calc_bonds, but only determines the potential energy
- * for the perturbed interactions.
- * The shift forces in fr are not affected.
- */
-
-real posres(int nbonds,
- const t_iatom forceatoms[], const t_iparams forceparams[],
- const rvec x[], rvec f[], rvec vir_diag,
- t_pbc *pbc,
- real lambda, real *dvdlambda,
- int refcoord_scaling, int ePBC, rvec comA, rvec comB);
-/* Position restraints require a different pbc treatment from other bondeds */
-
-real fbposres(int nbonds,
- const t_iatom forceatoms[], const t_iparams forceparams[],
- const rvec x[], rvec f[], rvec vir_diag,
- t_pbc *pbc, int refcoord_scaling, int ePBC, rvec com);
-/* Flat-bottom posres. Same PBC treatment as in normal position restraints */
-
-real bond_angle(const rvec xi, const rvec xj, const rvec xk,
- const t_pbc *pbc,
- rvec r_ij, rvec r_kj, real *costh,
- int *t1, int *t2); /* out */
-/* Calculate bond-angle. No PBC is taken into account (use mol-shift) */
-
-real dih_angle(const rvec xi, const rvec xj, const rvec xk, const rvec xl,
- const t_pbc *pbc,
- rvec r_ij, rvec r_kj, rvec r_kl, rvec m, rvec n, /* out */
- real *sign,
- int *t1, int *t2, int *t3);
-/* Calculate dihedral-angle. No PBC is taken into account (use mol-shift) */
-
-void do_dih_fup(int i, int j, int k, int l, real ddphi,
- rvec r_ij, rvec r_kj, rvec r_kl,
- rvec m, rvec n, rvec f[], rvec fshift[],
- const t_pbc *pbc, const t_graph *g,
- const rvec *x, int t1, int t2, int t3);
-/* Do an update of the forces for dihedral potentials */
-
-void make_dp_periodic(real *dp);
-/* make a dihedral fall in the range (-pi,pi) */
-
-/*************************************************************************
- *
- * Bonded force functions
- *
- *************************************************************************/
-t_ifunc bonds, g96bonds, morse_bonds, cubic_bonds, FENE_bonds, restraint_bonds;
-t_ifunc angles, g96angles, cross_bond_bond, cross_bond_angle, urey_bradley, quartic_angles, linear_angles;
-t_ifunc restrangles;
-t_ifunc pdihs, idihs, rbdihs;
-t_ifunc restrdihs, cbtdihs;
-t_ifunc tab_bonds, tab_angles, tab_dihs;
-t_ifunc polarize, anharm_polarize, water_pol, thole_pol, angres, angresz, dihres, unimplemented;
-
-
-/* Divided the bonded interactions over the threads, count=fr->nthreads
- * and set up the bonded thread-force buffer reduction.
- * This should be called each time the bonded setup changes;
- * i.e. at start-up without domain decomposition and at DD.
- */
-void setup_bonded_threading(t_forcerec *fr, t_idef *idef);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _bondf_h */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_LEGACYHEADERS_CALCGRID_H
+#define GMX_LEGACYHEADERS_CALCGRID_H
-#include "typedefs.h"
+#include <stdio.h>
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#ifdef __cplusplus
}
#endif
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
#ifndef _calcmu_h
#define _calcmu_h
+#include <stdio.h>
-#include "typedefs.h"
-#include "network.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _chargegroup_h
#define _chargegroup_h
-#include "sysstuff.h"
-#include "typedefs.h"
+#include <stdio.h>
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#endif
-void calc_chargegroup_radii(const gmx_mtop_t *mtop, rvec *x,
+struct gmx_mtop_t;
+struct t_block;
+
+void calc_chargegroup_radii(const struct gmx_mtop_t *mtop, rvec *x,
real *rvdw1, real *rvdw2,
real *rcoul1, real *rcoul2);
/* This routine calculates the two largest charge group radii in x,
* separately for VdW and Coulomb interactions.
*/
-void calc_cgcm(FILE *log, int cg0, int cg1, t_block *cgs,
+void calc_cgcm(FILE *log, int cg0, int cg1, struct t_block *cgs,
rvec pos[], rvec cg_cm[]);
/* Routine to compute centers of geometry of charge groups. No periodicity
* is used.
*/
void put_charge_groups_in_box (FILE *log, int cg0, int cg1,
- int ePBC, matrix box, t_block *cgs,
+ int ePBC, matrix box, struct t_block *cgs,
rvec pos[],
rvec cg_cm[]);
/* This routine puts charge groups in the periodic box, keeping them
#define _checkpoint_h
-#include "typedefs.h"
-#include "../fileio/gmxfio.h"
-#include "../fileio/filenm.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
#ifndef _constr_h
#define _constr_h
-#include "typedefs.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_pbc;
+
enum
{
econqCoord, /* Constrain coordinates (mass weighted) */
gmx_bool bCalcVir, /* Calculate r x m delta_r */
tensor vir_r_m_dr, /* sum r x m delta_r */
gmx_bool bDumpOnError, /* Dump debugging stuff on error*/
- int econq, /* which type of constrainint is occurring */
- t_vetavars *vetavar); /* veta for pressure control */
+ int econq); /* which type of constraint is occurring */
/* Shake all the atoms blockwise. It is assumed that all the constraints
* in the idef->shakes field are sorted, to ascending block nr. The
* sblock array points into the idef->shakes.iatoms field, with block 0
real dOH, real dHH);
/* Initializes and returns a structure with SETTLE parameters */
-void csettle(gmx_settledata_t settled,
- int nsettle, /* Number of settles */
- t_iatom iatoms[], /* The settle iatom list */
- const t_pbc *pbc, /* PBC data pointer, can be NULL */
- real b4[], /* Old coordinates */
- real after[], /* New coords, to be settled */
- real invdt, /* 1/delta_t */
- real *v, /* Also constrain v if v!=NULL */
- int calcvir_atom_end, /* Calculate r x m delta_r up to this atom */
- tensor vir_r_m_dr, /* sum r x m delta_r */
- int *xerror,
- t_vetavars *vetavar /* variables for pressure control */
+void csettle(gmx_settledata_t settled,
+ int nsettle, /* Number of settles */
+ t_iatom iatoms[], /* The settle iatom list */
+ const struct t_pbc *pbc, /* PBC data pointer, can be NULL */
+ real b4[], /* Old coordinates */
+ real after[], /* New coords, to be settled */
+ real invdt, /* 1/delta_t */
+ real *v, /* Also constrain v if v!=NULL */
+ int calcvir_atom_end, /* Calculate r x m delta_r up to this atom */
+ tensor vir_r_m_dr, /* sum r x m delta_r */
+ int *xerror
);
void settle_proj(gmx_settledata_t settled, int econq,
int nsettle, t_iatom iatoms[],
- const t_pbc *pbc, /* PBC data pointer, can be NULL */
+ const struct t_pbc *pbc, /* PBC data pointer, can be NULL */
rvec x[],
rvec *der, rvec *derp,
- int CalcVirAtomEnd, tensor vir_r_m_dder,
- t_vetavars *vetavar);
+ int CalcVirAtomEnd, tensor vir_r_m_dder);
/* Analytical algorithm to subtract the components of derivatives
* of coordinates working on settle type constraint.
*/
-void cshake(atom_id iatom[], int ncon, int *nnit, int maxnit,
- real dist2[], real xp[], real rij[], real m2[], real omega,
- real invmass[], real tt[], real lagr[], int *nerror);
+void cshake(const atom_id iatom[], int ncon, int *nnit, int maxnit,
+ const real dist2[], real xp[], const real rij[], const real m2[], real omega,
+ const real invmass[], const real tt[], real lagr[], int *nerror);
/* Regular iterative shake */
void crattle(atom_id iatom[], int ncon, int *nnit, int maxnit,
real dist2[], real vp[], real rij[], real m2[], real omega,
- real invmass[], real tt[], real lagr[], int *nerror, real invdt, t_vetavars *vetavar);
+ real invmass[], real tt[], real lagr[], int *nerror, real invdt);
gmx_bool constrain(FILE *log, gmx_bool bLog, gmx_bool bEner,
gmx_constr_t constr,
t_idef *idef,
t_inputrec *ir,
- gmx_ekindata_t *ekind,
t_commrec *cr,
gmx_int64_t step, int delta_step,
real step_scaling,
gmx_bool bMolPBC, matrix box,
real lambda, real *dvdlambda,
rvec *v, tensor *vir,
- t_nrnb *nrnb, int econq, gmx_bool bPscal, real veta, real vetanew);
+ t_nrnb *nrnb, int econq);
/*
* When econq=econqCoord constrains coordinates xprime using th
* directions in x, min_proj is not used.
*
* If vir!=NULL calculate the constraint virial.
*
- * if veta != NULL, constraints are done assuming isotropic pressure control
- * (i.e. constraining rdot.r = (v + veta*r).r = 0 instead of v
- *
- * Init_constraints must have be called once, before calling constrain.
- *
* Return TRUE if OK, FALSE in case of shake error
*
*/
gmx_lincsdata_t lincsd, t_mdatoms *md,
t_commrec *cr,
rvec *x, rvec *xprime, rvec *min_proj,
- matrix box, t_pbc *pbc,
+ matrix box, struct t_pbc *pbc,
real lambda, real *dvdlambda,
real invdt, rvec *v,
gmx_bool bCalcVir, tensor vir_r_m_dr,
#ifndef _disre_h
#define _disre_h
-#include "sysstuff.h"
-#include "typedefs.h"
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_pbc;
+
void init_disres(FILE *fplog, const gmx_mtop_t *mtop,
t_inputrec *ir, const t_commrec *cr,
t_fcdata *fcd, t_state *state, gmx_bool bIsREMD);
*/
void calc_disres_R_6(int nfa, const t_iatom *fa, const t_iparams ip[],
- const rvec *x, const t_pbc *pbc,
+ const rvec *x, const struct t_pbc *pbc,
t_fcdata *fcd, history_t *hist);
/* Calculates r and r^-3 (inst. and time averaged) for all pairs
* and the ensemble averaged r^-6 (inst. and time averaged) for all restraints
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _ebin_h
#define _ebin_h
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "../fileio/enxio.h"
+#include <stdio.h>
+
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/legacyheaders/types/energy.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
#define _force_h
-#include "typedefs.h"
-#include "types/force_flags.h"
-#include "pbc.h"
-#include "network.h"
-#include "tgroup.h"
-#include "vsite.h"
-#include "genborn.h"
-
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/timing/wallcycle.h"
#ifdef __cplusplus
extern "C" {
#endif
-void gmx_print_sepdvdl(FILE *fplog, const char *s, real v, real dvdlambda);
+struct t_graph;
+struct t_pbc;
void calc_vir(int nxf, rvec x[], rvec f[], tensor vir,
gmx_bool bScrewPBC, matrix box);
/* Calculate virial for nxf atoms, and add it to vir */
void f_calc_vir(int i0, int i1, rvec x[], rvec f[], tensor vir,
- t_graph *g, rvec shift_vec[]);
+ struct t_graph *g, rvec shift_vec[]);
/* Calculate virial taking periodicity into account */
-real RF_excl_correction(const t_forcerec *fr, t_graph *g,
+real RF_excl_correction(const t_forcerec *fr, struct t_graph *g,
const t_mdatoms *mdatoms, const t_blocka *excl,
- rvec x[], rvec f[], rvec *fshift, const t_pbc *pbc,
+ rvec x[], rvec f[], rvec *fshift, const struct t_pbc *pbc,
real lambda, real *dvdlambda);
/* Calculate the reaction-field energy correction for this node:
* epsfac q_i q_j (k_rf r_ij^2 - c_rf)
* message to fplog/stderr.
*/
-gmx_bool uses_simple_tables(int cutoff_scheme,
- nonbonded_verlet_t *nbv,
- int group);
+gmx_bool uses_simple_tables(int cutoff_scheme,
+ struct nonbonded_verlet_t *nbv,
+ int group);
/* Returns whether simple tables (i.e. not for use with GPUs) are used
* with the type of kernel indicated.
*/
tensor vir_force,
t_mdatoms *mdatoms,
gmx_enerdata_t *enerd, t_fcdata *fcd,
- real *lambda, t_graph *graph,
+ real *lambda, struct t_graph *graph,
t_forcerec *fr,
gmx_vsite_t *vsite, rvec mu_tot,
double t, FILE *field, gmx_edsam_t ed,
gmx_bool bDoLongRangeNS);
/* Call the neighborsearcher */
-extern void do_force_lowlevel(FILE *fplog,
- gmx_int64_t step,
- t_forcerec *fr,
+extern void do_force_lowlevel(t_forcerec *fr,
t_inputrec *ir,
t_idef *idef,
t_commrec *cr,
t_fcdata *fcd,
gmx_localtop_t *top,
gmx_genborn_t *born,
- t_atomtypes *atype,
gmx_bool bBornRadii,
matrix box,
t_lambda *fepvals,
real *lambda,
- t_graph *graph,
+ struct t_graph *graph,
t_blocka *excl,
rvec mu_tot[2],
int flags,
float *cycles_pme);
/* Call all the force routines */
+void free_gpu_resources(const t_forcerec *fr,
+ const t_commrec *cr,
+ const gmx_gpu_info_t *gpu_info,
+ const gmx_gpu_opt_t *gpu_opt);
+
#ifdef __cplusplus
}
#endif
#ifndef _genborn_h
#define _genborn_h
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
#define STILL_P5INV (1.0/STILL_P5)
#define STILL_PIP5 (M_PI*STILL_P5)
+struct t_graph;
+struct t_pbc;
/* Initialise GB stuff */
int init_gb(gmx_genborn_t **p_born,
/* Bonded GB interactions */
real gb_bonds_tab(rvec x[], rvec f[], rvec fshift[], real *charge, real *p_gbtabscale,
real *invsqrta, real *dvda, real *GBtab, t_idef *idef, real epsilon_r,
- real gb_epsilon_solvent, real facel, const t_pbc *pbc, const t_graph *graph);
+ real gb_epsilon_solvent, real facel, const struct t_pbc *pbc,
+ const struct t_graph *graph);
void
calc_gb_forces(t_commrec *cr, t_mdatoms *md, gmx_genborn_t *born, gmx_localtop_t *top,
rvec x[], rvec f[], t_forcerec *fr, t_idef *idef, int gb_algorithm, int sa_algorithm, t_nrnb *nrnb,
- const t_pbc *pbc, const t_graph *graph, gmx_enerdata_t *enerd);
+ const struct t_pbc *pbc, const struct t_graph *graph, gmx_enerdata_t *enerd);
int
make_gb_nblist(t_commrec *cr, int gb_algorithm,
rvec x[], matrix box,
- t_forcerec *fr, t_idef *idef, t_graph *graph, gmx_genborn_t *born);
+ t_forcerec *fr, t_idef *idef, struct t_graph *graph, gmx_genborn_t *born);
void
make_local_gb(const t_commrec *cr, gmx_genborn_t *born, int gb_algorithm);
GMX_CPUID_VENDOR_AMD,
GMX_CPUID_VENDOR_FUJITSU,
GMX_CPUID_VENDOR_IBM,
+ GMX_CPUID_VENDOR_ARM,
GMX_CPUID_NVENDORS
};
GMX_CPUID_FEATURE_X86_TDT, /* TSC deadline timer */
GMX_CPUID_FEATURE_X86_X2APIC, /* Extended xAPIC Support */
GMX_CPUID_FEATURE_X86_XOP, /* AMD extended instructions, only AMD for now */
+ GMX_CPUID_FEATURE_ARM_NEON, /* 32-bit ARM NEON */
+ GMX_CPUID_FEATURE_ARM_NEON_ASIMD, /* 64-bit ARM AArch64 Advanced SIMD */
+ GMX_CPUID_FEATURE_IBM_QPX, /* IBM QPX SIMD (BlueGene/Q and later) */
+ GMX_CPUID_FEATURE_IBM_VMX, /* IBM VMX SIMD (Altivec on Power6 and later) */
+ GMX_CPUID_FEATURE_IBM_VSX, /* IBM VSX SIMD (Power7 and later) */
GMX_CPUID_NFEATURES
};
GMX_CPUID_SIMD_X86_AVX2_256,
GMX_CPUID_SIMD_SPARC64_HPC_ACE,
GMX_CPUID_SIMD_IBM_QPX,
+ GMX_CPUID_SIMD_IBM_VMX,
+ GMX_CPUID_SIMD_IBM_VSX,
+ GMX_CPUID_SIMD_ARM_NEON,
+ GMX_CPUID_SIMD_ARM_NEON_ASIMD,
GMX_CPUID_NSIMD
};
#ifndef GMX_HARDWARE_DETECT_H
#define GMX_HARDWARE_DETECT_H
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
/* the init and consistency functions depend on commrec that may not be
consistent in cuda because MPI types don't exist there. */
#ifndef __CUDACC__
-/* return a pointer to a global hwinfo structure. */
+/* Construct the global hwinfo structure and return a pointer to
+ it. Caller is responsible for freeing this pointer. */
gmx_hw_info_t *gmx_detect_hardware(FILE *fplog, const t_commrec *cr,
gmx_bool bDetectGPUs);
#ifndef _gmx_ga2la_h
#define _gmx_ga2la_h
-#include "typedefs.h"
-#include "types/commrec.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/smalloc.h"
#ifdef __cplusplus
#ifndef _gmx_hash_h
#define _gmx_hash_h
-#include "typedefs.h"
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
#ifdef __cplusplus
extern "C" {
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef GMX_OMP_NTHREADS
-#define GMX_OMP_NTHREADS
+#ifndef GMX_OMP_NTHREADS_H
+#define GMX_OMP_NTHREADS_H
#include <stdio.h>
-#include "typedefs.h"
+
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
}
#endif
-/*! Enum values corresponding to multithreaded algorithmic modules. */
+struct t_commrec;
+
+/** Enum values corresponding to multithreaded algorithmic modules. */
typedef enum module_nth
{
/* Default is meant to be used in OMP regions outside the named
emntNR
} module_nth_t;
-/*! Initializes the per-module thread count. It is compatible with tMPI,
- * thread-safety is ensured (for the features available with tMPI).
- * This function should caled only once during the initialization of mdrun. */
-void gmx_omp_nthreads_init(FILE *fplog, t_commrec *cr,
+/*! \brief
+ * Initializes the per-module thread count.
+ *
+ * It is compatible with tMPI, thread-safety is ensured (for the features
+ * available with tMPI).
+ * This function should caled only once during the initialization of mdrun. */
+void gmx_omp_nthreads_init(FILE *fplog, struct t_commrec *cr,
int nthreads_hw_avail,
int omp_nthreads_req,
int omp_nthreads_pme_req,
gmx_bool bCurrNodePMEOnly,
gmx_bool bFullOmpSupport);
-/*! Returns the number of threads to be used in the given module m. */
+/*! \brief
+ * Returns the number of threads to be used in the given module \p mod. */
int gmx_omp_nthreads_get(int mod);
-/*! \brief Sets the number of threads to be used in module. Intended
- * for use in testing. */
+/*! \brief Sets the number of threads to be used in module.
+ *
+ * Intended for use in testing. */
void gmx_omp_nthreads_set(int mod, int nthreads);
-/*! Read the OMP_NUM_THREADS env. var. and check against the value set on the command line. */
+/*! \brief
+ * Read the OMP_NUM_THREADS env. var. and check against the value set on the
+ * command line. */
void gmx_omp_nthreads_read_env(int *nthreads_omp,
gmx_bool bIsSimMaster);
}
#endif
-#endif /* GMX_OMP_NTHREADS */
+#endif
*/
#ifndef GMX_THREAD_AFFINITY_H_
#define GMX_THREAD_AFFINITY_H_
-#include "typedefs.h"
+
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/types/hw_info.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
} /* fixes auto-indentation problems */
#endif
+struct t_commrec;
+
/* Sets the thread affinity using the requested setting stored in hw_opt.
* The hardware topologu is requested from hwinfo, when present.
*/
void
-gmx_set_thread_affinity(FILE *fplog,
- const t_commrec *cr,
- gmx_hw_opt_t *hw_opt,
- const gmx_hw_info_t *hwinfo);
+gmx_set_thread_affinity(FILE *fplog,
+ const struct t_commrec *cr,
+ gmx_hw_opt_t *hw_opt,
+ const gmx_hw_info_t *hwinfo);
/* Check the process affinity mask and if it is found to be non-zero,
* will honor it and disable mdrun internal affinity setting.
* made by the OpenMP library.
*
* Note that this will only work on Linux as we use a GNU feature.
+ * With bAfterOpenmpInit false, it will also detect whether OpenMP environment
+ * variables for setting the affinity are set.
*/
void
-gmx_check_thread_affinity_set(FILE *fplog, const t_commrec *cr,
+gmx_check_thread_affinity_set(FILE *fplog, const struct t_commrec *cr,
gmx_hw_opt_t *hw_opt, int ncpus,
gmx_bool bAfterOpenmpInit);
#ifndef GMX_INPUTREC_H
#define GMX_INPUTREC_H
-#include "types/inputrec.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
#ifdef __cplusplus
extern "C"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _macros_h
#define _macros_h
-#include "typedefs.h" /* for real definition only */
-
/* no extern "C" for this header because it only defines Macros */
-/*
- * With the macros below you don't
- * have to use an index if you don't wan't to. You can eg. use
- * angle.C0[23] instead if angle.c[0][23].
- * In a similar fashion, you can use angle.AI[3] instead of
- * angle.a[0][3]
- */
#ifndef __cplusplus
-#define AI a[0]
-#define AJ a[1]
-#define AK a[2]
-#define AL a[3]
-#define AM a[4]
-#define C0 c[0]
-#define C1 c[1]
-#define C2 c[2]
+#include <stdlib.h>
#ifndef min
#define min(a, b) (((a) < (b)) ? (a) : (b) )
#include <stdio.h>
-#include "typedefs.h"
-#include "network.h"
-#include "../fileio/filenm.h"
+
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
#endif
-int gmx_gethostname(char *name, size_t len);
-/* Sets the hostname to the value given by gethostname, if available,
- * and to "unknown" otherwise. name should have at least size len.
- * Returns 0 on success, -1 on error.
- */
-
void gmx_log_open(const char *fn, const t_commrec *cr,
- gmx_bool bMasterOnly, gmx_bool bAppendFiles, FILE**);
+ gmx_bool bAppendFiles, FILE**);
/* Open the log file, if necessary (nprocs > 1) the logfile name is
* communicated around the ring.
*/
#define _md_logging_h
#include <stdio.h>
-#include "typedefs.h"
#ifdef __cplusplus
extern "C" {
#endif
-void md_print_info(const t_commrec *cr, FILE *fplog,
+struct t_commrec;
+
+void md_print_info(const struct t_commrec *cr, FILE *fplog,
const char *fmt, ...);
/* Print an general information message to stderr on the master node
* and to fplog if fplog!=NULL.
* the arguments after that contain the values to be printed, as in printf.
*/
-void md_print_warn(const t_commrec *cr, FILE *fplog,
+void md_print_warn(const struct t_commrec *cr, FILE *fplog,
const char *fmt, ...);
/* As md_print_info above, but for important notices or warnings.
* The only difference with md_print_info is that a newline is printed
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _md_support_h
#define _md_support_h
-#include "typedefs.h"
-#include "types/globsig.h"
-#include "sim_util.h"
-#include "vcm.h"
+#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vcm.h"
+#include "gromacs/legacyheaders/types/globsig.h"
+#include "gromacs/timing/wallcycle.h"
#ifdef __cplusplus
extern "C" {
#define CGLO_PRESSURE (1<<8)
/* Sum the constraint term in global computation */
#define CGLO_CONSTRAINT (1<<9)
-/* we are using an integrator that requires iteration over some steps - currently not used*/
-#define CGLO_ITERATE (1<<10)
-/* it is the first time we are iterating (or, only once through is required */
-#define CGLO_FIRSTITERATE (1<<11)
/* Reading ekin from the trajectory */
-#define CGLO_READEKIN (1<<12)
+#define CGLO_READEKIN (1<<10)
/* we need to reset the ekin rescaling factor here */
-#define CGLO_SCALEEKIN (1<<13)
+#define CGLO_SCALEEKIN (1<<11)
/* return the number of steps between global communcations */
#ifndef _mdatoms_h
#define _mdatoms_h
-#include "typedefs.h"
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#endif
-t_mdatoms *init_mdatoms(FILE *fp, gmx_mtop_t *mtop, gmx_bool bFreeEnergy);
+struct gmx_mtop_t;
+
+t_mdatoms *init_mdatoms(FILE *fp, struct gmx_mtop_t *mtop, gmx_bool bFreeEnergy);
-void atoms2md(gmx_mtop_t *mtop, t_inputrec *ir,
+void atoms2md(struct gmx_mtop_t *mtop, t_inputrec *ir,
int nindex, int *index,
int homenr,
t_mdatoms *md);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _mdebin_h
#define _mdebin_h
-#include "typedefs.h"
-#include "sysstuff.h"
-#include "ebin.h"
-#include "../fileio/enxio.h"
-#include "types/state.h"
+#include <stdio.h>
+
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/legacyheaders/ebin.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/state.h"
#ifdef __cplusplus
extern "C" {
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stdio.h>
#include <time.h>
-#include "typedefs.h"
-#include "network.h"
-#include "sim_util.h"
-#include "tgroup.h"
-#include "../fileio/filenm.h"
-#include "mshift.h"
-#include "mdebin.h"
-#include "vcm.h"
-#include "vsite.h"
-#include "update.h"
-#include "types/membedt.h"
-#include "types/globsig.h"
+
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/vcm.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/types/globsig.h"
+#include "gromacs/legacyheaders/types/membedt.h"
+#include "gromacs/timing/wallcycle.h"
#ifdef __cplusplus
extern "C" {
#define MD_POLARISE (1<<2)
#define MD_RERUN (1<<4)
#define MD_RERUN_VSITE (1<<5)
-#define MD_SEPPOT (1<<7)
#define MD_DDBONDCHECK (1<<10)
#define MD_DDBONDCOMM (1<<11)
#define MD_CONFOUT (1<<12)
#define MD_STARTFROMCPT (1<<18)
#define MD_RESETCOUNTERSHALFWAY (1<<19)
#define MD_TUNEPME (1<<20)
-#define MD_TESTVERLET (1<<22)
#define MD_IMDWAIT (1<<23)
#define MD_IMDTERM (1<<24)
#define MD_IMDPULL (1<<25)
const char *deviceOptions, int imdport, unsigned long Flags);
/* Driver routine, that calls the different methods */
+void bcast_state(const struct t_commrec *cr, t_state *state);
+/* Broadcasts state from the master to all nodes in cr->mpi_comm_mygroup.
+ */
+
#ifdef __cplusplus
}
#endif
#define _names_h
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
#include <stdio.h>
-#include "types/simple.h"
-#include "typedefs.h"
-#include "main.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/fatalerror.h"
#ifdef __cplusplus
extern "C" {
#endif
-t_commrec *init_commrec(void);
+struct gmx_domdec_t;
+struct gmx_multisim_t;
+struct t_commrec;
+
+struct t_commrec *init_commrec(void);
/* Allocate, initialize and return the commrec. */
-t_commrec *reinitialize_commrec_for_this_thread(const t_commrec *cro);
+struct t_commrec *reinitialize_commrec_for_this_thread(const struct t_commrec *cro);
/* Initialize communication records for thread-parallel simulations.
Must be called on all threads before any communication takes place by
the individual threads. Copies the original commrec to
thread-local versions (a small memory leak results because we don't
deallocate the old shared version). */
-void gmx_fill_commrec_from_mpi(t_commrec *cr);
+void gmx_fill_commrec_from_mpi(struct t_commrec *cr);
/* Continues t_commrec construction */
-int gmx_node_num(void);
-/* return the number of nodes in the ring */
-
-int gmx_node_rank(void);
-/* return the rank of the node */
-
-int gmx_physicalnode_id_hash(void);
-/* Return a non-negative hash that is, hopefully, unique for each physical node.
- * This hash is useful for determining hardware locality.
- */
-
-void gmx_setup_nodecomm(FILE *fplog, t_commrec *cr);
+void gmx_setup_nodecomm(FILE *fplog, struct t_commrec *cr);
/* Sets up fast global communication for clusters with multi-core nodes */
-void gmx_init_intranode_counters(t_commrec *cr);
+void gmx_init_intranode_counters(struct t_commrec *cr);
/* Initializes intra-physical-node MPI process/thread counts and ID. */
-gmx_bool gmx_mpi_initialized(void);
-/* return TRUE when MPI_Init has been called.
- * return FALSE when MPI_Init has not been called OR
- * when GROMACS was compiled without MPI support.
- */
-
-void gmx_barrier(const t_commrec *cr);
+void gmx_barrier(const struct t_commrec *cr);
/* Wait till all processes in cr->mpi_comm_mygroup have reached the barrier */
-void gmx_bcast(int nbytes, void *b, const t_commrec *cr);
+void gmx_bcast(int nbytes, void *b, const struct t_commrec *cr);
/* Broadcast nbytes bytes from the master to cr->mpi_comm_mygroup */
-void gmx_bcast_sim(int nbytes, void *b, const t_commrec *cr);
+void gmx_bcast_sim(int nbytes, void *b, const struct t_commrec *cr);
/* Broadcast nbytes bytes from the sim master to cr->mpi_comm_mysim */
-void gmx_sumi(int nr, int r[], const t_commrec *cr);
+void gmx_sumi(int nr, int r[], const struct t_commrec *cr);
/* Calculate the global sum of an array of ints */
-void gmx_sumli(int nr, gmx_int64_t r[], const t_commrec *cr);
+void gmx_sumli(int nr, gmx_int64_t r[], const struct t_commrec *cr);
/* Calculate the global sum of an array of large ints */
-void gmx_sumf(int nr, float r[], const t_commrec *cr);
+void gmx_sumf(int nr, float r[], const struct t_commrec *cr);
/* Calculate the global sum of an array of floats */
-void gmx_sumd(int nr, double r[], const t_commrec *cr);
+void gmx_sumd(int nr, double r[], const struct t_commrec *cr);
/* Calculate the global sum of an array of doubles */
-void gmx_sumi_sim(int nr, int r[], const gmx_multisim_t *ms);
+void gmx_sumi_sim(int nr, int r[], const struct gmx_multisim_t *ms);
/* Calculate the sum over the simulations of an array of ints */
-void gmx_sumli_sim(int nr, gmx_int64_t r[], const gmx_multisim_t *ms);
+void gmx_sumli_sim(int nr, gmx_int64_t r[], const struct gmx_multisim_t *ms);
/* Calculate the sum over the simulations of an array of large ints */
-void gmx_sumf_sim(int nr, float r[], const gmx_multisim_t *ms);
+void gmx_sumf_sim(int nr, float r[], const struct gmx_multisim_t *ms);
/* Calculate the sum over the simulations of an array of floats */
-void gmx_sumd_sim(int nr, double r[], const gmx_multisim_t *ms);
+void gmx_sumd_sim(int nr, double r[], const struct gmx_multisim_t *ms);
/* Calculate the sum over the simulations of an array of doubles */
-void gmx_abort(int nodeid, int nnodes, int errorno);
-/* Abort the parallel run */
-
#ifdef GMX_DOUBLE
#define gmx_sum gmx_sumd
#define gmx_sum_sim gmx_sumd_sim
#define gmx_sum_sim gmx_sumf_sim
#endif
+gmx_bool gmx_fexist_master(const char *fname, struct t_commrec *cr);
+/* Return TRUE when fname exists, FALSE otherwise, bcast from master to others */
+
+void
+gmx_fatal_collective(int f_errno, const char *file, int line,
+ const struct t_commrec *cr, struct gmx_domdec_t *dd,
+ const char *fmt, ...);
+/* As gmx_fatal declared in utility/fatalerror.h,
+ * but only the master process prints the error message.
+ * This should only be called one of the following two situations:
+ * 1) On all nodes in cr->mpi_comm_mysim, with cr!=NULL,dd==NULL.
+ * 2) On all nodes in dd->mpi_comm_all, with cr==NULL,dd!=NULL.
+ * This will call MPI_Finalize instead of MPI_Abort when possible,
+ * This is useful for handling errors in code that is executed identically
+ * for all processes.
+ */
+
+/* This doesn't currently work if enabled (needs some header cleanup). */
#ifdef DEBUG_GMX
#define debug_gmx() do { FILE *fp = debug ? debug : stderr; \
if (bDebugMode()) { fprintf(fp, "rank=%d, %s %d\n", gmx_mpi_initialized() ? gmx_node_rank() : -1, __FILE__, __LINE__); } fflush(fp); } while (0)
#ifndef _nonbonded_h
#define _nonbonded_h
-#include "typedefs.h"
-#include "pbc.h"
-#include "network.h"
-#include "tgroup.h"
-#include "genborn.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
} /* fixes auto-indentation problems */
#endif
-
-
void
gmx_nonbonded_setup(t_forcerec * fr,
gmx_bool bGenericKernelOnly);
t_nrnb *nrnb, real *lambda, real dvdlambda[],
int nls, int eNL, int flags);
-/* Calculate VdW/charge listed pair interactions (usually 1-4 interactions).
- * global_atom_index is only passed for printing error messages.
- */
-real
-do_nonbonded_listed(int ftype, int nbonds, const t_iatom iatoms[], const t_iparams iparams[],
- const rvec x[], rvec f[], rvec fshift[], const t_pbc *pbc, const t_graph *g,
- real *lambda, real *dvdl, const t_mdatoms *md, const t_forcerec *fr,
- gmx_grppairener_t *grppener, int *global_atom_index);
-
#ifdef __cplusplus
}
#endif
#ifndef _nrnb_h
#define _nrnb_h
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
*/
void print_perf(FILE *out, double nodetime, double realtime,
- gmx_int64_t nsteps, real delta_t,
+ gmx_int64_t nsteps, double delta_t,
double nbfs, double mflop);
/* Prints the performance, nbfs and mflop come from print_flop */
#define _ns_h
#include <stdio.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "pbc.h"
-#include "tgroup.h"
-#include "network.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
int read_nblist(FILE *in, FILE *out, int **mat, int natoms, gmx_bool bSymm);
/* Returns total number of neighbors. If bSymm the matrix is symmetrized. */
-int natoms_beyond_ns_buffer(t_inputrec *ir, t_forcerec *fr, t_block *cgs,
- matrix scale_tot, rvec *x);
-/* Returns the number of atoms that moved beyond the ns buffer */
-
void reallocate_nblist(t_nblist *nl);
/* List reallocation, only exported for Verlet scheme use with FEP */
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
#endif
-#define GRID_STDDEV_FAC sqrt(3)
-#define NSGRID_STDDEV_FAC 2.0
-/*
- * GRID_STDDEV_FAC * stddev is used to estimate the interaction density.
- * sqrt(3) gives a uniform load for a rectangular block of cg's.
- * For a sphere it is not a bad approximation for 4x1x1 up to 4x2x2.
+/*! \brief Used when estimating the interaction density.
+ *
+ * GRID_STDDEV_FAC * stddev estimates the interaction density. The
+ * value sqrt(3) == 1.73205080757 gives a uniform load for a
+ * rectangular 3D block of charge groups. For a sphere, it is not a
+ * bad approximation for 4x1x1 up to 4x2x2.
*
- * The extent of the neighborsearch grid is a bit larger than sqrt(3)
+ * \todo It would be nicer to use sqrt(3) here, when all code that
+ * includes this file is in C++, which will let us cope with the
+ * std::sqrt<T> on Windows. */
+static const real GRID_STDDEV_FAC = 1.73205080757;
+
+/*! \brief The extent of the neighborsearch grid is a bit larger than sqrt(3)
* to account for less dense regions at the edges of the system.
*/
+static const real NSGRID_STDDEV_FAC = 2.0;
#define NSGRID_SIGNAL_MOVED_FAC 4
/* A cell index of NSGRID_SIGNAL_MOVED_FAC*ncells signals
#ifndef _oenv_h
#define _oenv_h
-#include "types/simple.h"
-#include "types/oenv.h"
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef __cplusplus
extern "C" {
int output_env_get_verbosity(const output_env_t oenv);
/* return the verbosity */
-int output_env_get_debug_level(const output_env_t oenv);
-/* return the debug level */
-
const char *output_env_get_time_unit(const output_env_t oenv);
/* return time unit (e.g. ps or ns) */
xvg_format_t output_env_get_xvg_format(const output_env_t oenv);
/* Returns enum (see above) for xvg output formatting */
-const char *output_env_get_program_name(const output_env_t oenv);
-/* return the program name */
-
-const char *output_env_get_cmd_line(const output_env_t oenv);
-/* return the command line */
-
-const char *output_env_get_short_program_name(const output_env_t oenv);
-/* get the short version (without path component) of the program name */
+/*! \brief
+ * Returns display name for the currently running program.
+ */
+const char *output_env_get_program_display_name(const output_env_t oenv);
#ifdef __cplusplus
}
void output_env_init(output_env_t *oenvp,
const gmx::ProgramContextInterface &context,
time_unit_t tmu, gmx_bool view, xvg_format_t xvg_format,
- int verbosity, int debug_level);
+ int verbosity);
/* initialize an output_env structure, setting the command line,
the default time value a gmx_boolean view that is set to TRUE when the
user requests direct viewing of graphs,
the graph formatting type, the verbosity, and debug level */
+
+/*! \brief
+ * Returns gmx::ProgramContextInterface from an output_env structure.
+ */
+const gmx::ProgramContextInterface &
+output_env_get_program_context(const output_env_t oenv);
+
#endif
#endif
#ifndef _orires_h
#define _orires_h
-#include "sysstuff.h"
-#include "typedefs.h"
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_pbc;
+
void init_orires(FILE *fplog, const gmx_mtop_t *mtop,
rvec x[],
const t_inputrec *ir,
real calc_orires_dev(const gmx_multisim_t *ms,
int nfa, const t_iatom fa[], const t_iparams ip[],
const t_mdatoms *md, const rvec x[],
- const t_pbc *pbc, t_fcdata *fcd, history_t *hist);
+ const struct t_pbc *pbc, t_fcdata *fcd, history_t *hist);
/*
* Calculates the time averaged D matrices, the S matrix for each experiment.
* Returns the weighted RMS deviation of the orientation restraints.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _perf_est_h
#define _perf_est_h
-#include "typedefs.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
#endif
-int n_bonded_dx(gmx_mtop_t *mtop, gmx_bool bExcl);
+struct gmx_mtop_t;
+
+int n_bonded_dx(struct gmx_mtop_t *mtop, gmx_bool bExcl);
/* Returns the number of pbc_rvec_sub calls required for bonded interactions.
* This number is also roughly proportional to the computational cost.
*/
-float pme_load_estimate(gmx_mtop_t *mtop, t_inputrec *ir, matrix box);
+float pme_load_estimate(struct gmx_mtop_t *mtop, t_inputrec *ir, matrix box);
/* Returns an estimate for the relative load of the PME mesh calculation
* in the total force calculation.
* This estimate is reasonable for recent Intel and AMD x86_64 CPUs.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _QMMM_h
#define _QMMM_h
-#include "typedefs.h"
-#include "pbc.h"
-#include "network.h"
-#include "tgroup.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _rbin_h
#define _rbin_h
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "network.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_commrec;
+
typedef struct {
int nreal;
int maxreal;
int add_bind(t_bin *b, int nr, double r[]);
/* Add reals to the bin. Returns index */
-void sum_bin(t_bin *b, t_commrec *cr);
+void sum_bin(t_bin *b, struct t_commrec *cr);
/* Globally sum the reals in the bin */
void extract_binr(t_bin *b, int index, int nr, real r[]);
#include <string.h>
-#include "typedefs.h"
-#include "warninp.h"
+#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "typedefs.h"
-#include "vsite.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/timing/wallcycle.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_graph;
+
/* Initialization function, also predicts the initial shell postions.
* If x!=NULL, the shells are predict for the global coordinates x.
*/
tensor force_vir,
t_mdatoms *md,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- t_graph *graph,
+ struct t_graph *graph,
gmx_groups_t *groups,
gmx_shellfc_t shfc,
t_forcerec *fr,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <signal.h>
-#include "typedefs.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
#ifndef _sim_util_h
#define _sim_util_h
-#include "typedefs.h"
-#include "mdebin.h"
-#include "update.h"
-#include "vcm.h"
-#include "../fileio/enxio.h"
-#include "../fileio/mdoutf.h"
-#include "../timing/walltime_accounting.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/mdoutf.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/vcm.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_graph;
+
typedef struct gmx_global_stat *gmx_global_stat_t;
void do_pbc_first(FILE *log, matrix box, t_forcerec *fr,
- t_graph *graph, rvec x[]);
+ struct t_graph *graph, rvec x[]);
void do_pbc_first_mtop(FILE *fplog, int ePBC, matrix box,
gmx_mtop_t *mtop, rvec x[]);
t_inputrec *inputrec,
t_nrnb nrnb[], gmx_wallcycle_t wcycle,
gmx_walltime_accounting_t walltime_accounting,
- wallclock_gpu_t *gputimes,
+ struct nonbonded_verlet_t *nbv,
gmx_bool bWriteStat);
void calc_enervirdiff(FILE *fplog, int eDispCorr, t_forcerec *fr);
-void calc_dispcorr(FILE *fplog, t_inputrec *ir, t_forcerec *fr,
- gmx_int64_t step, int natoms,
+void calc_dispcorr(t_inputrec *ir, t_forcerec *fr,
+ int natoms,
matrix box, real lambda, tensor pres, tensor virial,
real *prescorr, real *enercorr, real *dvdlcorr);
gmx_wallcycle_t wcycle);
/* Routine in sim_util.c */
+gmx_bool use_GPU(const struct nonbonded_verlet_t *nbv);
+
#ifdef __cplusplus
}
#endif
#ifndef _splitter_h
#define _splitter_h
-#include "typedefs.h"
-#include "types/inputrec.h"
+#include <stdio.h>
+
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_blocka;
+struct t_idef;
+
void gen_sblocks(FILE *fp, int at_start, int at_end,
- t_idef *idef, t_blocka *sblock,
+ struct t_idef *idef, struct t_blocka *sblock,
gmx_bool bSettle);
/* Generate shake blocks from the constraint list. Set bSettle to yes for shake
* blocks including settles. You normally do not want this.
#ifndef _tables_h
#define _tables_h
-#include "types/simple.h"
-#include "types/interaction_const.h"
+#include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef __cplusplus
extern "C" {
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _tgroup_h
#define _tgroup_h
-#include "typedefs.h"
-#include "network.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stdio.h>
-#include "typedefs.h"
-#include "../fileio/tpxio.h"
+
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
#define NOTSET -12345
#include <sys/types.h>
-#include "sysstuff.h"
-#include "types/simple.h"
-#include "types/enums.h"
-#include "types/block.h"
-#include "types/symtab.h"
-#include "types/idef.h"
-#include "types/atoms.h"
-#include "../fileio/trx.h"
-#include "types/topology.h"
-#include "types/energy.h"
-#include "types/inputrec.h"
-#include "types/ishift.h"
-#include "types/graph.h"
-#include "types/nrnb.h"
-#include "types/nblist.h"
-#include "types/nbnxn_pairlist.h"
-#include "types/nsgrid.h"
-#include "types/forcerec.h"
-#include "types/fcdata.h"
-#include "types/mdatom.h"
-#include "types/pbc.h"
-#include "types/ifunc.h"
-#include "types/group.h"
-#include "types/state.h"
-#include "types/shellfc.h"
-#include "types/constr.h"
-#include "types/matrix.h"
-#include "types/oenv.h"
+
+#include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/constr.h"
+#include "gromacs/legacyheaders/types/energy.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/fcdata.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/legacyheaders/types/group.h"
+#include "gromacs/legacyheaders/types/ifunc.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
+#include "gromacs/legacyheaders/types/nblist.h"
+#include "gromacs/legacyheaders/types/nrnb.h"
+#include "gromacs/legacyheaders/types/nsgrid.h"
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/legacyheaders/types/shellfc.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/state.h"
+#include "gromacs/topology/topology.h"
#ifdef __cplusplus
extern "C" {
#endif
-/*
- * Memory (re)allocation can be VERY slow, especially with some
- * MPI libraries that replace the standard malloc and realloc calls.
- * To avoid slow memory allocation we use over_alloc to set the memory
- * allocation size for large data blocks. Since this scales the size
- * with a factor, we use log(n) realloc calls instead of n.
- * This can reduce allocation times from minutes to seconds.
- */
-/* This factor leads to 4 realloc calls to double the array size */
-#define OVER_ALLOC_FAC 1.19
-
-void set_over_alloc_dd(gmx_bool set);
-/* Turns over allocation for variable size atoms/cg/top arrays on or off,
- * default is off.
- */
-
-int over_alloc_dd(int n);
-/* Returns n when domain decomposition over allocation is off.
- * Returns OVER_ALLOC_FAC*n + 100 when over allocation in on.
- * This is to avoid frequent reallocation
- * during domain decomposition in mdrun.
- */
-
-/* Over allocation for small data types: int, real etc. */
-#define over_alloc_small(n) (int)(OVER_ALLOC_FAC*(n) + 8000)
-
-/* Over allocation for large data types: complex structs */
-#define over_alloc_large(n) (int)(OVER_ALLOC_FAC*(n) + 1000)
-
int gmx_int64_to_int(gmx_int64_t step, const char *warn);
/* Convert a gmx_int64_t value to int.
* If warn!=NULL a warning message will be written
* "WARNING during %s:", where warn is printed in %s.
*/
-#define STEPSTRSIZE 22
-
-char *gmx_step_str(gmx_int64_t i, char *buf);
-/* Prints a gmx_int64_t value in buf and returns the pointer to buf.
- * buf should be large enough to contain i: STEPSTRSIZE (22) chars.
- * When multiple gmx_int64_t values are printed in the same printf call,
- * be sure to call gmx_step_str with different buffers.
- */
-
/* Functions to initiate and delete structures *
* These functions are defined in gmxlib/typedefs.c
*/
-void init_block(t_block *block);
-void init_blocka(t_blocka *block);
-void init_atom (t_atoms *at);
-void init_mtop(gmx_mtop_t *mtop);
-void init_top(t_topology *top);
void init_inputrec(t_inputrec *ir);
void init_energyhistory(energyhistory_t * enerhist);
void done_energyhistory(energyhistory_t * enerhist);
void init_df_history(df_history_t *dfhist, int nlambda);
void done_df_history(df_history_t *dfhist);
void copy_df_history(df_history_t * df_dest, df_history_t *df_source);
-
-void copy_blocka(const t_blocka *src, t_blocka *dest);
-
-void done_block(t_block *block);
-void done_blocka(t_blocka *block);
-void done_atom (t_atoms *at);
-void done_moltype(gmx_moltype_t *molt);
-void done_molblock(gmx_molblock_t *molb);
-void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab);
-void done_top(t_topology *top);
void done_inputrec(t_inputrec *ir);
void done_state(t_state *state);
void preserve_box_shape(t_inputrec *ir, matrix box_rel, matrix b);
/* Preserve the box shape, b can be box or boxv */
-void stupid_fill_block(t_block *grp, int natom, gmx_bool bOneIndexGroup);
-/* Fill a block structure with numbers identical to the index
- * (0, 1, 2, .. natom-1)
- * If bOneIndexGroup, then all atoms are lumped in one index group,
- * otherwise there is one atom per index entry
- */
-
-void stupid_fill_blocka(t_blocka *grp, int natom);
-/* Fill a block structure with numbers identical to the index
- * (0, 1, 2, .. natom-1)
- * There is one atom per index entry
- */
-
-void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo);
-/* allocate memory for the arrays, set nr to natoms and nres to 0
- * set pdbinfo to NULL or allocate memory for it */
-
-t_atoms *copy_t_atoms(t_atoms *src);
-/* copy an atoms struct from src to a new one */
-
-void add_t_atoms(t_atoms *atoms, int natom_extra, int nres_extra);
-/* allocate extra space for more atoms and or residues */
-
-void t_atoms_set_resinfo(t_atoms *atoms, int atom_ind, t_symtab *symtab,
- const char *resname, int resnr, unsigned char ic,
- int chainnum, char chainid);
-/* Set the residue name, number, insertion code and chain identifier
- * of atom index atom_ind.
- */
-
-void free_t_atoms(t_atoms *atoms, gmx_bool bFreeNames);
-/* Free all the arrays and set the nr and nres to 0.
- * bFreeNames tells if to free the atom and residue name strings,
- * don't free them if they still need to be used in e.g. the topology struct.
- */
-
-t_atoms *mtop2atoms(gmx_mtop_t *mtop);
-/* generate a t_atoms struct for the system from gmx_mtop_t */
-
real max_cutoff(real cutoff1, real cutoff2);
/* Returns the maximum of the cut-off's, taking into account that 0=inf. */
-/* Following are forward declarations for structures in commrec.h */
-typedef struct t_commrec t_commrec;
-typedef struct gmx_domdec_t gmx_domdec_t;
-typedef struct gmx_multisim_t gmx_multisim_t;
-typedef struct gmx_domdec_zones_t gmx_domdec_zones_t;
-typedef struct gmx_ddbox_t gmx_ddbox_t;
-
#ifdef __cplusplus
}
#endif
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+# includes: Nothing to build, just installation
+file(GLOB HEADERS RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.h)
+list(REMOVE_ITEM HEADERS commrec.h)
+gmx_install_headers(${HEADERS})
#ifndef _commrec_h
#define _commrec_h
-#include "../../utility/gmxmpi.h"
-#include "../typedefs.h"
-#include "idef.h"
+#include <stddef.h>
+
+#include "gromacs/legacyheaders/types/commrec_fwd.h" // IWYU pragma: export
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
gmx_nodecomm_t nc;
/* For domain decomposition */
- gmx_domdec_t *dd;
+ struct gmx_domdec_t *dd;
/* The duties of this node, see the defines above */
- int duty;
+ int duty;
- gmx_multisim_t *ms;
+ struct gmx_multisim_t *ms;
/* these buffers are used as destination buffers if MPI_IN_PLACE isn't
supported.*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _dlb_h
-#define _dlb_h
+#ifndef GMX_TYPES_COMMREC_FWD_H
+#define GMX_TYPES_COMMREC_FWD_H
-#include "typedefs.h"
+typedef struct t_commrec t_commrec;
+typedef struct gmx_domdec_t gmx_domdec_t;
+typedef struct gmx_multisim_t gmx_multisim_t;
+typedef struct gmx_domdec_zones_t gmx_domdec_zones_t;
+typedef struct gmx_ddbox_t gmx_ddbox_t;
-extern void count_nb(t_commrec *cr, t_nsborder *nsb, t_block *cgs, int nns,
- int nlr, t_idef *idef, int ngner);
-
-#endif /* _dlb_h */
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "simple.h"
+#ifndef GMX_TYPES_ENERGY_H
+#define GMX_TYPES_ENERGY_H
+
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef __cplusplus
extern "C" {
#ifdef __cplusplus
}
#endif
+
+#endif
/* flat-bottom posres geometries */
enum {
efbposresZERO, efbposresSPHERE, efbposresCYLINDER, efbposresX, efbposresY, efbposresZ,
- efbposresNR
+ efbposresCYLINDERX, efbposresCYLINDERY, efbposresCYLINDERZ, efbposresNR
};
enum {
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _fcdata_h
#define _fcdata_h
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
#ifdef __cplusplus
extern "C" {
#endif
double **v;
} t_oriresdata;
+typedef struct {
+ int n; /* n+1 is the number of points */
+ real scale; /* distance between two points */
+ real *data; /* the actual table data, per point there are 4 numbers */
+} bondedtable_t;
+
/*
* Data struct used in the force calculation routines
* for storing the tables for bonded interactions and
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2012, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_FORCE_NS (1<<2)
/* Update long-range neighborlists */
#define GMX_FORCE_LRNS (1<<3)
-/* Calculate bonded energies/forces */
-#define GMX_FORCE_BONDED (1<<4)
+/* Calculate listed energies/forces (e.g. bonds, restraints, 1-4, FEP non-bonded) */
+#define GMX_FORCE_LISTED (1<<4)
/* Store long-range forces in a separate array */
#define GMX_FORCE_SEPLRF (1<<5)
/* Calculate non-bonded energies/forces */
#define GMX_FORCE_DO_LR (1<<11)
/* Normally one want all energy terms and forces */
-#define GMX_FORCE_ALLFORCES (GMX_FORCE_BONDED | GMX_FORCE_NONBONDED | GMX_FORCE_FORCES)
+#define GMX_FORCE_ALLFORCES (GMX_FORCE_LISTED | GMX_FORCE_NONBONDED | GMX_FORCE_FORCES)
#ifdef __cplusplus
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "ns.h"
-#include "genborn.h"
-#include "qmmmrec.h"
-#include "idef.h"
-#include "nb_verlet.h"
-#include "interaction_const.h"
-#include "hw_info.h"
+#ifndef GMX_LEGACYHEADERS_TYPES_FORCEREC_H
+#define GMX_LEGACYHEADERS_TYPES_FORCEREC_H
+
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/genborn.h"
+#include "gromacs/legacyheaders/types/hw_info.h"
+#include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/legacyheaders/types/nblist.h"
+#include "gromacs/legacyheaders/types/ns.h"
+#include "gromacs/legacyheaders/types/qmmmrec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
/* Abstract type for PME that is defined only in the routine that use them. */
typedef struct gmx_pme *gmx_pme_t;
-
-
+struct nonbonded_verlet_t;
/* Structure describing the data in a single table */
typedef struct
} cginfo_mb_t;
-/* ewald table type */
-typedef struct ewald_tab *ewald_tab_t;
+/* Forward declaration of type for managing Ewald tables */
+struct gmx_ewald_tab_t;
-typedef struct {
- rvec *f;
- int f_nalloc;
- unsigned red_mask; /* Mask for marking which parts of f are filled */
- rvec *fshift;
- real ener[F_NRE];
- gmx_grppairener_t grpp;
- real Vcorr_q;
- real Vcorr_lj;
- real dvdl[efptNR];
- tensor vir_q;
- tensor vir_lj;
-} f_thread_t;
+typedef struct f_thread_t f_thread_t;
typedef struct {
interaction_const_t *ic;
real sc_r_power;
real sc_sigma6_def;
real sc_sigma6_min;
- gmx_bool bSepDVDL;
/* NS Stuff */
int eeltype;
rvec *shift_vec;
/* The neighborlists including tables */
- int nnblists;
- int *gid2nblists;
- t_nblists *nblists;
+ int nnblists;
+ int *gid2nblists;
+ t_nblists *nblists;
- int cutoff_scheme; /* group- or Verlet-style cutoff */
- gmx_bool bNonbonded; /* true if nonbonded calculations are *not* turned off */
- nonbonded_verlet_t *nbv;
+ int cutoff_scheme; /* group- or Verlet-style cutoff */
+ gmx_bool bNonbonded; /* true if nonbonded calculations are *not* turned off */
+ struct nonbonded_verlet_t *nbv;
/* The wall tables (if used) */
int nwall;
tensor vir_lj_recip;
/* PME/Ewald stuff */
- gmx_bool bEwald;
- real ewaldcoeff_q;
- real ewaldcoeff_lj;
- ewald_tab_t ewald_table;
+ gmx_bool bEwald;
+ real ewaldcoeff_q;
+ real ewaldcoeff_lj;
+ struct gmx_ewald_tab_t *ewald_table;
/* Virial Stuff */
rvec *fshift;
#ifdef __cplusplus
}
#endif
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_LEGACYHEADERS_TYPES_GENBORN_H
+#define GMX_LEGACYHEADERS_TYPES_GENBORN_H
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#endif
-#include "simple.h"
-
typedef struct
{
int nbonds;
#ifdef __cplusplus
}
#endif
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
data). This means that the only meaningful values are positive,
negative or zero. */
enum {
- eglsNABNSB, eglsCHKPT, eglsSTOPCOND, eglsRESETCOUNTERS, eglsNR
+ eglsCHKPT, eglsSTOPCOND, eglsRESETCOUNTERS, eglsNR
};
typedef struct {
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef _types_graph_h
-#define _types_graph_h
-
-#include "idef.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-
-typedef enum {
- egcolWhite, egcolGrey, egcolBlack, egcolNR
-} egCol;
-
-typedef struct {
- int at0; /* The first atom the graph was constructed for */
- int at1; /* The last atom the graph was constructed for */
- int nnodes; /* The number of nodes, nnodes=at_end-at_start */
- int nbound; /* The number of nodes with edges */
- int at_start; /* The first connected atom in this graph */
- int at_end; /* The last+1 connected atom in this graph */
- int *nedge; /* For each node the number of edges */
- atom_id **edge; /* For each node, the actual edges (bidirect.) */
- gmx_bool bScrewPBC; /* Screw boundary conditions */
- ivec *ishift; /* Shift for each particle */
- int negc;
- egCol *egc; /* color of each node */
-} t_graph;
-
-
-#define SHIFT_IVEC(g, i) ((g)->ishift[i])
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _types_graph_h */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_LEGACYHEADERS_TYPES_GROUP_H
+#define GMX_LEGACYHEADERS_TYPES_GROUP_H
-
-#include "simple.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#ifdef __cplusplus
}
#endif
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef HWINFO_H
#define HWINFO_H
-#include "simple.h"
-#include "nbnxn_cuda_types_ext.h"
-#include "../gmx_cpuid.h"
+#include "gromacs/legacyheaders/gmx_cpuid.h"
+#include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef __cplusplus
extern "C" {
/* GPU device selection information -- for now with only CUDA devices */
typedef struct
{
- char *gpu_id; /* GPU id's to use, each specified as chars */
- gmx_bool bUserSet; /* true if the GPUs in cuda_dev_use are manually provided by the user */
+ char *gpu_id; /* GPU id's to use, each specified as chars */
+ gmx_bool bUserSet; /* true if the GPUs in cuda_dev_use are manually provided by the user */
- int ncuda_dev_use; /* number of device (IDs) selected to be used */
- int *cuda_dev_use; /* device index list providing GPU to PP rank mapping, GPUs can be listed multiple times when ranks share them */
+ int ncuda_dev_compatible; /* number of compatible GPU devices that could be used */
+ int *cuda_dev_compatible; /* array of compatible GPU device IDs, from which automatic selection occurs */
+ int ncuda_dev_use; /* number of GPU devices selected to be used, either by the user or automatically */
+ int *cuda_dev_use; /* array mapping from PP rank index to GPU device ID; GPU IDs can be listed multiple times when ranks share them */
} gmx_gpu_opt_t;
/* Threading and GPU options, can be set automatically or by the user */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _ifunc_h
#define _ifunc_h
-#include "idef.h"
-#include "mdatom.h"
-#include "fcdata.h"
-#include "graph.h"
-#include "pbc.h"
+#include "gromacs/legacyheaders/types/fcdata.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
+#include "gromacs/topology/idef.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_graph;
+struct t_pbc;
typedef real t_ifunc (int nbonds, const t_iatom iatoms[],
const t_iparams iparams[],
const rvec x[], rvec f[], rvec fshift[],
- const t_pbc *pbc, const t_graph *g,
+ const struct t_pbc *pbc, const struct t_graph *g,
real lambda, real *dvdlambda,
const t_mdatoms *md, t_fcdata *fcd,
int *ddgatindex);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _inputrec_h_
#define _inputrec_h_
+#include <stdio.h>
-#include "simple.h"
-#include "enums.h"
-#include "../sysstuff.h"
-#include "../../swap/enums.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/swap/enums.h"
#ifdef __cplusplus
extern "C" {
} t_IMD;
/* Abstract types for position swapping only defined in swapcoords.c */
-typedef struct swap *gmx_swapcoords_t;
+typedef struct t_swap *gmx_swapcoords_t;
typedef struct {
int nstswap; /* Every how many steps a swap is attempted? */
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _INTERACTION_CONST_
-#define _INTERACTION_CONST_
+#ifndef GMX_LEGACYHEADERS_INTERACTION_CONST_H
+#define GMX_LEGACYHEADERS_INTERACTION_CONST_H
+
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
}
#endif
-#endif /* _INTERACTION_CONST_ */
+#endif
#ifndef _mdatom_h
#define _mdatom_h
-#include "simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef __cplusplus
extern "C" {
t_nrnb;
-typedef struct gmx_wallcycle *gmx_wallcycle_t;
-
#ifdef __cplusplus
}
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "nsgrid.h"
-#include "nblist.h"
+#ifndef GMX_LEGACYHEADERS_TYPES_NS_H
+#define GMX_LEGACYHEADERS_TYPES_NS_H
+
+#include "gromacs/legacyheaders/types/nblist.h"
+#include "gromacs/legacyheaders/types/nsgrid.h"
#ifdef __cplusplus
extern "C" {
#ifdef __cplusplus
}
#endif
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define _nsgrid_h
-#include "simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef __cplusplus
extern "C" {
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifndef _pbc_h
-#define _pbc_h
-
-
-#include "simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/* Maximum number of combinations of single triclinic box vectors
- * required to shift atoms that are within a brick of the size of
- * the diagonal of the box to within the maximum cut-off distance.
- */
-#define MAX_NTRICVEC 12
-
-typedef struct {
- int ePBC;
- int ndim_ePBC;
- int ePBCDX;
- int dim;
- matrix box;
- rvec fbox_diag;
- rvec hbox_diag;
- rvec mhbox_diag;
- real max_cutoff2;
- gmx_bool bLimitDistance;
- real limit_distance2;
- int ntric_vec;
- ivec tric_shift[MAX_NTRICVEC];
- rvec tric_vec[MAX_NTRICVEC];
-} t_pbc;
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_LEGACYHEADERS_TYPES_QMMMREC_H
+#define GMX_LEGACYHEADERS_TYPES_QMMMREC_H
-#include "simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef __cplusplus
extern "C" {
#ifdef __cplusplus
}
#endif
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_LEGACYHEADERS_TYPES_RGB_H
+#define GMX_LEGACYHEADERS_TYPES_RGB_H
-#ifndef _sysstuff_h
-#define _sysstuff_h
+#include "gromacs/utility/real.h"
-#ifndef _386_
-#include <stdlib.h>
-#endif
-#include <stdio.h>
-#include <errno.h>
-#include <signal.h>
-#include <limits.h>
-#include <time.h>
+typedef struct {
+ real r, g, b;
+} t_rgb;
-#endif /* _sysstuff_h */
+#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
#ifndef _simple_h
#define _simple_h
-/* Information about integer data type sizes */
-#include <limits.h>
-#define __STDC_LIMIT_MACROS
-#include <stdint.h>
-#ifndef _MSC_VER
-#define __STDC_FORMAT_MACROS
-#include <inttypes.h>
-#endif
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-#define XX 0 /* Defines for indexing in */
-#define YY 1 /* vectors */
-#define ZZ 2
-#define DIM 3 /* Dimension of vectors */
-#define XXXX 0 /* defines to index matrices */
-#define XXYY 1
-#define XXZZ 2
-#define YYXX 3
-#define YYYY 4
-#define YYZZ 5
-#define ZZXX 6
-#define ZZYY 7
-#define ZZZZ 8
-
-/* There is no standard size for 'bool' in C++, so when
- * we previously defined it to int for C code the data types
- * (and structs) would have different size depending on your compiler,
- * both at gromacs build time and when you use the library.
- * The only way around this is to NOT assume anything about the C++ type,
- * so we cannot use the name 'bool' in our C code anymore.
- */
-
-typedef int gmx_bool;
-
-#ifndef FALSE
-# define FALSE 0
-#endif
-#ifndef TRUE
-# define TRUE 1
-#endif
-#define BOOL_NR 2
-
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
typedef int atom_id; /* To indicate an atoms id */
#define NO_ATID (atom_id)(~0) /* Use this to indicate invalid atid */
-/*! \brief Double precision accuracy */
-#define GMX_DOUBLE_EPS 2.2204460492503131e-16
-
-/*! \brief Maximum double precision value - reduced 1 unit in last digit for MSVC */
-#define GMX_DOUBLE_MAX 1.7976931348623157e+308
-
-/*! \brief Minimum double precision value */
-#define GMX_DOUBLE_MIN 2.2250738585072014e-308
-
-/*! \brief Single precision accuracy */
-#define GMX_FLOAT_EPS 1.19209290e-07F
-
-/*! \brief Maximum single precision value - reduced 1 unit in last digit for MSVC */
-#define GMX_FLOAT_MAX 3.40282346E+38F
-
-/*! \brief Minimum single precision value */
-#define GMX_FLOAT_MIN 1.175494351E-38F
-
-#ifdef __PGI
-/* The portland group x86 C/C++ compilers do not treat negative zero initializers
- * correctly, but "optimizes" them to positive zero, so we implement it explicitly.
- * These constructs are optimized to simple loads at compile time. If you want to
- * use them on other compilers those have to support gcc preprocessor extensions.
- * Note: These initializers might be sensitive to the endianness (which can
- * be different for byte and word order), so check that it works for your platform
- * and add a separate section if necessary before adding to the ifdef above.
- */
-# define GMX_DOUBLE_NEGZERO ({ const union { int di[2]; double d; } _gmx_dzero = {0, -2147483648}; _gmx_dzero.d; })
-# define GMX_FLOAT_NEGZERO ({ const union { int fi; float f; } _gmx_fzero = {-2147483648}; _gmx_fzero.f; })
-#else
-/*! \brief Negative zero in double */
-# define GMX_DOUBLE_NEGZERO (-0.0)
-
-/*! \brief Negative zero in float */
-# define GMX_FLOAT_NEGZERO (-0.0f)
-#endif
-
-
-/* Check whether we already have a real type! */
-#ifdef GMX_DOUBLE
-
-#ifndef HAVE_REAL
-typedef double real;
-#define HAVE_REAL
-#endif
-
-#define GMX_MPI_REAL MPI_DOUBLE
-#define GMX_REAL_EPS GMX_DOUBLE_EPS
-#define GMX_REAL_MIN GMX_DOUBLE_MIN
-#define GMX_REAL_MAX GMX_DOUBLE_MAX
-#define GMX_REAL_NEGZERO GMX_DOUBLE_NEGZERO
-#define gmx_real_fullprecision_pfmt "%21.14e"
-#else
-
-#ifndef HAVE_REAL
-typedef float real;
-#define HAVE_REAL
-#endif
-
-#define GMX_MPI_REAL MPI_FLOAT
-#define GMX_REAL_EPS GMX_FLOAT_EPS
-#define GMX_REAL_MIN GMX_FLOAT_MIN
-#define GMX_REAL_MAX GMX_FLOAT_MAX
-#define GMX_REAL_NEGZERO GMX_FLOAT_NEGZERO
-#define gmx_real_fullprecision_pfmt "%14.7e"
-#endif
-
-typedef real rvec[DIM];
-
-typedef double dvec[DIM];
-
-typedef real matrix[DIM][DIM];
-
-typedef real tensor[DIM][DIM];
-
-typedef int ivec[DIM];
-
-typedef int imatrix[DIM][DIM];
-
-#ifdef _MSC_VER
-typedef __int32 gmx_int32_t;
-#define GMX_PRId32 "I32d"
-#define GMX_SCNd32 "I32d"
-
-typedef __int64 gmx_int64_t;
-#define GMX_PRId64 "I64d"
-#define GMX_SCNd64 "I64d"
-
-typedef unsigned __int32 gmx_uint32_t;
-#define GMX_PRIu32 "I32u"
-#define GMX_SCNu32 "I32u"
-
-typedef unsigned __int64 gmx_uint64_t;
-#define GMX_PRIu64 "I64u"
-#define GMX_SCNu64 "I64u"
-#else
-typedef int32_t gmx_int32_t;
-#define GMX_PRId32 PRId32
-#define GMX_SCNd32 SCNd32
-
-typedef int64_t gmx_int64_t;
-#define GMX_PRId64 PRId64
-#define GMX_SCNd64 SCNd64
-
-typedef uint32_t gmx_uint32_t;
-#define GMX_PRIu32 PRIu32
-#define GMX_SCNu32 SCNu32
-
-typedef uint64_t gmx_uint64_t;
-#define GMX_PRIu64 PRIu64
-#define GMX_SCNu64 SCNu64
-#endif
-
-#define GMX_INT32_MAX INT32_MAX
-#define GMX_INT32_MIN INT32_MIN
-
-#define GMX_INT64_MAX INT64_MAX
-#define GMX_INT64_MIN INT64_MIN
-
-#define GMX_UINT32_MAX UINT32_MAX
-#define GMX_UINT32_MIN UINT32_MIN
-
-#define GMX_UINT64_MAX UINT64_MAX
-#define GMX_UINT64_MIN UINT64_MIN
-
-#if !defined __cplusplus && _MSC_VER
-#define gmx_inline __inline
-#else
-/* C++ or C99 */
-#define gmx_inline inline
-#endif
-
-/* ICC, GCC, MSVC, Pathscale, PGI, XLC support __restrict.
- * Any other compiler can be added here. We cannot
- * use restrict because it is in C99 but not in C++ */
-#define gmx_restrict __restrict
-
-/*
- * These attributes suppress compiler warnings about unused function arguments
- * by marking them as possibly unused. Some arguments are unused but
- * have to be retained to preserve a function signature
- * that must match that of another function.
- * Some arguments are only used in *some* code paths (e.g. MPI)
- */
-
-#ifndef gmx_unused
-#ifdef __GNUC__
-/* GCC, clang, and some ICC pretending to be GCC */
-# define gmx_unused __attribute__ ((unused))
-#elif (defined(__INTEL_COMPILER) || defined(__ECC)) && !defined(_MSC_VER)
-/* ICC on *nix */
-# define gmx_unused __attribute__ ((unused))
-#elif defined(__PGI)
-/* Portland group compilers */
-# define gmx_unused __attribute__ ((unused))
-#elif defined _MSC_VER
-/* MSVC */
-# define gmx_unused /*@unused@*/
-#elif defined(__xlC__)
-/* IBM */
-# define gmx_unused __attribute__ ((unused))
-#else
-# define gmx_unused
-#endif
-#endif
-
-/* Standard sizes for char* string buffers */
-#define STRLEN 4096
-#define BIG_STRLEN 1048576
-
-
-#ifdef __cplusplus
-}
-#endif
-
#endif
#define _state_h_
-#include "simple.h"
-#include "../../swap/enums.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/swap/enums.h"
#ifdef __cplusplus
extern "C" {
#ifndef _update_h
#define _update_h
-#include "typedefs.h"
-#include "mshift.h"
-#include "tgroup.h"
-#include "network.h"
-#include "vec.h"
-
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/timing/wallcycle.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_graph;
+
/* Abstract type for stochastic dynamics */
typedef struct gmx_update *gmx_update_t;
gmx_int64_t step,
real *dvdlambda, /* FEP stuff */
t_inputrec *inputrec, /* input record and box stuff */
- gmx_ekindata_t *ekind,
t_mdatoms *md,
t_state *state,
gmx_bool bMolPBC,
- t_graph *graph,
+ struct t_graph *graph,
rvec force[], /* forces on home particles */
t_idef *idef,
tensor vir_part,
gmx_update_t upd,
gmx_constr_t constr,
gmx_bool bFirstHalf,
- gmx_bool bCalcVir,
- real vetanew);
+ gmx_bool bCalcVir);
/* Return TRUE if OK, FALSE in case of Shake Error */
t_mdatoms *md,
t_state *state,
rvec force[], /* forces on home particles */
- matrix *scale_tot,
matrix pcoupl_mu,
t_nrnb *nrnb,
gmx_update_t upd);
/* Return TRUE if OK, FALSE in case of Shake Error */
void calc_ke_part(t_state *state, t_grpopts *opts, t_mdatoms *md,
- gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel, gmx_bool bSaveOld);
+ gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel);
/*
* Compute the partial kinetic energy for home particles;
* will be accumulated in the calling routine.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _vcm_h
#define _vcm_h
-#include "sysstuff.h"
-#include "typedefs.h"
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct gmx_groups_t;
typedef struct {
int nr; /* Number of groups */
char **group_name; /* These two are copies to pointers in */
} t_vcm;
-t_vcm *init_vcm(FILE *fp, gmx_groups_t *groups, t_inputrec *ir);
+t_vcm *init_vcm(FILE *fp, struct gmx_groups_t *groups, t_inputrec *ir);
/* Do a per group center of mass things */
void calc_vcm_grp(int start, int homenr, t_mdatoms *md,
#ifndef _viewit_h
#define _viewit_h
-#include "typedefs.h"
-#include "../fileio/filenm.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/types/oenv.h"
#ifdef __cplusplus
extern "C" {
#endif
-
void do_view(const output_env_t oenv, const char *fn, const char *opts);
/* forks off appropriate command to view file.
* currently eps, xpm, xvg and pdb are supported
#define _vsite_h
#include <stdio.h>
-#include "typedefs.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/pbcutil/ishift.h"
#ifdef __cplusplus
extern "C" {
int th_ind_nalloc; /* Size of th_ind */
} gmx_vsite_t;
+struct t_graph;
+
void construct_vsites(gmx_vsite_t *vsite,
rvec x[],
real dt, rvec v[],
rvec x[], rvec f[], rvec *fshift,
gmx_bool VirCorr, matrix vir,
t_nrnb *nrnb, t_idef *idef,
- int ePBC, gmx_bool bMolPBC, t_graph *g, matrix box,
+ int ePBC, gmx_bool bMolPBC, struct t_graph *g, matrix box,
t_commrec *cr);
/* Spread the force operating on the vsite atoms on the surrounding atoms.
* If fshift!=NULL also update the shift forces.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _warninp_h
#define _warninp_h
-#include "typedefs.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
libdir=@CMAKE_INSTALL_PREFIX@/@LIB_INSTALL_DIR@
-includedir=@CMAKE_INSTALL_PREFIX@/@INCL_INSTALL_DIR@
Name: libgromacs@GMX_LIBS_SUFFIX@
Description: Gromacs library
URL: http://www.gromacs.org
-Version: @PROJECT_VERSION@
+Version: @GMX_VERSION_STRING@
Requires: @PKG_FFT@ @PKG_XML@
Libs.private: @CMAKE_THREAD_LIBS_INIT@ @PKG_DL_LIBS@ @OpenMP_LINKER_FLAGS@
Libs: -L${libdir} -lgromacs@GMX_LIBS_SUFFIX@ @PKG_FFT_LIBS@ -lm
-Cflags: -I${includedir} @PKG_CFLAGS@
+Cflags: @PKG_CFLAGS@
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
set(LIBGROMACS_SOURCES
${LIBGROMACS_SOURCES} ${LINEARALGEBRA_SOURCES} PARENT_SCOPE)
-set(LINEARALGEBRA_PUBLIC_HEADERS
+gmx_install_headers(
eigensolver.h
matrix.h
- mtxio.h
- sparsematrix.h)
-gmx_install_headers(linearalgebra ${LINEARALGEBRA_PUBLIC_HEADERS})
+ sparsematrix.h
+ )
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "eigensolver.h"
+#include "gmxpre.h"
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "eigensolver.h"
#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_lapack.h"
#include "gmx_arpack.h"
+#include "gmx_lapack.h"
void
eigensolver(real * a,
#ifndef GMX_LINEARALGEBRA_EIGENSOLVER_H
#define GMX_LINEARALGEBRA_EIGENSOLVER_H
-#include "../legacyheaders/types/simple.h"
-
-#include "sparsematrix.h"
+#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2004 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
+#include "gmx_arpack.h"
+
#include <math.h>
#include <string.h>
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gmx_arpack.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
#include "gmx_blas.h"
#include "gmx_lapack.h"
+
static void
F77_FUNC(dstqrb, DSTQRB) (int * n,
double * d__,
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2004 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ARPACK_H
#define GMX_ARPACK_H
-#ifdef HAVE_CONFIG_H
#include "config.h"
-#endif
#ifdef __cplusplus
extern "C" {
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*! \cond */
-#ifdef HAVE_CONFIG_H
#include "config.h"
-#endif
-/* Suppress Cygwin compiler warnings from using newlib version of
- * ctype.h */
-#ifdef GMX_CYGWIN
-#undef toupper
-#endif
+/* These are not required by this file, but by the internal BLAS
+ * implementation. In principle, they could be included in each file
+ * that requires them, but this is simpler. Since the header is internal
+ * to the linearyalgebra/ module, the added complexity may not be worth it. */
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#include <ctype.h>
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include <math.h>
#include <ctype.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
double
#include <ctype.h>
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
void
#include <ctype.h>
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include <ctype.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
void
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
void
#include <ctype.h>
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
void
#include <ctype.h>
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
void
#include <ctype.h>
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
void
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
void
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
float
#include <math.h>
#include <ctype.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
void
#include <ctype.h>
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
void
#include <ctype.h>
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
void
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
void
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
void
#include <ctype.h>
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
void
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*! \cond */
-#ifdef HAVE_CONFIG_H
#include "config.h"
-#endif
-/* Suppress Cygwin compiler warnings from using newlib version of
- * ctype.h */
-#ifdef GMX_CYGWIN
-#undef toupper
-#endif
+/* These are not required by this file, but by the internal LAPACK
+ * implementation. In principle, they could be included in each file
+ * that requires them, but this is simpler. Since the header is internal
+ * to the linearyalgebra/ module, the added complexity may not be worth it. */
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(dbdsdc,DBDSDC)(const char *uplo,
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(dbdsqr,DBDSQR)(const char *uplo,
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(dlaed6,DLAED6)(int *kniter,
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <stdlib.h>
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
#include "../gmx_lapack.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
double
F77_FUNC(dlapy2,DLAPY2)(double * x, double * y)
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(dlarf,DLARF)(const char *side,
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
#include <ctype.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(dlartg,DLARTG)(double *f,
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include <ctype.h>
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(dlasd2,DLASD2)(int *nl,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(dlasd4,DLASD4)(int *n,
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(dlasq1,DLASQ1)(int *n,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#ifdef _MSC_VER
#pragma warning(disable: 4723) /*division by zero - is used on purpose here*/
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(dlasq6,DLASQ6)(int *i0,
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
void
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
void
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(dlasv2,DLASV2)(double *f,
#include <ctype.h>
#include "../gmx_lapack.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(dorml2,DORML2)(const char *side,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(dstebz,DSTEBZ)(const char *range,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(dstegr,DSTEGR)(const char *jobz,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(dstein,DSTEIN)(int *n,
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(dsterf,DSTERF)(int *n,
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <ctype.h>
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(dtrtri,DTRTRI)(const char *uplo,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(sbdsdc,SBDSDC)(const char *uplo,
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(sbdsqr,SBDSQR)(const char *uplo,
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(slaed6,SLAED6)(int *kniter,
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <stdlib.h>
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
#include "../gmx_lapack.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
float
F77_FUNC(slapy2,SLAPY2)(float * x, float * y)
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(slarf,SLARF)(const char *side,
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
#include <ctype.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(slartg,SLARTG)(float *f,
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include <ctype.h>
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(slasd2,SLASD2)(int *nl,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(slasd4,SLASD4)(int *n,
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(slasq1,SLASQ1)(int *n,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#ifdef _MSC_VER
#pragma warning(disable: 4723) /*division by zero - is used on purpose here*/
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(slasq6,SLASQ6)(int *i0,
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
void
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
void
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(slasv2,SLASV2)(float *f,
#include <ctype.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_lapack.h"
void
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(sstebz,SSTEBZ)(const char *range,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(sstegr,SSTEGR)(const char *jobz,
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(sstein,SSTEIN)(int *n,
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(ssterf,SSTERF)(int *n,
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include <ctype.h>
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
#include "../gmx_blas.h"
#include "../gmx_lapack.h"
#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "types/simple.h"
+#include "gromacs/utility/real.h"
void
F77_FUNC(strtri,STRTRI)(const char *uplo,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
#include "matrix.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "config.h"
#include <stdio.h>
-#include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/legacyheaders/vec.h"
-
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "gmx_lapack.h"
{
ax += a0[i]*a[j][i];
}
- chi2 += sqr(y[j]-ax);
+ chi2 += (y[j] - ax) * (y[j] - ax);
}
sfree(atx);
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
+#include "gmxpre.h"
+
#include "nrjac.h"
#include <math.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
static gmx_inline
#ifndef GMX_LINEARALGEBRA_NRJAC_H
#define GMX_LINEARALGEBRA_NRJAC_H
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
#include "sparsematrix.h"
#include <assert.h>
-#include <stdlib.h>
#include <stdio.h>
+#include <stdlib.h>
#include "gromacs/utility/smalloc.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stdio.h>
-#include "../legacyheaders/types/simple.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2009,2013, by the GROMACS development team, led by
+# Copyright (c) 2014,2015, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-# - Define function to check we are compiling for CRAY XT catamount
-#
-# GMX_TEST_CATAMOUNT(VARIABLE)
-#
-# VARIABLE will be set to true if we are compiling for catamount
-#
+file(GLOB LISTED_FORCES_SOURCES *.cpp)
+set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${LISTED_FORCES_SOURCES} PARENT_SCOPE)
+
+gmx_install_headers(listed-forces.h)
-function(GMX_TEST_CATAMOUNT VARIABLE)
- include(CheckCSourceCompiles)
- check_c_source_compiles(
- "int
-main()
-{
-#if defined __QK_USER__
- return 0;
-#else
-# error not catamount
-#endif
-}" CATAMOUNT_COMPILE_OK)
- set(${VARIABLE} ${CATAMOUNT_COMPILE_OK} PARENT_SCOPE)
-endfunction()
+if (BUILD_TESTING)
+# add_subdirectory(tests)
+endif()
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+/*! \internal \file
+ *
+ * \brief This file defines low-level functions necessary for
+ * computing energies and forces for listed interactions.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \ingroup module_listed-forces
+ */
+#include "gmxpre.h"
+
+#include "bonded.h"
-#include <math.h>
#include <assert.h>
-#include "physics.h"
-#include "vec.h"
-#include "gromacs/math/utilities.h"
-#include "txtdump.h"
-#include "bondf.h"
-#include "gromacs/utility/smalloc.h"
-#include "pbc.h"
-#include "ns.h"
-#include "macros.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "mshift.h"
-#include "main.h"
-#include "disre.h"
-#include "orires.h"
-#include "force.h"
-#include "nonbonded.h"
-#include "restcbt.h"
+#include <cmath>
+
+#include <algorithm>
+
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/simd/simd.h"
#include "gromacs/simd/simd_math.h"
#include "gromacs/simd/vector_operations.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
-/* Find a better place for this? */
+#include "listed-internal.h"
+#include "pairs.h"
+#include "restcbt.h"
+
+/*! \brief Mysterious CMAP coefficient matrix */
const int cmap_coeff_matrix[] = {
1, 0, -3, 2, 0, 0, 0, 0, -3, 0, 9, -6, 2, 0, -6, 4,
0, 0, 0, 0, 0, 0, 0, 0, 3, 0, -9, 6, -2, 0, 6, -4,
};
-
-int glatnr(int *global_atom_index, int i)
-{
- int atnr;
-
- if (global_atom_index == NULL)
- {
- atnr = i + 1;
- }
- else
- {
- atnr = global_atom_index[i] + 1;
- }
-
- return atnr;
-}
-
+/*! \brief Compute dx = xi - xj, modulo PBC if non-NULL
+ *
+ * \todo This kind of code appears in many places. Consolidate it */
static int pbc_rvec_sub(const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
{
if (pbc)
gmx_simd_real_t bxx;
} pbc_simd_t;
-/* Set the SIMD pbc data from a normal t_pbc struct */
+/*! \brief Set the SIMD pbc data from a normal t_pbc struct */
static void set_pbc_simd(const t_pbc *pbc, pbc_simd_t *pbc_simd)
{
rvec inv_bdiag;
}
}
-/* Correct distance vector *dx,*dy,*dz for PBC using SIMD */
+/*! \brief Correct distance vector *dx,*dy,*dz for PBC using SIMD */
static gmx_inline void
pbc_dx_simd(gmx_simd_real_t *dx, gmx_simd_real_t *dy, gmx_simd_real_t *dz,
const pbc_simd_t *pbc)
#endif /* GMX_SIMD_HAVE_REAL */
-/*
- * Morse potential bond by Frank Everdij
+/*! \brief Morse potential bond
*
- * Three parameters needed:
+ * By Frank Everdij. Three parameters needed:
*
* b0 = equilibrium distance in nm
* be = beta in nm^-1 (actually, it's nu_e*Sqrt(2*pi*pi*mu/D_e))
* Note: the potential is referenced to be +cb at infinite separation
* and zero at the equilibrium distance!
*/
-
real morse_bonds(int nbonds,
const t_iatom forceatoms[], const t_iparams forceparams[],
const rvec x[], rvec f[], rvec fshift[],
return vtot;
}
+//! \cond
real cubic_bonds(int nbonds,
const t_iatom forceatoms[], const t_iparams forceparams[],
const rvec x[], rvec f[], rvec fshift[],
const real half = 0.5;
const real one = 1.0;
real bm, kb;
- real dr, dr2, bm2, omdr2obm2, fbond, vbond, fij, vtot;
+ real dr2, bm2, omdr2obm2, fbond, vbond, fij, vtot;
rvec dx;
int i, m, ki, type, ai, aj;
ivec dt;
kk[YY] = sqr(qS)*ONE_4PI_EPS0/forceparams[type0].wpol.al_y;
kk[ZZ] = sqr(qS)*ONE_4PI_EPS0/forceparams[type0].wpol.al_z;
r_HH = 1.0/forceparams[type0].wpol.rHH;
- r_OD = 1.0/forceparams[type0].wpol.rOD;
if (debug)
{
fprintf(debug, "WPOL: qS = %10.5f aS = %5d\n", qS, aS);
rvec fshift[], real afac)
{
rvec r12;
- real r12sq, r12_1, r12n, r12bar, v0, v1, fscal, ebar, fff;
+ real r12sq, r12_1, r12bar, v0, v1, fscal, ebar, fff;
int m, t;
t = pbc_rvec_sub(pbc, xi, xj, r12); /* 3 */
int gmx_unused *global_atom_index)
{
/* Interaction between two pairs of particles with opposite charge */
- int i, type, a1, da1, a2, da2;
- real q1, q2, qq, a, al1, al2, afac;
- real V = 0;
+ int i, type, a1, da1, a2, da2;
+ real q1, q2, qq, a, al1, al2, afac;
+ real V = 0;
+ const real minusOneOnSix = -1.0/6.0;
for (i = 0; (i < nbonds); )
{
al1 = forceparams[type].thole.alpha1;
al2 = forceparams[type].thole.alpha2;
qq = q1*q2;
- afac = a*pow(al1*al2, -1.0/6.0);
+ afac = a*pow(al1*al2, minusOneOnSix);
V += do_1_thole(x[a1], x[a2], f[a1], f[a2], pbc, qq, fshift, afac);
V += do_1_thole(x[da1], x[a2], f[da1], f[a2], pbc, -qq, fshift, afac);
V += do_1_thole(x[a1], x[da2], f[a1], f[da2], pbc, -qq, fshift, afac);
#ifdef GMX_SIMD_HAVE_REAL
-/* As angles, but using SIMD to calculate many dihedrals at once.
+/* As angles, but using SIMD to calculate many angles at once.
* This routines does not calculate energies and shift forces.
*/
-static gmx_inline void
+void
angles_noener_simd(int nbonds,
const t_iatom forceatoms[], const t_iparams forceparams[],
const rvec x[], rvec f[],
rvec m, rvec n, rvec f[])
{
rvec f_i, f_j, f_k, f_l;
- rvec uvec, vvec, svec, dx_jl;
+ rvec uvec, vvec, svec;
real iprm, iprn, nrkj, nrkj2, nrkj_1, nrkj_2;
real a, b, p, q, toler;
- ivec jt, dt_ij, dt_kj, dt_lj;
iprm = iprod(m, m); /* 5 */
iprn = iprod(n, n); /* 5 */
}
/* As pdihs above, but without calculating energies and shift forces */
-static void
+void
pdihs_noener(int nbonds,
const t_iatom forceatoms[], const t_iparams forceparams[],
const rvec x[], rvec f[],
#ifdef GMX_SIMD_HAVE_REAL
/* As pdihs_noner above, but using SIMD to calculate many dihedrals at once */
-static void
+void
pdihs_noener_simd(int nbonds,
const t_iatom forceatoms[], const t_iparams forceparams[],
const rvec x[], rvec f[],
const int nfa1 = 5;
int i, iu, s;
int type, ai[GMX_SIMD_REAL_WIDTH], aj[GMX_SIMD_REAL_WIDTH], ak[GMX_SIMD_REAL_WIDTH], al[GMX_SIMD_REAL_WIDTH];
- real ddphi;
real dr_array[3*DIM*GMX_SIMD_REAL_WIDTH+GMX_SIMD_REAL_WIDTH], *dr;
real buf_array[7*GMX_SIMD_REAL_WIDTH+GMX_SIMD_REAL_WIDTH], *buf;
- real *cp, *phi0, *mult, *phi, *p, *q, *sf_i, *msf_l;
+ real *cp, *phi0, *mult, *p, *q;
gmx_simd_real_t phi0_S, phi_S;
gmx_simd_real_t mx_S, my_S, mz_S;
gmx_simd_real_t nx_S, ny_S, nz_S;
mult = buf + 2*GMX_SIMD_REAL_WIDTH;
p = buf + 3*GMX_SIMD_REAL_WIDTH;
q = buf + 4*GMX_SIMD_REAL_WIDTH;
- sf_i = buf + 5*GMX_SIMD_REAL_WIDTH;
- msf_l = buf + 6*GMX_SIMD_REAL_WIDTH;
set_pbc_simd(pbc, &pbc_simd);
const int nfa1 = 5;
int i, iu, s, j;
int type, ai[GMX_SIMD_REAL_WIDTH], aj[GMX_SIMD_REAL_WIDTH], ak[GMX_SIMD_REAL_WIDTH], al[GMX_SIMD_REAL_WIDTH];
- real ddphi;
real dr_array[3*DIM*GMX_SIMD_REAL_WIDTH+GMX_SIMD_REAL_WIDTH], *dr;
real buf_array[(NR_RBDIHS + 4)*GMX_SIMD_REAL_WIDTH+GMX_SIMD_REAL_WIDTH], *buf;
- real *parm, *phi, *p, *q, *sf_i, *msf_l;
+ real *parm, *p, *q;
gmx_simd_real_t phi_S;
gmx_simd_real_t ddphi_S, cosfac_S;
parm = buf;
p = buf + (NR_RBDIHS + 0)*GMX_SIMD_REAL_WIDTH;
q = buf + (NR_RBDIHS + 1)*GMX_SIMD_REAL_WIDTH;
- sf_i = buf + (NR_RBDIHS + 2)*GMX_SIMD_REAL_WIDTH;
- msf_l = buf + (NR_RBDIHS + 3)*GMX_SIMD_REAL_WIDTH;
set_pbc_simd(pbc, &pbc_simd);
dvdl_term += 0.5*(kB - kA)*dp2 - kk*dphi0*dp;
- do_dih_fup(ai, aj, ak, al, (real)(-ddphi), r_ij, r_kj, r_kl, m, n,
+ do_dih_fup(ai, aj, ak, al, -ddphi, r_ij, r_kj, r_kl, m, n,
f, fshift, pbc, g, x, t1, t2, t3); /* 112 */
/* 218 TOTAL */
#ifdef DEBUG
return vtot;
}
-
-/*! \brief returns dx, rdist, and dpdl for functions posres() and fbposres()
- */
-static void posres_dx(const rvec x, const rvec pos0A, const rvec pos0B,
- const rvec comA_sc, const rvec comB_sc,
- real lambda,
- t_pbc *pbc, int refcoord_scaling, int npbcdim,
- rvec dx, rvec rdist, rvec dpdl)
-{
- int m, d;
- real posA, posB, L1, ref = 0.;
- rvec pos;
-
- L1 = 1.0-lambda;
-
- for (m = 0; m < DIM; m++)
- {
- posA = pos0A[m];
- posB = pos0B[m];
- if (m < npbcdim)
- {
- switch (refcoord_scaling)
- {
- case erscNO:
- ref = 0;
- rdist[m] = L1*posA + lambda*posB;
- dpdl[m] = posB - posA;
- break;
- case erscALL:
- /* Box relative coordinates are stored for dimensions with pbc */
- posA *= pbc->box[m][m];
- posB *= pbc->box[m][m];
- assert(npbcdim <= DIM);
- for (d = m+1; d < npbcdim; d++)
- {
- posA += pos0A[d]*pbc->box[d][m];
- posB += pos0B[d]*pbc->box[d][m];
- }
- ref = L1*posA + lambda*posB;
- rdist[m] = 0;
- dpdl[m] = posB - posA;
- break;
- case erscCOM:
- ref = L1*comA_sc[m] + lambda*comB_sc[m];
- rdist[m] = L1*posA + lambda*posB;
- dpdl[m] = comB_sc[m] - comA_sc[m] + posB - posA;
- break;
- default:
- gmx_fatal(FARGS, "No such scaling method implemented");
- }
- }
- else
- {
- ref = L1*posA + lambda*posB;
- rdist[m] = 0;
- dpdl[m] = posB - posA;
- }
-
- /* We do pbc_dx with ref+rdist,
- * since with only ref we can be up to half a box vector wrong.
- */
- pos[m] = ref + rdist[m];
- }
-
- if (pbc)
- {
- pbc_dx(pbc, x, pos, dx);
- }
- else
- {
- rvec_sub(x, pos, dx);
- }
-}
-
-/*! \brief Adds forces of flat-bottomed positions restraints to f[]
- * and fixes vir_diag. Returns the flat-bottomed potential. */
-real fbposres(int nbonds,
- const t_iatom forceatoms[], const t_iparams forceparams[],
- const rvec x[], rvec f[], rvec vir_diag,
- t_pbc *pbc,
- int refcoord_scaling, int ePBC, rvec com)
-/* compute flat-bottomed positions restraints */
-{
- int i, ai, m, d, type, npbcdim = 0, fbdim;
- const t_iparams *pr;
- real vtot, kk, v;
- real ref = 0, dr, dr2, rpot, rfb, rfb2, fact, invdr;
- rvec com_sc, rdist, pos, dx, dpdl, fm;
- gmx_bool bInvert;
-
- npbcdim = ePBC2npbcdim(ePBC);
-
- if (refcoord_scaling == erscCOM)
- {
- clear_rvec(com_sc);
- for (m = 0; m < npbcdim; m++)
- {
- assert(npbcdim <= DIM);
- for (d = m; d < npbcdim; d++)
- {
- com_sc[m] += com[d]*pbc->box[d][m];
- }
- }
- }
-
- vtot = 0.0;
- for (i = 0; (i < nbonds); )
- {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- pr = &forceparams[type];
-
- /* same calculation as for normal posres, but with identical A and B states, and lambda==0 */
- posres_dx(x[ai], forceparams[type].fbposres.pos0, forceparams[type].fbposres.pos0,
- com_sc, com_sc, 0.0,
- pbc, refcoord_scaling, npbcdim,
- dx, rdist, dpdl);
-
- clear_rvec(fm);
- v = 0.0;
-
- kk = pr->fbposres.k;
- rfb = pr->fbposres.r;
- rfb2 = sqr(rfb);
-
- /* with rfb<0, push particle out of the sphere/cylinder/layer */
- bInvert = FALSE;
- if (rfb < 0.)
- {
- bInvert = TRUE;
- rfb = -rfb;
- }
-
- switch (pr->fbposres.geom)
- {
- case efbposresSPHERE:
- /* spherical flat-bottom posres */
- dr2 = norm2(dx);
- if (dr2 > 0.0 &&
- ( (dr2 > rfb2 && bInvert == FALSE ) || (dr2 < rfb2 && bInvert == TRUE ) )
- )
- {
- dr = sqrt(dr2);
- v = 0.5*kk*sqr(dr - rfb);
- fact = -kk*(dr-rfb)/dr; /* Force pointing to the center pos0 */
- svmul(fact, dx, fm);
- }
- break;
- case efbposresCYLINDER:
- /* cylidrical flat-bottom posres in x-y plane. fm[ZZ] = 0. */
- dr2 = sqr(dx[XX])+sqr(dx[YY]);
- if (dr2 > 0.0 &&
- ( (dr2 > rfb2 && bInvert == FALSE ) || (dr2 < rfb2 && bInvert == TRUE ) )
- )
- {
- dr = sqrt(dr2);
- invdr = 1./dr;
- v = 0.5*kk*sqr(dr - rfb);
- fm[XX] = -kk*(dr-rfb)*dx[XX]*invdr; /* Force pointing to the center */
- fm[YY] = -kk*(dr-rfb)*dx[YY]*invdr;
- }
- break;
- case efbposresX: /* fbdim=XX */
- case efbposresY: /* fbdim=YY */
- case efbposresZ: /* fbdim=ZZ */
- /* 1D flat-bottom potential */
- fbdim = pr->fbposres.geom - efbposresX;
- dr = dx[fbdim];
- if ( ( dr > rfb && bInvert == FALSE ) || ( 0 < dr && dr < rfb && bInvert == TRUE ) )
- {
- v = 0.5*kk*sqr(dr - rfb);
- fm[fbdim] = -kk*(dr - rfb);
- }
- else if ( (dr < (-rfb) && bInvert == FALSE ) || ( (-rfb) < dr && dr < 0 && bInvert == TRUE ))
- {
- v = 0.5*kk*sqr(dr + rfb);
- fm[fbdim] = -kk*(dr + rfb);
- }
- break;
- }
-
- vtot += v;
-
- for (m = 0; (m < DIM); m++)
- {
- f[ai][m] += fm[m];
- /* Here we correct for the pbc_dx which included rdist */
- vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm[m];
- }
- }
-
- return vtot;
-}
-
-
-real posres(int nbonds,
- const t_iatom forceatoms[], const t_iparams forceparams[],
- const rvec x[], rvec f[], rvec vir_diag,
- t_pbc *pbc,
- real lambda, real *dvdlambda,
- int refcoord_scaling, int ePBC, rvec comA, rvec comB)
-{
- int i, ai, m, d, type, ki, npbcdim = 0;
- const t_iparams *pr;
- real L1;
- real vtot, kk, fm;
- real posA, posB, ref = 0;
- rvec comA_sc, comB_sc, rdist, dpdl, pos, dx;
- gmx_bool bForceValid = TRUE;
-
- if ((f == NULL) || (vir_diag == NULL)) /* should both be null together! */
- {
- bForceValid = FALSE;
- }
-
- npbcdim = ePBC2npbcdim(ePBC);
-
- if (refcoord_scaling == erscCOM)
- {
- clear_rvec(comA_sc);
- clear_rvec(comB_sc);
- for (m = 0; m < npbcdim; m++)
- {
- assert(npbcdim <= DIM);
- for (d = m; d < npbcdim; d++)
- {
- comA_sc[m] += comA[d]*pbc->box[d][m];
- comB_sc[m] += comB[d]*pbc->box[d][m];
- }
- }
- }
-
- L1 = 1.0 - lambda;
-
- vtot = 0.0;
- for (i = 0; (i < nbonds); )
- {
- type = forceatoms[i++];
- ai = forceatoms[i++];
- pr = &forceparams[type];
-
- /* return dx, rdist, and dpdl */
- posres_dx(x[ai], forceparams[type].posres.pos0A, forceparams[type].posres.pos0B,
- comA_sc, comB_sc, lambda,
- pbc, refcoord_scaling, npbcdim,
- dx, rdist, dpdl);
-
- for (m = 0; (m < DIM); m++)
- {
- kk = L1*pr->posres.fcA[m] + lambda*pr->posres.fcB[m];
- fm = -kk*dx[m];
- vtot += 0.5*kk*dx[m]*dx[m];
- *dvdlambda +=
- 0.5*(pr->posres.fcB[m] - pr->posres.fcA[m])*dx[m]*dx[m]
- + fm*dpdl[m];
-
- /* Here we correct for the pbc_dx which included rdist */
- if (bForceValid)
- {
- f[ai][m] += fm;
- vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm;
- }
- }
- }
-
- return vtot;
-}
-
static real low_angres(int nbonds,
const t_iatom forceatoms[], const t_iparams forceparams[],
const rvec x[], rvec f[], rvec fshift[],
real vtot = 0;
int ai, aj, ak, al, i, k, type, t1, t2, t3;
real phi0A, phi0B, dphiA, dphiB, kfacA, kfacB, phi0, dphi, kfac;
- real phi, ddphi, ddp, ddp2, dp, sign, d2r, fc, L1;
+ real phi, ddphi, ddp, ddp2, dp, sign, d2r, L1;
rvec r_ij, r_kj, r_kl, m, n;
L1 = 1.0-lambda;
{
int i, d, ai, aj, ak, type, m;
int t1, t2;
- rvec r_ij, r_kj;
real v, vtot;
ivec jt, dt_ij, dt_kj;
rvec f_i, f_j, f_k;
t1 = pbc_rvec_sub(pbc, x[ai], x[aj], vec_temp);
pbc_rvec_sub(pbc, x[aj], x[ai], delta_ante);
t2 = pbc_rvec_sub(pbc, x[ak], x[aj], delta_crnt);
- t3 = pbc_rvec_sub(pbc, x[ak], x[al], vec_temp);
+ pbc_rvec_sub(pbc, x[ak], x[al], vec_temp);
pbc_rvec_sub(pbc, x[al], x[ak], delta_post);
/* This function computes factors needed for restricted angle potential.
pbc_rvec_sub(pbc, x[aj], x[ai], delta_ante);
t2 = pbc_rvec_sub(pbc, x[ak], x[aj], vec_temp);
pbc_rvec_sub(pbc, x[ak], x[aj], delta_crnt);
- t3 = pbc_rvec_sub(pbc, x[ak], x[al], vec_temp);
+ pbc_rvec_sub(pbc, x[ak], x[al], vec_temp);
pbc_rvec_sub(pbc, x[al], x[ak], delta_post);
/* \brief Compute factors for CBT potential
return vtot;
}
-int cmap_setup_grid_index(int ip, int grid_spacing, int *ipm1, int *ipp1, int *ipp2)
+//! \endcond
+
+/*! \brief Mysterious undocumented function */
+static int
+cmap_setup_grid_index(int ip, int grid_spacing, int *ipm1, int *ipp1, int *ipp2)
{
int im1, ip1, ip2;
}
-real cmap_dihs(int nbonds,
- const t_iatom forceatoms[], const t_iparams forceparams[],
- const gmx_cmap_t *cmap_grid,
- const rvec x[], rvec f[], rvec fshift[],
- const t_pbc *pbc, const t_graph *g,
- real gmx_unused lambda, real gmx_unused *dvdlambda,
- const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
- int gmx_unused *global_atom_index)
+real
+cmap_dihs(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const gmx_cmap_t *cmap_grid,
+ const rvec x[], rvec f[], rvec fshift[],
+ const struct t_pbc *pbc, const struct t_graph *g,
+ real gmx_unused lambda, real gmx_unused *dvdlambda,
+ const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
+ int gmx_unused *global_atom_index)
{
int i, j, k, n, idx;
int ai, aj, ak, al, am;
int t11, t21, t31, t12, t22, t32;
int iphi1, ip1m1, ip1p1, ip1p2;
int iphi2, ip2m1, ip2p1, ip2p2;
- int l1, l2, l3, l4;
- int pos1, pos2, pos3, pos4, tmp;
+ int l1, l2, l3;
+ int pos1, pos2, pos3, pos4;
real ty[4], ty1[4], ty2[4], ty12[4], tc[16], tx[16];
- real phi1, psi1, cos_phi1, sin_phi1, sign1, xphi1;
- real phi2, psi2, cos_phi2, sin_phi2, sign2, xphi2;
- real dx, xx, tt, tu, e, df1, df2, ddf1, ddf2, ddf12, vtot;
+ real phi1, cos_phi1, sin_phi1, sign1, xphi1;
+ real phi2, cos_phi2, sin_phi2, sign2, xphi2;
+ real dx, xx, tt, tu, e, df1, df2, vtot;
real ra21, rb21, rg21, rg1, rgr1, ra2r1, rb2r1, rabr1;
real ra22, rb22, rg22, rg2, rgr2, ra2r2, rb2r2, rabr2;
real fg1, hg1, fga1, hgb1, gaa1, gbb1;
b1[1] = r1_kl[2]*r1_kj[0]-r1_kl[0]*r1_kj[2];
b1[2] = r1_kl[0]*r1_kj[1]-r1_kl[1]*r1_kj[0]; /* 9 */
- tmp = pbc_rvec_sub(pbc, x[a1l], x[a1k], h1);
+ pbc_rvec_sub(pbc, x[a1l], x[a1k], h1);
ra21 = iprod(a1, a1); /* 5 */
rb21 = iprod(b1, b1); /* 5 */
b2[1] = r2_kl[2]*r2_kj[0]-r2_kl[0]*r2_kj[2];
b2[2] = r2_kl[0]*r2_kj[1]-r2_kl[1]*r2_kj[0]; /* 9 */
- tmp = pbc_rvec_sub(pbc, x[a2l], x[a2k], h2);
+ pbc_rvec_sub(pbc, x[a2l], x[a2k], h2);
ra22 = iprod(a2, a2); /* 5 */
rb22 = iprod(b2, b2); /* 5 */
dx = 2*M_PI / cmap_grid->grid_spacing;
/* Where on the grid are we */
- iphi1 = (int)(xphi1/dx);
- iphi2 = (int)(xphi2/dx);
+ iphi1 = static_cast<int>(xphi1/dx);
+ iphi2 = static_cast<int>(xphi2/dx);
iphi1 = cmap_setup_grid_index(iphi1, cmap_grid->grid_spacing, &ip1m1, &ip1p1, &ip1p2);
iphi2 = cmap_setup_grid_index(iphi2, cmap_grid->grid_spacing, &ip2m1, &ip2p1, &ip2p2);
e = 0;
df1 = 0;
df2 = 0;
- ddf1 = 0;
- ddf2 = 0;
- ddf12 = 0;
for (i = 3; i >= 0; i--)
{
e = tt * e + ((tc[i*4+3]*tu+tc[i*4+2])*tu + tc[i*4+1])*tu+tc[i*4];
df1 = tu * df1 + (3.0*tc[l1]*tt+2.0*tc[l2])*tt+tc[l3];
df2 = tt * df2 + (3.0*tc[i*4+3]*tu+2.0*tc[i*4+2])*tu+tc[i*4+1];
- ddf1 = tu * ddf1 + 2.0*3.0*tc[l1]*tt+2.0*tc[l2];
- ddf2 = tt * ddf2 + 2.0*3.0*tc[4*i+3]*tu+2.0*tc[4*i+2];
}
- ddf12 = tc[5] + 2.0*tc[9]*tt + 3.0*tc[13]*tt*tt + 2.0*tu*(tc[6]+2.0*tc[10]*tt+3.0*tc[14]*tt*tt) +
- 3.0*tu*tu*(tc[7]+2.0*tc[11]*tt+3.0*tc[15]*tt*tt);
-
fac = RAD2DEG/dx;
df1 = df1 * fac;
df2 = df2 * fac;
- ddf1 = ddf1 * fac * fac;
- ddf2 = ddf2 * fac * fac;
- ddf12 = ddf12 * fac * fac;
/* CMAP energy */
vtot += e;
}
-
+//! \cond
/***********************************************************
*
* G R O M O S 9 6 F U N C T I O N S
/* Potential from Lawrence and Skimmer, Chem. Phys. Lett. 372 (2003)
* pp. 842-847
*/
- int i, ai, aj, ak, type, m, t1, t2, t3;
+ int i, ai, aj, ak, type, m, t1, t2;
rvec r_ij, r_kj, r_ik;
real vtot, vrt, s1, s2, s3, r1, r2, r3, r1e, r2e, r3e, krt, k1, k2, k3;
rvec f_i, f_j, f_k;
/* Compute distance vectors ... */
t1 = pbc_rvec_sub(pbc, x[ai], x[aj], r_ij);
t2 = pbc_rvec_sub(pbc, x[ak], x[aj], r_kj);
- t3 = pbc_rvec_sub(pbc, x[ai], x[ak], r_ik);
+ pbc_rvec_sub(pbc, x[ai], x[ak], r_ik);
/* ... and their lengths */
r1 = norm(r_ij);
{
real k, tabscale, *VFtab, rt, eps, eps2, Yt, Ft, Geps, Heps2, Fp, VV, FF;
int n0, nnn;
- real v, f, dvdlambda;
+ real dvdlambda;
k = (1.0 - lambda)*kA + lambda*kB;
VFtab = table->data;
rt = r*tabscale;
- n0 = rt;
+ n0 = static_cast<int>(rt);
if (n0 >= table->n)
{
gmx_fatal(FARGS, "A tabulated %s interaction table number %d is out of the table range: r %f, between table indices %d and %d, table length %d",
if (cos_theta2 < 1)
{
int m;
- real snt, st, sth;
+ real st, sth;
real cik, cii, ckk;
real nrkj2, nrij2;
rvec f_i, f_j, f_k;
return vtot;
}
-/* Return if this is a potential calculated in bondfree.c,
- * i.e. an interaction that actually calculates a potential and
- * works on multiple atoms (not e.g. a connection or a position restraint).
- */
-static gmx_inline gmx_bool ftype_is_bonded_potential(int ftype)
-{
- return
- (interaction_function[ftype].flags & IF_BOND) &&
- !(ftype == F_CONNBONDS || ftype == F_POSRES || ftype == F_FBPOSRES) &&
- (ftype < F_GB12 || ftype > F_GB14);
-}
-
-static void divide_bondeds_over_threads(t_idef *idef, int nthreads)
-{
- int ftype;
- int nat1;
- int t;
- int il_nr_thread;
-
- idef->nthreads = nthreads;
-
- if (F_NRE*(nthreads+1) > idef->il_thread_division_nalloc)
- {
- idef->il_thread_division_nalloc = F_NRE*(nthreads+1);
- snew(idef->il_thread_division, idef->il_thread_division_nalloc);
- }
-
- for (ftype = 0; ftype < F_NRE; ftype++)
- {
- if (ftype_is_bonded_potential(ftype))
- {
- nat1 = interaction_function[ftype].nratoms + 1;
-
- for (t = 0; t <= nthreads; t++)
- {
- /* Divide the interactions equally over the threads.
- * When the different types of bonded interactions
- * are distributed roughly equally over the threads,
- * this should lead to well localized output into
- * the force buffer on each thread.
- * If this is not the case, a more advanced scheme
- * (not implemented yet) will do better.
- */
- il_nr_thread = (((idef->il[ftype].nr/nat1)*t)/nthreads)*nat1;
-
- /* Ensure that distance restraint pairs with the same label
- * end up on the same thread.
- * This is slighlty tricky code, since the next for iteration
- * may have an initial il_nr_thread lower than the final value
- * in the previous iteration, but this will anyhow be increased
- * to the approriate value again by this while loop.
- */
- while (ftype == F_DISRES &&
- il_nr_thread > 0 &&
- il_nr_thread < idef->il[ftype].nr &&
- idef->iparams[idef->il[ftype].iatoms[il_nr_thread]].disres.label ==
- idef->iparams[idef->il[ftype].iatoms[il_nr_thread-nat1]].disres.label)
- {
- il_nr_thread += nat1;
- }
-
- idef->il_thread_division[ftype*(nthreads+1)+t] = il_nr_thread;
- }
- }
- }
-}
-
-static unsigned
-calc_bonded_reduction_mask(const t_idef *idef,
- int shift,
- int t, int nt)
-{
- unsigned mask;
- int ftype, nb, nat1, nb0, nb1, i, a;
-
- mask = 0;
-
- for (ftype = 0; ftype < F_NRE; ftype++)
- {
- if (ftype_is_bonded_potential(ftype))
- {
- nb = idef->il[ftype].nr;
- if (nb > 0)
- {
- nat1 = interaction_function[ftype].nratoms + 1;
-
- /* Divide this interaction equally over the threads.
- * This is not stored: should match division in calc_bonds.
- */
- nb0 = idef->il_thread_division[ftype*(nt+1)+t];
- nb1 = idef->il_thread_division[ftype*(nt+1)+t+1];
-
- for (i = nb0; i < nb1; i += nat1)
- {
- for (a = 1; a < nat1; a++)
- {
- mask |= (1U << (idef->il[ftype].iatoms[i+a]>>shift));
- }
- }
- }
- }
- }
-
- return mask;
-}
-
-void setup_bonded_threading(t_forcerec *fr, t_idef *idef)
-{
-#define MAX_BLOCK_BITS 32
- int t;
- int ctot, c, b;
-
- assert(fr->nthreads >= 1);
-
- /* Divide the bonded interaction over the threads */
- divide_bondeds_over_threads(idef, fr->nthreads);
-
- if (fr->nthreads == 1)
- {
- fr->red_nblock = 0;
-
- return;
- }
-
- /* We divide the force array in a maximum of 32 blocks.
- * Minimum force block reduction size is 2^6=64.
- */
- fr->red_ashift = 6;
- while (fr->natoms_force > (int)(MAX_BLOCK_BITS*(1U<<fr->red_ashift)))
- {
- fr->red_ashift++;
- }
- if (debug)
- {
- fprintf(debug, "bonded force buffer block atom shift %d bits\n",
- fr->red_ashift);
- }
-
- /* Determine to which blocks each thread's bonded force calculation
- * contributes. Store this is a mask for each thread.
- */
-#pragma omp parallel for num_threads(fr->nthreads) schedule(static)
- for (t = 1; t < fr->nthreads; t++)
- {
- fr->f_t[t].red_mask =
- calc_bonded_reduction_mask(idef, fr->red_ashift, t, fr->nthreads);
- }
-
- /* Determine the maximum number of blocks we need to reduce over */
- fr->red_nblock = 0;
- ctot = 0;
- for (t = 0; t < fr->nthreads; t++)
- {
- c = 0;
- for (b = 0; b < MAX_BLOCK_BITS; b++)
- {
- if (fr->f_t[t].red_mask & (1U<<b))
- {
- fr->red_nblock = max(fr->red_nblock, b+1);
- c++;
- }
- }
- if (debug)
- {
- fprintf(debug, "thread %d flags %x count %d\n",
- t, fr->f_t[t].red_mask, c);
- }
- ctot += c;
- }
- if (debug)
- {
- fprintf(debug, "Number of blocks to reduce: %d of size %d\n",
- fr->red_nblock, 1<<fr->red_ashift);
- fprintf(debug, "Reduction density %.2f density/#thread %.2f\n",
- ctot*(1<<fr->red_ashift)/(double)fr->natoms_force,
- ctot*(1<<fr->red_ashift)/(double)(fr->natoms_force*fr->nthreads));
- }
-}
-
-static void zero_thread_forces(f_thread_t *f_t, int n,
- int nblock, int blocksize)
-{
- int b, a0, a1, a, i, j;
-
- if (n > f_t->f_nalloc)
- {
- f_t->f_nalloc = over_alloc_large(n);
- srenew(f_t->f, f_t->f_nalloc);
- }
-
- if (f_t->red_mask != 0)
- {
- for (b = 0; b < nblock; b++)
- {
- if (f_t->red_mask && (1U<<b))
- {
- a0 = b*blocksize;
- a1 = min((b+1)*blocksize, n);
- for (a = a0; a < a1; a++)
- {
- clear_rvec(f_t->f[a]);
- }
- }
- }
- }
- for (i = 0; i < SHIFTS; i++)
- {
- clear_rvec(f_t->fshift[i]);
- }
- for (i = 0; i < F_NRE; i++)
- {
- f_t->ener[i] = 0;
- }
- for (i = 0; i < egNR; i++)
- {
- for (j = 0; j < f_t->grpp.nener; j++)
- {
- f_t->grpp.ener[i][j] = 0;
- }
- }
- for (i = 0; i < efptNR; i++)
- {
- f_t->dvdl[i] = 0;
- }
-}
-
-static void reduce_thread_force_buffer(int n, rvec *f,
- int nthreads, f_thread_t *f_t,
- int nblock, int block_size)
-{
- /* The max thread number is arbitrary,
- * we used a fixed number to avoid memory management.
- * Using more than 16 threads is probably never useful performance wise.
- */
-#define MAX_BONDED_THREADS 256
- int b;
-
- if (nthreads > MAX_BONDED_THREADS)
- {
- gmx_fatal(FARGS, "Can not reduce bonded forces on more than %d threads",
- MAX_BONDED_THREADS);
- }
-
- /* This reduction can run on any number of threads,
- * independently of nthreads.
- */
-#pragma omp parallel for num_threads(nthreads) schedule(static)
- for (b = 0; b < nblock; b++)
- {
- rvec *fp[MAX_BONDED_THREADS];
- int nfb, ft, fb;
- int a0, a1, a;
-
- /* Determine which threads contribute to this block */
- nfb = 0;
- for (ft = 1; ft < nthreads; ft++)
- {
- if (f_t[ft].red_mask & (1U<<b))
- {
- fp[nfb++] = f_t[ft].f;
- }
- }
- if (nfb > 0)
- {
- /* Reduce force buffers for threads that contribute */
- a0 = b *block_size;
- a1 = (b+1)*block_size;
- a1 = min(a1, n);
- for (a = a0; a < a1; a++)
- {
- for (fb = 0; fb < nfb; fb++)
- {
- rvec_inc(f[a], fp[fb][a]);
- }
- }
- }
- }
-}
-
-static void reduce_thread_forces(int n, rvec *f, rvec *fshift,
- real *ener, gmx_grppairener_t *grpp, real *dvdl,
- int nthreads, f_thread_t *f_t,
- int nblock, int block_size,
- gmx_bool bCalcEnerVir,
- gmx_bool bDHDL)
-{
- if (nblock > 0)
- {
- /* Reduce the bonded force buffer */
- reduce_thread_force_buffer(n, f, nthreads, f_t, nblock, block_size);
- }
-
- /* When necessary, reduce energy and virial using one thread only */
- if (bCalcEnerVir)
- {
- int t, i, j;
-
- for (i = 0; i < SHIFTS; i++)
- {
- for (t = 1; t < nthreads; t++)
- {
- rvec_inc(fshift[i], f_t[t].fshift[i]);
- }
- }
- for (i = 0; i < F_NRE; i++)
- {
- for (t = 1; t < nthreads; t++)
- {
- ener[i] += f_t[t].ener[i];
- }
- }
- for (i = 0; i < egNR; i++)
- {
- for (j = 0; j < f_t[1].grpp.nener; j++)
- {
- for (t = 1; t < nthreads; t++)
- {
-
- grpp->ener[i][j] += f_t[t].grpp.ener[i][j];
- }
- }
- }
- if (bDHDL)
- {
- for (i = 0; i < efptNR; i++)
- {
-
- for (t = 1; t < nthreads; t++)
- {
- dvdl[i] += f_t[t].dvdl[i];
- }
- }
- }
- }
-}
-
-static real calc_one_bond(FILE *fplog, int thread,
- int ftype, const t_idef *idef,
- rvec x[], rvec f[], rvec fshift[],
- t_forcerec *fr,
- const t_pbc *pbc, const t_graph *g,
- gmx_grppairener_t *grpp,
- t_nrnb *nrnb,
- real *lambda, real *dvdl,
- const t_mdatoms *md, t_fcdata *fcd,
- gmx_bool bCalcEnerVir,
- int *global_atom_index, gmx_bool bPrintSepPot)
-{
- int nat1, nbonds, efptFTYPE;
- real v = 0;
- t_iatom *iatoms;
- int nb0, nbn;
-
- if (IS_RESTRAINT_TYPE(ftype))
- {
- efptFTYPE = efptRESTRAINT;
- }
- else
- {
- efptFTYPE = efptBONDED;
- }
-
- nat1 = interaction_function[ftype].nratoms + 1;
- nbonds = idef->il[ftype].nr/nat1;
- iatoms = idef->il[ftype].iatoms;
-
- nb0 = idef->il_thread_division[ftype*(idef->nthreads+1)+thread];
- nbn = idef->il_thread_division[ftype*(idef->nthreads+1)+thread+1] - nb0;
-
- if (!IS_LISTED_LJ_C(ftype))
- {
- if (ftype == F_CMAP)
- {
- v = cmap_dihs(nbn, iatoms+nb0,
- idef->iparams, &idef->cmap_grid,
- (const rvec*)x, f, fshift,
- pbc, g, lambda[efptFTYPE], &(dvdl[efptFTYPE]),
- md, fcd, global_atom_index);
- }
-#ifdef GMX_SIMD_HAVE_REAL
- else if (ftype == F_ANGLES &&
- !bCalcEnerVir && fr->efep == efepNO)
- {
- /* No energies, shift forces, dvdl */
- angles_noener_simd(nbn, idef->il[ftype].iatoms+nb0,
- idef->iparams,
- (const rvec*)x, f,
- pbc, g, lambda[efptFTYPE], md, fcd,
- global_atom_index);
- v = 0;
- }
-#endif
- else if (ftype == F_PDIHS &&
- !bCalcEnerVir && fr->efep == efepNO)
- {
- /* No energies, shift forces, dvdl */
-#ifdef GMX_SIMD_HAVE_REAL
- pdihs_noener_simd
-#else
- pdihs_noener
-#endif
- (nbn, idef->il[ftype].iatoms+nb0,
- idef->iparams,
- (const rvec*)x, f,
- pbc, g, lambda[efptFTYPE], md, fcd,
- global_atom_index);
- v = 0;
- }
-#ifdef GMX_SIMD_HAVE_REAL
- else if (ftype == F_RBDIHS &&
- !bCalcEnerVir && fr->efep == efepNO)
- {
- /* No energies, shift forces, dvdl */
- rbdihs_noener_simd(nbn, idef->il[ftype].iatoms+nb0,
- idef->iparams,
- (const rvec*)x, f,
- pbc, g, lambda[efptFTYPE], md, fcd,
- global_atom_index);
- v = 0;
- }
-#endif
- else
- {
- v = interaction_function[ftype].ifunc(nbn, iatoms+nb0,
- idef->iparams,
- (const rvec*)x, f, fshift,
- pbc, g, lambda[efptFTYPE], &(dvdl[efptFTYPE]),
- md, fcd, global_atom_index);
- }
- if (bPrintSepPot)
- {
- fprintf(fplog, " %-23s #%4d V %12.5e dVdl %12.5e\n",
- interaction_function[ftype].longname,
- nbonds, v, lambda[efptFTYPE]);
- }
- }
- else
- {
- v = do_nonbonded_listed(ftype, nbn, iatoms+nb0, idef->iparams, (const rvec*)x, f, fshift,
- pbc, g, lambda, dvdl, md, fr, grpp, global_atom_index);
-
- if (bPrintSepPot)
- {
- fprintf(fplog, " %-5s + %-15s #%4d dVdl %12.5e\n",
- interaction_function[ftype].longname,
- interaction_function[F_LJ14].longname, nbonds, dvdl[efptVDW]);
- fprintf(fplog, " %-5s + %-15s #%4d dVdl %12.5e\n",
- interaction_function[ftype].longname,
- interaction_function[F_COUL14].longname, nbonds, dvdl[efptCOUL]);
- }
- }
-
- if (thread == 0)
- {
- inc_nrnb(nrnb, interaction_function[ftype].nrnb_ind, nbonds);
- }
-
- return v;
-}
-
-void calc_bonds(FILE *fplog, const gmx_multisim_t *ms,
- const t_idef *idef,
- rvec x[], history_t *hist,
- rvec f[], t_forcerec *fr,
- const t_pbc *pbc, const t_graph *g,
- gmx_enerdata_t *enerd, t_nrnb *nrnb,
- real *lambda,
- const t_mdatoms *md,
- t_fcdata *fcd, int *global_atom_index,
- t_atomtypes gmx_unused *atype, gmx_genborn_t gmx_unused *born,
- int force_flags,
- gmx_bool bPrintSepPot, gmx_int64_t step)
-{
- gmx_bool bCalcEnerVir;
- int i;
- real v, dvdl[efptNR], dvdl_dum[efptNR]; /* The dummy array is to have a place to store the dhdl at other values
- of lambda, which will be thrown away in the end*/
- const t_pbc *pbc_null;
- char buf[22];
- int thread;
-
- assert(fr->nthreads == idef->nthreads);
-
- bCalcEnerVir = (force_flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY));
-
- for (i = 0; i < efptNR; i++)
- {
- dvdl[i] = 0.0;
- }
- if (fr->bMolPBC)
- {
- pbc_null = pbc;
- }
- else
- {
- pbc_null = NULL;
- }
- if (bPrintSepPot)
- {
- fprintf(fplog, "Step %s: bonded V and dVdl for this rank\n",
- gmx_step_str(step, buf));
- }
-
-#ifdef DEBUG
- if (g && debug)
- {
- p_graph(debug, "Bondage is fun", g);
- }
-#endif
-
- /* Do pre force calculation stuff which might require communication */
- if (idef->il[F_ORIRES].nr)
- {
- enerd->term[F_ORIRESDEV] =
- calc_orires_dev(ms, idef->il[F_ORIRES].nr,
- idef->il[F_ORIRES].iatoms,
- idef->iparams, md, (const rvec*)x,
- pbc_null, fcd, hist);
- }
- if (idef->il[F_DISRES].nr)
- {
- calc_disres_R_6(idef->il[F_DISRES].nr,
- idef->il[F_DISRES].iatoms,
- idef->iparams, (const rvec*)x, pbc_null,
- fcd, hist);
-#ifdef GMX_MPI
- if (fcd->disres.nsystems > 1)
- {
- gmx_sum_sim(2*fcd->disres.nres, fcd->disres.Rt_6, ms);
- }
-#endif
- }
-
-#pragma omp parallel for num_threads(fr->nthreads) schedule(static)
- for (thread = 0; thread < fr->nthreads; thread++)
- {
- int ftype;
- real *epot, v;
- /* thread stuff */
- rvec *ft, *fshift;
- real *dvdlt;
- gmx_grppairener_t *grpp;
-
- if (thread == 0)
- {
- ft = f;
- fshift = fr->fshift;
- epot = enerd->term;
- grpp = &enerd->grpp;
- dvdlt = dvdl;
- }
- else
- {
- zero_thread_forces(&fr->f_t[thread], fr->natoms_force,
- fr->red_nblock, 1<<fr->red_ashift);
-
- ft = fr->f_t[thread].f;
- fshift = fr->f_t[thread].fshift;
- epot = fr->f_t[thread].ener;
- grpp = &fr->f_t[thread].grpp;
- dvdlt = fr->f_t[thread].dvdl;
- }
- /* Loop over all bonded force types to calculate the bonded forces */
- for (ftype = 0; (ftype < F_NRE); ftype++)
- {
- if (idef->il[ftype].nr > 0 && ftype_is_bonded_potential(ftype))
- {
- v = calc_one_bond(fplog, thread, ftype, idef, x,
- ft, fshift, fr, pbc_null, g, grpp,
- nrnb, lambda, dvdlt,
- md, fcd, bCalcEnerVir,
- global_atom_index, bPrintSepPot);
- epot[ftype] += v;
- }
- }
- }
- if (fr->nthreads > 1)
- {
- reduce_thread_forces(fr->natoms_force, f, fr->fshift,
- enerd->term, &enerd->grpp, dvdl,
- fr->nthreads, fr->f_t,
- fr->red_nblock, 1<<fr->red_ashift,
- bCalcEnerVir,
- force_flags & GMX_FORCE_DHDL);
- }
- if (force_flags & GMX_FORCE_DHDL)
- {
- for (i = 0; i < efptNR; i++)
- {
- enerd->dvdl_nonlin[i] += dvdl[i];
- }
- }
-
- /* Copy the sum of violations for the distance restraints from fcd */
- if (fcd)
- {
- enerd->term[F_DISRESVIOL] = fcd->disres.sumviol;
-
- }
-}
-
-void calc_bonds_lambda(FILE *fplog,
- const t_idef *idef,
- rvec x[],
- t_forcerec *fr,
- const t_pbc *pbc, const t_graph *g,
- gmx_grppairener_t *grpp, real *epot, t_nrnb *nrnb,
- real *lambda,
- const t_mdatoms *md,
- t_fcdata *fcd,
- int *global_atom_index)
-{
- int i, ftype, nr_nonperturbed, nr;
- real v;
- real dvdl_dum[efptNR];
- rvec *f, *fshift;
- const t_pbc *pbc_null;
- t_idef idef_fe;
-
- if (fr->bMolPBC)
- {
- pbc_null = pbc;
- }
- else
- {
- pbc_null = NULL;
- }
-
- /* Copy the whole idef, so we can modify the contents locally */
- idef_fe = *idef;
- idef_fe.nthreads = 1;
- snew(idef_fe.il_thread_division, F_NRE*(idef_fe.nthreads+1));
-
- /* We already have the forces, so we use temp buffers here */
- snew(f, fr->natoms_force);
- snew(fshift, SHIFTS);
-
- /* Loop over all bonded force types to calculate the bonded energies */
- for (ftype = 0; (ftype < F_NRE); ftype++)
- {
- if (ftype_is_bonded_potential(ftype))
- {
- /* Set the work range of thread 0 to the perturbed bondeds only */
- nr_nonperturbed = idef->il[ftype].nr_nonperturbed;
- nr = idef->il[ftype].nr;
- idef_fe.il_thread_division[ftype*2+0] = nr_nonperturbed;
- idef_fe.il_thread_division[ftype*2+1] = nr;
-
- /* This is only to get the flop count correct */
- idef_fe.il[ftype].nr = nr - nr_nonperturbed;
-
- if (nr - nr_nonperturbed > 0)
- {
- v = calc_one_bond(fplog, 0, ftype, &idef_fe,
- x, f, fshift, fr, pbc_null, g,
- grpp, nrnb, lambda, dvdl_dum,
- md, fcd, TRUE,
- global_atom_index, FALSE);
- epot[ftype] += v;
- }
- }
- }
-
- sfree(fshift);
- sfree(f);
-
- sfree(idef_fe.il_thread_division);
-}
+//! \endcond
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ *
+ * \brief This file contains declarations necessary for low-level
+ * functions for computing energies and forces for bonded interactions.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_listed-forces
+ */
+
+#ifndef GMX_LISTED_FORCES_BONDED_H
+#define GMX_LISTED_FORCES_BONDED_H
+
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/types/fcdata.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/legacyheaders/types/ifunc.h"
+#include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
+#include "gromacs/legacyheaders/types/nrnb.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/simd/simd.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/utility/basedefinitions.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+struct gmx_wallcycle;
+struct t_graph;
+struct t_pbc;
+
+/*! \brief Calculate bond-angle. No PBC is taken into account (use mol-shift) */
+real bond_angle(const rvec xi, const rvec xj, const rvec xk,
+ const struct t_pbc *pbc,
+ rvec r_ij, rvec r_kj, real *costh,
+ int *t1, int *t2); /* out */
+
+/*! \brief Calculate dihedral-angle. No PBC is taken into account (use mol-shift) */
+real dih_angle(const rvec xi, const rvec xj, const rvec xk, const rvec xl,
+ const struct t_pbc *pbc,
+ rvec r_ij, rvec r_kj, rvec r_kl, rvec m, rvec n, /* out */
+ real *sign,
+ int *t1, int *t2, int *t3);
+
+/*! \brief Do an update of the forces for dihedral potentials */
+void do_dih_fup(int i, int j, int k, int l, real ddphi,
+ rvec r_ij, rvec r_kj, rvec r_kl,
+ rvec m, rvec n, rvec f[], rvec fshift[],
+ const struct t_pbc *pbc, const struct t_graph *g,
+ const rvec *x, int t1, int t2, int t3);
+
+/*! \brief Make a dihedral fall in the range (-pi,pi) */
+void make_dp_periodic(real *dp);
+
+/*! \brief Compute CMAP dihedral energies and forces */
+real
+ cmap_dihs(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const gmx_cmap_t *cmap_grid,
+ const rvec x[], rvec f[], rvec fshift[],
+ const struct t_pbc *pbc, const struct t_graph *g,
+ real gmx_unused lambda, real gmx_unused *dvdlambda,
+ const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
+ int gmx_unused *global_atom_index);
+
+//! \cond
+/*************************************************************************
+ *
+ * Bonded force functions
+ *
+ *************************************************************************/
+t_ifunc bonds, g96bonds, morse_bonds, cubic_bonds, FENE_bonds, restraint_bonds;
+t_ifunc angles, g96angles, cross_bond_bond, cross_bond_angle, urey_bradley, quartic_angles, linear_angles;
+t_ifunc restrangles;
+t_ifunc pdihs, idihs, rbdihs;
+t_ifunc restrdihs, cbtdihs;
+t_ifunc tab_bonds, tab_angles, tab_dihs;
+t_ifunc polarize, anharm_polarize, water_pol, thole_pol, angres, angresz, dihres, unimplemented;
+
+/* As pdihs(), but without calculating energies and shift forces */
+void
+ pdihs_noener(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[],
+ const struct t_pbc gmx_unused *pbc,
+ const struct t_graph gmx_unused *g,
+ real lambda,
+ const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
+ int gmx_unused *global_atom_index);
+
+#ifdef GMX_SIMD_HAVE_REAL
+
+/* As angles(), but using SIMD to calculate many angles at once.
+ * This routines does not calculate energies and shift forces.
+ */
+void
+ angles_noener_simd(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[],
+ const struct t_pbc *pbc,
+ const struct t_graph gmx_unused *g,
+ real gmx_unused lambda,
+ const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
+ int gmx_unused *global_atom_index);
+
+/* As pdihs_noener(), but using SIMD to calculate many dihedrals at once. */
+void
+ pdihs_noener_simd(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[],
+ const struct t_pbc *pbc,
+ const struct t_graph gmx_unused *g,
+ real gmx_unused lambda,
+ const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
+ int gmx_unused *global_atom_index);
+
+#endif
+
+//! \endcond
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief This file defines high-level functions for mdrun to compute
+ * energies and forces for listed interactions.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \ingroup module_listed-forces
+ */
+#include "gmxpre.h"
+
+#include "listed-forces.h"
+
+#include "config.h"
+
+#include <assert.h>
+
+#include <algorithm>
+
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/listed-forces/position-restraints.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/forcerec-threading.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/simd/simd.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "pairs.h"
+
+namespace
+{
+
+/*! \brief Return true if ftype is an explicit pair-listed LJ or
+ * COULOMB interaction type: bonded LJ (usually 1-4), or special
+ * listed non-bonded for FEP. */
+bool
+isPairInteraction(int ftype)
+{
+ return ((ftype) >= F_LJ14 && (ftype) <= F_LJC_PAIRS_NB);
+}
+
+/*! \brief Zero thread-local force-output buffers */
+void
+zero_thread_forces(f_thread_t *f_t, int n,
+ int nblock, int blocksize)
+{
+ int b, a0, a1, a, i, j;
+
+ if (n > f_t->f_nalloc)
+ {
+ f_t->f_nalloc = over_alloc_large(n);
+ srenew(f_t->f, f_t->f_nalloc);
+ }
+
+ if (!bitmask_is_zero(f_t->red_mask))
+ {
+ for (b = 0; b < nblock; b++)
+ {
+ if (bitmask_is_set(f_t->red_mask, b))
+ {
+ a0 = b*blocksize;
+ a1 = std::min((b+1)*blocksize, n);
+ for (a = a0; a < a1; a++)
+ {
+ clear_rvec(f_t->f[a]);
+ }
+ }
+ }
+ }
+ for (i = 0; i < SHIFTS; i++)
+ {
+ clear_rvec(f_t->fshift[i]);
+ }
+ for (i = 0; i < F_NRE; i++)
+ {
+ f_t->ener[i] = 0;
+ }
+ for (i = 0; i < egNR; i++)
+ {
+ for (j = 0; j < f_t->grpp.nener; j++)
+ {
+ f_t->grpp.ener[i][j] = 0;
+ }
+ }
+ for (i = 0; i < efptNR; i++)
+ {
+ f_t->dvdl[i] = 0;
+ }
+}
+
+/*! \brief The max thread number is arbitrary, we used a fixed number
+ * to avoid memory management. Using more than 16 threads is probably
+ * never useful performance wise. */
+#define MAX_BONDED_THREADS 256
+
+/*! \brief Reduce thread-local force buffers */
+void
+reduce_thread_force_buffer(int n, rvec *f,
+ int nthreads, f_thread_t *f_t,
+ int nblock, int block_size)
+{
+ int b;
+
+ if (nthreads > MAX_BONDED_THREADS)
+ {
+ gmx_fatal(FARGS, "Can not reduce bonded forces on more than %d threads",
+ MAX_BONDED_THREADS);
+ }
+
+ /* This reduction can run on any number of threads,
+ * independently of nthreads.
+ */
+#pragma omp parallel for num_threads(nthreads) schedule(static)
+ for (b = 0; b < nblock; b++)
+ {
+ rvec *fp[MAX_BONDED_THREADS];
+ int nfb, ft, fb;
+ int a0, a1, a;
+
+ /* Determine which threads contribute to this block */
+ nfb = 0;
+ for (ft = 1; ft < nthreads; ft++)
+ {
+ if (bitmask_is_set(f_t[ft].red_mask, b))
+ {
+ fp[nfb++] = f_t[ft].f;
+ }
+ }
+ if (nfb > 0)
+ {
+ /* Reduce force buffers for threads that contribute */
+ a0 = b *block_size;
+ a1 = (b+1)*block_size;
+ a1 = std::min(a1, n);
+ for (a = a0; a < a1; a++)
+ {
+ for (fb = 0; fb < nfb; fb++)
+ {
+ rvec_inc(f[a], fp[fb][a]);
+ }
+ }
+ }
+ }
+}
+
+/*! \brief Reduce thread-local forces */
+void
+reduce_thread_forces(int n, rvec *f, rvec *fshift,
+ real *ener, gmx_grppairener_t *grpp, real *dvdl,
+ int nthreads, f_thread_t *f_t,
+ int nblock, int block_size,
+ gmx_bool bCalcEnerVir,
+ gmx_bool bDHDL)
+{
+ if (nblock > 0)
+ {
+ /* Reduce the bonded force buffer */
+ reduce_thread_force_buffer(n, f, nthreads, f_t, nblock, block_size);
+ }
+
+ /* When necessary, reduce energy and virial using one thread only */
+ if (bCalcEnerVir)
+ {
+ int t, i, j;
+
+ for (i = 0; i < SHIFTS; i++)
+ {
+ for (t = 1; t < nthreads; t++)
+ {
+ rvec_inc(fshift[i], f_t[t].fshift[i]);
+ }
+ }
+ for (i = 0; i < F_NRE; i++)
+ {
+ for (t = 1; t < nthreads; t++)
+ {
+ ener[i] += f_t[t].ener[i];
+ }
+ }
+ for (i = 0; i < egNR; i++)
+ {
+ for (j = 0; j < f_t[1].grpp.nener; j++)
+ {
+ for (t = 1; t < nthreads; t++)
+ {
+
+ grpp->ener[i][j] += f_t[t].grpp.ener[i][j];
+ }
+ }
+ }
+ if (bDHDL)
+ {
+ for (i = 0; i < efptNR; i++)
+ {
+
+ for (t = 1; t < nthreads; t++)
+ {
+ dvdl[i] += f_t[t].dvdl[i];
+ }
+ }
+ }
+ }
+}
+
+/*! \brief Calculate one element of the list of bonded interactions
+ for this thread */
+real
+calc_one_bond(int thread,
+ int ftype, const t_idef *idef,
+ const rvec x[], rvec f[], rvec fshift[],
+ t_forcerec *fr,
+ const t_pbc *pbc, const t_graph *g,
+ gmx_grppairener_t *grpp,
+ t_nrnb *nrnb,
+ real *lambda, real *dvdl,
+ const t_mdatoms *md, t_fcdata *fcd,
+ gmx_bool bCalcEnerVir,
+ int *global_atom_index)
+{
+ int nat1, nbonds, efptFTYPE;
+ real v = 0;
+ t_iatom *iatoms;
+ int nb0, nbn;
+
+ if (IS_RESTRAINT_TYPE(ftype))
+ {
+ efptFTYPE = efptRESTRAINT;
+ }
+ else
+ {
+ efptFTYPE = efptBONDED;
+ }
+
+ nat1 = interaction_function[ftype].nratoms + 1;
+ nbonds = idef->il[ftype].nr/nat1;
+ iatoms = idef->il[ftype].iatoms;
+
+ nb0 = idef->il_thread_division[ftype*(idef->nthreads+1)+thread];
+ nbn = idef->il_thread_division[ftype*(idef->nthreads+1)+thread+1] - nb0;
+
+ if (!isPairInteraction(ftype))
+ {
+ if (ftype == F_CMAP)
+ {
+ v = cmap_dihs(nbn, iatoms+nb0,
+ idef->iparams, &idef->cmap_grid,
+ x, f, fshift,
+ pbc, g, lambda[efptFTYPE], &(dvdl[efptFTYPE]),
+ md, fcd, global_atom_index);
+ }
+#ifdef GMX_SIMD_HAVE_REAL
+ else if (ftype == F_ANGLES &&
+ !bCalcEnerVir && fr->efep == efepNO)
+ {
+ /* No energies, shift forces, dvdl */
+ angles_noener_simd(nbn, idef->il[ftype].iatoms+nb0,
+ idef->iparams,
+ x, f,
+ pbc, g, lambda[efptFTYPE], md, fcd,
+ global_atom_index);
+ v = 0;
+ }
+#endif
+ else if (ftype == F_PDIHS &&
+ !bCalcEnerVir && fr->efep == efepNO)
+ {
+ /* No energies, shift forces, dvdl */
+#ifdef GMX_SIMD_HAVE_REAL
+ pdihs_noener_simd
+#else
+ pdihs_noener
+#endif
+ (nbn, idef->il[ftype].iatoms+nb0,
+ idef->iparams,
+ x, f,
+ pbc, g, lambda[efptFTYPE], md, fcd,
+ global_atom_index);
+ v = 0;
+ }
+ else
+ {
+ v = interaction_function[ftype].ifunc(nbn, iatoms+nb0,
+ idef->iparams,
+ x, f, fshift,
+ pbc, g, lambda[efptFTYPE], &(dvdl[efptFTYPE]),
+ md, fcd, global_atom_index);
+ }
+ }
+ else
+ {
+ v = do_pairs(ftype, nbn, iatoms+nb0, idef->iparams, x, f, fshift,
+ pbc, g, lambda, dvdl, md, fr, grpp, global_atom_index);
+ }
+
+ if (thread == 0)
+ {
+ inc_nrnb(nrnb, interaction_function[ftype].nrnb_ind, nbonds);
+ }
+
+ return v;
+}
+
+} // namespace
+
+gmx_bool
+ftype_is_bonded_potential(int ftype)
+{
+ return
+ (interaction_function[ftype].flags & IF_BOND) &&
+ !(ftype == F_CONNBONDS || ftype == F_POSRES || ftype == F_FBPOSRES) &&
+ (ftype < F_GB12 || ftype > F_GB14);
+}
+
+void calc_listed(const gmx_multisim_t *ms,
+ const t_idef *idef,
+ const rvec x[], history_t *hist,
+ rvec f[], t_forcerec *fr,
+ const struct t_pbc *pbc,
+ const struct t_pbc *pbc_full,
+ const struct t_graph *g,
+ gmx_enerdata_t *enerd, t_nrnb *nrnb,
+ real *lambda,
+ const t_mdatoms *md,
+ t_fcdata *fcd, int *global_atom_index,
+ int force_flags)
+{
+ gmx_bool bCalcEnerVir;
+ int i;
+ real dvdl[efptNR]; /* The dummy array is to have a place to store the dhdl at other values
+ of lambda, which will be thrown away in the end*/
+ const t_pbc *pbc_null;
+ int thread;
+
+ assert(fr->nthreads == idef->nthreads);
+
+ bCalcEnerVir = (force_flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY));
+
+ for (i = 0; i < efptNR; i++)
+ {
+ dvdl[i] = 0.0;
+ }
+ if (fr->bMolPBC)
+ {
+ pbc_null = pbc;
+ }
+ else
+ {
+ pbc_null = NULL;
+ }
+
+#ifdef DEBUG
+ if (g && debug)
+ {
+ p_graph(debug, "Bondage is fun", g);
+ }
+#endif
+
+ if (idef->il[F_POSRES].nr > 0)
+ {
+ posres_wrapper(nrnb, idef, pbc_full, x, enerd, lambda, fr);
+ }
+
+ if (idef->il[F_FBPOSRES].nr > 0)
+ {
+ fbposres_wrapper(nrnb, idef, pbc_full, x, enerd, fr);
+ }
+
+ /* Do pre force calculation stuff which might require communication */
+ if (idef->il[F_ORIRES].nr)
+ {
+ enerd->term[F_ORIRESDEV] =
+ calc_orires_dev(ms, idef->il[F_ORIRES].nr,
+ idef->il[F_ORIRES].iatoms,
+ idef->iparams, md, x,
+ pbc_null, fcd, hist);
+ }
+ if (idef->il[F_DISRES].nr)
+ {
+ calc_disres_R_6(idef->il[F_DISRES].nr,
+ idef->il[F_DISRES].iatoms,
+ idef->iparams, x, pbc_null,
+ fcd, hist);
+#ifdef GMX_MPI
+ if (fcd->disres.nsystems > 1)
+ {
+ gmx_sum_sim(2*fcd->disres.nres, fcd->disres.Rt_6, ms);
+ }
+#endif
+ }
+
+#pragma omp parallel for num_threads(fr->nthreads) schedule(static)
+ for (thread = 0; thread < fr->nthreads; thread++)
+ {
+ int ftype;
+ real *epot, v;
+ /* thread stuff */
+ rvec *ft, *fshift;
+ real *dvdlt;
+ gmx_grppairener_t *grpp;
+
+ if (thread == 0)
+ {
+ ft = f;
+ fshift = fr->fshift;
+ epot = enerd->term;
+ grpp = &enerd->grpp;
+ dvdlt = dvdl;
+ }
+ else
+ {
+ zero_thread_forces(&fr->f_t[thread], fr->natoms_force,
+ fr->red_nblock, 1<<fr->red_ashift);
+
+ ft = fr->f_t[thread].f;
+ fshift = fr->f_t[thread].fshift;
+ epot = fr->f_t[thread].ener;
+ grpp = &fr->f_t[thread].grpp;
+ dvdlt = fr->f_t[thread].dvdl;
+ }
+ /* Loop over all bonded force types to calculate the bonded forces */
+ for (ftype = 0; (ftype < F_NRE); ftype++)
+ {
+ if (idef->il[ftype].nr > 0 && ftype_is_bonded_potential(ftype))
+ {
+ v = calc_one_bond(thread, ftype, idef, x,
+ ft, fshift, fr, pbc_null, g, grpp,
+ nrnb, lambda, dvdlt,
+ md, fcd, bCalcEnerVir,
+ global_atom_index);
+ epot[ftype] += v;
+ }
+ }
+ }
+ if (fr->nthreads > 1)
+ {
+ reduce_thread_forces(fr->natoms_force, f, fr->fshift,
+ enerd->term, &enerd->grpp, dvdl,
+ fr->nthreads, fr->f_t,
+ fr->red_nblock, 1<<fr->red_ashift,
+ bCalcEnerVir,
+ force_flags & GMX_FORCE_DHDL);
+ }
+ if (force_flags & GMX_FORCE_DHDL)
+ {
+ for (i = 0; i < efptNR; i++)
+ {
+ enerd->dvdl_nonlin[i] += dvdl[i];
+ }
+ }
+
+ /* Copy the sum of violations for the distance restraints from fcd */
+ if (fcd)
+ {
+ enerd->term[F_DISRESVIOL] = fcd->disres.sumviol;
+
+ }
+}
+
+void calc_listed_lambda(const t_idef *idef,
+ const rvec x[],
+ t_forcerec *fr,
+ const struct t_pbc *pbc, const struct t_graph *g,
+ gmx_grppairener_t *grpp, real *epot, t_nrnb *nrnb,
+ real *lambda,
+ const t_mdatoms *md,
+ t_fcdata *fcd,
+ int *global_atom_index)
+{
+ int ftype, nr_nonperturbed, nr;
+ real v;
+ real dvdl_dum[efptNR] = {0};
+ rvec *f, *fshift;
+ const t_pbc *pbc_null;
+ t_idef idef_fe;
+
+ if (fr->bMolPBC)
+ {
+ pbc_null = pbc;
+ }
+ else
+ {
+ pbc_null = NULL;
+ }
+
+ /* Copy the whole idef, so we can modify the contents locally */
+ idef_fe = *idef;
+ idef_fe.nthreads = 1;
+ snew(idef_fe.il_thread_division, F_NRE*(idef_fe.nthreads+1));
+
+ /* We already have the forces, so we use temp buffers here */
+ snew(f, fr->natoms_force);
+ snew(fshift, SHIFTS);
+
+ /* Loop over all bonded force types to calculate the bonded energies */
+ for (ftype = 0; (ftype < F_NRE); ftype++)
+ {
+ if (ftype_is_bonded_potential(ftype))
+ {
+ /* Set the work range of thread 0 to the perturbed bondeds only */
+ nr_nonperturbed = idef->il[ftype].nr_nonperturbed;
+ nr = idef->il[ftype].nr;
+ idef_fe.il_thread_division[ftype*2+0] = nr_nonperturbed;
+ idef_fe.il_thread_division[ftype*2+1] = nr;
+
+ /* This is only to get the flop count correct */
+ idef_fe.il[ftype].nr = nr - nr_nonperturbed;
+
+ if (nr - nr_nonperturbed > 0)
+ {
+ v = calc_one_bond(0, ftype, &idef_fe,
+ x, f, fshift, fr, pbc_null, g,
+ grpp, nrnb, lambda, dvdl_dum,
+ md, fcd, TRUE,
+ global_atom_index);
+ epot[ftype] += v;
+ }
+ }
+ }
+
+ sfree(fshift);
+ sfree(f);
+
+ sfree(idef_fe.il_thread_division);
+}
+
+void
+do_force_listed(gmx_wallcycle *wcycle,
+ matrix box,
+ const t_lambda *fepvals,
+ const gmx_multisim_t *ms,
+ const t_idef *idef,
+ const rvec x[],
+ history_t *hist,
+ rvec f[],
+ t_forcerec *fr,
+ const struct t_pbc *pbc,
+ const struct t_graph *graph,
+ gmx_enerdata_t *enerd,
+ t_nrnb *nrnb,
+ real *lambda,
+ const t_mdatoms *md,
+ t_fcdata *fcd,
+ int *global_atom_index,
+ int flags)
+{
+ t_pbc pbc_full; /* Full PBC is needed for position restraints */
+
+ if (!(flags & GMX_FORCE_LISTED))
+ {
+ return;
+ }
+
+ wallcycle_sub_start(wcycle, ewcsLISTED);
+
+ if ((idef->il[F_POSRES].nr > 0) ||
+ (idef->il[F_FBPOSRES].nr > 0))
+ {
+ set_pbc(&pbc_full, fr->ePBC, box);
+ }
+ calc_listed(ms, idef, x, hist, f, fr, pbc, &pbc_full,
+ graph, enerd, nrnb, lambda, md, fcd,
+ global_atom_index, flags);
+
+ /* Check if we have to determine energy differences
+ * at foreign lambda's.
+ */
+ if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL))
+ {
+ posres_wrapper_lambda(fepvals, idef, &pbc_full, x, enerd, lambda, fr);
+
+ if (idef->ilsort != ilsortNO_FE)
+ {
+ if (idef->ilsort != ilsortFE_SORTED)
+ {
+ gmx_incons("The bonded interactions are not sorted for free energy");
+ }
+ for (int i = 0; i < enerd->n_lambda; i++)
+ {
+ real lam_i[efptNR];
+
+ reset_foreign_enerdata(enerd);
+ for (int j = 0; j < efptNR; j++)
+ {
+ lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
+ }
+ calc_listed_lambda(idef, x, fr, pbc, graph, &(enerd->foreign_grpp), enerd->foreign_term, nrnb, lam_i, md,
+ fcd, global_atom_index);
+ sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
+ enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
+ }
+ }
+ }
+ debug_gmx();
+
+ wallcycle_sub_stop(wcycle, ewcsLISTED);
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \defgroup module_listed-forces Interactions between lists of particles
+ * \ingroup group_mdrun
+ *
+ * \brief Handles computing energies and forces for listed
+ * interactions.
+ *
+ * Located here is the the code for
+ * - computing energies and forces for interactions between a small
+ number of particles, e.g bonds, position restraints and listed
+ non-bonded interactions (e.g. 1-4).
+ * - high-level functions used by mdrun for computing a set of such
+ quantities
+ * - managing thread-wise decomposition, thread-local buffer output,
+ and reduction of output data across threads.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ */
+/*! \file
+ *
+ * \brief This file contains declarations of high-level functions used
+ * by mdrun to compute energies and forces for listed interactions.
+ *
+ * Clients of libgromacs that want to evaluate listed interactions
+ * should call functions declared here.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \inpublicapi
+ * \ingroup module_listed-forces
+ */
+#ifndef GMX_LISTED_FORCES_LISTED_FORCES_H
+#define GMX_LISTED_FORCES_LISTED_FORCES_H
+
+#include "gromacs/legacyheaders/typedefs.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*! \brief Return whether this is an interaction that actually
+ * calculates a potential and works on multiple atoms (not e.g. a
+ * connection or a position restraint).
+ *
+ * \todo This function could go away when idef is not a big bucket of
+ * everything. */
+gmx_bool
+ftype_is_bonded_potential(int ftype);
+
+/*! \brief Calculates all listed force interactions.
+ *
+ * Note that pbc_full is used only for position restraints, and is
+ * not initialized if there are none. */
+void calc_listed(const gmx_multisim_t *ms,
+ const t_idef *idef,
+ const rvec x[], history_t *hist,
+ rvec f[], t_forcerec *fr,
+ const struct t_pbc *pbc, const struct t_pbc *pbc_full,
+ const struct t_graph *g,
+ gmx_enerdata_t *enerd, t_nrnb *nrnb, real *lambda,
+ const t_mdatoms *md,
+ t_fcdata *fcd, int *ddgatindex,
+ int force_flags);
+
+/*! \brief As calc_listed(), but only determines the potential energy
+ * for the perturbed interactions.
+ *
+ * The shift forces in fr are not affected. */
+void calc_listed_lambda(const t_idef *idef,
+ const rvec x[],
+ t_forcerec *fr,
+ const struct t_pbc *pbc, const struct t_graph *g,
+ gmx_grppairener_t *grpp, real *epot, t_nrnb *nrnb,
+ real *lambda,
+ const t_mdatoms *md,
+ t_fcdata *fcd, int *global_atom_index);
+
+/*! \brief Do all aspects of energy and force calculations for mdrun
+ * on the set of listed interactions */
+void
+do_force_listed(struct gmx_wallcycle *wcycle,
+ matrix box,
+ const t_lambda *fepvals,
+ const gmx_multisim_t *ms,
+ const t_idef *idef,
+ const rvec x[],
+ history_t *hist,
+ rvec f[],
+ t_forcerec *fr,
+ const struct t_pbc *pbc,
+ const struct t_graph *graph,
+ gmx_enerdata_t *enerd,
+ t_nrnb *nrnb,
+ real *lambda,
+ const t_mdatoms *md,
+ t_fcdata *fcd,
+ int *global_atom_index,
+ int flags);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief This file defines functions needed internally by the module.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_listed-forces
+ */
+#include "gmxpre.h"
+
+#include "listed-internal.h"
+
+#include <cstdlib>
+
+int glatnr(int *global_atom_index, int i)
+{
+ int atnr;
+
+ if (global_atom_index == NULL)
+ {
+ atnr = i + 1;
+ }
+ else
+ {
+ atnr = global_atom_index[i] + 1;
+ }
+
+ return atnr;
+}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \internal \file
+ *
+ * \brief This file contains declarations for functions needed
+ * internally by the module.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_listed-forces
+ */
+#ifndef GMX_LISTED_FORCES_LISTED_INTERNAL_H
+#define GMX_LISTED_FORCES_LISTED_INTERNAL_H
-
-#ifndef _correl_h
-#define _correl_h
-
-#include "typedefs.h"
-#include "gromacs/fft/fft.h"
-
-typedef struct {
- int n;
- gmx_fft_t fft_setup;
- real *buf1, *buf2, *abuf;
-} correl_t;
-
-extern correl_t *init_correl(int n);
-extern void done_correl(correl_t *c);
-
-extern void correl(real data1[], real data2[], int n, real ans[]);
-extern void four1(real data[], int nn, int isign);
+/*! \brief Returns the global topology atom number belonging to local
+ * atom index i.
+ *
+ * This function is intended for writing ascii output and returns atom
+ * numbers starting at 1. When global_atom_index=NULL returns i+1.
+ */
+int
+glatnr(int *global_atom_index, int i);
#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief This file defines functions for managing threading of listed
+ * interactions.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_listed-forces
+ */
+#include "gmxpre.h"
+
+#include "manage-threading.h"
+
+#include <assert.h>
+
+#include <algorithm>
+
+#include "gromacs/listed-forces/listed-forces.h"
+#include "gromacs/mdlib/forcerec-threading.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
+
+//! Divides listed interactions over threads
+static void divide_bondeds_over_threads(t_idef *idef, int nthreads)
+{
+ int ftype;
+ int nat1;
+ int t;
+ int il_nr_thread;
+
+ idef->nthreads = nthreads;
+
+ if (F_NRE*(nthreads+1) > idef->il_thread_division_nalloc)
+ {
+ idef->il_thread_division_nalloc = F_NRE*(nthreads+1);
+ snew(idef->il_thread_division, idef->il_thread_division_nalloc);
+ }
+
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (ftype_is_bonded_potential(ftype))
+ {
+ nat1 = interaction_function[ftype].nratoms + 1;
+
+ for (t = 0; t <= nthreads; t++)
+ {
+ /* Divide the interactions equally over the threads.
+ * When the different types of bonded interactions
+ * are distributed roughly equally over the threads,
+ * this should lead to well localized output into
+ * the force buffer on each thread.
+ * If this is not the case, a more advanced scheme
+ * (not implemented yet) will do better.
+ */
+ il_nr_thread = (((idef->il[ftype].nr/nat1)*t)/nthreads)*nat1;
+
+ /* Ensure that distance restraint pairs with the same label
+ * end up on the same thread.
+ * This is slighlty tricky code, since the next for iteration
+ * may have an initial il_nr_thread lower than the final value
+ * in the previous iteration, but this will anyhow be increased
+ * to the approriate value again by this while loop.
+ */
+ while (ftype == F_DISRES &&
+ il_nr_thread > 0 &&
+ il_nr_thread < idef->il[ftype].nr &&
+ idef->iparams[idef->il[ftype].iatoms[il_nr_thread]].disres.label ==
+ idef->iparams[idef->il[ftype].iatoms[il_nr_thread-nat1]].disres.label)
+ {
+ il_nr_thread += nat1;
+ }
+
+ idef->il_thread_division[ftype*(nthreads+1)+t] = il_nr_thread;
+ }
+ }
+ }
+}
+
+//! Construct a reduction mask for which interaction was computed on which thread
+static void
+calc_bonded_reduction_mask(gmx_bitmask_t *mask,
+ const t_idef *idef,
+ int shift,
+ int t, int nt)
+{
+ int ftype, nb, nat1, nb0, nb1, i, a;
+ bitmask_clear(mask);
+
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (ftype_is_bonded_potential(ftype))
+ {
+ nb = idef->il[ftype].nr;
+ if (nb > 0)
+ {
+ nat1 = interaction_function[ftype].nratoms + 1;
+
+ /* Divide this interaction equally over the threads.
+ * This is not stored: should match division in calc_bonds.
+ */
+ nb0 = idef->il_thread_division[ftype*(nt+1)+t];
+ nb1 = idef->il_thread_division[ftype*(nt+1)+t+1];
+
+ for (i = nb0; i < nb1; i += nat1)
+ {
+ for (a = 1; a < nat1; a++)
+ {
+ bitmask_set_bit(mask, idef->il[ftype].iatoms[i+a]>>shift);
+ }
+ }
+ }
+ }
+ }
+}
+
+
+/*! \brief We divide the force array in a maximum of BITMASK_SIZE (default 32) blocks.
+ * Minimum force block reduction size is thus 2^6=64.
+ */
+const int maxBlockBits = BITMASK_SIZE;
+
+void setup_bonded_threading(t_forcerec *fr, t_idef *idef)
+{
+ int t;
+ int ctot, c, b;
+
+ assert(fr->nthreads >= 1);
+
+ /* Divide the bonded interaction over the threads */
+ divide_bondeds_over_threads(idef, fr->nthreads);
+
+ if (fr->nthreads == 1)
+ {
+ fr->red_nblock = 0;
+
+ return;
+ }
+
+ fr->red_ashift = 6;
+ while (fr->natoms_force > (int)(maxBlockBits*(1U<<fr->red_ashift)))
+ {
+ fr->red_ashift++;
+ }
+ if (debug)
+ {
+ fprintf(debug, "bonded force buffer block atom shift %d bits\n",
+ fr->red_ashift);
+ }
+
+ /* Determine to which blocks each thread's bonded force calculation
+ * contributes. Store this is a mask for each thread.
+ */
+#pragma omp parallel for num_threads(fr->nthreads) schedule(static)
+ for (t = 1; t < fr->nthreads; t++)
+ {
+ calc_bonded_reduction_mask(&fr->f_t[t].red_mask,
+ idef, fr->red_ashift, t, fr->nthreads);
+ }
+
+ /* Determine the maximum number of blocks we need to reduce over */
+ fr->red_nblock = 0;
+ ctot = 0;
+ for (t = 0; t < fr->nthreads; t++)
+ {
+ c = 0;
+ for (b = 0; b < maxBlockBits; b++)
+ {
+ if (bitmask_is_set(fr->f_t[t].red_mask, b))
+ {
+ fr->red_nblock = std::max(fr->red_nblock, b+1);
+ c++;
+ }
+ }
+ if (debug)
+ {
+#if BITMASK_SIZE <= 64 //move into bitmask when it is C++
+ std::string flags = gmx::formatString("%x", fr->f_t[t].red_mask);
+#else
+ std::string flags = gmx::formatAndJoin(fr->f_t[t].red_mask,
+ fr->f_t[t].red_mask+BITMASK_ALEN,
+ "", gmx::StringFormatter("%x"));
+#endif
+ fprintf(debug, "thread %d flags %s count %d\n",
+ t, flags.c_str(), c);
+ }
+ ctot += c;
+ }
+ if (debug)
+ {
+ fprintf(debug, "Number of blocks to reduce: %d of size %d\n",
+ fr->red_nblock, 1<<fr->red_ashift);
+ fprintf(debug, "Reduction density %.2f density/#thread %.2f\n",
+ ctot*(1<<fr->red_ashift)/(double)fr->natoms_force,
+ ctot*(1<<fr->red_ashift)/(double)(fr->natoms_force*fr->nthreads));
+ }
+}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef GMX_GMXPREPROCESS_ADDCONF_H
-#define GMX_GMXPREPROCESS_ADDCONF_H
+/*! \libinternal \file
+ * \brief Declares functions for managing threading of listed forces
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_listed-forces
+ */
+#ifndef GMX_LISTED_FORCES_MANAGE_THREADING_H
+#define GMX_LISTED_FORCES_MANAGE_THREADING_H
-#include "typedefs.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/topology/idef.h"
#ifdef __cplusplus
extern "C" {
#endif
-extern
-void add_conf(t_atoms *atoms, rvec **x, rvec **v, real **r, gmx_bool bSrenew,
- int ePBC, matrix box, gmx_bool bInsert,
- t_atoms *atoms_solvt, rvec *x_solvt, rvec *v_solvt, real *r_solvt,
- gmx_bool bVerbose, real rshell, int max_sol, const output_env_t oenv);
-/* Add two conformations together, without generating overlap.
- * When not inserting, don't check overlap in the middle of the box.
- * If rshell > 0, keep all the residues around the protein (0..natoms_prot-1)
- * that are within rshell distance.
- * If max_sol > 0, add max max_sol solvent molecules.
+/*! \brief Divide the listed interactions over the threads
+ *
+ * Uses fr->nthreads for the number of threads, and sets up the
+ * thread-force buffer reduction. This should be called each time the
+ * bonded setup changes; i.e. at start-up without domain decomposition
+ * and at DD.
*/
+void setup_bonded_threading(t_forcerec *fr, t_idef *idef);
#ifdef __cplusplus
}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief This file defines functions for "pair" interactions
+ * (i.e. listed non-bonded interactions, e.g. 1-4 interactions)
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \ingroup module_listed-forces
+ */
+#include "gmxpre.h"
+
+#include "pairs.h"
+
+#include <cmath>
+
+#include "gromacs/legacyheaders/types/group.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/fatalerror.h"
+
+#include "listed-internal.h"
+
+namespace
+{
+
+/*! \brief Issue a warning if a listed interaction is beyond a table limit */
+void
+warning_rlimit(const rvec *x, int ai, int aj, int * global_atom_index, real r, real rlimit)
+{
+ gmx_warning("Listed nonbonded interaction between particles %d and %d\n"
+ "at distance %.3f which is larger than the table limit %.3f nm.\n\n"
+ "This is likely either a 1,4 interaction, or a listed interaction inside\n"
+ "a smaller molecule you are decoupling during a free energy calculation.\n"
+ "Since interactions at distances beyond the table cannot be computed,\n"
+ "they are skipped until they are inside the table limit again. You will\n"
+ "only see this message once, even if it occurs for several interactions.\n\n"
+ "IMPORTANT: This should not happen in a stable simulation, so there is\n"
+ "probably something wrong with your system. Only change the table-extension\n"
+ "distance in the mdp file if you are really sure that is the reason.\n",
+ glatnr(global_atom_index, ai), glatnr(global_atom_index, aj), r, rlimit);
+
+ if (debug)
+ {
+ fprintf(debug,
+ "%8f %8f %8f\n%8f %8f %8f\n1-4 (%d,%d) interaction not within cut-off! r=%g. Ignored\n",
+ x[ai][XX], x[ai][YY], x[ai][ZZ], x[aj][XX], x[aj][YY], x[aj][ZZ],
+ glatnr(global_atom_index, ai), glatnr(global_atom_index, aj), r);
+ }
+}
+
+/*! \brief Compute the energy and force for a single pair interaction */
+real
+evaluate_single(real r2, real tabscale, real *vftab,
+ real qq, real c6, real c12, real *velec, real *vvdw)
+{
+ real rinv, r, rtab, eps, eps2, Y, F, Geps, Heps2, Fp, VVe, FFe, VVd, FFd, VVr, FFr, fscal;
+ int ntab;
+
+ /* Do the tabulated interactions - first table lookup */
+ rinv = gmx_invsqrt(r2);
+ r = r2*rinv;
+ rtab = r*tabscale;
+ ntab = static_cast<int>(rtab);
+ eps = rtab-ntab;
+ eps2 = eps*eps;
+ ntab = 12*ntab;
+ /* Electrostatics */
+ Y = vftab[ntab];
+ F = vftab[ntab+1];
+ Geps = eps*vftab[ntab+2];
+ Heps2 = eps2*vftab[ntab+3];
+ Fp = F+Geps+Heps2;
+ VVe = Y+eps*Fp;
+ FFe = Fp+Geps+2.0*Heps2;
+ /* Dispersion */
+ Y = vftab[ntab+4];
+ F = vftab[ntab+5];
+ Geps = eps*vftab[ntab+6];
+ Heps2 = eps2*vftab[ntab+7];
+ Fp = F+Geps+Heps2;
+ VVd = Y+eps*Fp;
+ FFd = Fp+Geps+2.0*Heps2;
+ /* Repulsion */
+ Y = vftab[ntab+8];
+ F = vftab[ntab+9];
+ Geps = eps*vftab[ntab+10];
+ Heps2 = eps2*vftab[ntab+11];
+ Fp = F+Geps+Heps2;
+ VVr = Y+eps*Fp;
+ FFr = Fp+Geps+2.0*Heps2;
+
+ *velec = qq*VVe;
+ *vvdw = c6*VVd+c12*VVr;
+
+ fscal = -(qq*FFe+c6*FFd+c12*FFr)*tabscale*rinv;
+
+ return fscal;
+}
+
+/*! \brief Compute the energy and force for a single pair interaction under FEP */
+real
+free_energy_evaluate_single(real r2, real sc_r_power, real alpha_coul,
+ real alpha_vdw, real tabscale, real *vftab,
+ real qqA, real c6A, real c12A, real qqB,
+ real c6B, real c12B, real LFC[2], real LFV[2], real DLF[2],
+ real lfac_coul[2], real lfac_vdw[2], real dlfac_coul[2],
+ real dlfac_vdw[2], real sigma6_def, real sigma6_min,
+ real sigma2_def, real sigma2_min,
+ real *velectot, real *vvdwtot, real *dvdl)
+{
+ real rp, rpm2, rtab, eps, eps2, Y, F, Geps, Heps2, Fp, VV, FF, fscal;
+ real qq[2], c6[2], c12[2], sigma6[2], sigma2[2], sigma_pow[2];
+ real alpha_coul_eff, alpha_vdw_eff, dvdl_coul, dvdl_vdw;
+ real rpinv, r_coul, r_vdw, velecsum, vvdwsum;
+ real fscal_vdw[2], fscal_elec[2];
+ real velec[2], vvdw[2];
+ int i, ntab;
+ const real half = 0.5;
+ const real minusOne = -1.0;
+ const real oneThird = 1.0 / 3.0;
+ const real one = 1.0;
+ const real two = 2.0;
+ const real six = 6.0;
+ const real fourtyeight = 48.0;
+
+ qq[0] = qqA;
+ qq[1] = qqB;
+ c6[0] = c6A;
+ c6[1] = c6B;
+ c12[0] = c12A;
+ c12[1] = c12B;
+
+ if (sc_r_power == six)
+ {
+ rpm2 = r2*r2; /* r4 */
+ rp = rpm2*r2; /* r6 */
+ }
+ else if (sc_r_power == fourtyeight)
+ {
+ rp = r2*r2*r2; /* r6 */
+ rp = rp*rp; /* r12 */
+ rp = rp*rp; /* r24 */
+ rp = rp*rp; /* r48 */
+ rpm2 = rp/r2; /* r46 */
+ }
+ else
+ {
+ rp = std::pow(r2, half * sc_r_power); /* not currently supported as input, but can handle it */
+ rpm2 = rp/r2;
+ }
+
+ /* Loop over state A(0) and B(1) */
+ for (i = 0; i < 2; i++)
+ {
+ if ((c6[i] > 0) && (c12[i] > 0))
+ {
+ /* The c6 & c12 coefficients now contain the constants 6.0 and 12.0, respectively.
+ * Correct for this by multiplying with (1/12.0)/(1/6.0)=6.0/12.0=0.5.
+ */
+ sigma6[i] = half*c12[i]/c6[i];
+ sigma2[i] = std::pow(half*c12[i]/c6[i], oneThird);
+ /* should be able to get rid of this ^^^ internal pow call eventually. Will require agreement on
+ what data to store externally. Can't be fixed without larger scale changes, so not 5.0 */
+ if (sigma6[i] < sigma6_min) /* for disappearing coul and vdw with soft core at the same time */
+ {
+ sigma6[i] = sigma6_min;
+ sigma2[i] = sigma2_min;
+ }
+ }
+ else
+ {
+ sigma6[i] = sigma6_def;
+ sigma2[i] = sigma2_def;
+ }
+ if (sc_r_power == six)
+ {
+ sigma_pow[i] = sigma6[i];
+ }
+ else if (sc_r_power == fourtyeight)
+ {
+ sigma_pow[i] = sigma6[i]*sigma6[i]; /* sigma^12 */
+ sigma_pow[i] = sigma_pow[i]*sigma_pow[i]; /* sigma^24 */
+ sigma_pow[i] = sigma_pow[i]*sigma_pow[i]; /* sigma^48 */
+ }
+ else
+ { /* not really supported as input, but in here for testing the general case*/
+ sigma_pow[i] = std::pow(sigma2[i], sc_r_power/2);
+ }
+ }
+
+ /* only use softcore if one of the states has a zero endstate - softcore is for avoiding infinities!*/
+ if ((c12[0] > 0) && (c12[1] > 0))
+ {
+ alpha_vdw_eff = 0;
+ alpha_coul_eff = 0;
+ }
+ else
+ {
+ alpha_vdw_eff = alpha_vdw;
+ alpha_coul_eff = alpha_coul;
+ }
+
+ /* Loop over A and B states again */
+ for (i = 0; i < 2; i++)
+ {
+ fscal_elec[i] = 0;
+ fscal_vdw[i] = 0;
+ velec[i] = 0;
+ vvdw[i] = 0;
+
+ /* Only spend time on A or B state if it is non-zero */
+ if ( (qq[i] != 0) || (c6[i] != 0) || (c12[i] != 0) )
+ {
+ /* Coulomb */
+ rpinv = one/(alpha_coul_eff*lfac_coul[i]*sigma_pow[i]+rp);
+ r_coul = std::pow(rpinv, minusOne / sc_r_power);
+
+ /* Electrostatics table lookup data */
+ rtab = r_coul*tabscale;
+ ntab = static_cast<int>(rtab);
+ eps = rtab-ntab;
+ eps2 = eps*eps;
+ ntab = 12*ntab;
+ /* Electrostatics */
+ Y = vftab[ntab];
+ F = vftab[ntab+1];
+ Geps = eps*vftab[ntab+2];
+ Heps2 = eps2*vftab[ntab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+eps*Fp;
+ FF = Fp+Geps+two*Heps2;
+ velec[i] = qq[i]*VV;
+ fscal_elec[i] = -qq[i]*FF*r_coul*rpinv*tabscale;
+
+ /* Vdw */
+ rpinv = one/(alpha_vdw_eff*lfac_vdw[i]*sigma_pow[i]+rp);
+ r_vdw = std::pow(rpinv, minusOne / sc_r_power);
+ /* Vdw table lookup data */
+ rtab = r_vdw*tabscale;
+ ntab = static_cast<int>(rtab);
+ eps = rtab-ntab;
+ eps2 = eps*eps;
+ ntab = 12*ntab;
+ /* Dispersion */
+ Y = vftab[ntab+4];
+ F = vftab[ntab+5];
+ Geps = eps*vftab[ntab+6];
+ Heps2 = eps2*vftab[ntab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+eps*Fp;
+ FF = Fp+Geps+two*Heps2;
+ vvdw[i] = c6[i]*VV;
+ fscal_vdw[i] = -c6[i]*FF;
+
+ /* Repulsion */
+ Y = vftab[ntab+8];
+ F = vftab[ntab+9];
+ Geps = eps*vftab[ntab+10];
+ Heps2 = eps2*vftab[ntab+11];
+ Fp = F+Geps+Heps2;
+ VV = Y+eps*Fp;
+ FF = Fp+Geps+two*Heps2;
+ vvdw[i] += c12[i]*VV;
+ fscal_vdw[i] -= c12[i]*FF;
+ fscal_vdw[i] *= r_vdw*rpinv*tabscale;
+ }
+ }
+ /* Now we have velec[i], vvdw[i], and fscal[i] for both states */
+ /* Assemble A and B states */
+ velecsum = 0;
+ vvdwsum = 0;
+ dvdl_coul = 0;
+ dvdl_vdw = 0;
+ fscal = 0;
+ for (i = 0; i < 2; i++)
+ {
+ velecsum += LFC[i]*velec[i];
+ vvdwsum += LFV[i]*vvdw[i];
+
+ fscal += (LFC[i]*fscal_elec[i]+LFV[i]*fscal_vdw[i])*rpm2;
+
+ dvdl_coul += velec[i]*DLF[i] + LFC[i]*alpha_coul_eff*dlfac_coul[i]*fscal_elec[i]*sigma_pow[i];
+ dvdl_vdw += vvdw[i]*DLF[i] + LFV[i]*alpha_vdw_eff*dlfac_vdw[i]*fscal_vdw[i]*sigma_pow[i];
+ }
+
+ dvdl[efptCOUL] += dvdl_coul;
+ dvdl[efptVDW] += dvdl_vdw;
+
+ *velectot = velecsum;
+ *vvdwtot = vvdwsum;
+
+ return fscal;
+}
+
+} // namespace
+
+real
+do_pairs(int ftype, int nbonds,
+ const t_iatom iatoms[], const t_iparams iparams[],
+ const rvec x[], rvec f[], rvec fshift[],
+ const struct t_pbc *pbc, const struct t_graph *g,
+ real *lambda, real *dvdl,
+ const t_mdatoms *md,
+ const t_forcerec *fr, gmx_grppairener_t *grppener,
+ int *global_atom_index)
+{
+ real qq, c6, c12;
+ rvec dx;
+ ivec dt;
+ int i, itype, ai, aj, gid;
+ int fshift_index;
+ real r2;
+ real fscal, velec, vvdw;
+ real * energygrp_elec;
+ real * energygrp_vdw;
+ static gmx_bool warned_rlimit = FALSE;
+ /* Free energy stuff */
+ gmx_bool bFreeEnergy;
+ real LFC[2], LFV[2], DLF[2], lfac_coul[2], lfac_vdw[2], dlfac_coul[2], dlfac_vdw[2];
+ real qqB, c6B, c12B, sigma2_def, sigma2_min;
+ const real oneThird = 1.0 / 3.0;
+
+ switch (ftype)
+ {
+ case F_LJ14:
+ case F_LJC14_Q:
+ energygrp_elec = grppener->ener[egCOUL14];
+ energygrp_vdw = grppener->ener[egLJ14];
+ break;
+ case F_LJC_PAIRS_NB:
+ energygrp_elec = grppener->ener[egCOULSR];
+ energygrp_vdw = grppener->ener[egLJSR];
+ break;
+ default:
+ energygrp_elec = NULL; /* Keep compiler happy */
+ energygrp_vdw = NULL; /* Keep compiler happy */
+ gmx_fatal(FARGS, "Unknown function type %d in do_nonbonded14", ftype);
+ break;
+ }
+
+ if (fr->efep != efepNO)
+ {
+ /* Lambda factor for state A=1-lambda and B=lambda */
+ LFC[0] = 1.0 - lambda[efptCOUL];
+ LFV[0] = 1.0 - lambda[efptVDW];
+ LFC[1] = lambda[efptCOUL];
+ LFV[1] = lambda[efptVDW];
+
+ /*derivative of the lambda factor for state A and B */
+ DLF[0] = -1;
+ DLF[1] = 1;
+
+ /* precalculate */
+ sigma2_def = pow(fr->sc_sigma6_def, oneThird);
+ sigma2_min = pow(fr->sc_sigma6_min, oneThird);
+
+ for (i = 0; i < 2; i++)
+ {
+ lfac_coul[i] = (fr->sc_power == 2 ? (1-LFC[i])*(1-LFC[i]) : (1-LFC[i]));
+ dlfac_coul[i] = DLF[i]*fr->sc_power/fr->sc_r_power*(fr->sc_power == 2 ? (1-LFC[i]) : 1);
+ lfac_vdw[i] = (fr->sc_power == 2 ? (1-LFV[i])*(1-LFV[i]) : (1-LFV[i]));
+ dlfac_vdw[i] = DLF[i]*fr->sc_power/fr->sc_r_power*(fr->sc_power == 2 ? (1-LFV[i]) : 1);
+ }
+ }
+ else
+ {
+ sigma2_min = sigma2_def = 0;
+ }
+
+ bFreeEnergy = FALSE;
+ for (i = 0; (i < nbonds); )
+ {
+ itype = iatoms[i++];
+ ai = iatoms[i++];
+ aj = iatoms[i++];
+ gid = GID(md->cENER[ai], md->cENER[aj], md->nenergrp);
+
+ /* Get parameters */
+ switch (ftype)
+ {
+ case F_LJ14:
+ bFreeEnergy =
+ (fr->efep != efepNO &&
+ ((md->nPerturbed && (md->bPerturbed[ai] || md->bPerturbed[aj])) ||
+ iparams[itype].lj14.c6A != iparams[itype].lj14.c6B ||
+ iparams[itype].lj14.c12A != iparams[itype].lj14.c12B));
+ qq = md->chargeA[ai]*md->chargeA[aj]*fr->epsfac*fr->fudgeQQ;
+ c6 = iparams[itype].lj14.c6A;
+ c12 = iparams[itype].lj14.c12A;
+ break;
+ case F_LJC14_Q:
+ qq = iparams[itype].ljc14.qi*iparams[itype].ljc14.qj*fr->epsfac*iparams[itype].ljc14.fqq;
+ c6 = iparams[itype].ljc14.c6;
+ c12 = iparams[itype].ljc14.c12;
+ break;
+ case F_LJC_PAIRS_NB:
+ qq = iparams[itype].ljcnb.qi*iparams[itype].ljcnb.qj*fr->epsfac;
+ c6 = iparams[itype].ljcnb.c6;
+ c12 = iparams[itype].ljcnb.c12;
+ break;
+ default:
+ /* Cannot happen since we called gmx_fatal() above in this case */
+ qq = c6 = c12 = 0; /* Keep compiler happy */
+ break;
+ }
+
+ /* To save flops in the optimized kernels, c6/c12 have 6.0/12.0 derivative prefactors
+ * included in the general nfbp array now. This means the tables are scaled down by the
+ * same factor, so when we use the original c6/c12 parameters from iparams[] they must
+ * be scaled up.
+ */
+ c6 *= 6.0;
+ c12 *= 12.0;
+
+ /* Do we need to apply full periodic boundary conditions? */
+ if (fr->bMolPBC == TRUE)
+ {
+ fshift_index = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
+ }
+ else
+ {
+ fshift_index = CENTRAL;
+ rvec_sub(x[ai], x[aj], dx);
+ }
+ r2 = norm2(dx);
+
+ if (r2 >= fr->tab14.r*fr->tab14.r)
+ {
+ /* This check isn't race free. But it doesn't matter because if a race occurs the only
+ * disadvantage is that the warning is printed twice */
+ if (warned_rlimit == FALSE)
+ {
+ warning_rlimit(x, ai, aj, global_atom_index, sqrt(r2), fr->tab14.r);
+ warned_rlimit = TRUE;
+ }
+ continue;
+ }
+
+ if (bFreeEnergy)
+ {
+ /* Currently free energy is only supported for F_LJ14, so no need to check for that if we got here */
+ qqB = md->chargeB[ai]*md->chargeB[aj]*fr->epsfac*fr->fudgeQQ;
+ c6B = iparams[itype].lj14.c6B*6.0;
+ c12B = iparams[itype].lj14.c12B*12.0;
+
+ fscal = free_energy_evaluate_single(r2, fr->sc_r_power, fr->sc_alphacoul, fr->sc_alphavdw,
+ fr->tab14.scale, fr->tab14.data, qq, c6, c12, qqB, c6B, c12B,
+ LFC, LFV, DLF, lfac_coul, lfac_vdw, dlfac_coul, dlfac_vdw,
+ fr->sc_sigma6_def, fr->sc_sigma6_min, sigma2_def, sigma2_min, &velec, &vvdw, dvdl);
+ }
+ else
+ {
+ /* Evaluate tabulated interaction without free energy */
+ fscal = evaluate_single(r2, fr->tab14.scale, fr->tab14.data, qq, c6, c12, &velec, &vvdw);
+ }
+
+ energygrp_elec[gid] += velec;
+ energygrp_vdw[gid] += vvdw;
+ svmul(fscal, dx, dx);
+
+ /* Add the forces */
+ rvec_inc(f[ai], dx);
+ rvec_dec(f[aj], dx);
+
+ if (g)
+ {
+ /* Correct the shift forces using the graph */
+ ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
+ fshift_index = IVEC2IS(dt);
+ }
+ if (fshift_index != CENTRAL)
+ {
+ rvec_inc(fshift[fshift_index], dx);
+ rvec_dec(fshift[CENTRAL], dx);
+ }
+ }
+ return 0.0;
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief This file declares functions for "pair" interactions
+ * (i.e. listed non-bonded interactions, e.g. 1-4 interactions)
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \ingroup module_listed-forces
+ */
+#ifndef GMX_LISTED_FORCES_PAIRS_H
+#define GMX_LISTED_FORCES_PAIRS_H
+
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
+struct t_graph;
+struct t_pbc;
+
+/*! \brief Calculate VdW/charge listed pair interactions (usually 1-4
+ * interactions).
+ *
+ * global_atom_index is only passed for printing error messages.
+ */
+real
+do_pairs(int ftype, int nbonds, const t_iatom iatoms[], const t_iparams iparams[],
+ const rvec x[], rvec f[], rvec fshift[],
+ const struct t_pbc *pbc, const struct t_graph *g,
+ real *lambda, real *dvdl, const t_mdatoms *md, const t_forcerec *fr,
+ gmx_grppairener_t *grppener, int *global_atom_index);
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief This file defines low-level functions necessary for
+ * computing energies and forces for position restraints.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \ingroup module_listed-forces
+ */
+
+#include "gmxpre.h"
+
+#include "position-restraints.h"
+
+#include <assert.h>
+
+#include <cmath>
+
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/utility/basedefinitions.h"
+
+namespace
+{
+
+/*! \brief returns dx, rdist, and dpdl for functions posres() and fbposres()
+ */
+void posres_dx(const rvec x, const rvec pos0A, const rvec pos0B,
+ const rvec comA_sc, const rvec comB_sc,
+ real lambda,
+ const t_pbc *pbc, int refcoord_scaling, int npbcdim,
+ rvec dx, rvec rdist, rvec dpdl)
+{
+ int m, d;
+ real posA, posB, L1, ref = 0.;
+ rvec pos;
+
+ L1 = 1.0-lambda;
+
+ for (m = 0; m < DIM; m++)
+ {
+ posA = pos0A[m];
+ posB = pos0B[m];
+ if (m < npbcdim)
+ {
+ switch (refcoord_scaling)
+ {
+ case erscNO:
+ ref = 0;
+ rdist[m] = L1*posA + lambda*posB;
+ dpdl[m] = posB - posA;
+ break;
+ case erscALL:
+ /* Box relative coordinates are stored for dimensions with pbc */
+ posA *= pbc->box[m][m];
+ posB *= pbc->box[m][m];
+ assert(npbcdim <= DIM);
+ for (d = m+1; d < npbcdim; d++)
+ {
+ posA += pos0A[d]*pbc->box[d][m];
+ posB += pos0B[d]*pbc->box[d][m];
+ }
+ ref = L1*posA + lambda*posB;
+ rdist[m] = 0;
+ dpdl[m] = posB - posA;
+ break;
+ case erscCOM:
+ ref = L1*comA_sc[m] + lambda*comB_sc[m];
+ rdist[m] = L1*posA + lambda*posB;
+ dpdl[m] = comB_sc[m] - comA_sc[m] + posB - posA;
+ break;
+ default:
+ gmx_fatal(FARGS, "No such scaling method implemented");
+ }
+ }
+ else
+ {
+ ref = L1*posA + lambda*posB;
+ rdist[m] = 0;
+ dpdl[m] = posB - posA;
+ }
+
+ /* We do pbc_dx with ref+rdist,
+ * since with only ref we can be up to half a box vector wrong.
+ */
+ pos[m] = ref + rdist[m];
+ }
+
+ if (pbc)
+ {
+ pbc_dx(pbc, x, pos, dx);
+ }
+ else
+ {
+ rvec_sub(x, pos, dx);
+ }
+}
+
+/*! \brief Computes forces and potential for flat-bottom cylindrical restraints.
+ * Returns the flat-bottom potential. */
+real do_fbposres_cylinder(int fbdim, rvec fm, rvec dx, real rfb, real kk, gmx_bool bInvert)
+{
+ int d;
+ real dr, dr2, invdr, v, rfb2;
+
+ dr2 = 0.0;
+ rfb2 = sqr(rfb);
+ v = 0.0;
+
+ for (d = 0; d < DIM; d++)
+ {
+ if (d != fbdim)
+ {
+ dr2 += sqr(dx[d]);
+ }
+ }
+
+ if (dr2 > 0.0 &&
+ ( (dr2 > rfb2 && bInvert == FALSE ) || (dr2 < rfb2 && bInvert == TRUE ) )
+ )
+ {
+ dr = sqrt(dr2);
+ invdr = 1./dr;
+ v = 0.5*kk*sqr(dr - rfb);
+ for (d = 0; d < DIM; d++)
+ {
+ if (d != fbdim)
+ {
+ fm[d] = -kk*(dr-rfb)*dx[d]*invdr; /* Force pointing to the center */
+ }
+ }
+ }
+
+ return v;
+}
+
+/*! \brief Adds forces of flat-bottomed positions restraints to f[]
+ * and fixes vir_diag.
+ *
+ * Returns the flat-bottomed potential. Same PBC treatment as in
+ * normal position restraints */
+real fbposres(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[], rvec vir_diag,
+ const t_pbc *pbc,
+ int refcoord_scaling, int ePBC, rvec com)
+/* compute flat-bottomed positions restraints */
+{
+ int i, ai, m, d, type, npbcdim = 0, fbdim;
+ const t_iparams *pr;
+ real vtot, kk, v;
+ real dr, dr2, rfb, rfb2, fact;
+ rvec com_sc, rdist, dx, dpdl, fm;
+ gmx_bool bInvert;
+
+ npbcdim = ePBC2npbcdim(ePBC);
+
+ if (refcoord_scaling == erscCOM)
+ {
+ clear_rvec(com_sc);
+ for (m = 0; m < npbcdim; m++)
+ {
+ assert(npbcdim <= DIM);
+ for (d = m; d < npbcdim; d++)
+ {
+ com_sc[m] += com[d]*pbc->box[d][m];
+ }
+ }
+ }
+
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ pr = &forceparams[type];
+
+ /* same calculation as for normal posres, but with identical A and B states, and lambda==0 */
+ posres_dx(x[ai], forceparams[type].fbposres.pos0, forceparams[type].fbposres.pos0,
+ com_sc, com_sc, 0.0,
+ pbc, refcoord_scaling, npbcdim,
+ dx, rdist, dpdl);
+
+ clear_rvec(fm);
+ v = 0.0;
+
+ kk = pr->fbposres.k;
+ rfb = pr->fbposres.r;
+ rfb2 = sqr(rfb);
+
+ /* with rfb<0, push particle out of the sphere/cylinder/layer */
+ bInvert = FALSE;
+ if (rfb < 0.)
+ {
+ bInvert = TRUE;
+ rfb = -rfb;
+ }
+
+ switch (pr->fbposres.geom)
+ {
+ case efbposresSPHERE:
+ /* spherical flat-bottom posres */
+ dr2 = norm2(dx);
+ if (dr2 > 0.0 &&
+ ( (dr2 > rfb2 && bInvert == FALSE ) || (dr2 < rfb2 && bInvert == TRUE ) )
+ )
+ {
+ dr = sqrt(dr2);
+ v = 0.5*kk*sqr(dr - rfb);
+ fact = -kk*(dr-rfb)/dr; /* Force pointing to the center pos0 */
+ svmul(fact, dx, fm);
+ }
+ break;
+ case efbposresCYLINDERX:
+ /* cylindrical flat-bottom posres in y-z plane. fm[XX] = 0. */
+ fbdim = XX;
+ v = do_fbposres_cylinder(fbdim, fm, dx, rfb, kk, bInvert);
+ break;
+ case efbposresCYLINDERY:
+ /* cylindrical flat-bottom posres in x-z plane. fm[YY] = 0. */
+ fbdim = YY;
+ v = do_fbposres_cylinder(fbdim, fm, dx, rfb, kk, bInvert);
+ break;
+ case efbposresCYLINDER:
+ /* equivalent to efbposresCYLINDERZ for backwards compatibility */
+ case efbposresCYLINDERZ:
+ /* cylindrical flat-bottom posres in x-y plane. fm[ZZ] = 0. */
+ fbdim = ZZ;
+ v = do_fbposres_cylinder(fbdim, fm, dx, rfb, kk, bInvert);
+ break;
+ case efbposresX: /* fbdim=XX */
+ case efbposresY: /* fbdim=YY */
+ case efbposresZ: /* fbdim=ZZ */
+ /* 1D flat-bottom potential */
+ fbdim = pr->fbposres.geom - efbposresX;
+ dr = dx[fbdim];
+ if ( ( dr > rfb && bInvert == FALSE ) || ( 0 < dr && dr < rfb && bInvert == TRUE ) )
+ {
+ v = 0.5*kk*sqr(dr - rfb);
+ fm[fbdim] = -kk*(dr - rfb);
+ }
+ else if ( (dr < (-rfb) && bInvert == FALSE ) || ( (-rfb) < dr && dr < 0 && bInvert == TRUE ))
+ {
+ v = 0.5*kk*sqr(dr + rfb);
+ fm[fbdim] = -kk*(dr + rfb);
+ }
+ break;
+ }
+
+ vtot += v;
+
+ for (m = 0; (m < DIM); m++)
+ {
+ f[ai][m] += fm[m];
+ /* Here we correct for the pbc_dx which included rdist */
+ vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm[m];
+ }
+ }
+
+ return vtot;
+}
+
+
+/*! \brief Compute energies and forces for position restraints
+ *
+ * Note that position restraints require a different pbc treatment
+ * from other bondeds */
+real posres(int nbonds,
+ const t_iatom forceatoms[], const t_iparams forceparams[],
+ const rvec x[], rvec f[], rvec vir_diag,
+ const struct t_pbc *pbc,
+ real lambda, real *dvdlambda,
+ int refcoord_scaling, int ePBC, rvec comA, rvec comB)
+{
+ int i, ai, m, d, type, npbcdim = 0;
+ const t_iparams *pr;
+ real L1;
+ real vtot, kk, fm;
+ rvec comA_sc, comB_sc, rdist, dpdl, dx;
+ gmx_bool bForceValid = TRUE;
+
+ if ((f == NULL) || (vir_diag == NULL)) /* should both be null together! */
+ {
+ bForceValid = FALSE;
+ }
+
+ npbcdim = ePBC2npbcdim(ePBC);
+
+ if (refcoord_scaling == erscCOM)
+ {
+ clear_rvec(comA_sc);
+ clear_rvec(comB_sc);
+ for (m = 0; m < npbcdim; m++)
+ {
+ assert(npbcdim <= DIM);
+ for (d = m; d < npbcdim; d++)
+ {
+ comA_sc[m] += comA[d]*pbc->box[d][m];
+ comB_sc[m] += comB[d]*pbc->box[d][m];
+ }
+ }
+ }
+
+ L1 = 1.0 - lambda;
+
+ vtot = 0.0;
+ for (i = 0; (i < nbonds); )
+ {
+ type = forceatoms[i++];
+ ai = forceatoms[i++];
+ pr = &forceparams[type];
+
+ /* return dx, rdist, and dpdl */
+ posres_dx(x[ai], forceparams[type].posres.pos0A, forceparams[type].posres.pos0B,
+ comA_sc, comB_sc, lambda,
+ pbc, refcoord_scaling, npbcdim,
+ dx, rdist, dpdl);
+
+ for (m = 0; (m < DIM); m++)
+ {
+ kk = L1*pr->posres.fcA[m] + lambda*pr->posres.fcB[m];
+ fm = -kk*dx[m];
+ vtot += 0.5*kk*dx[m]*dx[m];
+ *dvdlambda +=
+ 0.5*(pr->posres.fcB[m] - pr->posres.fcA[m])*dx[m]*dx[m]
+ + fm*dpdl[m];
+
+ /* Here we correct for the pbc_dx which included rdist */
+ if (bForceValid)
+ {
+ f[ai][m] += fm;
+ vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm;
+ }
+ }
+ }
+
+ return vtot;
+}
+
+} // namespace
+
+void
+posres_wrapper(t_nrnb *nrnb,
+ const t_idef *idef,
+ const struct t_pbc *pbc,
+ const rvec x[],
+ gmx_enerdata_t *enerd,
+ real *lambda,
+ t_forcerec *fr)
+{
+ real v, dvdl;
+
+ dvdl = 0;
+ v = posres(idef->il[F_POSRES].nr, idef->il[F_POSRES].iatoms,
+ idef->iparams_posres,
+ x, fr->f_novirsum, fr->vir_diag_posres,
+ fr->ePBC == epbcNONE ? NULL : pbc,
+ lambda[efptRESTRAINT], &dvdl,
+ fr->rc_scaling, fr->ePBC, fr->posres_com, fr->posres_comB);
+ enerd->term[F_POSRES] += v;
+ /* If just the force constant changes, the FEP term is linear,
+ * but if k changes, it is not.
+ */
+ enerd->dvdl_nonlin[efptRESTRAINT] += dvdl;
+ inc_nrnb(nrnb, eNR_POSRES, idef->il[F_POSRES].nr/2);
+}
+
+void
+posres_wrapper_lambda(const t_lambda *fepvals,
+ const t_idef *idef,
+ const struct t_pbc *pbc,
+ const rvec x[],
+ gmx_enerdata_t *enerd,
+ real *lambda,
+ t_forcerec *fr)
+{
+ real v;
+ int i;
+
+ if (0 == idef->il[F_POSRES].nr)
+ {
+ return;
+ }
+
+ for (i = 0; i < enerd->n_lambda; i++)
+ {
+ real dvdl_dum = 0, lambda_dum;
+
+ lambda_dum = (i == 0 ? lambda[efptRESTRAINT] : fepvals->all_lambda[efptRESTRAINT][i-1]);
+ v = posres(idef->il[F_POSRES].nr, idef->il[F_POSRES].iatoms,
+ idef->iparams_posres,
+ x, NULL, NULL,
+ fr->ePBC == epbcNONE ? NULL : pbc, lambda_dum, &dvdl_dum,
+ fr->rc_scaling, fr->ePBC, fr->posres_com, fr->posres_comB);
+ enerd->enerpart_lambda[i] += v;
+ }
+}
+
+/*! \brief Helper function that wraps calls to fbposres for
+ free-energy perturbation */
+void fbposres_wrapper(t_nrnb *nrnb,
+ const t_idef *idef,
+ const struct t_pbc *pbc,
+ const rvec x[],
+ gmx_enerdata_t *enerd,
+ t_forcerec *fr)
+{
+ real v;
+
+ v = fbposres(idef->il[F_FBPOSRES].nr, idef->il[F_FBPOSRES].iatoms,
+ idef->iparams_fbposres,
+ x, fr->f_novirsum, fr->vir_diag_posres,
+ fr->ePBC == epbcNONE ? NULL : pbc,
+ fr->rc_scaling, fr->ePBC, fr->posres_com);
+ enerd->term[F_FBPOSRES] += v;
+ inc_nrnb(nrnb, eNR_FBPOSRES, idef->il[F_FBPOSRES].nr/2);
+}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef GMX_LEGACYHEADERS_TYPES_MATRIX_H
-#define GMX_LEGACYHEADERS_TYPES_MATRIX_H
+/*! \libinternal \file
+ *
+ * \brief This file contains declarations necessary for low-level
+ * functions for computing energies and forces for position
+ * restraints.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_listed-forces
+ */
-#ifdef __cplusplus
-extern "C" {
-#endif
+#ifndef GMX_LISTED_FORCES_POSITION_RESTRAINTS_H
+#define GMX_LISTED_FORCES_POSITION_RESTRAINTS_H
-#include "simple.h"
+#include <stdio.h>
-typedef struct {
- real r, g, b;
-} t_rgb;
+#include "gromacs/legacyheaders/typedefs.h"
-typedef struct {
- char c1; /* should all be non-zero (and printable and not '"') */
- char c2; /*
- * should all be zero (single char color names: smaller xpm's)
- * or should all be non-zero (double char color names: more colors)
- */
-} t_xpmelmt;
+#ifdef __cplusplus
+extern "C" {
+#endif
-typedef short t_matelmt;
+struct t_pbc;
-typedef struct {
- t_xpmelmt code; /* see comment for t_xpmelmt */
- const char *desc;
- t_rgb rgb;
-} t_mapping;
+/*! \brief Helper function that wraps calls to posres */
+void
+posres_wrapper(t_nrnb *nrnb,
+ const t_idef *idef,
+ const struct t_pbc *pbc,
+ const rvec x[],
+ gmx_enerdata_t *enerd,
+ real *lambda,
+ t_forcerec *fr);
-#define MAT_SPATIAL_X (1<<0)
-#define MAT_SPATIAL_Y (1<<1)
-/* Defines if x and y are spatial dimensions,
- * when not, there are n axis ticks at the middle of the elements,
- * when set, there are n+1 axis ticks at the edges of the elements.
- */
+/*! \brief Helper function that wraps calls to posres for free-energy
+ pertubation */
+void
+posres_wrapper_lambda(const t_lambda *fepvals,
+ const t_idef *idef,
+ const struct t_pbc *pbc,
+ const rvec x[],
+ gmx_enerdata_t *enerd,
+ real *lambda,
+ t_forcerec *fr);
-typedef struct {
- unsigned int flags; /* The possible flags are defined above */
- int nx, ny;
- int y0;
- char title[256];
- char legend[256];
- char label_x[256];
- char label_y[256];
- gmx_bool bDiscrete;
- real *axis_x;
- real *axis_y;
- t_matelmt **matrix;
- int nmap;
- t_mapping *map;
-} t_matrix;
-/* title matrix title
- * legend label for the continuous legend
- * label_x label for the x-axis
- * label_y label for the y-axis
- * nx, ny size of the matrix
- * axis_x[] the x-ticklabels
- * axis_y[] the y-ticklables
- * *matrix[] element x,y is matrix[x][y]
- * nmap number of color levels for the output(?)
- */
+/*! \brief Helper function that wraps calls to fbposres for
+ free-energy perturbation */
+void fbposres_wrapper(t_nrnb *nrnb,
+ const t_idef *idef,
+ const struct t_pbc *pbc,
+ const rvec x[],
+ gmx_enerdata_t *enerd,
+ t_forcerec *fr);
#ifdef __cplusplus
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \internal \file
+ *
+ * \brief
+ * This file contains function definitions necessary
+ * for computations of forces due to restricted angle, restricted dihedral and
+ * combined bending-torsion potentials.
+ *
+ * \author Nicolae Goga
+ *
+ * \ingroup module_listed-forces
+ */
+#include "gmxpre.h"
+
+#include "restcbt.h"
#include <math.h>
-#include <assert.h>
-#include "physics.h"
-#include "vec.h"
+
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
-#include "txtdump.h"
-#include "bondf.h"
-#include "gromacs/utility/smalloc.h"
-#include "pbc.h"
-#include "ns.h"
-#include "macros.h"
-#include "names.h"
-#include "mshift.h"
-#include "main.h"
-#include "disre.h"
-#include "orires.h"
-#include "force.h"
-#include "nonbonded.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/idef.h"
/* This function computes factors needed for restricted angle potential.
* For explanations on formula used see file "restcbt.h" */
real *prefactor_phi, real *v)
{
- real phi0, sine_phi0, cosine_phi0;
+ real phi0, cosine_phi0;
real k_torsion;
real c_self_ante, c_self_crnt, c_self_post;
real c_cros_ante, c_cros_acrs, c_cros_post;
real sine_phi_sq, cosine_phi;
real delta_cosine, term_phi_phi0;
real ratio_phi_ante, ratio_phi_post;
- real cos_phi, norm_phi;
+ real norm_phi;
/* Read parameters phi0 and k_torsion */
phi0 = forceparams[type].pdihs.phiA * DEG2RAD;
cosine_phi0 = cos(phi0);
- sine_phi0 = sin(phi0);
k_torsion = forceparams[type].pdihs.cpA;
/* Computation of the cosine of the dihedral angle. The scalar ("dot") product method
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-/*! \libinternal \file
+/*! \internal \file
*
*
* \brief
* This file contains function declarations necessary
for computations of forces due to restricted angle, restricted dihedral and
combined bending-torsion potentials.
-
*
* \author Nicolae Goga
*
- * \inlibraryapi
+ * \ingroup module_listed-forces
*/
-#ifndef _restcbt_h
-#define _restcbt_h
-
-
-#ifdef __cplusplus
-extern "C" {
-#endif
+#ifndef GMX_LISTED_FORCES_RESTCBT_H
+#define GMX_LISTED_FORCES_RESTCBT_H
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/idef.h"
/*! \brief This function computes factors needed for restricted angle potentials.
*
rvec f_theta_post_aj, rvec f_theta_post_ak, rvec f_theta_post_al,
real * v);
-
-#ifdef __cplusplus
-}
#endif
-
-#endif /* _restcbt_h */
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "3dtransforms.h"
+
+#include <math.h>
+#include <stdio.h>
+
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+
+#define N 4
+
+void gmx_mat4_copy(mat4 a, mat4 b)
+{
+ for (int i = 0; i < N; ++i)
+ {
+ for (int j = 0; j < N; ++j)
+ {
+ b[i][j] = a[i][j];
+ }
+ }
+}
+
+void gmx_mat4_transform_point(mat4 m, rvec x, vec4 v)
+{
+ int i;
+
+ for (i = 0; (i < N); i++)
+ {
+ v[i] = m[XX][i]*x[XX]+m[YY][i]*x[YY]+m[ZZ][i]*x[ZZ]+m[WW][i];
+ }
+}
+
+void gmx_mat4_mmul(mat4 A, mat4 B, mat4 C)
+{
+ int i, j, k;
+
+ for (i = 0; i < N; i++)
+ {
+ for (j = 0; j < N; j++)
+ {
+ A[i][j] = 0;
+ for (k = 0; (k < N); k++)
+ {
+ A[i][j] += B[i][k]*C[k][j];
+ }
+ }
+ }
+}
+
+void gmx_mat4_init_unity(mat4 m)
+{
+ int i, j;
+
+ for (i = 0; (i < N); i++)
+ {
+ for (j = 0; (j < N); j++)
+ {
+ if (i == j)
+ {
+ m[i][j] = 1.0;
+ }
+ else
+ {
+ m[i][j] = 0.0;
+ }
+ }
+ }
+}
+
+void gmx_mat4_init_rotation(int axis, real angle, mat4 A)
+{
+ gmx_mat4_init_unity(A);
+
+ switch (axis)
+ {
+ case XX:
+ A[YY][YY] = cos(angle);
+ A[YY][ZZ] = -sin(angle);
+ A[ZZ][YY] = sin(angle);
+ A[ZZ][ZZ] = cos(angle);
+ break;
+ case YY:
+ A[XX][XX] = cos(angle);
+ A[XX][ZZ] = sin(angle);
+ A[ZZ][XX] = -sin(angle);
+ A[ZZ][ZZ] = cos(angle);
+ break;
+ case ZZ:
+ A[XX][XX] = cos(angle);
+ A[XX][YY] = -sin(angle);
+ A[YY][XX] = sin(angle);
+ A[YY][YY] = cos(angle);
+ break;
+ default:
+ gmx_fatal(FARGS, "Error: invalid axis: %d", axis);
+ }
+}
+
+void gmx_mat4_init_translation(real tx, real ty, real tz, mat4 A)
+{
+ gmx_mat4_init_unity(A);
+ A[3][XX] = tx;
+ A[3][YY] = ty;
+ A[3][ZZ] = tz;
+}
+
+void gmx_mat4_print(FILE *fp, const char *s, mat4 A)
+{
+ int i, j;
+
+ if (fp)
+ {
+ fprintf(fp, "%s: ", s);
+ for (i = 0; i < N; i++)
+ {
+ fprintf(fp, "\t");
+ for (j = 0; j < N; j++)
+ {
+ fprintf(fp, "%10.5f", A[i][j]);
+ }
+ fprintf(fp, "\n");
+ }
+ }
+}
+
+void gmx_vec4_print(FILE *fp, const char *s, vec4 a)
+{
+ int j;
+
+ if (fp)
+ {
+ fprintf(fp, "%s: ", s);
+ for (j = 0; j < N; j++)
+ {
+ fprintf(fp, "%10.5f", a[j]);
+ }
+ fprintf(fp, "\n");
+ }
+}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _nlistheuristics_h
-#define _nlistheuristics_h
+#ifndef GMX_MATH_3DTRANSFORMS_H
+#define GMX_MATH_3DTRANSFORMS_H
+
+#include <stdio.h>
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#endif
-#if 0
-}
-/* Hack to make automatic indenting work */
-#endif
+/** Index for the fourth dimension for `vec4`. */
+#define WW 3
+
+/*! \brief
+ * 4D vector type used in 3D transformations.
+ *
+ * In \Gromacs, only a limited set of 3D transformations are used, and all of
+ * them operate on coordinates, so the fourth element is assumed to be one and
+ * ignored in all contexts.
+ */
+typedef real vec4[4];
+
+/*! \brief
+ * 4D matrix type used in 3D transformations.
+ */
+typedef real mat4[4][4];
+
+void gmx_mat4_copy(mat4 a, mat4 b);
+
+void gmx_mat4_transform_point(mat4 m, rvec x, vec4 v);
+
+/*! \brief
+ * Computes the product of two `mat4` matrices as A = B * C.
+ *
+ * Note that the order of operands is different from mmul() in vec.h!
+ */
+void gmx_mat4_mmul(mat4 A, mat4 B, mat4 C);
-typedef struct {
- gmx_bool bGStatEveryStep;
- gmx_int64_t step_ns;
- gmx_int64_t step_nscheck;
- gmx_int64_t nns;
- matrix scale_tot;
- int nabnsb;
- double s1;
- double s2;
- double ab;
- double lt_runav;
- double lt_runav2;
-} gmx_nlheur_t;
+void gmx_mat4_init_unity(mat4 m);
-void reset_nlistheuristics(gmx_nlheur_t *nlh, gmx_int64_t step);
+void gmx_mat4_init_rotation(int axis, real angle, mat4 A);
-void init_nlistheuristics(gmx_nlheur_t *nlh,
- gmx_bool bGStatEveryStep, gmx_int64_t step);
+void gmx_mat4_init_translation(real tx, real ty, real tz, mat4 A);
-void update_nliststatistics(gmx_nlheur_t *nlh, gmx_int64_t step);
+void gmx_mat4_print(FILE *fp, const char *s, mat4 A);
-void set_nlistheuristics(gmx_nlheur_t *nlh, gmx_bool bReset, gmx_int64_t step);
+void gmx_vec4_print(FILE *fp, const char *s, vec4 a);
#ifdef __cplusplus
}
file(GLOB MATH_SOURCES *.cpp *.c)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${MATH_SOURCES} PARENT_SCOPE)
-set(MATH_PUBLIC_HEADERS
- 3dview.h
- gmxcomplex.h
+gmx_install_headers(
+ 3dtransforms.h
+ calculate-ewald-splitting-coefficient.h
do_fit.h
+ gmxcomplex.h
+ units.h
utilities.h
+ vec.h
+ vectypes.h
)
-gmx_install_headers(math ${MATH_PUBLIC_HEADERS})
if (BUILD_TESTING)
-# add_subdirectory(tests)
+ add_subdirectory(tests)
endif()
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "calculate-ewald-splitting-coefficient.h"
+
+#include <cmath>
+
+#include "gromacs/math/utilities.h"
+#include "gromacs/utility/real.h"
+
+real calc_ewaldcoeff_q(real rc, real rtol)
+{
+ real beta = 5, low, high;
+ int n, i = 0;
+
+ do
+ {
+ i++;
+ beta *= 2;
+ }
+ while (gmx_erfc(beta*rc) > rtol);
+
+ /* Do a binary search with tolerance 2^-60 */
+ n = i+60;
+ low = 0;
+ high = beta;
+ for (i = 0; i < n; i++)
+ {
+ beta = (low+high)/2;
+ if (gmx_erfc(beta*rc) > rtol)
+ {
+ low = beta;
+ }
+ else
+ {
+ high = beta;
+ }
+ }
+ return beta;
+}
+
+static real compute_lj_function(real beta, real rc)
+{
+ real xrc, xrc2, xrc4, result;
+ xrc = beta*rc;
+ xrc2 = xrc*xrc;
+ xrc4 = xrc2*xrc2;
+ result = std::exp(-xrc2)*(1 + xrc2 + xrc4/2.0);
+
+ return result;
+}
+
+real calc_ewaldcoeff_lj(real rc, real rtol)
+{
+ real beta = 5, low, high;
+ int n, i = 0;
+
+ do
+ {
+ i++;
+ beta *= 2.0;
+ }
+ while (compute_lj_function(beta, rc) > rtol);
+
+ /* Do a binary search with tolerance 2^-60 */
+ n = i + 60;
+ low = 0;
+ high = beta;
+ for (i = 0; i < n; ++i)
+ {
+ beta = (low + high) / 2.0;
+ if (compute_lj_function(beta, rc) > rtol)
+ {
+ low = beta;
+ }
+ else
+ {
+ high = beta;
+ }
+ }
+ return beta;
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ *
+ * \brief Declares functions for computing Ewald splitting coefficients
+ *
+ * These belong in the maths module because they do simple maths and
+ * are used many parts of Gromacs.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \inpublicapi
+ */
+#ifndef GMX_MATH_CALCULATE_EWALD_SPLITTING_COEFFICIENT_H
+#define GMX_MATH_CALCULATE_EWALD_SPLITTING_COEFFICIENT_H
+
+#include "gromacs/utility/real.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*! \brief Computes the Ewald splitting coefficient for Coulomb
+ *
+ * Returns a value of beta that satisfies rtol > erfc(beta * rc)
+ * (and is very close to equality). That value is used the same way in
+ * all Coulomb-based Ewald methods.
+ *
+ * \param[in] rc Cutoff radius
+ * \param[in] rtol Required maximum value of the short-ranged
+ * potential at the cutoff (ie. ewald-rtol)
+ * \return The value of the splitting coefficient that
+ * produces the required dtol at rc.
+ */
+real
+calc_ewaldcoeff_q(real rc, real rtol);
+
+/*! \brief Computes the Ewald splitting coefficient for LJ
+ *
+ * Returns a value of beta that satisfies dtol > erfc(beta * rc) * (1
+ * + beta^2 * rc^2 + 0.5 * beta^4 * rc^4) (and is very close to
+ * equality), which is used in LJ-PME.
+ *
+ * \param[in] rc Cutoff radius
+ * \param[in] rtol Required maximum value of the short-ranged
+ * potential at the cutoff (ie. ewald-rtol-lj)
+ * \return The value of the splitting coefficient that
+ * produces the required dtol at rc.
+ */
+real
+calc_ewaldcoeff_lj(real rc, real rtol);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
#include "do_fit.h"
-#include "gromacs/math/utilities.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "txtdump.h"
+#include <math.h>
+#include <stdio.h>
#include "gromacs/linearalgebra/nrjac.h"
-#include "gmx_fatal.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
real calc_similar_ind(gmx_bool bRho, int nind, atom_id *index, real mass[],
#ifndef GMX_MATH_DO_FIT_H
#define GMX_MATH_DO_FIT_H
-#include "../legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#define GMX_MATH_GMXCOMPLEX_H
#include <math.h>
-#include "../legacyheaders/types/simple.h"
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
typedef struct {
real re, im;
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/* This file is completely threadsafe - keep it that way! */
+#include "gmxpre.h"
+
+#include "gromacs/math/vec.h"
+
+/** Exponential lookup table - 256 floats */
+const unsigned int gmx_invsqrt_exptab[256] = {
+ 0x5f000000, 0x5e800000, 0x5e800000, 0x5e000000,
+ 0x5e000000, 0x5d800000, 0x5d800000, 0x5d000000,
+ 0x5d000000, 0x5c800000, 0x5c800000, 0x5c000000,
+ 0x5c000000, 0x5b800000, 0x5b800000, 0x5b000000,
+ 0x5b000000, 0x5a800000, 0x5a800000, 0x5a000000,
+ 0x5a000000, 0x59800000, 0x59800000, 0x59000000,
+ 0x59000000, 0x58800000, 0x58800000, 0x58000000,
+ 0x58000000, 0x57800000, 0x57800000, 0x57000000,
+ 0x57000000, 0x56800000, 0x56800000, 0x56000000,
+ 0x56000000, 0x55800000, 0x55800000, 0x55000000,
+ 0x55000000, 0x54800000, 0x54800000, 0x54000000,
+ 0x54000000, 0x53800000, 0x53800000, 0x53000000,
+ 0x53000000, 0x52800000, 0x52800000, 0x52000000,
+ 0x52000000, 0x51800000, 0x51800000, 0x51000000,
+ 0x51000000, 0x50800000, 0x50800000, 0x50000000,
+ 0x50000000, 0x4f800000, 0x4f800000, 0x4f000000,
+ 0x4f000000, 0x4e800000, 0x4e800000, 0x4e000000,
+ 0x4e000000, 0x4d800000, 0x4d800000, 0x4d000000,
+ 0x4d000000, 0x4c800000, 0x4c800000, 0x4c000000,
+ 0x4c000000, 0x4b800000, 0x4b800000, 0x4b000000,
+ 0x4b000000, 0x4a800000, 0x4a800000, 0x4a000000,
+ 0x4a000000, 0x49800000, 0x49800000, 0x49000000,
+ 0x49000000, 0x48800000, 0x48800000, 0x48000000,
+ 0x48000000, 0x47800000, 0x47800000, 0x47000000,
+ 0x47000000, 0x46800000, 0x46800000, 0x46000000,
+ 0x46000000, 0x45800000, 0x45800000, 0x45000000,
+ 0x45000000, 0x44800000, 0x44800000, 0x44000000,
+ 0x44000000, 0x43800000, 0x43800000, 0x43000000,
+ 0x43000000, 0x42800000, 0x42800000, 0x42000000,
+ 0x42000000, 0x41800000, 0x41800000, 0x41000000,
+ 0x41000000, 0x40800000, 0x40800000, 0x40000000,
+ 0x40000000, 0x3f800000, 0x3f800000, 0x3f000000,
+ 0x3f000000, 0x3e800000, 0x3e800000, 0x3e000000,
+ 0x3e000000, 0x3d800000, 0x3d800000, 0x3d000000,
+ 0x3d000000, 0x3c800000, 0x3c800000, 0x3c000000,
+ 0x3c000000, 0x3b800000, 0x3b800000, 0x3b000000,
+ 0x3b000000, 0x3a800000, 0x3a800000, 0x3a000000,
+ 0x3a000000, 0x39800000, 0x39800000, 0x39000000,
+ 0x39000000, 0x38800000, 0x38800000, 0x38000000,
+ 0x38000000, 0x37800000, 0x37800000, 0x37000000,
+ 0x37000000, 0x36800000, 0x36800000, 0x36000000,
+ 0x36000000, 0x35800000, 0x35800000, 0x35000000,
+ 0x35000000, 0x34800000, 0x34800000, 0x34000000,
+ 0x34000000, 0x33800000, 0x33800000, 0x33000000,
+ 0x33000000, 0x32800000, 0x32800000, 0x32000000,
+ 0x32000000, 0x31800000, 0x31800000, 0x31000000,
+ 0x31000000, 0x30800000, 0x30800000, 0x30000000,
+ 0x30000000, 0x2f800000, 0x2f800000, 0x2f000000,
+ 0x2f000000, 0x2e800000, 0x2e800000, 0x2e000000,
+ 0x2e000000, 0x2d800000, 0x2d800000, 0x2d000000,
+ 0x2d000000, 0x2c800000, 0x2c800000, 0x2c000000,
+ 0x2c000000, 0x2b800000, 0x2b800000, 0x2b000000,
+ 0x2b000000, 0x2a800000, 0x2a800000, 0x2a000000,
+ 0x2a000000, 0x29800000, 0x29800000, 0x29000000,
+ 0x29000000, 0x28800000, 0x28800000, 0x28000000,
+ 0x28000000, 0x27800000, 0x27800000, 0x27000000,
+ 0x27000000, 0x26800000, 0x26800000, 0x26000000,
+ 0x26000000, 0x25800000, 0x25800000, 0x25000000,
+ 0x25000000, 0x24800000, 0x24800000, 0x24000000,
+ 0x24000000, 0x23800000, 0x23800000, 0x23000000,
+ 0x23000000, 0x22800000, 0x22800000, 0x22000000,
+ 0x22000000, 0x21800000, 0x21800000, 0x21000000,
+ 0x21000000, 0x20800000, 0x20800000, 0x20000000,
+ 0x20000000, 0x1f800000, 0x1f800000, 0x1f000000
+};
+
+/** Mantissa lookup table - 4096 floats */
+const unsigned int gmx_invsqrt_fracttab[4096] = {
+ 0x3504f3, 0x34f9a4, 0x34ee57, 0x34e30c, 0x34d7c3, 0x34cc7c, 0x34c137, 0x34b5f5,
+ 0x34aab4, 0x349f76, 0x34943a, 0x348900, 0x347dc7, 0x347291, 0x34675e, 0x345c2c,
+ 0x3450fc, 0x3445ce, 0x343aa3, 0x342f79, 0x342452, 0x34192c, 0x340e09, 0x3402e8,
+ 0x33f7c9, 0x33ecac, 0x33e191, 0x33d678, 0x33cb61, 0x33c04c, 0x33b539, 0x33aa28,
+ 0x339f19, 0x33940d, 0x338902, 0x337df9, 0x3372f3, 0x3367ee, 0x335cec, 0x3351eb,
+ 0x3346ed, 0x333bf0, 0x3330f6, 0x3325fd, 0x331b07, 0x331013, 0x330520, 0x32fa30,
+ 0x32ef41, 0x32e455, 0x32d96b, 0x32ce82, 0x32c39c, 0x32b8b7, 0x32add5, 0x32a2f5,
+ 0x329816, 0x328d3a, 0x32825f, 0x327787, 0x326cb0, 0x3261dc, 0x325709, 0x324c38,
+ 0x32416a, 0x32369d, 0x322bd2, 0x32210a, 0x321643, 0x320b7e, 0x3200bb, 0x31f5fa,
+ 0x31eb3b, 0x31e07e, 0x31d5c3, 0x31cb0a, 0x31c053, 0x31b59d, 0x31aaea, 0x31a038,
+ 0x319589, 0x318adb, 0x318030, 0x317586, 0x316ade, 0x316038, 0x315594, 0x314af2,
+ 0x314052, 0x3135b4, 0x312b18, 0x31207d, 0x3115e5, 0x310b4e, 0x3100b9, 0x30f627,
+ 0x30eb96, 0x30e107, 0x30d67a, 0x30cbee, 0x30c165, 0x30b6dd, 0x30ac58, 0x30a1d4,
+ 0x309752, 0x308cd2, 0x308254, 0x3077d8, 0x306d5e, 0x3062e5, 0x30586e, 0x304dfa,
+ 0x304387, 0x303916, 0x302ea7, 0x302439, 0x3019ce, 0x300f64, 0x3004fc, 0x2ffa96,
+ 0x2ff032, 0x2fe5d0, 0x2fdb6f, 0x2fd111, 0x2fc6b4, 0x2fbc59, 0x2fb200, 0x2fa7a9,
+ 0x2f9d53, 0x2f9300, 0x2f88ae, 0x2f7e5e, 0x2f7410, 0x2f69c3, 0x2f5f79, 0x2f5530,
+ 0x2f4ae9, 0x2f40a4, 0x2f3661, 0x2f2c1f, 0x2f21df, 0x2f17a1, 0x2f0d65, 0x2f032b,
+ 0x2ef8f2, 0x2eeebc, 0x2ee487, 0x2eda53, 0x2ed022, 0x2ec5f2, 0x2ebbc5, 0x2eb199,
+ 0x2ea76e, 0x2e9d46, 0x2e931f, 0x2e88fa, 0x2e7ed7, 0x2e74b5, 0x2e6a96, 0x2e6078,
+ 0x2e565c, 0x2e4c41, 0x2e4229, 0x2e3812, 0x2e2dfd, 0x2e23e9, 0x2e19d8, 0x2e0fc8,
+ 0x2e05ba, 0x2dfbad, 0x2df1a3, 0x2de79a, 0x2ddd93, 0x2dd38d, 0x2dc989, 0x2dbf87,
+ 0x2db587, 0x2dab89, 0x2da18c, 0x2d9791, 0x2d8d97, 0x2d83a0, 0x2d79aa, 0x2d6fb6,
+ 0x2d65c3, 0x2d5bd2, 0x2d51e3, 0x2d47f6, 0x2d3e0a, 0x2d3420, 0x2d2a38, 0x2d2051,
+ 0x2d166c, 0x2d0c89, 0x2d02a8, 0x2cf8c8, 0x2ceeea, 0x2ce50d, 0x2cdb33, 0x2cd15a,
+ 0x2cc782, 0x2cbdad, 0x2cb3d9, 0x2caa06, 0x2ca036, 0x2c9667, 0x2c8c99, 0x2c82ce,
+ 0x2c7904, 0x2c6f3b, 0x2c6575, 0x2c5bb0, 0x2c51ed, 0x2c482b, 0x2c3e6b, 0x2c34ad,
+ 0x2c2af0, 0x2c2135, 0x2c177b, 0x2c0dc4, 0x2c040e, 0x2bfa59, 0x2bf0a6, 0x2be6f5,
+ 0x2bdd46, 0x2bd398, 0x2bc9eb, 0x2bc041, 0x2bb698, 0x2bacf0, 0x2ba34b, 0x2b99a6,
+ 0x2b9004, 0x2b8663, 0x2b7cc4, 0x2b7326, 0x2b698a, 0x2b5ff0, 0x2b5657, 0x2b4cc0,
+ 0x2b432a, 0x2b3996, 0x2b3004, 0x2b2673, 0x2b1ce4, 0x2b1357, 0x2b09cb, 0x2b0040,
+ 0x2af6b7, 0x2aed30, 0x2ae3ab, 0x2ada27, 0x2ad0a4, 0x2ac724, 0x2abda4, 0x2ab427,
+ 0x2aaaab, 0x2aa130, 0x2a97b7, 0x2a8e40, 0x2a84ca, 0x2a7b56, 0x2a71e3, 0x2a6872,
+ 0x2a5f03, 0x2a5595, 0x2a4c29, 0x2a42be, 0x2a3955, 0x2a2fed, 0x2a2687, 0x2a1d23,
+ 0x2a13c0, 0x2a0a5e, 0x2a00fe, 0x29f7a0, 0x29ee43, 0x29e4e8, 0x29db8e, 0x29d236,
+ 0x29c8e0, 0x29bf8b, 0x29b637, 0x29ace5, 0x29a395, 0x299a46, 0x2990f8, 0x2987ad,
+ 0x297e62, 0x297519, 0x296bd2, 0x29628c, 0x295948, 0x295005, 0x2946c4, 0x293d85,
+ 0x293446, 0x292b0a, 0x2921cf, 0x291895, 0x290f5d, 0x290626, 0x28fcf1, 0x28f3be,
+ 0x28ea8c, 0x28e15b, 0x28d82c, 0x28cefe, 0x28c5d2, 0x28bca8, 0x28b37f, 0x28aa57,
+ 0x28a131, 0x28980c, 0x288ee9, 0x2885c7, 0x287ca7, 0x287389, 0x286a6b, 0x286150,
+ 0x285835, 0x284f1c, 0x284605, 0x283cef, 0x2833db, 0x282ac8, 0x2821b7, 0x2818a7,
+ 0x280f98, 0x28068b, 0x27fd80, 0x27f475, 0x27eb6d, 0x27e266, 0x27d960, 0x27d05c,
+ 0x27c759, 0x27be57, 0x27b557, 0x27ac59, 0x27a35c, 0x279a60, 0x279166, 0x27886d,
+ 0x277f76, 0x277680, 0x276d8c, 0x276499, 0x275ba7, 0x2752b7, 0x2749c9, 0x2740db,
+ 0x2737f0, 0x272f05, 0x27261c, 0x271d35, 0x27144f, 0x270b6a, 0x270287, 0x26f9a5,
+ 0x26f0c4, 0x26e7e5, 0x26df08, 0x26d62c, 0x26cd51, 0x26c477, 0x26bba0, 0x26b2c9,
+ 0x26a9f4, 0x26a120, 0x26984e, 0x268f7d, 0x2686ad, 0x267ddf, 0x267512, 0x266c47,
+ 0x26637d, 0x265ab4, 0x2651ed, 0x264927, 0x264063, 0x2637a0, 0x262ede, 0x26261e,
+ 0x261d5f, 0x2614a2, 0x260be6, 0x26032b, 0x25fa72, 0x25f1ba, 0x25e903, 0x25e04e,
+ 0x25d79a, 0x25cee7, 0x25c636, 0x25bd87, 0x25b4d8, 0x25ac2b, 0x25a37f, 0x259ad5,
+ 0x25922c, 0x258985, 0x2580de, 0x257839, 0x256f96, 0x2566f4, 0x255e53, 0x2555b3,
+ 0x254d15, 0x254479, 0x253bdd, 0x253343, 0x252aaa, 0x252213, 0x25197d, 0x2510e8,
+ 0x250855, 0x24ffc3, 0x24f732, 0x24eea3, 0x24e615, 0x24dd88, 0x24d4fc, 0x24cc72,
+ 0x24c3ea, 0x24bb62, 0x24b2dc, 0x24aa57, 0x24a1d4, 0x249952, 0x2490d1, 0x248852,
+ 0x247fd3, 0x247756, 0x246edb, 0x246661, 0x245de8, 0x245570, 0x244cfa, 0x244485,
+ 0x243c11, 0x24339f, 0x242b2e, 0x2422be, 0x241a4f, 0x2411e2, 0x240976, 0x24010c,
+ 0x23f8a2, 0x23f03a, 0x23e7d4, 0x23df6e, 0x23d70a, 0x23cea7, 0x23c646, 0x23bde6,
+ 0x23b587, 0x23ad29, 0x23a4cc, 0x239c71, 0x239417, 0x238bbf, 0x238368, 0x237b12,
+ 0x2372bd, 0x236a69, 0x236217, 0x2359c6, 0x235177, 0x234928, 0x2340db, 0x23388f,
+ 0x233045, 0x2327fb, 0x231fb3, 0x23176c, 0x230f27, 0x2306e2, 0x22fe9f, 0x22f65e,
+ 0x22ee1d, 0x22e5de, 0x22dda0, 0x22d563, 0x22cd28, 0x22c4ed, 0x22bcb4, 0x22b47c,
+ 0x22ac46, 0x22a411, 0x229bdd, 0x2293aa, 0x228b78, 0x228348, 0x227b19, 0x2272eb,
+ 0x226abe, 0x226293, 0x225a69, 0x225240, 0x224a18, 0x2241f2, 0x2239cc, 0x2231a8,
+ 0x222985, 0x222164, 0x221944, 0x221124, 0x220907, 0x2200ea, 0x21f8ce, 0x21f0b4,
+ 0x21e89b, 0x21e083, 0x21d86d, 0x21d057, 0x21c843, 0x21c030, 0x21b81e, 0x21b00e,
+ 0x21a7fe, 0x219ff0, 0x2197e3, 0x218fd8, 0x2187cd, 0x217fc4, 0x2177bc, 0x216fb5,
+ 0x2167af, 0x215faa, 0x2157a7, 0x214fa5, 0x2147a4, 0x213fa4, 0x2137a5, 0x212fa8,
+ 0x2127ac, 0x211fb1, 0x2117b7, 0x210fbe, 0x2107c7, 0x20ffd0, 0x20f7db, 0x20efe7,
+ 0x20e7f5, 0x20e003, 0x20d813, 0x20d023, 0x20c835, 0x20c048, 0x20b85d, 0x20b072,
+ 0x20a889, 0x20a0a1, 0x2098ba, 0x2090d4, 0x2088ef, 0x20810b, 0x207929, 0x207148,
+ 0x206968, 0x206189, 0x2059ab, 0x2051cf, 0x2049f3, 0x204219, 0x203a40, 0x203268,
+ 0x202a91, 0x2022bb, 0x201ae7, 0x201313, 0x200b41, 0x200370, 0x1ffba0, 0x1ff3d1,
+ 0x1fec04, 0x1fe437, 0x1fdc6c, 0x1fd4a2, 0x1fccd9, 0x1fc511, 0x1fbd4a, 0x1fb584,
+ 0x1fadc0, 0x1fa5fc, 0x1f9e3a, 0x1f9679, 0x1f8eb9, 0x1f86fa, 0x1f7f3c, 0x1f777f,
+ 0x1f6fc4, 0x1f680a, 0x1f6050, 0x1f5898, 0x1f50e1, 0x1f492b, 0x1f4176, 0x1f39c3,
+ 0x1f3210, 0x1f2a5f, 0x1f22af, 0x1f1aff, 0x1f1351, 0x1f0ba4, 0x1f03f8, 0x1efc4e,
+ 0x1ef4a4, 0x1eecfb, 0x1ee554, 0x1eddae, 0x1ed608, 0x1ece64, 0x1ec6c1, 0x1ebf1f,
+ 0x1eb77f, 0x1eafdf, 0x1ea840, 0x1ea0a3, 0x1e9906, 0x1e916b, 0x1e89d1, 0x1e8238,
+ 0x1e7aa0, 0x1e7309, 0x1e6b73, 0x1e63de, 0x1e5c4a, 0x1e54b8, 0x1e4d26, 0x1e4596,
+ 0x1e3e06, 0x1e3678, 0x1e2eeb, 0x1e275f, 0x1e1fd4, 0x1e184a, 0x1e10c1, 0x1e0939,
+ 0x1e01b3, 0x1dfa2d, 0x1df2a8, 0x1deb25, 0x1de3a2, 0x1ddc21, 0x1dd4a1, 0x1dcd22,
+ 0x1dc5a3, 0x1dbe26, 0x1db6aa, 0x1daf2f, 0x1da7b6, 0x1da03d, 0x1d98c5, 0x1d914e,
+ 0x1d89d9, 0x1d8264, 0x1d7af1, 0x1d737e, 0x1d6c0d, 0x1d649c, 0x1d5d2d, 0x1d55bf,
+ 0x1d4e52, 0x1d46e5, 0x1d3f7a, 0x1d3810, 0x1d30a7, 0x1d293f, 0x1d21d8, 0x1d1a73,
+ 0x1d130e, 0x1d0baa, 0x1d0447, 0x1cfce6, 0x1cf585, 0x1cee25, 0x1ce6c7, 0x1cdf69,
+ 0x1cd80d, 0x1cd0b1, 0x1cc957, 0x1cc1fe, 0x1cbaa5, 0x1cb34e, 0x1cabf8, 0x1ca4a2,
+ 0x1c9d4e, 0x1c95fb, 0x1c8ea9, 0x1c8758, 0x1c8008, 0x1c78b8, 0x1c716a, 0x1c6a1d,
+ 0x1c62d1, 0x1c5b86, 0x1c543c, 0x1c4cf3, 0x1c45ab, 0x1c3e65, 0x1c371f, 0x1c2fda,
+ 0x1c2896, 0x1c2153, 0x1c1a11, 0x1c12d0, 0x1c0b90, 0x1c0452, 0x1bfd14, 0x1bf5d7,
+ 0x1bee9b, 0x1be760, 0x1be027, 0x1bd8ee, 0x1bd1b6, 0x1bca7f, 0x1bc349, 0x1bbc15,
+ 0x1bb4e1, 0x1badae, 0x1ba67c, 0x1b9f4c, 0x1b981c, 0x1b90ed, 0x1b89bf, 0x1b8292,
+ 0x1b7b67, 0x1b743c, 0x1b6d12, 0x1b65e9, 0x1b5ec1, 0x1b579a, 0x1b5074, 0x1b4950,
+ 0x1b422c, 0x1b3b09, 0x1b33e7, 0x1b2cc6, 0x1b25a6, 0x1b1e87, 0x1b1769, 0x1b104c,
+ 0x1b0930, 0x1b0215, 0x1afafb, 0x1af3e2, 0x1aecc9, 0x1ae5b2, 0x1ade9c, 0x1ad787,
+ 0x1ad073, 0x1ac95f, 0x1ac24d, 0x1abb3c, 0x1ab42b, 0x1aad1c, 0x1aa60d, 0x1a9f00,
+ 0x1a97f3, 0x1a90e8, 0x1a89dd, 0x1a82d4, 0x1a7bcb, 0x1a74c3, 0x1a6dbd, 0x1a66b7,
+ 0x1a5fb2, 0x1a58ae, 0x1a51ab, 0x1a4aa9, 0x1a43a8, 0x1a3ca8, 0x1a35a9, 0x1a2eab,
+ 0x1a27ae, 0x1a20b1, 0x1a19b6, 0x1a12bc, 0x1a0bc2, 0x1a04ca, 0x19fdd2, 0x19f6dc,
+ 0x19efe6, 0x19e8f2, 0x19e1fe, 0x19db0b, 0x19d419, 0x19cd28, 0x19c638, 0x19bf49,
+ 0x19b85b, 0x19b16e, 0x19aa82, 0x19a396, 0x199cac, 0x1995c3, 0x198eda, 0x1987f3,
+ 0x19810c, 0x197a26, 0x197342, 0x196c5e, 0x19657b, 0x195e99, 0x1957b8, 0x1950d8,
+ 0x1949f8, 0x19431a, 0x193c3d, 0x193560, 0x192e85, 0x1927aa, 0x1920d1, 0x1919f8,
+ 0x191320, 0x190c49, 0x190573, 0x18fe9e, 0x18f7ca, 0x18f0f7, 0x18ea24, 0x18e353,
+ 0x18dc82, 0x18d5b3, 0x18cee4, 0x18c816, 0x18c149, 0x18ba7d, 0x18b3b2, 0x18ace8,
+ 0x18a61f, 0x189f56, 0x18988f, 0x1891c8, 0x188b03, 0x18843e, 0x187d7a, 0x1876b7,
+ 0x186ff5, 0x186934, 0x186274, 0x185bb4, 0x1854f6, 0x184e38, 0x18477c, 0x1840c0,
+ 0x183a05, 0x18334b, 0x182c92, 0x1825da, 0x181f23, 0x18186c, 0x1811b7, 0x180b02,
+ 0x18044e, 0x17fd9b, 0x17f6e9, 0x17f038, 0x17e988, 0x17e2d9, 0x17dc2a, 0x17d57d,
+ 0x17ced0, 0x17c824, 0x17c179, 0x17bacf, 0x17b426, 0x17ad7e, 0x17a6d6, 0x17a030,
+ 0x17998a, 0x1792e5, 0x178c41, 0x17859e, 0x177efc, 0x17785b, 0x1771ba, 0x176b1b,
+ 0x17647c, 0x175dde, 0x175741, 0x1750a5, 0x174a0a, 0x17436f, 0x173cd6, 0x17363d,
+ 0x172fa5, 0x17290f, 0x172278, 0x171be3, 0x17154f, 0x170ebb, 0x170829, 0x170197,
+ 0x16fb06, 0x16f476, 0x16ede7, 0x16e759, 0x16e0cb, 0x16da3e, 0x16d3b3, 0x16cd28,
+ 0x16c69e, 0x16c014, 0x16b98c, 0x16b305, 0x16ac7e, 0x16a5f8, 0x169f73, 0x1698ef,
+ 0x16926c, 0x168be9, 0x168568, 0x167ee7, 0x167867, 0x1671e8, 0x166b6a, 0x1664ec,
+ 0x165e70, 0x1657f4, 0x165179, 0x164aff, 0x164486, 0x163e0d, 0x163796, 0x16311f,
+ 0x162aa9, 0x162434, 0x161dc0, 0x16174d, 0x1610da, 0x160a68, 0x1603f8, 0x15fd88,
+ 0x15f718, 0x15f0aa, 0x15ea3c, 0x15e3d0, 0x15dd64, 0x15d6f9, 0x15d08e, 0x15ca25,
+ 0x15c3bc, 0x15bd55, 0x15b6ee, 0x15b087, 0x15aa22, 0x15a3be, 0x159d5a, 0x1596f7,
+ 0x159095, 0x158a34, 0x1583d3, 0x157d74, 0x157715, 0x1570b7, 0x156a5a, 0x1563fd,
+ 0x155da2, 0x155747, 0x1550ed, 0x154a94, 0x15443c, 0x153de4, 0x15378e, 0x153138,
+ 0x152ae3, 0x15248e, 0x151e3b, 0x1517e8, 0x151197, 0x150b45, 0x1504f5, 0x14fea6,
+ 0x14f857, 0x14f209, 0x14ebbc, 0x14e570, 0x14df25, 0x14d8da, 0x14d290, 0x14cc47,
+ 0x14c5ff, 0x14bfb7, 0x14b971, 0x14b32b, 0x14ace6, 0x14a6a1, 0x14a05e, 0x149a1b,
+ 0x1493d9, 0x148d98, 0x148758, 0x148118, 0x147ada, 0x14749c, 0x146e5f, 0x146822,
+ 0x1461e7, 0x145bac, 0x145572, 0x144f38, 0x144900, 0x1442c8, 0x143c91, 0x14365b,
+ 0x143026, 0x1429f1, 0x1423be, 0x141d8b, 0x141758, 0x141127, 0x140af6, 0x1404c6,
+ 0x13fe97, 0x13f869, 0x13f23b, 0x13ec0f, 0x13e5e3, 0x13dfb7, 0x13d98d, 0x13d363,
+ 0x13cd3a, 0x13c712, 0x13c0eb, 0x13bac4, 0x13b49e, 0x13ae79, 0x13a855, 0x13a231,
+ 0x139c0e, 0x1395ec, 0x138fcb, 0x1389ab, 0x13838b, 0x137d6c, 0x13774e, 0x137130,
+ 0x136b13, 0x1364f8, 0x135edc, 0x1358c2, 0x1352a8, 0x134c8f, 0x134677, 0x134060,
+ 0x133a49, 0x133433, 0x132e1e, 0x13280a, 0x1321f6, 0x131be3, 0x1315d1, 0x130fc0,
+ 0x1309af, 0x13039f, 0x12fd90, 0x12f782, 0x12f174, 0x12eb67, 0x12e55b, 0x12df50,
+ 0x12d945, 0x12d33b, 0x12cd32, 0x12c72a, 0x12c122, 0x12bb1b, 0x12b515, 0x12af10,
+ 0x12a90b, 0x12a307, 0x129d04, 0x129702, 0x129100, 0x128aff, 0x1284ff, 0x127eff,
+ 0x127900, 0x127302, 0x126d05, 0x126708, 0x12610d, 0x125b11, 0x125517, 0x124f1d,
+ 0x124925, 0x12432c, 0x123d35, 0x12373e, 0x123148, 0x122b53, 0x12255e, 0x121f6b,
+ 0x121978, 0x121385, 0x120d94, 0x1207a3, 0x1201b3, 0x11fbc3, 0x11f5d4, 0x11efe6,
+ 0x11e9f9, 0x11e40d, 0x11de21, 0x11d836, 0x11d24b, 0x11cc62, 0x11c679, 0x11c090,
+ 0x11baa9, 0x11b4c2, 0x11aedc, 0x11a8f7, 0x11a312, 0x119d2e, 0x11974b, 0x119168,
+ 0x118b87, 0x1185a6, 0x117fc5, 0x1179e5, 0x117407, 0x116e28, 0x11684b, 0x11626e,
+ 0x115c92, 0x1156b6, 0x1150dc, 0x114b02, 0x114529, 0x113f50, 0x113978, 0x1133a1,
+ 0x112dca, 0x1127f5, 0x112220, 0x111c4b, 0x111678, 0x1110a5, 0x110ad3, 0x110501,
+ 0x10ff30, 0x10f960, 0x10f391, 0x10edc2, 0x10e7f4, 0x10e226, 0x10dc5a, 0x10d68e,
+ 0x10d0c3, 0x10caf8, 0x10c52e, 0x10bf65, 0x10b99c, 0x10b3d5, 0x10ae0e, 0x10a847,
+ 0x10a281, 0x109cbc, 0x1096f8, 0x109134, 0x108b72, 0x1085af, 0x107fee, 0x107a2d,
+ 0x10746d, 0x106ead, 0x1068ee, 0x106330, 0x105d73, 0x1057b6, 0x1051fa, 0x104c3e,
+ 0x104684, 0x1040ca, 0x103b10, 0x103558, 0x102fa0, 0x1029e8, 0x102432, 0x101e7c,
+ 0x1018c6, 0x101312, 0x100d5e, 0x1007ab, 0x1001f8, 0xffc46, 0xff695, 0xff0e4,
+ 0xfeb35, 0xfe585, 0xfdfd7, 0xfda29, 0xfd47c, 0xfcecf, 0xfc923, 0xfc378,
+ 0xfbdce, 0xfb824, 0xfb27b, 0xfacd2, 0xfa72a, 0xfa183, 0xf9bdd, 0xf9637,
+ 0xf9092, 0xf8aed, 0xf854a, 0xf7fa6, 0xf7a04, 0xf7462, 0xf6ec1, 0xf6920,
+ 0xf6381, 0xf5de1, 0xf5843, 0xf52a5, 0xf4d08, 0xf476b, 0xf41cf, 0xf3c34,
+ 0xf369a, 0xf3100, 0xf2b66, 0xf25ce, 0xf2036, 0xf1a9f, 0xf1508, 0xf0f72,
+ 0xf09dd, 0xf0448, 0xefeb4, 0xef921, 0xef38e, 0xeedfc, 0xee86b, 0xee2da,
+ 0xedd4a, 0xed7ba, 0xed22b, 0xecc9d, 0xec710, 0xec183, 0xebbf7, 0xeb66b,
+ 0xeb0e0, 0xeab56, 0xea5cc, 0xea043, 0xe9abb, 0xe9533, 0xe8fac, 0xe8a26,
+ 0xe84a0, 0xe7f1b, 0xe7996, 0xe7413, 0xe6e8f, 0xe690d, 0xe638b, 0xe5e0a,
+ 0xe5889, 0xe5309, 0xe4d8a, 0xe480b, 0xe428d, 0xe3d0f, 0xe3792, 0xe3216,
+ 0xe2c9b, 0xe2720, 0xe21a5, 0xe1c2c, 0xe16b3, 0xe113a, 0xe0bc3, 0xe064c,
+ 0xe00d5, 0xdfb5f, 0xdf5ea, 0xdf075, 0xdeb01, 0xde58e, 0xde01b, 0xddaa9,
+ 0xdd538, 0xdcfc7, 0xdca57, 0xdc4e7, 0xdbf78, 0xdba0a, 0xdb49c, 0xdaf2f,
+ 0xda9c2, 0xda457, 0xd9eeb, 0xd9981, 0xd9417, 0xd8ead, 0xd8945, 0xd83dc,
+ 0xd7e75, 0xd790e, 0xd73a8, 0xd6e42, 0xd68dd, 0xd6379, 0xd5e15, 0xd58b2,
+ 0xd534f, 0xd4ded, 0xd488c, 0xd432b, 0xd3dcb, 0xd386c, 0xd330d, 0xd2dae,
+ 0xd2851, 0xd22f4, 0xd1d97, 0xd183b, 0xd12e0, 0xd0d86, 0xd082c, 0xd02d2,
+ 0xcfd79, 0xcf821, 0xcf2ca, 0xced73, 0xce81c, 0xce2c7, 0xcdd72, 0xcd81d,
+ 0xcd2c9, 0xccd76, 0xcc823, 0xcc2d1, 0xcbd7f, 0xcb82f, 0xcb2de, 0xcad8f,
+ 0xca83f, 0xca2f1, 0xc9da3, 0xc9856, 0xc9309, 0xc8dbd, 0xc8871, 0xc8326,
+ 0xc7ddc, 0xc7892, 0xc7349, 0xc6e01, 0xc68b9, 0xc6372, 0xc5e2b, 0xc58e5,
+ 0xc539f, 0xc4e5a, 0xc4916, 0xc43d2, 0xc3e8f, 0xc394c, 0xc340a, 0xc2ec9,
+ 0xc2988, 0xc2448, 0xc1f08, 0xc19c9, 0xc148b, 0xc0f4d, 0xc0a10, 0xc04d3,
+ 0xbff97, 0xbfa5b, 0xbf521, 0xbefe6, 0xbeaad, 0xbe573, 0xbe03b, 0xbdb03,
+ 0xbd5cb, 0xbd095, 0xbcb5e, 0xbc629, 0xbc0f4, 0xbbbbf, 0xbb68b, 0xbb158,
+ 0xbac25, 0xba6f3, 0xba1c1, 0xb9c90, 0xb9760, 0xb9230, 0xb8d01, 0xb87d2,
+ 0xb82a4, 0xb7d76, 0xb7849, 0xb731d, 0xb6df1, 0xb68c6, 0xb639b, 0xb5e71,
+ 0xb5948, 0xb541f, 0xb4ef6, 0xb49cf, 0xb44a7, 0xb3f81, 0xb3a5b, 0xb3535,
+ 0xb3010, 0xb2aec, 0xb25c8, 0xb20a5, 0xb1b82, 0xb1660, 0xb113e, 0xb0c1d,
+ 0xb06fd, 0xb01dd, 0xafcbe, 0xaf79f, 0xaf281, 0xaed64, 0xae847, 0xae32a,
+ 0xade0e, 0xad8f3, 0xad3d8, 0xacebe, 0xac9a4, 0xac48b, 0xabf73, 0xaba5b,
+ 0xab544, 0xab02d, 0xaab17, 0xaa601, 0xaa0ec, 0xa9bd7, 0xa96c3, 0xa91b0,
+ 0xa8c9d, 0xa878a, 0xa8279, 0xa7d67, 0xa7857, 0xa7347, 0xa6e37, 0xa6928,
+ 0xa641a, 0xa5f0c, 0xa59fe, 0xa54f2, 0xa4fe5, 0xa4ada, 0xa45ce, 0xa40c4,
+ 0xa3bba, 0xa36b0, 0xa31a7, 0xa2c9f, 0xa2797, 0xa2290, 0xa1d89, 0xa1883,
+ 0xa137d, 0xa0e78, 0xa0974, 0xa0470, 0x9ff6c, 0x9fa69, 0x9f567, 0x9f065,
+ 0x9eb64, 0x9e663, 0x9e163, 0x9dc63, 0x9d764, 0x9d266, 0x9cd68, 0x9c86a,
+ 0x9c36d, 0x9be71, 0x9b975, 0x9b47a, 0x9af7f, 0x9aa85, 0x9a58b, 0x9a092,
+ 0x99b9a, 0x996a1, 0x991aa, 0x98cb3, 0x987bd, 0x982c7, 0x97dd1, 0x978dc,
+ 0x973e8, 0x96ef4, 0x96a01, 0x9650e, 0x9601c, 0x95b2b, 0x9563a, 0x95149,
+ 0x94c59, 0x94769, 0x9427a, 0x93d8c, 0x9389e, 0x933b1, 0x92ec4, 0x929d8,
+ 0x924ec, 0x92001, 0x91b16, 0x9162c, 0x91142, 0x90c59, 0x90770, 0x90288,
+ 0x8fda1, 0x8f8ba, 0x8f3d3, 0x8eeed, 0x8ea08, 0x8e523, 0x8e03e, 0x8db5b,
+ 0x8d677, 0x8d194, 0x8ccb2, 0x8c7d0, 0x8c2ef, 0x8be0e, 0x8b92e, 0x8b44e,
+ 0x8af6f, 0x8aa91, 0x8a5b2, 0x8a0d5, 0x89bf8, 0x8971b, 0x8923f, 0x88d64,
+ 0x88889, 0x883ae, 0x87ed4, 0x879fb, 0x87522, 0x87049, 0x86b71, 0x8669a,
+ 0x861c3, 0x85ced, 0x85817, 0x85341, 0x84e6d, 0x84998, 0x844c5, 0x83ff1,
+ 0x83b1e, 0x8364c, 0x8317a, 0x82ca9, 0x827d8, 0x82308, 0x81e39, 0x81969,
+ 0x8149b, 0x80fcd, 0x80aff, 0x80632, 0x80165, 0x7fc99, 0x7f7cd, 0x7f302,
+ 0x7ee37, 0x7e96d, 0x7e4a4, 0x7dfdb, 0x7db12, 0x7d64a, 0x7d182, 0x7ccbb,
+ 0x7c7f5, 0x7c32f, 0x7be69, 0x7b9a4, 0x7b4df, 0x7b01b, 0x7ab58, 0x7a695,
+ 0x7a1d2, 0x79d10, 0x7984f, 0x7938e, 0x78ecd, 0x78a0d, 0x7854d, 0x7808e,
+ 0x77bd0, 0x77712, 0x77254, 0x76d97, 0x768da, 0x7641e, 0x75f63, 0x75aa8,
+ 0x755ed, 0x75133, 0x74c79, 0x747c0, 0x74308, 0x73e50, 0x73998, 0x734e1,
+ 0x7302a, 0x72b74, 0x726be, 0x72209, 0x71d55, 0x718a0, 0x713ed, 0x70f3a,
+ 0x70a87, 0x705d5, 0x70123, 0x6fc72, 0x6f7c1, 0x6f311, 0x6ee61, 0x6e9b2,
+ 0x6e503, 0x6e055, 0x6dba7, 0x6d6f9, 0x6d24d, 0x6cda0, 0x6c8f4, 0x6c449,
+ 0x6bf9e, 0x6baf4, 0x6b64a, 0x6b1a0, 0x6acf7, 0x6a84f, 0x6a3a7, 0x69eff,
+ 0x69a58, 0x695b2, 0x6910c, 0x68c66, 0x687c1, 0x6831d, 0x67e78, 0x679d5,
+ 0x67532, 0x6708f, 0x66bed, 0x6674b, 0x662aa, 0x65e09, 0x65969, 0x654c9,
+ 0x65029, 0x64b8a, 0x646ec, 0x6424e, 0x63db1, 0x63914, 0x63477, 0x62fdb,
+ 0x62b40, 0x626a5, 0x6220a, 0x61d70, 0x618d6, 0x6143d, 0x60fa4, 0x60b0c,
+ 0x60674, 0x601dd, 0x5fd46, 0x5f8b0, 0x5f41a, 0x5ef85, 0x5eaf0, 0x5e65b,
+ 0x5e1c7, 0x5dd34, 0x5d8a1, 0x5d40e, 0x5cf7c, 0x5caea, 0x5c659, 0x5c1c9,
+ 0x5bd38, 0x5b8a9, 0x5b419, 0x5af8a, 0x5aafc, 0x5a66e, 0x5a1e1, 0x59d54,
+ 0x598c7, 0x5943b, 0x58fb0, 0x58b24, 0x5869a, 0x58210, 0x57d86, 0x578fd,
+ 0x57474, 0x56feb, 0x56b64, 0x566dc, 0x56255, 0x55dcf, 0x55949, 0x554c3,
+ 0x5503e, 0x54bb9, 0x54735, 0x542b1, 0x53e2e, 0x539ab, 0x53529, 0x530a7,
+ 0x52c25, 0x527a4, 0x52324, 0x51ea4, 0x51a24, 0x515a5, 0x51126, 0x50ca8,
+ 0x5082a, 0x503ad, 0x4ff30, 0x4fab4, 0x4f638, 0x4f1bc, 0x4ed41, 0x4e8c6,
+ 0x4e44c, 0x4dfd3, 0x4db59, 0x4d6e0, 0x4d268, 0x4cdf0, 0x4c979, 0x4c502,
+ 0x4c08b, 0x4bc15, 0x4b79f, 0x4b32a, 0x4aeb5, 0x4aa41, 0x4a5cd, 0x4a15a,
+ 0x49ce7, 0x49874, 0x49402, 0x48f91, 0x48b1f, 0x486af, 0x4823e, 0x47dce,
+ 0x4795f, 0x474f0, 0x47082, 0x46c14, 0x467a6, 0x46339, 0x45ecc, 0x45a60,
+ 0x455f4, 0x45189, 0x44d1e, 0x448b3, 0x44449, 0x43fdf, 0x43b76, 0x4370d,
+ 0x432a5, 0x42e3d, 0x429d6, 0x4256f, 0x42108, 0x41ca2, 0x4183c, 0x413d7,
+ 0x40f72, 0x40b0e, 0x406aa, 0x40247, 0x3fde4, 0x3f981, 0x3f51f, 0x3f0bd,
+ 0x3ec5c, 0x3e7fb, 0x3e39b, 0x3df3b, 0x3dadb, 0x3d67c, 0x3d21d, 0x3cdbf,
+ 0x3c961, 0x3c504, 0x3c0a7, 0x3bc4a, 0x3b7ee, 0x3b393, 0x3af37, 0x3aadd,
+ 0x3a682, 0x3a228, 0x39dcf, 0x39976, 0x3951d, 0x390c5, 0x38c6d, 0x38816,
+ 0x383bf, 0x37f69, 0x37b13, 0x376bd, 0x37268, 0x36e13, 0x369bf, 0x3656b,
+ 0x36117, 0x35cc4, 0x35872, 0x3541f, 0x34fce, 0x34b7c, 0x3472b, 0x342db,
+ 0x33e8b, 0x33a3b, 0x335ec, 0x3319d, 0x32d4f, 0x32901, 0x324b3, 0x32066,
+ 0x31c1a, 0x317cd, 0x31381, 0x30f36, 0x30aeb, 0x306a1, 0x30256, 0x2fe0d,
+ 0x2f9c3, 0x2f57a, 0x2f132, 0x2ecea, 0x2e8a2, 0x2e45b, 0x2e014, 0x2dbce,
+ 0x2d788, 0x2d343, 0x2cefd, 0x2cab9, 0x2c675, 0x2c231, 0x2bded, 0x2b9aa,
+ 0x2b568, 0x2b125, 0x2ace4, 0x2a8a2, 0x2a461, 0x2a021, 0x29be1, 0x297a1,
+ 0x29362, 0x28f23, 0x28ae4, 0x286a6, 0x28269, 0x27e2c, 0x279ef, 0x275b2,
+ 0x27176, 0x26d3b, 0x26900, 0x264c5, 0x2608b, 0x25c51, 0x25817, 0x253de,
+ 0x24fa6, 0x24b6d, 0x24735, 0x242fe, 0x23ec7, 0x23a90, 0x2365a, 0x23224,
+ 0x22def, 0x229ba, 0x22585, 0x22151, 0x21d1d, 0x218ea, 0x214b7, 0x21084,
+ 0x20c52, 0x20821, 0x203ef, 0x1ffbe, 0x1fb8e, 0x1f75e, 0x1f32e, 0x1eeff,
+ 0x1ead0, 0x1e6a1, 0x1e273, 0x1de45, 0x1da18, 0x1d5eb, 0x1d1bf, 0x1cd93,
+ 0x1c967, 0x1c53c, 0x1c111, 0x1bce6, 0x1b8bc, 0x1b493, 0x1b069, 0x1ac40,
+ 0x1a818, 0x1a3f0, 0x19fc8, 0x19ba1, 0x1977a, 0x19354, 0x18f2d, 0x18b08,
+ 0x186e2, 0x182be, 0x17e99, 0x17a75, 0x17651, 0x1722e, 0x16e0b, 0x169e9,
+ 0x165c6, 0x161a5, 0x15d83, 0x15963, 0x15542, 0x15122, 0x14d02, 0x148e3,
+ 0x144c4, 0x140a5, 0x13c87, 0x13869, 0x1344c, 0x1302f, 0x12c12, 0x127f6,
+ 0x123da, 0x11fbf, 0x11ba4, 0x11789, 0x1136f, 0x10f55, 0x10b3c, 0x10723,
+ 0x1030a, 0xfef2, 0xfada, 0xf6c2, 0xf2ab, 0xee95, 0xea7e, 0xe668,
+ 0xe253, 0xde3e, 0xda29, 0xd614, 0xd200, 0xcded, 0xc9da, 0xc5c7,
+ 0xc1b4, 0xbda2, 0xb990, 0xb57f, 0xb16e, 0xad5e, 0xa94e, 0xa53e,
+ 0xa12e, 0x9d1f, 0x9911, 0x9503, 0x90f5, 0x8ce7, 0x88da, 0x84ce,
+ 0x80c1, 0x7cb5, 0x78aa, 0x749f, 0x7094, 0x6c89, 0x687f, 0x6476,
+ 0x606d, 0x5c64, 0x585b, 0x5453, 0x504b, 0x4c44, 0x483d, 0x4436,
+ 0x4030, 0x3c2a, 0x3825, 0x3420, 0x301b, 0x2c17, 0x2813, 0x240f,
+ 0x200c, 0x1c09, 0x1807, 0x1405, 0x1003, 0xc02, 0x801, 0x400,
+ 0x7fffff, 0x7ff001, 0x7fe006, 0x7fd00d, 0x7fc018, 0x7fb025, 0x7fa036, 0x7f9049,
+ 0x7f8060, 0x7f7079, 0x7f6095, 0x7f50b5, 0x7f40d7, 0x7f30fc, 0x7f2124, 0x7f114f,
+ 0x7f017e, 0x7ef1af, 0x7ee1e2, 0x7ed219, 0x7ec253, 0x7eb290, 0x7ea2d0, 0x7e9312,
+ 0x7e8358, 0x7e73a0, 0x7e63eb, 0x7e543a, 0x7e448b, 0x7e34df, 0x7e2536, 0x7e1590,
+ 0x7e05ec, 0x7df64c, 0x7de6ae, 0x7dd714, 0x7dc77c, 0x7db7e7, 0x7da855, 0x7d98c6,
+ 0x7d893a, 0x7d79b0, 0x7d6a2a, 0x7d5aa6, 0x7d4b25, 0x7d3ba7, 0x7d2c2c, 0x7d1cb3,
+ 0x7d0d3e, 0x7cfdcb, 0x7cee5b, 0x7cdeee, 0x7ccf84, 0x7cc01d, 0x7cb0b8, 0x7ca156,
+ 0x7c91f7, 0x7c829b, 0x7c7342, 0x7c63eb, 0x7c5497, 0x7c4546, 0x7c35f8, 0x7c26ad,
+ 0x7c1764, 0x7c081e, 0x7bf8db, 0x7be99b, 0x7bda5d, 0x7bcb23, 0x7bbbeb, 0x7bacb5,
+ 0x7b9d83, 0x7b8e53, 0x7b7f26, 0x7b6ffc, 0x7b60d4, 0x7b51b0, 0x7b428e, 0x7b336e,
+ 0x7b2452, 0x7b1538, 0x7b0621, 0x7af70c, 0x7ae7fb, 0x7ad8ec, 0x7ac9e0, 0x7abad6,
+ 0x7aabcf, 0x7a9ccb, 0x7a8dca, 0x7a7ecb, 0x7a6fcf, 0x7a60d5, 0x7a51df, 0x7a42eb,
+ 0x7a33f9, 0x7a250b, 0x7a161f, 0x7a0735, 0x79f84f, 0x79e96b, 0x79da89, 0x79cbab,
+ 0x79bccf, 0x79adf5, 0x799f1f, 0x79904a, 0x798179, 0x7972aa, 0x7963de, 0x795515,
+ 0x79464e, 0x793789, 0x7928c8, 0x791a09, 0x790b4c, 0x78fc92, 0x78eddb, 0x78df27,
+ 0x78d075, 0x78c1c5, 0x78b319, 0x78a46e, 0x7895c7, 0x788722, 0x78787f, 0x7869e0,
+ 0x785b42, 0x784ca8, 0x783e10, 0x782f7a, 0x7820e7, 0x781257, 0x7803c9, 0x77f53e,
+ 0x77e6b5, 0x77d82f, 0x77c9ab, 0x77bb2a, 0x77acac, 0x779e30, 0x778fb6, 0x77813f,
+ 0x7772cb, 0x776459, 0x7755ea, 0x77477d, 0x773913, 0x772aab, 0x771c46, 0x770de3,
+ 0x76ff83, 0x76f125, 0x76e2ca, 0x76d472, 0x76c61b, 0x76b7c8, 0x76a977, 0x769b28,
+ 0x768cdc, 0x767e92, 0x76704b, 0x766206, 0x7653c4, 0x764584, 0x763747, 0x76290c,
+ 0x761ad3, 0x760c9d, 0x75fe6a, 0x75f039, 0x75e20a, 0x75d3de, 0x75c5b5, 0x75b78e,
+ 0x75a969, 0x759b46, 0x758d27, 0x757f09, 0x7570ee, 0x7562d6, 0x7554bf, 0x7546ac,
+ 0x75389a, 0x752a8c, 0x751c7f, 0x750e75, 0x75006d, 0x74f268, 0x74e465, 0x74d665,
+ 0x74c867, 0x74ba6b, 0x74ac72, 0x749e7b, 0x749087, 0x748295, 0x7474a5, 0x7466b8,
+ 0x7458cd, 0x744ae4, 0x743cfe, 0x742f1a, 0x742139, 0x74135a, 0x74057d, 0x73f7a3,
+ 0x73e9cb, 0x73dbf5, 0x73ce22, 0x73c051, 0x73b282, 0x73a4b6, 0x7396ec, 0x738925,
+ 0x737b60, 0x736d9d, 0x735fdc, 0x73521e, 0x734462, 0x7336a9, 0x7328f1, 0x731b3c,
+ 0x730d8a, 0x72ffd9, 0x72f22c, 0x72e480, 0x72d6d7, 0x72c92f, 0x72bb8b, 0x72ade8,
+ 0x72a048, 0x7292aa, 0x72850f, 0x727775, 0x7269de, 0x725c4a, 0x724eb7, 0x724127,
+ 0x723399, 0x72260e, 0x721884, 0x720afd, 0x71fd79, 0x71eff6, 0x71e276, 0x71d4f8,
+ 0x71c77c, 0x71ba02, 0x71ac8b, 0x719f16, 0x7191a3, 0x718433, 0x7176c5, 0x716959,
+ 0x715bef, 0x714e87, 0x714122, 0x7133bf, 0x71265e, 0x711900, 0x710ba3, 0x70fe49,
+ 0x70f0f1, 0x70e39b, 0x70d648, 0x70c8f6, 0x70bba7, 0x70ae5a, 0x70a110, 0x7093c7,
+ 0x708681, 0x70793d, 0x706bfb, 0x705ebb, 0x70517d, 0x704442, 0x703709, 0x7029d2,
+ 0x701c9d, 0x700f6a, 0x70023a, 0x6ff50c, 0x6fe7e0, 0x6fdab6, 0x6fcd8e, 0x6fc068,
+ 0x6fb345, 0x6fa624, 0x6f9904, 0x6f8be7, 0x6f7ecd, 0x6f71b4, 0x6f649d, 0x6f5789,
+ 0x6f4a77, 0x6f3d67, 0x6f3059, 0x6f234d, 0x6f1643, 0x6f093c, 0x6efc36, 0x6eef33,
+ 0x6ee232, 0x6ed533, 0x6ec836, 0x6ebb3b, 0x6eae42, 0x6ea14c, 0x6e9457, 0x6e8765,
+ 0x6e7a74, 0x6e6d86, 0x6e609a, 0x6e53b0, 0x6e46c8, 0x6e39e3, 0x6e2cff, 0x6e201d,
+ 0x6e133e, 0x6e0661, 0x6df985, 0x6decac, 0x6ddfd5, 0x6dd300, 0x6dc62d, 0x6db95c,
+ 0x6dac8d, 0x6d9fc0, 0x6d92f5, 0x6d862d, 0x6d7966, 0x6d6ca2, 0x6d5fdf, 0x6d531f,
+ 0x6d4660, 0x6d39a4, 0x6d2cea, 0x6d2032, 0x6d137c, 0x6d06c7, 0x6cfa15, 0x6ced65,
+ 0x6ce0b7, 0x6cd40b, 0x6cc761, 0x6cbab9, 0x6cae14, 0x6ca170, 0x6c94ce, 0x6c882e,
+ 0x6c7b90, 0x6c6ef5, 0x6c625b, 0x6c55c3, 0x6c492d, 0x6c3c9a, 0x6c3008, 0x6c2378,
+ 0x6c16ea, 0x6c0a5f, 0x6bfdd5, 0x6bf14d, 0x6be4c8, 0x6bd844, 0x6bcbc2, 0x6bbf42,
+ 0x6bb2c5, 0x6ba649, 0x6b99cf, 0x6b8d57, 0x6b80e2, 0x6b746e, 0x6b67fc, 0x6b5b8c,
+ 0x6b4f1e, 0x6b42b2, 0x6b3648, 0x6b29e0, 0x6b1d7a, 0x6b1116, 0x6b04b4, 0x6af854,
+ 0x6aebf5, 0x6adf99, 0x6ad33f, 0x6ac6e6, 0x6aba90, 0x6aae3b, 0x6aa1e9, 0x6a9598,
+ 0x6a8949, 0x6a7cfd, 0x6a70b2, 0x6a6469, 0x6a5822, 0x6a4bdd, 0x6a3f9a, 0x6a3359,
+ 0x6a271a, 0x6a1adc, 0x6a0ea1, 0x6a0267, 0x69f630, 0x69e9fa, 0x69ddc6, 0x69d195,
+ 0x69c565, 0x69b937, 0x69ad0b, 0x69a0e0, 0x6994b8, 0x698892, 0x697c6d, 0x69704a,
+ 0x69642a, 0x69580b, 0x694bee, 0x693fd3, 0x6933ba, 0x6927a2, 0x691b8d, 0x690f79,
+ 0x690368, 0x68f758, 0x68eb4a, 0x68df3e, 0x68d334, 0x68c72b, 0x68bb25, 0x68af20,
+ 0x68a31d, 0x68971d, 0x688b1d, 0x687f20, 0x687325, 0x68672c, 0x685b34, 0x684f3e,
+ 0x68434a, 0x683758, 0x682b68, 0x681f7a, 0x68138d, 0x6807a2, 0x67fbb9, 0x67efd2,
+ 0x67e3ed, 0x67d80a, 0x67cc28, 0x67c048, 0x67b46a, 0x67a88e, 0x679cb4, 0x6790dc,
+ 0x678505, 0x677930, 0x676d5d, 0x67618c, 0x6755bd, 0x6749ef, 0x673e23, 0x673259,
+ 0x672691, 0x671acb, 0x670f06, 0x670343, 0x66f782, 0x66ebc3, 0x66e006, 0x66d44a,
+ 0x66c891, 0x66bcd8, 0x66b122, 0x66a56e, 0x6699bb, 0x668e0a, 0x66825b, 0x6676ae,
+ 0x666b02, 0x665f58, 0x6653b0, 0x66480a, 0x663c66, 0x6630c3, 0x662522, 0x661983,
+ 0x660de5, 0x66024a, 0x65f6b0, 0x65eb17, 0x65df81, 0x65d3ec, 0x65c859, 0x65bcc8,
+ 0x65b139, 0x65a5ab, 0x659a1f, 0x658e95, 0x65830d, 0x657786, 0x656c01, 0x65607e,
+ 0x6554fc, 0x65497c, 0x653dfe, 0x653282, 0x652707, 0x651b8e, 0x651017, 0x6504a2,
+ 0x64f92e, 0x64edbc, 0x64e24c, 0x64d6dd, 0x64cb70, 0x64c005, 0x64b49c, 0x64a934,
+ 0x649dce, 0x64926a, 0x648707, 0x647ba6, 0x647047, 0x6464ea, 0x64598e, 0x644e34,
+ 0x6442db, 0x643784, 0x642c2f, 0x6420dc, 0x64158a, 0x640a3a, 0x63feec, 0x63f39f,
+ 0x63e854, 0x63dd0b, 0x63d1c3, 0x63c67d, 0x63bb39, 0x63aff7, 0x63a4b6, 0x639976,
+ 0x638e39, 0x6382fd, 0x6377c3, 0x636c8a, 0x636153, 0x63561e, 0x634aea, 0x633fb8,
+ 0x633488, 0x632959, 0x631e2c, 0x631301, 0x6307d7, 0x62fcaf, 0x62f189, 0x62e664,
+ 0x62db41, 0x62d01f, 0x62c500, 0x62b9e1, 0x62aec5, 0x62a3aa, 0x629890, 0x628d79,
+ 0x628263, 0x62774e, 0x626c3b, 0x62612a, 0x62561b, 0x624b0d, 0x624000, 0x6234f6,
+ 0x6229ed, 0x621ee5, 0x6213df, 0x6208db, 0x61fdd8, 0x61f2d7, 0x61e7d8, 0x61dcda,
+ 0x61d1de, 0x61c6e3, 0x61bbea, 0x61b0f3, 0x61a5fd, 0x619b09, 0x619016, 0x618525,
+ 0x617a36, 0x616f48, 0x61645b, 0x615971, 0x614e88, 0x6143a0, 0x6138ba, 0x612dd6,
+ 0x6122f3, 0x611812, 0x610d32, 0x610254, 0x60f778, 0x60ec9d, 0x60e1c4, 0x60d6ec,
+ 0x60cc16, 0x60c141, 0x60b66e, 0x60ab9c, 0x60a0cc, 0x6095fe, 0x608b31, 0x608066,
+ 0x60759c, 0x606ad4, 0x60600e, 0x605549, 0x604a85, 0x603fc3, 0x603503, 0x602a44,
+ 0x601f87, 0x6014cb, 0x600a11, 0x5fff58, 0x5ff4a1, 0x5fe9eb, 0x5fdf37, 0x5fd485,
+ 0x5fc9d4, 0x5fbf24, 0x5fb476, 0x5fa9ca, 0x5f9f1f, 0x5f9476, 0x5f89ce, 0x5f7f28,
+ 0x5f7483, 0x5f69df, 0x5f5f3e, 0x5f549d, 0x5f49ff, 0x5f3f62, 0x5f34c6, 0x5f2a2c,
+ 0x5f1f93, 0x5f14fc, 0x5f0a66, 0x5effd2, 0x5ef53f, 0x5eeaae, 0x5ee01f, 0x5ed591,
+ 0x5ecb04, 0x5ec079, 0x5eb5ef, 0x5eab67, 0x5ea0e0, 0x5e965b, 0x5e8bd8, 0x5e8155,
+ 0x5e76d5, 0x5e6c55, 0x5e61d8, 0x5e575c, 0x5e4ce1, 0x5e4268, 0x5e37f0, 0x5e2d79,
+ 0x5e2305, 0x5e1891, 0x5e0e1f, 0x5e03af, 0x5df940, 0x5deed3, 0x5de467, 0x5dd9fc,
+ 0x5dcf93, 0x5dc52b, 0x5dbac5, 0x5db061, 0x5da5fd, 0x5d9b9c, 0x5d913b, 0x5d86dc,
+ 0x5d7c7f, 0x5d7223, 0x5d67c9, 0x5d5d70, 0x5d5318, 0x5d48c2, 0x5d3e6d, 0x5d341a,
+ 0x5d29c8, 0x5d1f78, 0x5d1529, 0x5d0adc, 0x5d0090, 0x5cf645, 0x5cebfc, 0x5ce1b4,
+ 0x5cd76e, 0x5ccd29, 0x5cc2e6, 0x5cb8a4, 0x5cae63, 0x5ca424, 0x5c99e6, 0x5c8faa,
+ 0x5c856f, 0x5c7b36, 0x5c70fe, 0x5c66c7, 0x5c5c92, 0x5c525e, 0x5c482c, 0x5c3dfb,
+ 0x5c33cc, 0x5c299d, 0x5c1f71, 0x5c1546, 0x5c0b1c, 0x5c00f3, 0x5bf6cc, 0x5beca7,
+ 0x5be282, 0x5bd85f, 0x5bce3e, 0x5bc41e, 0x5bb9ff, 0x5bafe2, 0x5ba5c6, 0x5b9bac,
+ 0x5b9193, 0x5b877b, 0x5b7d65, 0x5b7350, 0x5b693d, 0x5b5f2a, 0x5b551a, 0x5b4b0a,
+ 0x5b40fd, 0x5b36f0, 0x5b2ce5, 0x5b22db, 0x5b18d3, 0x5b0ecc, 0x5b04c6, 0x5afac2,
+ 0x5af0bf, 0x5ae6bd, 0x5adcbd, 0x5ad2be, 0x5ac8c1, 0x5abec5, 0x5ab4ca, 0x5aaad1,
+ 0x5aa0d9, 0x5a96e2, 0x5a8ced, 0x5a82f9, 0x5a7906, 0x5a6f15, 0x5a6525, 0x5a5b37,
+ 0x5a514a, 0x5a475e, 0x5a3d74, 0x5a338b, 0x5a29a3, 0x5a1fbd, 0x5a15d8, 0x5a0bf4,
+ 0x5a0212, 0x59f831, 0x59ee51, 0x59e473, 0x59da96, 0x59d0ba, 0x59c6e0, 0x59bd07,
+ 0x59b330, 0x59a959, 0x599f84, 0x5995b1, 0x598bde, 0x59820e, 0x59783e, 0x596e70,
+ 0x5964a3, 0x595ad7, 0x59510d, 0x594744, 0x593d7c, 0x5933b6, 0x5929f1, 0x59202d,
+ 0x59166b, 0x590caa, 0x5902ea, 0x58f92b, 0x58ef6e, 0x58e5b3, 0x58dbf8, 0x58d23f,
+ 0x58c887, 0x58bed0, 0x58b51b, 0x58ab67, 0x58a1b4, 0x589803, 0x588e53, 0x5884a4,
+ 0x587af7, 0x58714b, 0x5867a0, 0x585df6, 0x58544e, 0x584aa7, 0x584101, 0x58375d,
+ 0x582dba, 0x582418, 0x581a77, 0x5810d8, 0x58073a, 0x57fd9d, 0x57f402, 0x57ea68,
+ 0x57e0cf, 0x57d737, 0x57cda1, 0x57c40c, 0x57ba78, 0x57b0e6, 0x57a754, 0x579dc5,
+ 0x579436, 0x578aa9, 0x57811c, 0x577792, 0x576e08, 0x576480, 0x575af9, 0x575173,
+ 0x5747ee, 0x573e6b, 0x5734e9, 0x572b68, 0x5721e9, 0x57186b, 0x570eee, 0x570572,
+ 0x56fbf8, 0x56f27e, 0x56e906, 0x56df90, 0x56d61a, 0x56cca6, 0x56c333, 0x56b9c1,
+ 0x56b051, 0x56a6e2, 0x569d74, 0x569407, 0x568a9b, 0x568131, 0x5677c8, 0x566e60,
+ 0x5664fa, 0x565b95, 0x565231, 0x5648ce, 0x563f6c, 0x56360c, 0x562cad, 0x56234f,
+ 0x5619f2, 0x561097, 0x56073c, 0x55fde3, 0x55f48c, 0x55eb35, 0x55e1e0, 0x55d88c,
+ 0x55cf39, 0x55c5e7, 0x55bc97, 0x55b347, 0x55a9f9, 0x55a0ad, 0x559761, 0x558e17,
+ 0x5584cd, 0x557b86, 0x55723f, 0x5568f9, 0x555fb5, 0x555672, 0x554d30, 0x5543ef,
+ 0x553ab0, 0x553171, 0x552834, 0x551ef8, 0x5515be, 0x550c84, 0x55034c, 0x54fa15,
+ 0x54f0df, 0x54e7aa, 0x54de77, 0x54d544, 0x54cc13, 0x54c2e3, 0x54b9b4, 0x54b087,
+ 0x54a75a, 0x549e2f, 0x549505, 0x548bdc, 0x5482b5, 0x54798e, 0x547069, 0x546745,
+ 0x545e22, 0x545500, 0x544be0, 0x5442c0, 0x5439a2, 0x543085, 0x542769, 0x541e4f,
+ 0x541535, 0x540c1d, 0x540306, 0x53f9f0, 0x53f0db, 0x53e7c7, 0x53deb5, 0x53d5a3,
+ 0x53cc93, 0x53c384, 0x53ba76, 0x53b169, 0x53a85e, 0x539f54, 0x53964a, 0x538d42,
+ 0x53843b, 0x537b36, 0x537231, 0x53692e, 0x53602b, 0x53572a, 0x534e2a, 0x53452b,
+ 0x533c2e, 0x533331, 0x532a36, 0x53213b, 0x531842, 0x530f4a, 0x530654, 0x52fd5e,
+ 0x52f469, 0x52eb76, 0x52e284, 0x52d993, 0x52d0a3, 0x52c7b4, 0x52bec6, 0x52b5d9,
+ 0x52acee, 0x52a404, 0x529b1b, 0x529233, 0x52894c, 0x528066, 0x527781, 0x526e9e,
+ 0x5265bb, 0x525cda, 0x5253fa, 0x524b1b, 0x52423d, 0x523960, 0x523084, 0x5227aa,
+ 0x521ed0, 0x5215f8, 0x520d21, 0x52044b, 0x51fb76, 0x51f2a2, 0x51e9cf, 0x51e0fe,
+ 0x51d82d, 0x51cf5e, 0x51c68f, 0x51bdc2, 0x51b4f6, 0x51ac2b, 0x51a361, 0x519a98,
+ 0x5191d1, 0x51890a, 0x518045, 0x517780, 0x516ebd, 0x5165fb, 0x515d3a, 0x51547a,
+ 0x514bbb, 0x5142fd, 0x513a41, 0x513185, 0x5128cb, 0x512011, 0x511759, 0x510ea2,
+ 0x5105ec, 0x50fd36, 0x50f483, 0x50ebd0, 0x50e31e, 0x50da6d, 0x50d1be, 0x50c90f,
+ 0x50c062, 0x50b7b5, 0x50af0a, 0x50a660, 0x509db7, 0x50950f, 0x508c68, 0x5083c2,
+ 0x507b1d, 0x507279, 0x5069d7, 0x506135, 0x505894, 0x504ff5, 0x504757, 0x503eb9,
+ 0x50361d, 0x502d82, 0x5024e8, 0x501c4f, 0x5013b7, 0x500b20, 0x50028a, 0x4ff9f5,
+ 0x4ff162, 0x4fe8cf, 0x4fe03d, 0x4fd7ad, 0x4fcf1d, 0x4fc68f, 0x4fbe01, 0x4fb575,
+ 0x4facea, 0x4fa460, 0x4f9bd7, 0x4f934e, 0x4f8ac7, 0x4f8241, 0x4f79bc, 0x4f7139,
+ 0x4f68b6, 0x4f6034, 0x4f57b3, 0x4f4f33, 0x4f46b5, 0x4f3e37, 0x4f35bb, 0x4f2d3f,
+ 0x4f24c5, 0x4f1c4b, 0x4f13d3, 0x4f0b5b, 0x4f02e5, 0x4efa70, 0x4ef1fb, 0x4ee988,
+ 0x4ee116, 0x4ed8a5, 0x4ed035, 0x4ec7c6, 0x4ebf58, 0x4eb6ea, 0x4eae7e, 0x4ea613,
+ 0x4e9daa, 0x4e9541, 0x4e8cd9, 0x4e8472, 0x4e7c0c, 0x4e73a7, 0x4e6b43, 0x4e62e1,
+ 0x4e5a7f, 0x4e521e, 0x4e49be, 0x4e4160, 0x4e3902, 0x4e30a5, 0x4e284a, 0x4e1fef,
+ 0x4e1796, 0x4e0f3d, 0x4e06e5, 0x4dfe8f, 0x4df639, 0x4dede5, 0x4de591, 0x4ddd3f,
+ 0x4dd4ed, 0x4dcc9d, 0x4dc44d, 0x4dbbff, 0x4db3b1, 0x4dab65, 0x4da319, 0x4d9acf,
+ 0x4d9285, 0x4d8a3d, 0x4d81f5, 0x4d79af, 0x4d7169, 0x4d6925, 0x4d60e2, 0x4d589f,
+ 0x4d505e, 0x4d481d, 0x4d3fde, 0x4d379f, 0x4d2f62, 0x4d2725, 0x4d1eea, 0x4d16af,
+ 0x4d0e76, 0x4d063d, 0x4cfe05, 0x4cf5cf, 0x4ced99, 0x4ce565, 0x4cdd31, 0x4cd4fe,
+ 0x4ccccd, 0x4cc49c, 0x4cbc6c, 0x4cb43e, 0x4cac10, 0x4ca3e3, 0x4c9bb8, 0x4c938d,
+ 0x4c8b63, 0x4c833a, 0x4c7b12, 0x4c72eb, 0x4c6ac6, 0x4c62a1, 0x4c5a7d, 0x4c525a,
+ 0x4c4a38, 0x4c4217, 0x4c39f7, 0x4c31d7, 0x4c29b9, 0x4c219c, 0x4c1980, 0x4c1165,
+ 0x4c094b, 0x4c0131, 0x4bf919, 0x4bf102, 0x4be8eb, 0x4be0d6, 0x4bd8c1, 0x4bd0ae,
+ 0x4bc89b, 0x4bc089, 0x4bb879, 0x4bb069, 0x4ba85a, 0x4ba04d, 0x4b9840, 0x4b9034,
+ 0x4b8829, 0x4b801f, 0x4b7816, 0x4b700e, 0x4b6807, 0x4b6001, 0x4b57fc, 0x4b4ff7,
+ 0x4b47f4, 0x4b3ff2, 0x4b37f0, 0x4b2ff0, 0x4b27f0, 0x4b1ff2, 0x4b17f4, 0x4b0ff7,
+ 0x4b07fc, 0x4b0001, 0x4af807, 0x4af00e, 0x4ae816, 0x4ae01f, 0x4ad829, 0x4ad034,
+ 0x4ac83f, 0x4ac04c, 0x4ab85a, 0x4ab068, 0x4aa878, 0x4aa088, 0x4a989a, 0x4a90ac,
+ 0x4a88bf, 0x4a80d3, 0x4a78e8, 0x4a70fe, 0x4a6915, 0x4a612d, 0x4a5946, 0x4a5160,
+ 0x4a497a, 0x4a4196, 0x4a39b2, 0x4a31d0, 0x4a29ee, 0x4a220d, 0x4a1a2d, 0x4a124f,
+ 0x4a0a71, 0x4a0294, 0x49fab7, 0x49f2dc, 0x49eb02, 0x49e328, 0x49db50, 0x49d378,
+ 0x49cba2, 0x49c3cc, 0x49bbf7, 0x49b423, 0x49ac50, 0x49a47e, 0x499cad, 0x4994dd,
+ 0x498d0d, 0x49853f, 0x497d71, 0x4975a5, 0x496dd9, 0x49660e, 0x495e44, 0x49567b,
+ 0x494eb3, 0x4946ec, 0x493f25, 0x493760, 0x492f9b, 0x4927d8, 0x492015, 0x491853,
+ 0x491092, 0x4908d2, 0x490113, 0x48f955, 0x48f198, 0x48e9db, 0x48e21f, 0x48da65,
+ 0x48d2ab, 0x48caf2, 0x48c33a, 0x48bb83, 0x48b3cd, 0x48ac18, 0x48a463, 0x489cb0,
+ 0x4894fd, 0x488d4b, 0x48859a, 0x487dea, 0x48763b, 0x486e8d, 0x4866df, 0x485f33,
+ 0x485787, 0x484fdd, 0x484833, 0x48408a, 0x4838e2, 0x48313b, 0x482994, 0x4821ef,
+ 0x481a4a, 0x4812a6, 0x480b04, 0x480362, 0x47fbc1, 0x47f420, 0x47ec81, 0x47e4e3,
+ 0x47dd45, 0x47d5a8, 0x47ce0c, 0x47c672, 0x47bed7, 0x47b73e, 0x47afa6, 0x47a80e,
+ 0x47a078, 0x4798e2, 0x47914d, 0x4789b9, 0x478226, 0x477a93, 0x477302, 0x476b71,
+ 0x4763e2, 0x475c53, 0x4754c5, 0x474d37, 0x4745ab, 0x473e20, 0x473695, 0x472f0b,
+ 0x472783, 0x471ffa, 0x471873, 0x4710ed, 0x470968, 0x4701e3, 0x46fa5f, 0x46f2dc,
+ 0x46eb5a, 0x46e3d9, 0x46dc59, 0x46d4d9, 0x46cd5a, 0x46c5dd, 0x46be60, 0x46b6e4,
+ 0x46af68, 0x46a7ee, 0x46a074, 0x4698fb, 0x469184, 0x468a0c, 0x468296, 0x467b21,
+ 0x4673ac, 0x466c39, 0x4664c6, 0x465d54, 0x4655e3, 0x464e72, 0x464703, 0x463f94,
+ 0x463826, 0x4630b9, 0x46294d, 0x4621e2, 0x461a77, 0x46130e, 0x460ba5, 0x46043d,
+ 0x45fcd6, 0x45f56f, 0x45ee0a, 0x45e6a5, 0x45df41, 0x45d7de, 0x45d07c, 0x45c91a,
+ 0x45c1ba, 0x45ba5a, 0x45b2fb, 0x45ab9d, 0x45a440, 0x459ce4, 0x459588, 0x458e2d,
+ 0x4586d3, 0x457f7a, 0x457822, 0x4570ca, 0x456974, 0x45621e, 0x455ac9, 0x455374,
+ 0x454c21, 0x4544ce, 0x453d7d, 0x45362c, 0x452edb, 0x45278c, 0x45203e, 0x4518f0,
+ 0x4511a3, 0x450a57, 0x45030c, 0x44fbc1, 0x44f477, 0x44ed2e, 0x44e5e6, 0x44de9f,
+ 0x44d759, 0x44d013, 0x44c8ce, 0x44c18a, 0x44ba47, 0x44b305, 0x44abc3, 0x44a482,
+ 0x449d42, 0x449603, 0x448ec5, 0x448787, 0x44804a, 0x44790e, 0x4471d3, 0x446a99,
+ 0x44635f, 0x445c26, 0x4454ee, 0x444db7, 0x444681, 0x443f4b, 0x443816, 0x4430e2,
+ 0x4429af, 0x44227c, 0x441b4b, 0x44141a, 0x440cea, 0x4405ba, 0x43fe8c, 0x43f75e,
+ 0x43f031, 0x43e905, 0x43e1da, 0x43daaf, 0x43d385, 0x43cc5c, 0x43c534, 0x43be0d,
+ 0x43b6e6, 0x43afc0, 0x43a89b, 0x43a177, 0x439a54, 0x439331, 0x438c0f, 0x4384ee,
+ 0x437dcd, 0x4376ae, 0x436f8f, 0x436871, 0x436154, 0x435a37, 0x43531b, 0x434c00,
+ 0x4344e6, 0x433dcd, 0x4336b4, 0x432f9c, 0x432885, 0x43216f, 0x431a5a, 0x431345,
+ 0x430c31, 0x43051e, 0x42fe0b, 0x42f6f9, 0x42efe9, 0x42e8d8, 0x42e1c9, 0x42daba,
+ 0x42d3ad, 0x42cca0, 0x42c593, 0x42be88, 0x42b77d, 0x42b073, 0x42a96a, 0x42a261,
+ 0x429b59, 0x429452, 0x428d4c, 0x428647, 0x427f42, 0x42783e, 0x42713b, 0x426a39,
+ 0x426337, 0x425c36, 0x425536, 0x424e37, 0x424738, 0x42403a, 0x42393d, 0x423241,
+ 0x422b45, 0x42244a, 0x421d50, 0x421657, 0x420f5e, 0x420866, 0x42016f, 0x41fa79,
+ 0x41f383, 0x41ec8e, 0x41e59a, 0x41dea7, 0x41d7b4, 0x41d0c2, 0x41c9d1, 0x41c2e1,
+ 0x41bbf1, 0x41b503, 0x41ae14, 0x41a727, 0x41a03a, 0x41994e, 0x419263, 0x418b79,
+ 0x41848f, 0x417da6, 0x4176be, 0x416fd7, 0x4168f0, 0x41620a, 0x415b25, 0x415440,
+ 0x414d5c, 0x414679, 0x413f97, 0x4138b6, 0x4131d5, 0x412af5, 0x412415, 0x411d37,
+ 0x411659, 0x410f7c, 0x41089f, 0x4101c3, 0x40fae9, 0x40f40e, 0x40ed35, 0x40e65c,
+ 0x40df84, 0x40d8ad, 0x40d1d6, 0x40cb00, 0x40c42b, 0x40bd57, 0x40b683, 0x40afb0,
+ 0x40a8de, 0x40a20c, 0x409b3b, 0x40946b, 0x408d9c, 0x4086cd, 0x408000, 0x407932,
+ 0x407266, 0x406b9a, 0x4064cf, 0x405e05, 0x40573b, 0x405072, 0x4049aa, 0x4042e3,
+ 0x403c1c, 0x403556, 0x402e91, 0x4027cc, 0x402109, 0x401a45, 0x401383, 0x400cc1,
+ 0x400600, 0x3fff40, 0x3ff880, 0x3ff1c2, 0x3feb03, 0x3fe446, 0x3fdd89, 0x3fd6cd,
+ 0x3fd012, 0x3fc957, 0x3fc29d, 0x3fbbe4, 0x3fb52c, 0x3fae74, 0x3fa7bd, 0x3fa107,
+ 0x3f9a51, 0x3f939c, 0x3f8ce8, 0x3f8634, 0x3f7f81, 0x3f78cf, 0x3f721e, 0x3f6b6d,
+ 0x3f64bd, 0x3f5e0e, 0x3f575f, 0x3f50b1, 0x3f4a04, 0x3f4357, 0x3f3cac, 0x3f3601,
+ 0x3f2f56, 0x3f28ac, 0x3f2203, 0x3f1b5b, 0x3f14b3, 0x3f0e0c, 0x3f0766, 0x3f00c1,
+ 0x3efa1c, 0x3ef377, 0x3eecd4, 0x3ee631, 0x3edf8f, 0x3ed8ee, 0x3ed24d, 0x3ecbad,
+ 0x3ec50e, 0x3ebe6f, 0x3eb7d1, 0x3eb134, 0x3eaa97, 0x3ea3fb, 0x3e9d60, 0x3e96c6,
+ 0x3e902c, 0x3e8993, 0x3e82fa, 0x3e7c62, 0x3e75cb, 0x3e6f35, 0x3e689f, 0x3e620a,
+ 0x3e5b76, 0x3e54e2, 0x3e4e4f, 0x3e47bd, 0x3e412b, 0x3e3a9a, 0x3e340a, 0x3e2d7a,
+ 0x3e26eb, 0x3e205d, 0x3e19cf, 0x3e1342, 0x3e0cb6, 0x3e062b, 0x3dffa0, 0x3df916,
+ 0x3df28c, 0x3dec03, 0x3de57b, 0x3ddef4, 0x3dd86d, 0x3dd1e7, 0x3dcb61, 0x3dc4dc,
+ 0x3dbe58, 0x3db7d5, 0x3db152, 0x3daad0, 0x3da44f, 0x3d9dce, 0x3d974e, 0x3d90ce,
+ 0x3d8a4f, 0x3d83d1, 0x3d7d54, 0x3d76d7, 0x3d705b, 0x3d69e0, 0x3d6365, 0x3d5ceb,
+ 0x3d5671, 0x3d4ff9, 0x3d4980, 0x3d4309, 0x3d3c92, 0x3d361c, 0x3d2fa7, 0x3d2932,
+ 0x3d22be, 0x3d1c4a, 0x3d15d7, 0x3d0f65, 0x3d08f4, 0x3d0283, 0x3cfc13, 0x3cf5a3,
+ 0x3cef34, 0x3ce8c6, 0x3ce259, 0x3cdbec, 0x3cd57f, 0x3ccf14, 0x3cc8a9, 0x3cc23f,
+ 0x3cbbd5, 0x3cb56c, 0x3caf04, 0x3ca89c, 0x3ca235, 0x3c9bcf, 0x3c9569, 0x3c8f04,
+ 0x3c889f, 0x3c823c, 0x3c7bd8, 0x3c7576, 0x3c6f14, 0x3c68b3, 0x3c6253, 0x3c5bf3,
+ 0x3c5593, 0x3c4f35, 0x3c48d7, 0x3c427a, 0x3c3c1d, 0x3c35c1, 0x3c2f66, 0x3c290b,
+ 0x3c22b1, 0x3c1c57, 0x3c15ff, 0x3c0fa7, 0x3c094f, 0x3c02f8, 0x3bfca2, 0x3bf64c,
+ 0x3beff7, 0x3be9a3, 0x3be34f, 0x3bdcfc, 0x3bd6aa, 0x3bd058, 0x3bca07, 0x3bc3b7,
+ 0x3bbd67, 0x3bb718, 0x3bb0c9, 0x3baa7b, 0x3ba42e, 0x3b9de1, 0x3b9795, 0x3b914a,
+ 0x3b8aff, 0x3b84b5, 0x3b7e6c, 0x3b7823, 0x3b71db, 0x3b6b93, 0x3b654c, 0x3b5f06,
+ 0x3b58c0, 0x3b527b, 0x3b4c36, 0x3b45f3, 0x3b3faf, 0x3b396d, 0x3b332b, 0x3b2cea,
+ 0x3b26a9, 0x3b2069, 0x3b1a2a, 0x3b13eb, 0x3b0dad, 0x3b076f, 0x3b0132, 0x3afaf6,
+ 0x3af4ba, 0x3aee7f, 0x3ae845, 0x3ae20b, 0x3adbd2, 0x3ad599, 0x3acf61, 0x3ac92a,
+ 0x3ac2f3, 0x3abcbd, 0x3ab688, 0x3ab053, 0x3aaa1f, 0x3aa3eb, 0x3a9db8, 0x3a9786,
+ 0x3a9154, 0x3a8b23, 0x3a84f2, 0x3a7ec2, 0x3a7893, 0x3a7264, 0x3a6c36, 0x3a6609,
+ 0x3a5fdc, 0x3a59b0, 0x3a5384, 0x3a4d59, 0x3a472f, 0x3a4105, 0x3a3adc, 0x3a34b4,
+ 0x3a2e8c, 0x3a2864, 0x3a223e, 0x3a1c18, 0x3a15f2, 0x3a0fcd, 0x3a09a9, 0x3a0385,
+ 0x39fd62, 0x39f740, 0x39f11e, 0x39eafd, 0x39e4dc, 0x39debc, 0x39d89d, 0x39d27e,
+ 0x39cc60, 0x39c642, 0x39c025, 0x39ba09, 0x39b3ed, 0x39add2, 0x39a7b7, 0x39a19d,
+ 0x399b84, 0x39956b, 0x398f53, 0x39893b, 0x398324, 0x397d0e, 0x3976f8, 0x3970e3,
+ 0x396ace, 0x3964ba, 0x395ea7, 0x395894, 0x395282, 0x394c70, 0x39465f, 0x39404f,
+ 0x393a3f, 0x393430, 0x392e21, 0x392813, 0x392206, 0x391bf9, 0x3915ed, 0x390fe1,
+ 0x3909d6, 0x3903cb, 0x38fdc1, 0x38f7b8, 0x38f1af, 0x38eba7, 0x38e5a0, 0x38df99,
+ 0x38d993, 0x38d38d, 0x38cd88, 0x38c783, 0x38c17f, 0x38bb7c, 0x38b579, 0x38af77,
+ 0x38a975, 0x38a374, 0x389d73, 0x389774, 0x389174, 0x388b76, 0x388577, 0x387f7a,
+ 0x38797d, 0x387381, 0x386d85, 0x38678a, 0x38618f, 0x385b95, 0x38559b, 0x384fa2,
+ 0x3849aa, 0x3843b2, 0x383dbb, 0x3837c5, 0x3831cf, 0x382bd9, 0x3825e4, 0x381ff0,
+ 0x3819fd, 0x381409, 0x380e17, 0x380825, 0x380234, 0x37fc43, 0x37f653, 0x37f063,
+ 0x37ea74, 0x37e485, 0x37de97, 0x37d8aa, 0x37d2bd, 0x37ccd1, 0x37c6e5, 0x37c0fa,
+ 0x37bb10, 0x37b526, 0x37af3d, 0x37a954, 0x37a36c, 0x379d84, 0x37979d, 0x3791b6,
+ 0x378bd0, 0x3785eb, 0x378006, 0x377a22, 0x37743e, 0x376e5b, 0x376879, 0x376297,
+ 0x375cb5, 0x3756d5, 0x3750f4, 0x374b15, 0x374535, 0x373f57, 0x373979, 0x37339b,
+ 0x372dbf, 0x3727e2, 0x372206, 0x371c2b, 0x371651, 0x371077, 0x370a9d, 0x3704c4,
+ 0x36feec, 0x36f914, 0x36f33d, 0x36ed66, 0x36e790, 0x36e1ba, 0x36dbe5, 0x36d611,
+ 0x36d03d, 0x36ca69, 0x36c497, 0x36bec4, 0x36b8f3, 0x36b321, 0x36ad51, 0x36a781,
+ 0x36a1b1, 0x369be2, 0x369614, 0x369046, 0x368a79, 0x3684ac, 0x367ee0, 0x367915,
+ 0x36734a, 0x366d7f, 0x3667b5, 0x3661ec, 0x365c23, 0x36565b, 0x365093, 0x364acc,
+ 0x364505, 0x363f3f, 0x363979, 0x3633b4, 0x362df0, 0x36282c, 0x362269, 0x361ca6,
+ 0x3616e4, 0x361122, 0x360b61, 0x3605a0, 0x35ffe0, 0x35fa20, 0x35f461, 0x35eea3,
+ 0x35e8e5, 0x35e328, 0x35dd6b, 0x35d7af, 0x35d1f3, 0x35cc38, 0x35c67d, 0x35c0c3,
+ 0x35bb09, 0x35b550, 0x35af98, 0x35a9e0, 0x35a429, 0x359e72, 0x3598bb, 0x359306,
+ 0x358d50, 0x35879c, 0x3581e8, 0x357c34, 0x357681, 0x3570ce, 0x356b1c, 0x35656b,
+ 0x355fba, 0x355a09, 0x355459, 0x354eaa, 0x3548fb, 0x35434d, 0x353d9f, 0x3537f2,
+ 0x353245, 0x352c99, 0x3526ee, 0x352143, 0x351b98, 0x3515ee, 0x351045, 0x350a9c
+};
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+gmx_add_unit_test(MathUnitTests math-test
+ vectypes.cpp
+ )
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests various corners of gmx::RVec implementation.
+ *
+ * The main point of these tests is to check that all different constructs
+ * using gmx::RVec compile, and that some of the non-trivial conversions
+ * to/from rvec work as intended.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_math
+ */
+#include "gmxpre.h"
+
+#include "gromacs/math/vectypes.h"
+
+#include <vector>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/math/vec.h"
+
+namespace
+{
+
+using gmx::RVec;
+
+TEST(RVecTest, CanBeStoredInVector)
+{
+ std::vector<RVec> v;
+ v.push_back(RVec(1, 2, 3));
+ v.resize(2);
+ EXPECT_EQ(1, v[0][XX]);
+ EXPECT_EQ(2, v[0][YY]);
+ EXPECT_EQ(3, v[0][ZZ]);
+}
+
+TEST(RVecTest, ConvertsImplicitlyFrom_rvec)
+{
+ std::vector<RVec> v;
+ rvec x = { 1, 2, 3 };
+ v.push_back(x);
+ EXPECT_EQ(1, v[0][XX]);
+ EXPECT_EQ(2, v[0][YY]);
+ EXPECT_EQ(3, v[0][ZZ]);
+}
+
+TEST(RVecTest, ConvertsImplicitlyTo_rvec)
+{
+ std::vector<RVec> v;
+ v.push_back(RVec(1, 2, 3));
+ rvec x;
+ copy_rvec(v[0], x);
+ EXPECT_EQ(1, x[XX]);
+ EXPECT_EQ(2, x[YY]);
+ EXPECT_EQ(3, x[ZZ]);
+}
+
+TEST(RVecTest, WorksAsMutable_rvec)
+{
+ std::vector<RVec> v;
+ v.push_back(RVec(1, 2, 3));
+ rvec x = {2, 3, 4};
+ copy_rvec(x, v[0]);
+ EXPECT_EQ(2, v[0][XX]);
+ EXPECT_EQ(3, v[0][YY]);
+ EXPECT_EQ(4, v[0][ZZ]);
+}
+
+TEST(RVecTest, WorksAs_rvec_Array)
+{
+ std::vector<RVec> v;
+ v.push_back(RVec(1, 2, 3));
+ v.push_back(RVec(2, 3, 4));
+ const rvec *r = as_rvec_array(&v[0]);
+ EXPECT_EQ(1, r[0][XX]);
+ EXPECT_EQ(2, r[0][YY]);
+ EXPECT_EQ(3, r[0][ZZ]);
+ EXPECT_EQ(2, r[1][XX]);
+ EXPECT_EQ(3, r[1][YY]);
+ EXPECT_EQ(4, r[1][ZZ]);
+}
+
+/*! \brief
+ * Helper function for testing RVec to rvec conversions.
+ */
+const rvec *testFunction(const rvec &x)
+{
+ return &x;
+}
+
+TEST(RVecTest, WorksAs_rvec_Reference)
+{
+ RVec v(1, 2, 3);
+ const rvec *r = testFunction(v.as_vec());
+ EXPECT_EQ(1, r[0][XX]);
+ EXPECT_EQ(2, r[0][YY]);
+ EXPECT_EQ(3, r[0][ZZ]);
+}
+
+} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2011,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
+#include "units.h"
+
#include <stdio.h>
+
#include "gromacs/utility/cstringutil.h"
-#include "physics.h"
double convert2gmx(double x, int unit)
{
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-#ifndef _physics_h
-#define _physics_h
+#ifndef GMX_MATH_UNITS_H
+#define GMX_MATH_UNITS_H
/*
* Physical constants to be used in Gromacs.
* be anywhere else in the code.
*/
-#include "../math/utilities.h"
+#include "gromacs/math/utilities.h"
#ifdef __cplusplus
extern "C" {
}
#endif
-
-#endif /* _physics_h */
+#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "gromacs/math/utilities.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "utilities.h"
-#include <math.h>
+#include "config.h"
+
+#include <assert.h>
#include <limits.h>
+#include <math.h>
+
#ifdef HAVE__FINITE
#include <float.h>
#endif
-#include <assert.h>
+#ifndef GMX_NATIVE_WINDOWS
+#include <fenv.h>
+#endif
int gmx_nint(real a)
{
{
if (x < 0)
{
- return (-pow(-x, 1.0/DIM));
+ return (-pow(-x, 1.0/3.0));
}
else
{
- return (pow(x, 1.0/DIM));
+ return (pow(x, 1.0/3.0));
}
}
gmx_bool gmx_isfinite(real gmx_unused x)
{
- gmx_bool returnval = TRUE;
- /* If no suitable function was found, assume the value is
- * finite. */
+ gmx_bool returnval;
#ifdef HAVE__FINITE
returnval = _finite(x);
returnval = isfinite(x);
#elif defined HAVE__ISFINITE
returnval = _isfinite(x);
+#else
+ /* If no suitable function was found, assume the value is
+ * finite. */
+ returnval = TRUE;
#endif
return returnval;
}
gmx_bool gmx_isnan(real x)
{
- /* cppcheck-suppress duplicateExpression */
return x != x;
}
}
return p;
}
+
+int gmx_feenableexcept()
+{
+#ifdef HAVE_FEENABLEEXCEPT
+ return feenableexcept(FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW);
+#elif (defined(__i386__) || defined(__x86_64__)) && defined(__APPLE__)
+ /* Author: David N. Williams
+ * License: Public Domain
+ *
+ * Might also work on non-Apple Unix. But should be tested
+ * before enabling.
+ */
+ unsigned int excepts = FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW;
+ static fenv_t fenv;
+ unsigned int new_excepts = excepts & FE_ALL_EXCEPT,
+ old_excepts; // previous masks
+
+ if (fegetenv (&fenv) )
+ {
+ return -1;
+ }
+ old_excepts = fenv.__control & FE_ALL_EXCEPT;
+
+ // unmask
+ fenv.__control &= ~new_excepts;
+ fenv.__mxcsr &= ~(new_excepts << 7);
+
+ return ( fesetenv (&fenv) ? -1 : old_excepts );
+#else
+ return -1;
+#endif
+}
#include <limits.h>
#include <math.h>
-#include "../legacyheaders/types/simple.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#define gmx_erfc(x) gmx_erfcf(x)
#endif
+#if defined(_MSC_VER) && _MSC_VER < 1800
+#define gmx_expm1(x) (exp(x)-1)
+#define gmx_log1p(x) log(1+x)
+#else
+#define gmx_expm1 expm1
+#define gmx_log1p log1p
+#endif
+
gmx_bool gmx_isfinite(real x);
gmx_bool gmx_isnan(real x);
unsigned int
gmx_log2i(unsigned int x);
-/*! /brief Multiply two large ints
+/*! \brief Multiply two large ints
*
- * \return False iff overflow occured
+ * \return False iff overflow occured
*/
gmx_bool
check_int_multiply_for_overflow(gmx_int64_t a,
int
gmx_greatest_common_divisor(int p, int q);
+
+/*! \brief Enable floating-point exceptions if supported on OS
+ *
+ * Enables division-by-zero, invalid, and overflow.
+ */
+int gmx_feenableexcept();
+
#ifdef __cplusplus
}
#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _vec_h
-#define _vec_h
+#ifndef GMX_MATH_VEC_H
+#define GMX_MATH_VEC_H
/*
collection of in-line ready operations:
HAVE_*SQRT*. This is no problem with public headers because
it is OK if user code uses a different rsqrt implementation */
#ifdef HAVE_CONFIG_H
-#include <config.h>
+#include "config.h"
#endif
-#include "types/simple.h"
-#include "../math/utilities.h"
-#include "typedefs.h"
-#include "sysstuff.h"
-#include "gmx_fatal.h"
#include <math.h>
-#include "physics.h"
+
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#define EXP_ADDR(val) (((val)&EXP_MASK)>>EXP_SHIFT)
#define FRACT_ADDR(val) (((val)&(FRACT_MASK|EXP_LSB))>>FRACT_SHIFT)
-extern const unsigned int *gmx_invsqrt_exptab;
-extern const unsigned int *gmx_invsqrt_fracttab;
+extern const unsigned int gmx_invsqrt_exptab[];
+extern const unsigned int gmx_invsqrt_fracttab[];
typedef union
{
b[ZZ] = a[ZZ];
}
-static gmx_inline void copy_rvecn(rvec *a, rvec *b, int startn, int endn)
+static gmx_inline void copy_rvecn(gmx_cxx_const rvec *a, rvec *b, int startn, int endn)
{
int i;
for (i = startn; i < endn; i++)
c[ZZ] = z;
}
-static gmx_inline void copy_mat(matrix a, matrix b)
+static gmx_inline void copy_mat(gmx_cxx_const matrix a, matrix b)
{
copy_rvec(a[XX], b[XX]);
copy_rvec(a[YY], b[YY]);
return atan2(wlen, s);
}
-static gmx_inline void mmul_ur0(matrix a, matrix b, matrix dest)
+static gmx_inline void mmul_ur0(gmx_cxx_const matrix a, gmx_cxx_const matrix b, matrix dest)
{
dest[XX][XX] = a[XX][XX]*b[XX][XX];
dest[XX][YY] = 0.0;
dest[ZZ][ZZ] = a[ZZ][ZZ]*b[ZZ][ZZ];
}
-static gmx_inline void mmul(matrix a, matrix b, matrix dest)
+static gmx_inline void mmul(gmx_cxx_const matrix a, gmx_cxx_const matrix b, matrix dest)
{
dest[XX][XX] = a[XX][XX]*b[XX][XX]+a[XX][YY]*b[YY][XX]+a[XX][ZZ]*b[ZZ][XX];
dest[YY][XX] = a[YY][XX]*b[XX][XX]+a[YY][YY]*b[YY][XX]+a[YY][ZZ]*b[ZZ][XX];
dest[ZZ][ZZ] = a[ZZ][XX]*b[XX][ZZ]+a[ZZ][YY]*b[YY][ZZ]+a[ZZ][ZZ]*b[ZZ][ZZ];
}
-static gmx_inline void transpose(matrix src, matrix dest)
+static gmx_inline void transpose(gmx_cxx_const matrix src, matrix dest)
{
dest[XX][XX] = src[XX][XX];
dest[YY][XX] = src[XX][YY];
dest[ZZ][ZZ] = src[ZZ][ZZ];
}
-static gmx_inline void tmmul(matrix a, matrix b, matrix dest)
+static gmx_inline void tmmul(gmx_cxx_const matrix a, gmx_cxx_const matrix b, matrix dest)
{
/* Computes dest=mmul(transpose(a),b,dest) - used in do_pr_pcoupl */
dest[XX][XX] = a[XX][XX]*b[XX][XX]+a[YY][XX]*b[YY][XX]+a[ZZ][XX]*b[ZZ][XX];
dest[ZZ][ZZ] = a[XX][ZZ]*b[XX][ZZ]+a[YY][ZZ]*b[YY][ZZ]+a[ZZ][ZZ]*b[ZZ][ZZ];
}
-static gmx_inline void mtmul(matrix a, matrix b, matrix dest)
+static gmx_inline void mtmul(gmx_cxx_const matrix a, gmx_cxx_const matrix b, matrix dest)
{
/* Computes dest=mmul(a,transpose(b),dest) - used in do_pr_pcoupl */
dest[XX][XX] = a[XX][XX]*b[XX][XX]+a[XX][YY]*b[XX][YY]+a[XX][ZZ]*b[XX][ZZ];
dest[ZZ][ZZ] = a[ZZ][XX]*b[ZZ][XX]+a[ZZ][YY]*b[ZZ][YY]+a[ZZ][ZZ]*b[ZZ][ZZ];
}
-static gmx_inline real det(matrix a)
+static gmx_inline real det(gmx_cxx_const matrix a)
{
return ( a[XX][XX]*(a[YY][YY]*a[ZZ][ZZ]-a[ZZ][YY]*a[YY][ZZ])
-a[YY][XX]*(a[XX][YY]*a[ZZ][ZZ]-a[ZZ][YY]*a[XX][ZZ])
}
-static gmx_inline void m_add(matrix a, matrix b, matrix dest)
+static gmx_inline void m_add(gmx_cxx_const matrix a, gmx_cxx_const matrix b, matrix dest)
{
dest[XX][XX] = a[XX][XX]+b[XX][XX];
dest[XX][YY] = a[XX][YY]+b[XX][YY];
dest[ZZ][ZZ] = a[ZZ][ZZ]+b[ZZ][ZZ];
}
-static gmx_inline void m_sub(matrix a, matrix b, matrix dest)
+static gmx_inline void m_sub(gmx_cxx_const matrix a, gmx_cxx_const matrix b, matrix dest)
{
dest[XX][XX] = a[XX][XX]-b[XX][XX];
dest[XX][YY] = a[XX][YY]-b[XX][YY];
dest[ZZ][ZZ] = a[ZZ][ZZ]-b[ZZ][ZZ];
}
-static gmx_inline void msmul(matrix m1, real r1, matrix dest)
+static gmx_inline void msmul(gmx_cxx_const matrix m1, real r1, matrix dest)
{
dest[XX][XX] = r1*m1[XX][XX];
dest[XX][YY] = r1*m1[XX][YY];
dest[ZZ][ZZ] = r1*m1[ZZ][ZZ];
}
-static gmx_inline void m_inv_ur0(matrix src, matrix dest)
+static gmx_inline void m_inv_ur0(gmx_cxx_const matrix src, matrix dest)
{
double tmp = src[XX][XX]*src[YY][YY]*src[ZZ][ZZ];
if (fabs(tmp) <= 100*GMX_REAL_MIN)
dest[YY][ZZ] = 0.0;
}
-static gmx_inline void m_inv(matrix src, matrix dest)
+static gmx_inline void m_inv(gmx_cxx_const matrix src, matrix dest)
{
const real smallreal = (real)1.0e-24;
const real largereal = (real)1.0e24;
dest[ZZ][ZZ] = c*(src[XX][XX]*src[YY][YY]-src[YY][XX]*src[XX][YY]);
}
-static gmx_inline void mvmul(matrix a, const rvec src, rvec dest)
+static gmx_inline void mvmul(gmx_cxx_const matrix a, const rvec src, rvec dest)
{
dest[XX] = a[XX][XX]*src[XX]+a[XX][YY]*src[YY]+a[XX][ZZ]*src[ZZ];
dest[YY] = a[YY][XX]*src[XX]+a[YY][YY]*src[YY]+a[YY][ZZ]*src[ZZ];
}
-static gmx_inline void mvmul_ur0(matrix a, const rvec src, rvec dest)
+static gmx_inline void mvmul_ur0(gmx_cxx_const matrix a, const rvec src, rvec dest)
{
dest[ZZ] = a[ZZ][XX]*src[XX]+a[ZZ][YY]*src[YY]+a[ZZ][ZZ]*src[ZZ];
dest[YY] = a[YY][XX]*src[XX]+a[YY][YY]*src[YY];
dest[XX] = a[XX][XX]*src[XX];
}
-static gmx_inline void tmvmul_ur0(matrix a, const rvec src, rvec dest)
+static gmx_inline void tmvmul_ur0(gmx_cxx_const matrix a, const rvec src, rvec dest)
{
dest[XX] = a[XX][XX]*src[XX]+a[YY][XX]*src[YY]+a[ZZ][XX]*src[ZZ];
dest[YY] = a[YY][YY]*src[YY]+a[ZZ][YY]*src[ZZ];
dest[ZZ] = linv*src[ZZ];
}
-static void calc_lll(rvec box, rvec lll)
+static void calc_lll(const rvec box, rvec lll)
{
lll[XX] = 2.0*M_PI/box[XX];
lll[YY] = 2.0*M_PI/box[YY];
lll[ZZ] = 2.0*M_PI/box[ZZ];
}
-static gmx_inline real trace(matrix m)
+static gmx_inline real trace(gmx_cxx_const matrix m)
{
return (m[XX][XX]+m[YY][YY]+m[ZZ][ZZ]);
}
}
/* Operations on multidimensional rvecs, used e.g. in edsam.c */
-static gmx_inline void m_rveccopy(int dim, rvec *a, rvec *b)
+static gmx_inline void m_rveccopy(int dim, gmx_cxx_const rvec *a, rvec *b)
{
/* b = a */
int i;
}
/*computer matrix vectors from base vectors and angles */
-static gmx_inline void matrix_convert(matrix box, rvec vec, rvec angle)
+static gmx_inline void matrix_convert(matrix box, const rvec vec, rvec angle)
{
svmul(DEG2RAD, angle, angle);
box[XX][XX] = vec[XX];
#ifdef __cplusplus
}
-
-static gmx_inline real det(const matrix a)
-{
- return ( a[XX][XX]*(a[YY][YY]*a[ZZ][ZZ]-a[ZZ][YY]*a[YY][ZZ])
- -a[YY][XX]*(a[XX][YY]*a[ZZ][ZZ]-a[ZZ][YY]*a[XX][ZZ])
- +a[ZZ][XX]*(a[XX][YY]*a[YY][ZZ]-a[YY][YY]*a[XX][ZZ]));
-}
-
-static gmx_inline void mvmul(const matrix a, const rvec src, rvec dest)
-{
- dest[XX] = a[XX][XX]*src[XX]+a[XX][YY]*src[YY]+a[XX][ZZ]*src[ZZ];
- dest[YY] = a[YY][XX]*src[XX]+a[YY][YY]*src[YY]+a[YY][ZZ]*src[ZZ];
- dest[ZZ] = a[ZZ][XX]*src[XX]+a[ZZ][YY]*src[YY]+a[ZZ][ZZ]*src[ZZ];
-}
-
-static gmx_inline void tmvmul_ur0(const matrix a, const rvec src, rvec dest)
-{
- dest[XX] = a[XX][XX]*src[XX]+a[YY][XX]*src[YY]+a[ZZ][XX]*src[ZZ];
- dest[YY] = a[YY][YY]*src[YY]+a[ZZ][YY]*src[ZZ];
- dest[ZZ] = a[ZZ][ZZ]*src[ZZ];
-}
-
#endif
-#endif /* _vec_h */
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_MATH_VECTYPES_H
+#define GMX_MATH_VECTYPES_H
+
+#include "gromacs/utility/real.h"
+
+#define XX 0 /* Defines for indexing in */
+#define YY 1 /* vectors */
+#define ZZ 2
+#define DIM 3 /* Dimension of vectors */
+
+typedef real rvec[DIM];
+
+typedef double dvec[DIM];
+
+typedef real matrix[DIM][DIM];
+
+typedef real tensor[DIM][DIM];
+
+typedef int ivec[DIM];
+
+typedef int imatrix[DIM][DIM];
+
+#ifdef __cplusplus
+
+namespace gmx
+{
+
+/*! \brief
+ * C++ class for 3D vectors.
+ *
+ * \tparam ValueType Type
+ *
+ * This class provides a C++ version of rvec/dvec/ivec that can be put into STL
+ * containers etc. It is more or less a drop-in replacement for `rvec` and
+ * friends: it can be used in most contexts that accept the equivalent C type.
+ * However, there are two cases where explicit conversion is necessary:
+ * - An array of these objects needs to be converted with as_vec_array() (or
+ * convenience methods like as_rvec_array()).
+ * - Passing an RVec as a `const rvec &` parameter to a function needs an
+ * explicit call to as_vec(). The implicit conversion should work for this
+ * as well, but cppcheck parses the necessary implicit conversion operator
+ * incorrectly and MSVC fails to compile code that relies on the implicit
+ * conversion, so the explicit method is necessary.
+ *
+ * For the array conversion to work, the compiler should not add any extra
+ * alignment/padding in the layout of this class; that this actually works as
+ * intended is tested in the unit tests.
+ *
+ * \inpublicapi
+ */
+template <typename ValueType>
+class BasicVector
+{
+ public:
+ //! Underlying raw C array type (rvec/dvec/ivec).
+ typedef ValueType RawArray[DIM];
+
+ //! Constructs default (uninitialized) vector.
+ BasicVector() {}
+ //! Constructs a vector from given values.
+ BasicVector(ValueType x, ValueType y, ValueType z)
+ {
+ x_[XX] = x;
+ x_[YY] = y;
+ x_[ZZ] = z;
+ }
+ /*! \brief
+ * Constructs a vector from given values.
+ *
+ * This constructor is not explicit to support implicit conversions
+ * that allow, e.g., calling `std::vector<RVec>:``:push_back()` directly
+ * with an `rvec` parameter.
+ */
+ BasicVector(const RawArray x)
+ {
+ x_[XX] = x[XX];
+ x_[YY] = x[YY];
+ x_[ZZ] = x[ZZ];
+ }
+ //! Indexing operator to make the class work as the raw array.
+ ValueType &operator[](int i) { return x_[i]; }
+ //! Indexing operator to make the class work as the raw array.
+ ValueType operator[](int i) const { return x_[i]; }
+ // The conversion functions below could more accurately return
+ // RawArray &, but this fails with cppcheck and does not solve the
+ // issue with MSVC, so as_vec() should be used instead.
+ //! Makes BasicVector usable in contexts where a raw C array is expected.
+ operator ValueType *() { return x_; }
+ //! Makes BasicVector usable in contexts where a raw C array is expected.
+ operator const ValueType *() const { return x_; }
+
+ //! Converts to a raw C array where implicit conversion does not work.
+ RawArray &as_vec() { return x_; }
+ //! Converts to a raw C array where implicit conversion does not work.
+ const RawArray &as_vec() const { return x_; }
+
+ private:
+ RawArray x_;
+};
+
+/*! \brief
+ * Casts a gmx::BasicVector array into an equivalent raw C array.
+ */
+template <typename ValueType> static inline
+typename BasicVector<ValueType>::RawArray *
+as_vec_array(BasicVector<ValueType> *x)
+{
+ return reinterpret_cast<typename BasicVector<ValueType>::RawArray *>(x);
+}
+
+/*! \brief
+ * Casts a gmx::BasicVector array into an equivalent raw C array.
+ */
+template <typename ValueType> static inline
+const typename BasicVector<ValueType>::RawArray *
+as_vec_array(const BasicVector<ValueType> *x)
+{
+ return reinterpret_cast<const typename BasicVector<ValueType>::RawArray *>(x);
+}
+
+//! Shorthand for C++ `rvec`-equivalent type.
+typedef BasicVector<real> RVec;
+//! Casts a gmx::RVec array into an `rvec` array.
+static inline rvec *as_rvec_array(RVec *x)
+{
+ return as_vec_array(x);
+}
+//! Casts a gmx::RVec array into an `rvec` array.
+static inline const rvec *as_rvec_array(const RVec *x)
+{
+ return as_vec_array(x);
+}
+
+} // namespace gmx
+
+#endif
+
+#endif
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2012,2013, by the GROMACS development team, led by
+# Copyright (c) 2010,2012,2013,2014, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# the research papers on the package. Check out http://www.gromacs.org.
file(GLOB MDLIB_SOURCES nbnxn_kernels/simd_4xn/*.c nbnxn_kernels/simd_2xnn/*.c nbnxn_kernels/*.c *.c *.cpp)
-set(MDLIB_SOURCES ${MDLIB_SOURCES} PARENT_SCOPE)
if(GMX_GPU)
add_subdirectory(nbnxn_cuda)
- set(GMX_GPU_LIBRARIES ${GMX_GPU_LIBRARIES} nbnxn_cuda PARENT_SCOPE)
+endif()
+
+set(MDLIB_SOURCES ${MDLIB_SOURCES} PARENT_SCOPE)
+if (BUILD_TESTING)
+ add_subdirectory(tests)
endif()
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
#include "adress.h"
-#include "gromacs/math/utilities.h"
-#include "pbc.h"
-#include "types/simple.h"
-#include "typedefs.h"
-#include "vec.h"
-#include "gmx_fatal.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/fatalerror.h"
real
adress_weight(rvec x,
#ifndef _adress_h_
#define _adress_h_
-#include "types/simple.h"
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
+
+#ifdef __cplusplus
+extern "C"
+{
+#endif
+
+struct t_pbc;
/** \brief calculates the AdResS weight of a particle
*
real adressr,
real adressw,
rvec * ref,
- t_pbc * pbc,
+ struct t_pbc * pbc,
t_forcerec * fr);
/** \brief update the weight of all coarse-grained particles in several charge groups for com vsites
rvec x[],
t_forcerec * fr,
t_mdatoms * mdatoms,
- t_pbc * pbc);
+ struct t_pbc * pbc);
/** \brief update the weight of all coarse-grained particles for cog vsites
*
rvec x[],
t_forcerec * fr,
t_mdatoms * mdatoms,
- t_pbc * pbc);
+ struct t_pbc * pbc);
/** \brief update the weight of all coarse-grained particles in several charge groups for atom vsites
*
rvec x[],
t_forcerec * fr,
t_mdatoms * mdatoms,
- t_pbc * pbc);
+ struct t_pbc * pbc);
/** \brief update the weight on per atom basis of all coarse-grained particles in several charge groups for atom vsites
*
rvec x[],
t_forcerec * fr,
t_mdatoms * mdatoms,
- t_pbc * pbc);
+ struct t_pbc * pbc);
/** \brief add AdResS IC thermodynamic force to f_novirsum
*
rvec f[],
t_forcerec * fr,
t_mdatoms * mdatoms,
- t_pbc * pbc);
+ struct t_pbc * pbc);
/** \brief checks weather a cpu calculates only coarse-grained or explicit interactions
* \return boolean if coarse-grained or not
*/
gmx_bool egp_coarsegrained(t_forcerec * fr, int egp_nr);
+
+#ifdef __cplusplus
+}
+#endif
+
#endif
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <string.h>
-#include "typedefs.h"
-#include "main.h"
-#include "mvdata.h"
-#include "types/commrec.h"
-#include "network.h"
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "symtab.h"
-#include "vec.h"
-#include "tgroup.h"
#define block_bc(cr, d) gmx_bcast( sizeof(d), &(d), (cr))
/* Probably the test for (nr) > 0 in the next macro is only needed
{
int i;
int *handle;
- char ***NM;
snew(handle, nr);
if (MASTER(cr))
{
- NM = *nm;
for (i = 0; (i < nr); i++)
{
- handle[i] = lookup_symtab(symtab, NM[i]);
+ handle[i] = lookup_symtab(symtab, (*nm)[i]);
}
}
nblock_bc(cr, nr, handle);
if (!MASTER(cr))
{
snew_bc(cr, *nm, nr);
- NM = *nm;
for (i = 0; (i < nr); i++)
{
(*nm)[i] = get_symtab_handle(symtab, handle[i]);
static void bc_atoms(const t_commrec *cr, t_symtab *symtab, t_atoms *atoms)
{
- int dummy;
-
block_bc(cr, atoms->nr);
snew_bc(cr, atoms->atom, atoms->nr);
nblock_bc(cr, atoms->nr, atoms->atom);
static void bc_groups(const t_commrec *cr, t_symtab *symtab,
int natoms, gmx_groups_t *groups)
{
- int dummy;
int g, n;
bc_grps(cr, groups->grps);
static void bc_cmap(const t_commrec *cr, gmx_cmap_t *cmap_grid)
{
- int i, j, nelem, ngrid;
+ int i, nelem, ngrid;
block_bc(cr, cmap_grid->ngrid);
block_bc(cr, cmap_grid->grid_spacing);
static void bc_ffparams(const t_commrec *cr, gmx_ffparams_t *ffp)
{
- int i;
-
block_bc(cr, ffp->ntypes);
block_bc(cr, ffp->atnr);
snew_bc(cr, ffp->functype, ffp->ntypes);
static void bc_imd(const t_commrec *cr, t_IMD *imd)
{
- int g;
-
block_bc(cr, *imd);
snew_bc(cr, imd->ind, imd->nat);
nblock_bc(cr, imd->nat, imd->ind);
static void bc_fepvals(const t_commrec *cr, t_lambda *fep)
{
- gmx_bool bAlloc = TRUE;
int i;
block_bc(cr, fep->nstdhdl);
static void bc_expandedvals(const t_commrec *cr, t_expanded *expand, int n_lambda)
{
- gmx_bool bAlloc = TRUE;
- int i;
-
block_bc(cr, expand->nstexpanded);
block_bc(cr, expand->elamstats);
block_bc(cr, expand->elmcmove);
static void bc_simtempvals(const t_commrec *cr, t_simtemp *simtemp, int n_lambda)
{
- gmx_bool bAlloc = TRUE;
- int i;
-
block_bc(cr, simtemp->simtemp_low);
block_bc(cr, simtemp->simtemp_high);
block_bc(cr, simtemp->eSimTempScale);
static void bc_inputrec(const t_commrec *cr, t_inputrec *inputrec)
{
- gmx_bool bAlloc = TRUE;
int i;
block_bc(cr, *inputrec);
static void bc_molblock(const t_commrec *cr, gmx_molblock_t *molb)
{
- gmx_bool bAlloc = TRUE;
-
block_bc(cr, molb->type);
block_bc(cr, molb->nmol);
block_bc(cr, molb->natoms_mol);
nblock_bc(cr, nr, atomtypes->S_hct);
}
-
+/*! \brief Broadcasts ir and mtop from the master to all nodes in
+ * cr->mpi_comm_mygroup. */
+static
void bcast_ir_mtop(const t_commrec *cr, t_inputrec *inputrec, gmx_mtop_t *mtop)
{
int i;
bc_block(cr, &mtop->mols);
bc_groups(cr, &mtop->symtab, mtop->natoms, &mtop->groups);
}
+
+void init_parallel(t_commrec *cr, t_inputrec *inputrec,
+ gmx_mtop_t *mtop)
+{
+ bcast_ir_mtop(cr, inputrec, mtop);
+}
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/calcmu.h"
#include <stdio.h>
#include <stdlib.h>
-#include "typedefs.h"
-#include "network.h"
-#include "vec.h"
-#include "physics.h"
-#include "main.h"
-#include "calcmu.h"
-#include "gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
void calc_mu(int start, int homenr, rvec x[], real q[], real qB[],
int nChargePerturbed,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include <algorithm>
+
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
-#include "sysstuff.h"
-#include "force.h"
-#include "vec.h"
-#include "mshift.h"
-#include "macros.h"
+#define XXXX 0
+#define XXYY 1
+#define XXZZ 2
+#define YYXX 3
+#define YYYY 4
+#define YYZZ 5
+#define ZZXX 6
+#define ZZYY 7
+#define ZZZZ 8
static void upd_vir(rvec vir, real dvx, real dvy, real dvz)
{
/* Calculate virial for bonded forces only when they belong to
* this node.
*/
- start = max(i0, g->at_start);
- end = min(i1, g->at_end);
+ start = std::max(i0, g->at_start);
+ end = std::min(i1, g->at_end);
#ifdef SAFE
lo_fcv2(start, end, x, f, vir, g->ishift, box, TRICLINIC(box));
#else
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "main.h"
-#include "constr.h"
-#include "copyrite.h"
-#include "physics.h"
-#include "vec.h"
-#include "pbc.h"
-#include "gromacs/utility/smalloc.h"
-#include "mdrun.h"
-#include "nrnb.h"
-#include "domdec.h"
-#include "mtop_util.h"
-#include "gmx_omp_nthreads.h"
+#include <stdlib.h>
+#include "gromacs/domdec/domdec.h"
#include "gromacs/fileio/gmxfio.h"
-#include "gmx_fatal.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/bitmask.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
int b0; /* first constraint for this thread */
real *bllen; /* the reference bond length */
int nth; /* The number of threads doing LINCS */
lincs_thread_t *th; /* LINCS thread division */
- unsigned *atf; /* atom flags for thread parallelization */
+ gmx_bitmask_t *atf; /* atom flags for thread parallelization */
int atf_nalloc; /* allocation size of atf */
/* arrays for temporary storage in the LINCS algorithm */
rvec *tmpv;
gmx_bool bCalcVir, tensor rmdf)
{
int b0, b1, b, i, j, k, n;
- real tmp0, tmp1, tmp2, im1, im2, mvb, rlen, len, wfac, lam;
+ real tmp0, tmp1, tmp2, mvb;
rvec dx;
int *bla, *blnr, *blbnb;
rvec *r;
gmx_bool bCalcVir, tensor vir_r_m_dr)
{
int b0, b1, b, i, j, k, n, iter;
- real tmp0, tmp1, tmp2, im1, im2, mvb, rlen, len, len2, dlen2, wfac;
+ real tmp0, tmp1, tmp2, mvb, rlen, len, len2, dlen2, wfac;
rvec dx;
int *bla, *blnr, *blbnb;
rvec *r;
dlen2 = 2*len2 - norm2(dx);
if (dlen2 < wfac*len2 && (nlocat == NULL || nlocat[b]))
{
+ /* not race free - see detailed comment in caller */
*warn = b;
}
if (dlen2 > 0)
li->triangle[li->ntriangle] = i;
li->tri_bits[li->ntriangle] = 0;
li->ntriangle++;
- if (li->blnr[i+1] - li->blnr[i] > sizeof(li->tri_bits[0])*8 - 1)
+ if (li->blnr[i+1] - li->blnr[i] > static_cast<int>(sizeof(li->tri_bits[0])*8 - 1))
{
gmx_fatal(FARGS, "A constraint is connected to %d constraints, this is more than the %d allowed for constraints participating in triangles",
li->blnr[i+1] - li->blnr[i],
{
lincs_thread_t *li_m;
int th;
- unsigned *atf;
+ gmx_bitmask_t *atf;
int a;
if (natoms > li->atf_nalloc)
/* Clear the atom flags */
for (a = 0; a < natoms; a++)
{
- atf[a] = 0;
+ bitmask_clear(&atf[a]);
+ }
+
+ if (li->nth > BITMASK_SIZE)
+ {
+ gmx_fatal(FARGS, "More than %d threads is not supported for LINCS.", BITMASK_SIZE);
}
for (th = 0; th < li->nth; th++)
li_th->b0 = (li->nc* th )/li->nth;
li_th->b1 = (li->nc*(th+1))/li->nth;
- if (th < sizeof(*atf)*8)
+ /* For each atom set a flag for constraints from each */
+ for (b = li_th->b0; b < li_th->b1; b++)
{
- /* For each atom set a flag for constraints from each */
- for (b = li_th->b0; b < li_th->b1; b++)
- {
- atf[li->bla[b*2] ] |= (1U<<th);
- atf[li->bla[b*2+1]] |= (1U<<th);
- }
+ bitmask_set_bit(&atf[li->bla[b*2]], th);
+ bitmask_set_bit(&atf[li->bla[b*2+1]], th);
}
}
for (th = 0; th < li->nth; th++)
{
lincs_thread_t *li_th;
- unsigned mask;
+ gmx_bitmask_t mask;
int b;
li_th = &li->th[th];
srenew(li_th->ind_r, li_th->ind_nalloc);
}
- if (th < sizeof(*atf)*8)
- {
- mask = (1U<<th) - 1U;
+ bitmask_init_low_bits(&mask, th);
- li_th->nind = 0;
- li_th->nind_r = 0;
- for (b = li_th->b0; b < li_th->b1; b++)
+ li_th->nind = 0;
+ li_th->nind_r = 0;
+ for (b = li_th->b0; b < li_th->b1; b++)
+ {
+ /* We let the constraint with the lowest thread index
+ * operate on atoms with constraints from multiple threads.
+ */
+ if (bitmask_is_disjoint(atf[li->bla[b*2]], mask) &&
+ bitmask_is_disjoint(atf[li->bla[b*2+1]], mask))
{
- /* We let the constraint with the lowest thread index
- * operate on atoms with constraints from multiple threads.
- */
- if (((atf[li->bla[b*2]] & mask) == 0) &&
- ((atf[li->bla[b*2+1]] & mask) == 0))
- {
- /* Add the constraint to the local atom update index */
- li_th->ind[li_th->nind++] = b;
- }
- else
- {
- /* Add the constraint to the rest block */
- li_th->ind_r[li_th->nind_r++] = b;
- }
+ /* Add the constraint to the local atom update index */
+ li_th->ind[li_th->nind++] = b;
}
- }
- else
- {
- /* We are out of bits, assign all constraints to rest */
- for (b = li_th->b0; b < li_th->b1; b++)
+ else
{
+ /* Add the constraint to the rest block */
li_th->ind_r[li_th->nind_r++] = b;
}
}
int i, k, ncc_alloc, ni, con, nconnect, concon;
int type, a1, a2;
real lenA = 0, lenB;
- gmx_bool bLocal;
li->nc = 0;
li->ncc = 0;
li->blnr[con] = nconnect;
for (i = 0; i < ni; i++)
{
- bLocal = TRUE;
type = iatom[3*i];
a1 = iatom[3*i+1];
a2 = iatom[3*i+2];
{
gmx_bool bCalcDHDL;
char buf[STRLEN], buf2[22], buf3[STRLEN];
- int i, warn, p_imax, error;
+ int i, warn, p_imax;
real ncons_loc, p_ssd, p_max = 0;
rvec dx;
gmx_bool bOK;
if (econqCoord)
{
/* dhdlambda contains dH/dlambda*dt^2, correct for this */
+ /* TODO This should probably use invdt, so that sd integrator scaling works properly */
dhdlambda /= ir->delta_t*ir->delta_t;
}
*dvdlambda += dhdlambda;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/constr.h"
#include <assert.h>
+#include <stdlib.h>
+
+#include <cmath>
+
+#include <algorithm>
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/fileio/confio.h"
-#include "types/commrec.h"
-#include "constr.h"
-#include "copyrite.h"
-#include "invblock.h"
-#include "main.h"
-#include "mdrun.h"
-#include "nrnb.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "physics.h"
-#include "names.h"
-#include "txtdump.h"
-#include "domdec.h"
-#include "gromacs/fileio/pdbio.h"
-#include "splitter.h"
-#include "mtop_util.h"
#include "gromacs/fileio/gmxfio.h"
-#include "macros.h"
-#include "gmx_omp_nthreads.h"
-#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/splitter.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
-
-#include "gmx_fatal.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/invblock.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
typedef struct gmx_constr {
int ncon_tot; /* The total number of constraints */
int nblocks; /* The number of SHAKE blocks */
int *sblock; /* The SHAKE blocks */
int sblock_nalloc; /* The allocation size of sblock */
- real *lagr; /* Lagrange multipliers for SHAKE */
+ real *lagr; /* -2 times the Lagrange multipliers for SHAKE */
int lagr_nalloc; /* The allocation size of lagr */
int maxwarn; /* The maximum number of warnings */
int warncount_lincs;
atom_id blocknr;
} t_sortblock;
-/* delta_t should be used instead of ir->delta_t, to permit the time
- step to be scaled by the calling code */
-static void *init_vetavars(t_vetavars *vars,
- gmx_bool constr_deriv,
- real veta, real vetanew,
- t_inputrec *ir, real delta_t,
- gmx_ekindata_t *ekind, gmx_bool bPscal)
-{
- double g;
- int i;
-
- /* first, set the alpha integrator variable */
- if ((ir->opts.nrdf[0] > 0) && bPscal)
- {
- vars->alpha = 1.0 + DIM/((double)ir->opts.nrdf[0]);
- }
- else
- {
- vars->alpha = 1.0;
- }
- g = 0.5*veta*delta_t;
- vars->rscale = exp(g)*series_sinhx(g);
- g = -0.25*vars->alpha*veta*delta_t;
- vars->vscale = exp(g)*series_sinhx(g);
- vars->rvscale = vars->vscale*vars->rscale;
- vars->veta = vetanew;
-
- if (constr_deriv)
- {
- snew(vars->vscale_nhc, ir->opts.ngtc);
- if ((ekind == NULL) || (!bPscal))
- {
- for (i = 0; i < ir->opts.ngtc; i++)
- {
- vars->vscale_nhc[i] = 1;
- }
- }
- else
- {
- for (i = 0; i < ir->opts.ngtc; i++)
- {
- vars->vscale_nhc[i] = ekind->tcstat[i].vscale_nhc;
- }
- }
- }
- else
- {
- vars->vscale_nhc = NULL;
- }
-
- return vars;
-}
-
-static void free_vetavars(t_vetavars *vars)
-{
- if (vars->vscale_nhc != NULL)
- {
- sfree(vars->vscale_nhc);
- }
-}
-
static int pcomp(const void *p1, const void *p2)
{
int db;
return db;
}
- min1 = min(a1->iatom[1], a1->iatom[2]);
- max1 = max(a1->iatom[1], a1->iatom[2]);
- min2 = min(a2->iatom[1], a2->iatom[2]);
- max2 = max(a2->iatom[1], a2->iatom[2]);
+ min1 = std::min(a1->iatom[1], a1->iatom[2]);
+ max1 = std::max(a1->iatom[1], a1->iatom[2]);
+ min2 = std::min(a2->iatom[1], a2->iatom[2]);
+ max2 = std::max(a2->iatom[1], a2->iatom[2]);
if (min1 == min2)
{
void too_many_constraint_warnings(int eConstrAlg, int warncount)
{
- const char *abort = "- aborting to avoid logfile runaway.\n"
- "This normally happens when your system is not sufficiently equilibrated,"
- "or if you are changing lambda too fast in free energy simulations.\n";
-
gmx_fatal(FARGS,
"Too many %s warnings (%d)\n"
"If you know what you are doing you can %s"
gmx_bool constrain(FILE *fplog, gmx_bool bLog, gmx_bool bEner,
struct gmx_constr *constr,
- t_idef *idef, t_inputrec *ir, gmx_ekindata_t *ekind,
+ t_idef *idef, t_inputrec *ir,
t_commrec *cr,
gmx_int64_t step, int delta_step,
real step_scaling,
gmx_bool bMolPBC, matrix box,
real lambda, real *dvdlambda,
rvec *v, tensor *vir,
- t_nrnb *nrnb, int econq, gmx_bool bPscal,
- real veta, real vetanew)
+ t_nrnb *nrnb, int econq)
{
gmx_bool bOK, bDump;
- int start, homenr, nrend;
- int i, j, d;
- int ncons, settle_error;
+ int start, homenr;
+ int i, j;
+ int settle_error;
tensor vir_r_m_dr;
- rvec *vstor;
real scaled_delta_t;
- real invdt, vir_fac, t;
+ real invdt, vir_fac = 0, t;
t_ilist *settle;
int nsettle;
t_pbc pbc, *pbc_null;
char buf[22];
- t_vetavars vetavar;
int nth, th;
if (econq == econqForceDispl && !EI_ENERGY_MINIMIZATION(ir->eI))
start = 0;
homenr = md->homenr;
- nrend = start+homenr;
scaled_delta_t = step_scaling * ir->delta_t;
- /* set constants for pressure control integration */
- init_vetavars(&vetavar, econq != econqCoord,
- veta, vetanew, ir, scaled_delta_t, ekind, bPscal);
-
/* Prepare time step for use in constraint implementations, and
avoid generating inf when ir->delta_t = 0. */
if (ir->delta_t == 0)
idef, ir, x, xprime, nrnb,
constr->lagr, lambda, dvdlambda,
invdt, v, vir != NULL, vir_r_m_dr,
- constr->maxwarn >= 0, econq, &vetavar);
+ constr->maxwarn >= 0, econq);
break;
case (econqVeloc):
bOK = bshakef(fplog, constr->shaked,
idef, ir, x, min_proj, nrnb,
constr->lagr, lambda, dvdlambda,
invdt, NULL, vir != NULL, vir_r_m_dr,
- constr->maxwarn >= 0, econq, &vetavar);
+ constr->maxwarn >= 0, econq);
break;
default:
gmx_fatal(FARGS, "Internal error, SHAKE called for constraining something else than coordinates");
x[0], xprime[0],
invdt, v ? v[0] : NULL, calcvir_atom_end,
th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
- th == 0 ? &settle_error : &constr->settle_error[th],
- &vetavar);
+ th == 0 ? &settle_error : &constr->settle_error[th]);
}
}
inc_nrnb(nrnb, eNR_SETTLE, nsettle);
pbc_null,
x,
xprime, min_proj, calcvir_atom_end,
- th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
- &vetavar);
+ th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th]);
}
}
/* This is an overestimate */
/* Combine virial and error info of the other threads */
for (i = 1; i < nth; i++)
{
- m_add(vir_r_m_dr, constr->vir_r_m_dr_th[i], vir_r_m_dr);
settle_error = constr->settle_error[i];
}
+ if (vir != NULL)
+ {
+ for (i = 1; i < nth; i++)
+ {
+ m_add(vir_r_m_dr, constr->vir_r_m_dr_th[i], vir_r_m_dr);
+ }
+ }
if (econq == econqCoord && settle_error >= 0)
{
{
char buf[256];
sprintf(buf,
- "\nstep " "%"GMX_PRId64 ": Water molecule starting at atom %d can not be "
+ "\nstep " "%" GMX_PRId64 ": Water molecule starting at atom %d can not be "
"settled.\nCheck for bad contacts and/or reduce the timestep if appropriate.\n",
step, ddglatnr(cr->dd, settle->iatoms[settle_error*(1+NRAL(F_SETTLE))+1]));
if (fplog)
}
}
- free_vetavars(&vetavar);
-
if (vir != NULL)
{
/* The normal uses of constrain() pass step_scaling = 1.0.
vir_fac = 0.5;
break;
default:
- vir_fac = 0;
gmx_incons("Unsupported constraint quantity for virial");
}
j, constr->nblocks, ncons);
for (i = 0; (i < ncons); i++)
{
- fprintf(stderr, "i: %5d sb[i].blocknr: %5u\n", i, sb[i].blocknr);
+ fprintf(stderr, "i: %5d sb[i].blocknr: %5d\n", i, sb[i].blocknr);
}
for (j = 0; (j <= constr->nblocks); j++)
{
if (EI_DYNAMICS(ir->eI))
{
lam1 = ir->fepvals->init_lambda + (ir->init_step + ir->nsteps)*ir->fepvals->delta_lambda;
- rmax = max(rmax, (1 - lam1)*sqrt(r2maxA) + lam1*sqrt(r2maxB));
+ rmax = std::max(rmax, (1 - lam1)*std::sqrt(r2maxA) + lam1*std::sqrt(r2maxB));
}
}
rmax = 0;
for (mt = 0; mt < mtop->nmoltype; mt++)
{
- rmax = max(rmax,
- constr_r_max_moltype(&mtop->moltype[mt],
- mtop->ffparams.iparams, ir));
+ rmax = std::max(rmax,
+ constr_r_max_moltype(&mtop->moltype[mt],
+ mtop->ffparams.iparams, ir));
}
if (fplog)
gmx_edsam_t ed, t_state *state,
t_commrec *cr)
{
- int ncon, nset, nmol, settle_type, i, natoms, mt, nflexcon;
+ int ncon, nset, nmol, settle_type, i, mt, nflexcon;
struct gmx_constr *constr;
char *env;
t_ilist *ilist;
}
}
+ if ((ncon + nset) > 0 && ir->epc == epcMTTK)
+ {
+ gmx_fatal(FARGS, "Constraints are not implemented with MTTK pressure control.");
+ }
+
constr->maxwarn = 999;
env = getenv("GMX_MAXCONSTRWARN");
if (env)
{
constr->maxwarn = 0;
- sscanf(env, "%d", &constr->maxwarn);
+ sscanf(env, "%8d", &constr->maxwarn);
if (fplog)
{
fprintf(fplog,
const t_block *cgs;
const t_ilist *il;
int mb;
- int nat, *at2cg, cg, a, ftype, i;
+ int *at2cg, cg, a, ftype, i;
gmx_bool bInterCG;
bInterCG = FALSE;
const t_block *cgs;
const t_ilist *il;
int mb;
- int nat, *at2cg, cg, a, ftype, i;
+ int *at2cg, cg, a, ftype, i;
gmx_bool bInterCG;
bInterCG = FALSE;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <assert.h>
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "update.h"
-#include "vec.h"
-#include "macros.h"
-#include "physics.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "txtdump.h"
-#include "nrnb.h"
+#include <algorithm>
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
-#include "update.h"
-#include "mdrun.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#define NTROTTERPARTS 3
{
/* general routine for both barostat and thermostat nose hoover chains */
- int i, j, mi, mj, jmax;
+ int i, j, mi, mj;
double Ekin, Efac, reft, kT, nd;
double dt;
t_grp_tcstat *tcstat;
{
iQinv = &(MassQ->QPinv[i*nh]);
nd = 1.0; /* THIS WILL CHANGE IF NOT ISOTROPIC */
- reft = max(0.0, opts->ref_t[0]);
+ reft = std::max<real>(0, opts->ref_t[0]);
Ekin = sqr(*veta)/MassQ->Winv;
}
else
iQinv = &(MassQ->Qinv[i*nh]);
tcstat = &ekind->tcstat[i];
nd = opts->nrdf[i];
- reft = max(0.0, opts->ref_t[i]);
+ reft = std::max<real>(0, opts->ref_t[i]);
if (bEkinAveVel)
{
Ekin = 2*trace(tcstat->ekinf)*tcstat->ekinscalef_nhc;
real pscal;
double alpha;
- int i, j, d, n, nwall;
- real T, GW, vol;
- tensor Winvm, ekinmod, localpres;
+ int nwall;
+ real GW, vol;
+ tensor ekinmod, localpres;
/* The heat bath is coupled to a separate barostat, the last temperature group. In the
2006 Tuckerman et al paper., the order is iL_{T_baro} iL {T_part}
* The pressure and compressibility always occur as a product,
* therefore the pressure unit drops out.
*/
- maxl = max(box[XX][XX], box[YY][YY]);
- maxl = max(maxl, box[ZZ][ZZ]);
+ maxl = std::max(box[XX][XX], box[YY][YY]);
+ maxl = std::max(maxl, box[ZZ][ZZ]);
for (d = 0; d < DIM; d++)
{
for (n = 0; n < DIM; n++)
{
int d, n;
real scalar_pressure, xy_pressure, p_corr_z;
- char *ptr, buf[STRLEN];
+ char buf[STRLEN];
/*
* Calculate the scaling matrix mu
if ((opts->tau_t[i] > 0) && (T > 0.0))
{
- reft = max(0.0, opts->ref_t[i]);
+ reft = std::max<real>(0, opts->ref_t[i]);
lll = sqrt(1.0 + (dt/opts->tau_t[i])*(reft/T-1.0));
- ekind->tcstat[i].lambda = max(min(lll, 1.25), 0.8);
+ ekind->tcstat[i].lambda = std::max<real>(std::min<real>(lll, 1.25), 0.8);
}
else
{
for (i = 0; (i < opts->ngtc); i++)
{
- reft = max(0.0, opts->ref_t[i]);
+ reft = std::max<real>(0, opts->ref_t[i]);
oldvxi = vxi[i];
vxi[i] += dt*MassQ->Qinv[i]*(ekind->tcstat[i].Th - reft);
xi[i] += dt*(oldvxi + vxi[i])*0.5;
t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno)
{
- int n, i, j, d, ntgrp, ngtc, gc = 0;
+ int n, i, d, ngtc, gc = 0;
t_grp_tcstat *tcstat;
t_grpopts *opts;
gmx_int64_t step_eff;
- real ecorr, pcorr, dvdlcorr;
- real bmass, qmass, reft, kT, dt, nd;
- tensor dumpres, dumvir;
+ real dt;
double *scalefac, dtc;
int *trotter_seq;
- rvec sumv = {0, 0, 0}, consk;
+ rvec sumv = {0, 0, 0};
gmx_bool bCouple;
if (trotter_seqno <= ettTSEQ2)
extern void init_npt_masses(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bInit)
{
- int n, i, j, d, ntgrp, ngtc, nnhpres, nh, gc = 0;
- t_grp_tcstat *tcstat;
+ int n, i, j, d, ngtc, nh;
t_grpopts *opts;
- real ecorr, pcorr, dvdlcorr;
- real bmass, qmass, reft, kT, dt, ndj, nd;
- tensor dumpres, dumvir;
+ real reft, kT, ndj, nd;
opts = &(ir->opts); /* just for ease of referencing */
ngtc = ir->opts.ngtc;
- nnhpres = state->nnhpres;
nh = state->nhchainlength;
if (ir->eI == eiMD)
{
if ((opts->tau_t[i] > 0) && (opts->ref_t[i] > 0))
{
- reft = max(0.0, opts->ref_t[i]);
+ reft = std::max<real>(0, opts->ref_t[i]);
nd = opts->nrdf[i];
kT = BOLTZ*reft;
for (j = 0; j < nh; j++)
}
else
{
- reft = 0.0;
for (j = 0; j < nh; j++)
{
MassQ->Qinv[i*nh+j] = 0.0;
int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bTrotter)
{
- int n, i, j, d, ntgrp, ngtc, nnhpres, nh, gc = 0;
- t_grp_tcstat *tcstat;
+ int i, j, nnhpres, nh;
t_grpopts *opts;
- real ecorr, pcorr, dvdlcorr;
- real bmass, qmass, reft, kT, dt, ndj, nd;
- tensor dumpres, dumvir;
+ real bmass, qmass, reft, kT;
int **trotter_seq;
opts = &(ir->opts); /* just for ease of referencing */
- ngtc = state->ngtc;
nnhpres = state->nnhpres;
nh = state->nhchainlength;
/* barostat temperature */
if ((ir->tau_p > 0) && (opts->ref_t[0] > 0))
{
- reft = max(0.0, opts->ref_t[0]);
+ reft = std::max<real>(0, opts->ref_t[0]);
kT = BOLTZ*reft;
for (i = 0; i < nnhpres; i++)
{
real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ)
{
- int i, j, nd, ndj, bmass, qmass, ngtcall;
- real ener_npt, reft, eta, kT, tau;
+ int i, j;
+ real nd, ndj;
+ real ener_npt, reft, kT;
double *ivxi, *ixi;
double *iQinv;
- real vol, dbaro, W, Q;
+ real vol;
int nh = state->nhchainlength;
ener_npt = 0;
ivxi = &state->nhpres_vxi[i*nh];
ixi = &state->nhpres_xi[i*nh];
iQinv = &(MassQ->QPinv[i*nh]);
- reft = max(ir->opts.ref_t[0], 0); /* using 'System' temperature */
+ reft = std::max<real>(ir->opts.ref_t[0], 0.0); /* using 'System' temperature */
kT = BOLTZ * reft;
for (j = 0; j < nh; j++)
iQinv = &(MassQ->Qinv[i*nh]);
nd = ir->opts.nrdf[i];
- reft = max(ir->opts.ref_t[i], 0);
+ reft = std::max<real>(ir->opts.ref_t[i], 0);
kT = BOLTZ * reft;
- if (nd > 0)
+ if (nd > 0.0)
{
if (IR_NVT_TROTTER(ir))
{
}
else
{
- ndj = 1;
+ ndj = 1.0;
}
ener_npt += ndj*ixi[j]*kT;
}
case eannPERIODIC:
/* calculate time modulo the period */
pert = opts->anneal_time[i][npoints-1];
- n = t / pert;
+ n = static_cast<int>(t / pert);
thist = t - n*pert; /* modulo time */
/* Make sure rounding didn't get us outside the interval */
if (fabs(thist-pert) < GMX_REAL_EPS*100)
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <stdio.h>
-#include "vec.h"
-#include "constr.h"
-#include "gmx_fatal.h"
+
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "pbc.h"
typedef struct
{
const t_pbc *pbc,
rvec x[],
rvec *der, rvec *derp,
- int calcvir_atom_end, tensor vir_r_m_dder,
- t_vetavars *vetavar)
+ int calcvir_atom_end, tensor vir_r_m_dder)
{
/* Settle for projection out constraint components
* of derivatives of the coordinates.
real imO, imH, dOH, dHH, invdOH, invdHH;
matrix invmat;
int i, m, m2, ow1, hw2, hw3;
- rvec roh2, roh3, rhh, dc, fc, fcv;
- rvec derm[3], derpm[3];
- real invvscale, vscale_nhc, veta;
- real kfacOH, kfacHH;
+ rvec roh2, roh3, rhh, dc, fc;
calcvir_atom_end *= DIM;
invdOH = p->invdOH;
invdHH = p->invdHH;
- veta = vetavar->veta;
- vscale_nhc = vetavar->vscale_nhc[0]; /* assume the first temperature control group. */
-
#ifdef PRAGMAS
#pragma ivdep
#endif
hw2 = iatoms[i*4+2];
hw3 = iatoms[i*4+3];
-
- for (m = 0; m < DIM; m++)
- {
- /* in the velocity case, these are the velocities, so we
- need to modify with the pressure control velocities! */
-
- derm[0][m] = vscale_nhc*der[ow1][m] + veta*x[ow1][m];
- derm[1][m] = vscale_nhc*der[hw2][m] + veta*x[hw2][m];
- derm[2][m] = vscale_nhc*der[hw3][m] + veta*x[hw3][m];
-
- }
- /* 27 flops */
-
if (pbc == NULL)
{
rvec_sub(x[ow1], x[hw2], roh2);
svmul(invdHH, rhh, rhh);
/* 18 flops */
- /* Determine the projections of der(modified) on the bonds */
+ /* Determine the projections of der on the bonds */
clear_rvec(dc);
for (m = 0; m < DIM; m++)
{
- dc[0] += (derm[0][m] - derm[1][m])*roh2[m];
- dc[1] += (derm[0][m] - derm[2][m])*roh3[m];
- dc[2] += (derm[1][m] - derm[2][m])*rhh [m];
+ dc[0] += (der[ow1][m] - der[hw2][m])*roh2[m];
+ dc[1] += (der[ow1][m] - der[hw3][m])*roh3[m];
+ dc[2] += (der[hw2][m] - der[hw3][m])*rhh [m];
}
/* 27 flops */
mvmul(invmat, dc, fc);
/* 15 flops */
- /* divide velocity by vscale_nhc for determining constrained velocities, since they
- have not yet been multiplied */
- svmul(1.0/vscale_nhc, fc, fcv);
- /* 7? flops */
-
/* Subtract the corrections from derp */
for (m = 0; m < DIM; m++)
{
- derp[ow1][m] -= imO*( fcv[0]*roh2[m] + fcv[1]*roh3[m]);
- derp[hw2][m] -= imH*(-fcv[0]*roh2[m] + fcv[2]*rhh [m]);
- derp[hw3][m] -= imH*(-fcv[1]*roh3[m] - fcv[2]*rhh [m]);
+ derp[ow1][m] -= imO*( fc[0]*roh2[m] + fc[1]*roh3[m]);
+ derp[hw2][m] -= imH*(-fc[0]*roh2[m] + fc[2]*rhh [m]);
+ derp[hw3][m] -= imH*(-fc[1]*roh3[m] - fc[2]*rhh [m]);
}
/* 45 flops */
for (m2 = 0; m2 < DIM; m2++)
{
vir_r_m_dder[m][m2] +=
- dOH*roh2[m]*roh2[m2]*fcv[0] +
- dOH*roh3[m]*roh3[m2]*fcv[1] +
- dHH*rhh [m]*rhh [m2]*fcv[2];
+ dOH*roh2[m]*roh2[m2]*fc[0] +
+ dOH*roh3[m]*roh3[m2]*fc[1] +
+ dHH*rhh [m]*rhh [m2]*fc[2];
}
}
}
}
-
- if (calcvir_atom_end > 0)
- {
- /* Correct r_m_dder, which will be used to calcualate the virial;
- * we need to use the unscaled multipliers in the virial.
- */
- msmul(vir_r_m_dder, 1.0/vetavar->vscale, vir_r_m_dder);
- }
}
real b4[], real after[],
real invdt, real *v, int CalcVirAtomEnd,
tensor vir_r_m_dr,
- int *error,
- t_vetavars *vetavar)
+ int *error)
{
/* ***************************************************************** */
/* ** */
/* Initialized data */
settleparam_t *p;
real wh, ra, rb, rc, irc2;
- real mOs, mHs, invdts;
+ real mO, mH;
/* Local variables */
- real gama, beta, alpa, xcom, ycom, zcom, al2be2, tmp, tmp2;
- real axlng, aylng, azlng, trns11, trns21, trns31, trns12, trns22,
- trns32, trns13, trns23, trns33, cosphi, costhe, sinphi, sinthe,
- cospsi, xaksxd, yaksxd, xakszd, yakszd, zakszd, zaksxd, xaksyd,
- xb0, yb0, zb0, xc0, yc0, zc0, xa1;
- real ya1, za1, xb1, yb1;
- real zb1, xc1, yc1, zc1, yaksyd, zaksyd, sinpsi, xa3, ya3, za3,
- xb3, yb3, zb3, xc3, yc3, zc3, xb0d, yb0d, xc0d, yc0d,
- za1d, xb1d, yb1d, zb1d, xc1d, yc1d, zc1d, ya2d, xb2d, yb2d, yc2d,
- xa3d, ya3d, za3d, xb3d, yb3d, zb3d, xc3d, yc3d, zc3d;
+ real gama, beta, alpa, xcom, ycom, zcom, al2be2, tmp, tmp2;
+ real axlng, aylng, azlng, trns11, trns21, trns31, trns12, trns22,
+ trns32, trns13, trns23, trns33, cosphi, costhe, sinphi, sinthe,
+ cospsi, xaksxd, yaksxd, xakszd, yakszd, zakszd, zaksxd, xaksyd,
+ xb0, yb0, zb0, xc0, yc0, zc0, xa1;
+ real ya1, za1, xb1, yb1;
+ real zb1, xc1, yc1, zc1, yaksyd, zaksyd, sinpsi, xa3, ya3, za3,
+ xb3, yb3, zb3, xc3, yc3, zc3, xb0d, yb0d, xc0d, yc0d,
+ za1d, xb1d, yb1d, zb1d, xc1d, yc1d, zc1d, ya2d, xb2d, yb2d, yc2d,
+ xa3d, ya3d, za3d, xb3d, yb3d, zb3d, xc3d, yc3d, zc3d;
real t1, t2;
real dax, day, daz, dbx, dby, dbz, dcx, dcy, dcz;
real mdax, mday, mdaz, mdbx, mdby, mdbz, mdcx, mdcy, mdcz;
CalcVirAtomEnd *= 3;
- p = &settled->massw;
- wh = p->wh;
- rc = p->rc;
- ra = p->ra;
- rb = p->rb;
- irc2 = p->irc2;
-
- mOs = p->mO / vetavar->rvscale;
- mHs = p->mH / vetavar->rvscale;
- invdts = invdt / vetavar->rscale;
+ p = &settled->massw;
+ wh = p->wh;
+ rc = p->rc;
+ ra = p->ra;
+ rb = p->rb;
+ irc2 = p->irc2;
+ mO = p->mO;
+ mH = p->mH;
#ifdef PRAGMAS
#pragma ivdep
if (v != NULL)
{
- v[ow1] += dax*invdts;
- v[ow1 + 1] += day*invdts;
- v[ow1 + 2] += daz*invdts;
- v[hw2] += dbx*invdts;
- v[hw2 + 1] += dby*invdts;
- v[hw2 + 2] += dbz*invdts;
- v[hw3] += dcx*invdts;
- v[hw3 + 1] += dcy*invdts;
- v[hw3 + 2] += dcz*invdts;
+ v[ow1] += dax*invdt;
+ v[ow1 + 1] += day*invdt;
+ v[ow1 + 2] += daz*invdt;
+ v[hw2] += dbx*invdt;
+ v[hw2 + 1] += dby*invdt;
+ v[hw2 + 2] += dbz*invdt;
+ v[hw3] += dcx*invdt;
+ v[hw3 + 1] += dcy*invdt;
+ v[hw3 + 2] += dcz*invdt;
/* 3*6 flops */
}
if (ow1 < CalcVirAtomEnd)
{
- mdax = mOs*dax;
- mday = mOs*day;
- mdaz = mOs*daz;
- mdbx = mHs*dbx;
- mdby = mHs*dby;
- mdbz = mHs*dbz;
- mdcx = mHs*dcx;
- mdcy = mHs*dcy;
- mdcz = mHs*dcz;
+ mdax = mO*dax;
+ mday = mO*day;
+ mdaz = mO*daz;
+ mdbx = mH*dbx;
+ mdby = mH*dby;
+ mdbz = mH*dbz;
+ mdcx = mH*dcx;
+ mdcy = mH*dcy;
+ mdcz = mH*dcz;
vir_r_m_dr[XX][XX] -= b4[ow1 ]*mdax + (b4[ow1 ]+xb0)*mdbx + (b4[ow1 ]+xc0)*mdcx;
vir_r_m_dr[XX][YY] -= b4[ow1 ]*mday + (b4[ow1 ]+xb0)*mdby + (b4[ow1 ]+xc0)*mdcy;
vir_r_m_dr[XX][ZZ] -= b4[ow1 ]*mdaz + (b4[ow1 ]+xb0)*mdbz + (b4[ow1 ]+xc0)*mdcz;
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2006,2007,2008,2009,2010,2012,2013,2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <assert.h>
-
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "constr.h"
-#include "types/commrec.h"
-#include "domdec.h"
-#include "domdec_network.h"
-#include "mtop_util.h"
-#include "gmx_ga2la.h"
-#include "gmx_hash.h"
-#include "gmx_omp_nthreads.h"
-#include "macros.h"
-
-#include "gmx_fatal.h"
-
-typedef struct {
- int nsend;
- int *a;
- int a_nalloc;
- int nrecv;
-} gmx_specatsend_t;
-
-typedef struct {
- int *ind;
- int nalloc;
- int n;
-} ind_req_t;
-
-typedef struct gmx_domdec_specat_comm {
- /* The number of indices to receive during the setup */
- int nreq[DIM][2][2];
- /* The atoms to send */
- gmx_specatsend_t spas[DIM][2];
- gmx_bool *bSendAtom;
- int bSendAtom_nalloc;
- /* Send buffers */
- int *ibuf;
- int ibuf_nalloc;
- rvec *vbuf;
- int vbuf_nalloc;
- rvec *vbuf2;
- int vbuf2_nalloc;
- /* The range in the local buffer(s) for received atoms */
- int at_start;
- int at_end;
-
- /* The atom indices we need from the surrounding cells.
- * We can gather the indices over nthread threads.
- */
- int nthread;
- ind_req_t *ireq;
-} gmx_domdec_specat_comm_t;
-
-typedef struct gmx_domdec_constraints {
- int *molb_con_offset;
- int *molb_ncon_mol;
- /* The fully local and connected constraints */
- int ncon;
- /* The global constraint number, only required for clearing gc_req */
- int *con_gl;
- int *con_nlocat;
- int con_nalloc;
- /* Boolean that tells if a global constraint index has been requested */
- char *gc_req;
- /* Global to local communicated constraint atom only index */
- gmx_hash_t ga2la;
-
- /* Multi-threading stuff */
- int nthread;
- t_ilist *ils;
-} gmx_domdec_constraints_t;
-
-
-static void dd_move_f_specat(gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac,
- rvec *f, rvec *fshift)
-{
- gmx_specatsend_t *spas;
- rvec *vbuf;
- int n, n0, n1, d, dim, dir, i;
- ivec vis;
- int is;
- gmx_bool bPBC, bScrew;
-
- n = spac->at_end;
- for (d = dd->ndim-1; d >= 0; d--)
- {
- dim = dd->dim[d];
- if (dd->nc[dim] > 2)
- {
- /* Pulse the grid forward and backward */
- spas = spac->spas[d];
- n0 = spas[0].nrecv;
- n1 = spas[1].nrecv;
- n -= n1 + n0;
- vbuf = spac->vbuf;
- /* Send and receive the coordinates */
- dd_sendrecv2_rvec(dd, d,
- f+n+n1, n0, vbuf, spas[0].nsend,
- f+n, n1, vbuf+spas[0].nsend, spas[1].nsend);
- for (dir = 0; dir < 2; dir++)
- {
- bPBC = ((dir == 0 && dd->ci[dim] == 0) ||
- (dir == 1 && dd->ci[dim] == dd->nc[dim]-1));
- bScrew = (bPBC && dd->bScrewPBC && dim == XX);
-
- spas = &spac->spas[d][dir];
- /* Sum the buffer into the required forces */
- if (!bPBC || (!bScrew && fshift == NULL))
- {
- for (i = 0; i < spas->nsend; i++)
- {
- rvec_inc(f[spas->a[i]], *vbuf);
- vbuf++;
- }
- }
- else
- {
- clear_ivec(vis);
- vis[dim] = (dir == 0 ? 1 : -1);
- is = IVEC2IS(vis);
- if (!bScrew)
- {
- /* Sum and add to shift forces */
- for (i = 0; i < spas->nsend; i++)
- {
- rvec_inc(f[spas->a[i]], *vbuf);
- rvec_inc(fshift[is], *vbuf);
- vbuf++;
- }
- }
- else
- {
- /* Rotate the forces */
- for (i = 0; i < spas->nsend; i++)
- {
- f[spas->a[i]][XX] += (*vbuf)[XX];
- f[spas->a[i]][YY] -= (*vbuf)[YY];
- f[spas->a[i]][ZZ] -= (*vbuf)[ZZ];
- if (fshift)
- {
- rvec_inc(fshift[is], *vbuf);
- }
- vbuf++;
- }
- }
- }
- }
- }
- else
- {
- /* Two cells, so we only need to communicate one way */
- spas = &spac->spas[d][0];
- n -= spas->nrecv;
- /* Send and receive the coordinates */
- dd_sendrecv_rvec(dd, d, dddirForward,
- f+n, spas->nrecv, spac->vbuf, spas->nsend);
- /* Sum the buffer into the required forces */
- if (dd->bScrewPBC && dim == XX &&
- (dd->ci[dim] == 0 ||
- dd->ci[dim] == dd->nc[dim]-1))
- {
- for (i = 0; i < spas->nsend; i++)
- {
- /* Rotate the force */
- f[spas->a[i]][XX] += spac->vbuf[i][XX];
- f[spas->a[i]][YY] -= spac->vbuf[i][YY];
- f[spas->a[i]][ZZ] -= spac->vbuf[i][ZZ];
- }
- }
- else
- {
- for (i = 0; i < spas->nsend; i++)
- {
- rvec_inc(f[spas->a[i]], spac->vbuf[i]);
- }
- }
- }
- }
-}
-
-void dd_move_f_vsites(gmx_domdec_t *dd, rvec *f, rvec *fshift)
-{
- if (dd->vsite_comm)
- {
- dd_move_f_specat(dd, dd->vsite_comm, f, fshift);
- }
-}
-
-void dd_clear_f_vsites(gmx_domdec_t *dd, rvec *f)
-{
- int i;
-
- if (dd->vsite_comm)
- {
- for (i = dd->vsite_comm->at_start; i < dd->vsite_comm->at_end; i++)
- {
- clear_rvec(f[i]);
- }
- }
-}
-
-static void dd_move_x_specat(gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac,
- matrix box,
- rvec *x0,
- rvec *x1, gmx_bool bX1IsCoord)
-{
- gmx_specatsend_t *spas;
- rvec *x, *vbuf, *rbuf;
- int nvec, v, n, nn, ns0, ns1, nr0, nr1, nr, d, dim, dir, i;
- gmx_bool bPBC, bScrew = FALSE;
- rvec shift = {0, 0, 0};
-
- nvec = 1;
- if (x1 != NULL)
- {
- nvec++;
- }
-
- n = spac->at_start;
- for (d = 0; d < dd->ndim; d++)
- {
- dim = dd->dim[d];
- if (dd->nc[dim] > 2)
- {
- /* Pulse the grid forward and backward */
- vbuf = spac->vbuf;
- for (dir = 0; dir < 2; dir++)
- {
- if (dir == 0 && dd->ci[dim] == 0)
- {
- bPBC = TRUE;
- bScrew = (dd->bScrewPBC && dim == XX);
- copy_rvec(box[dim], shift);
- }
- else if (dir == 1 && dd->ci[dim] == dd->nc[dim]-1)
- {
- bPBC = TRUE;
- bScrew = (dd->bScrewPBC && dim == XX);
- for (i = 0; i < DIM; i++)
- {
- shift[i] = -box[dim][i];
- }
- }
- else
- {
- bPBC = FALSE;
- bScrew = FALSE;
- }
- spas = &spac->spas[d][dir];
- for (v = 0; v < nvec; v++)
- {
- x = (v == 0 ? x0 : x1);
- /* Copy the required coordinates to the send buffer */
- if (!bPBC || (v == 1 && !bX1IsCoord))
- {
- /* Only copy */
- for (i = 0; i < spas->nsend; i++)
- {
- copy_rvec(x[spas->a[i]], *vbuf);
- vbuf++;
- }
- }
- else if (!bScrew)
- {
- /* Shift coordinates */
- for (i = 0; i < spas->nsend; i++)
- {
- rvec_add(x[spas->a[i]], shift, *vbuf);
- vbuf++;
- }
- }
- else
- {
- /* Shift and rotate coordinates */
- for (i = 0; i < spas->nsend; i++)
- {
- (*vbuf)[XX] = x[spas->a[i]][XX] + shift[XX];
- (*vbuf)[YY] = box[YY][YY] - x[spas->a[i]][YY] + shift[YY];
- (*vbuf)[ZZ] = box[ZZ][ZZ] - x[spas->a[i]][ZZ] + shift[ZZ];
- vbuf++;
- }
- }
- }
- }
- /* Send and receive the coordinates */
- spas = spac->spas[d];
- ns0 = spas[0].nsend;
- nr0 = spas[0].nrecv;
- ns1 = spas[1].nsend;
- nr1 = spas[1].nrecv;
- if (nvec == 1)
- {
- dd_sendrecv2_rvec(dd, d,
- spac->vbuf+ns0, ns1, x0+n, nr1,
- spac->vbuf, ns0, x0+n+nr1, nr0);
- }
- else
- {
- /* Communicate both vectors in one buffer */
- rbuf = spac->vbuf2;
- dd_sendrecv2_rvec(dd, d,
- spac->vbuf+2*ns0, 2*ns1, rbuf, 2*nr1,
- spac->vbuf, 2*ns0, rbuf+2*nr1, 2*nr0);
- /* Split the buffer into the two vectors */
- nn = n;
- for (dir = 1; dir >= 0; dir--)
- {
- nr = spas[dir].nrecv;
- for (v = 0; v < 2; v++)
- {
- x = (v == 0 ? x0 : x1);
- for (i = 0; i < nr; i++)
- {
- copy_rvec(*rbuf, x[nn+i]);
- rbuf++;
- }
- }
- nn += nr;
- }
- }
- n += nr0 + nr1;
- }
- else
- {
- spas = &spac->spas[d][0];
- /* Copy the required coordinates to the send buffer */
- vbuf = spac->vbuf;
- for (v = 0; v < nvec; v++)
- {
- x = (v == 0 ? x0 : x1);
- if (dd->bScrewPBC && dim == XX &&
- (dd->ci[XX] == 0 || dd->ci[XX] == dd->nc[XX]-1))
- {
- /* Here we only perform the rotation, the rest of the pbc
- * is handled in the constraint or viste routines.
- */
- for (i = 0; i < spas->nsend; i++)
- {
- (*vbuf)[XX] = x[spas->a[i]][XX];
- (*vbuf)[YY] = box[YY][YY] - x[spas->a[i]][YY];
- (*vbuf)[ZZ] = box[ZZ][ZZ] - x[spas->a[i]][ZZ];
- vbuf++;
- }
- }
- else
- {
- for (i = 0; i < spas->nsend; i++)
- {
- copy_rvec(x[spas->a[i]], *vbuf);
- vbuf++;
- }
- }
- }
- /* Send and receive the coordinates */
- if (nvec == 1)
- {
- dd_sendrecv_rvec(dd, d, dddirBackward,
- spac->vbuf, spas->nsend, x0+n, spas->nrecv);
- }
- else
- {
- /* Communicate both vectors in one buffer */
- rbuf = spac->vbuf2;
- dd_sendrecv_rvec(dd, d, dddirBackward,
- spac->vbuf, 2*spas->nsend, rbuf, 2*spas->nrecv);
- /* Split the buffer into the two vectors */
- nr = spas[0].nrecv;
- for (v = 0; v < 2; v++)
- {
- x = (v == 0 ? x0 : x1);
- for (i = 0; i < nr; i++)
- {
- copy_rvec(*rbuf, x[n+i]);
- rbuf++;
- }
- }
- }
- n += spas->nrecv;
- }
- }
-}
-
-void dd_move_x_constraints(gmx_domdec_t *dd, matrix box,
- rvec *x0, rvec *x1, gmx_bool bX1IsCoord)
-{
- if (dd->constraint_comm)
- {
- dd_move_x_specat(dd, dd->constraint_comm, box, x0, x1, bX1IsCoord);
- }
-}
-
-void dd_move_x_vsites(gmx_domdec_t *dd, matrix box, rvec *x)
-{
- if (dd->vsite_comm)
- {
- dd_move_x_specat(dd, dd->vsite_comm, box, x, NULL, FALSE);
- }
-}
-
-int *dd_constraints_nlocalatoms(gmx_domdec_t *dd)
-{
- if (dd->constraints)
- {
- return dd->constraints->con_nlocat;
- }
- else
- {
- return NULL;
- }
-}
-
-void dd_clear_local_constraint_indices(gmx_domdec_t *dd)
-{
- gmx_domdec_constraints_t *dc;
- int i;
-
- dc = dd->constraints;
-
- for (i = 0; i < dc->ncon; i++)
- {
- dc->gc_req[dc->con_gl[i]] = 0;
- }
-
- if (dd->constraint_comm)
- {
- gmx_hash_clear_and_optimize(dc->ga2la);
- }
-}
-
-void dd_clear_local_vsite_indices(gmx_domdec_t *dd)
-{
- int i;
-
- if (dd->vsite_comm)
- {
- gmx_hash_clear_and_optimize(dd->ga2la_vsite);
- }
-}
-
-static int setup_specat_communication(gmx_domdec_t *dd,
- ind_req_t *ireq,
- gmx_domdec_specat_comm_t *spac,
- gmx_hash_t ga2la_specat,
- int at_start,
- int vbuf_fac,
- const char *specat_type,
- const char *add_err)
-{
- int nsend[2], nlast, nsend_zero[2] = {0, 0}, *nsend_ptr;
- int d, dim, ndir, dir, nr, ns, i, nrecv_local, n0, start, indr, ind, buf[2];
- int nat_tot_specat, nat_tot_prev, nalloc_old;
- gmx_bool bPBC, bFirst;
- gmx_specatsend_t *spas;
-
- if (debug)
- {
- fprintf(debug, "Begin setup_specat_communication for %s\n", specat_type);
- }
-
- /* nsend[0]: the number of atoms requested by this node only,
- * we communicate this for more efficients checks
- * nsend[1]: the total number of requested atoms
- */
- nsend[0] = ireq->n;
- nsend[1] = nsend[0];
- nlast = nsend[1];
- for (d = dd->ndim-1; d >= 0; d--)
- {
- /* Pulse the grid forward and backward */
- dim = dd->dim[d];
- bPBC = (dim < dd->npbcdim);
- if (dd->nc[dim] == 2)
- {
- /* Only 2 cells, so we only need to communicate once */
- ndir = 1;
- }
- else
- {
- ndir = 2;
- }
- for (dir = 0; dir < ndir; dir++)
- {
- if (!bPBC &&
- dd->nc[dim] > 2 &&
- ((dir == 0 && dd->ci[dim] == dd->nc[dim] - 1) ||
- (dir == 1 && dd->ci[dim] == 0)))
- {
- /* No pbc: the fist/last cell should not request atoms */
- nsend_ptr = nsend_zero;
- }
- else
- {
- nsend_ptr = nsend;
- }
- /* Communicate the number of indices */
- dd_sendrecv_int(dd, d, dir == 0 ? dddirForward : dddirBackward,
- nsend_ptr, 2, spac->nreq[d][dir], 2);
- nr = spac->nreq[d][dir][1];
- if (nlast+nr > ireq->nalloc)
- {
- ireq->nalloc = over_alloc_dd(nlast+nr);
- srenew(ireq->ind, ireq->nalloc);
- }
- /* Communicate the indices */
- dd_sendrecv_int(dd, d, dir == 0 ? dddirForward : dddirBackward,
- ireq->ind, nsend_ptr[1], ireq->ind+nlast, nr);
- nlast += nr;
- }
- nsend[1] = nlast;
- }
- if (debug)
- {
- fprintf(debug, "Communicated the counts\n");
- }
-
- /* Search for the requested atoms and communicate the indices we have */
- nat_tot_specat = at_start;
- nrecv_local = 0;
- for (d = 0; d < dd->ndim; d++)
- {
- bFirst = (d == 0);
- /* Pulse the grid forward and backward */
- if (dd->dim[d] >= dd->npbcdim || dd->nc[dd->dim[d]] > 2)
- {
- ndir = 2;
- }
- else
- {
- ndir = 1;
- }
- nat_tot_prev = nat_tot_specat;
- for (dir = ndir-1; dir >= 0; dir--)
- {
- if (nat_tot_specat > spac->bSendAtom_nalloc)
- {
- nalloc_old = spac->bSendAtom_nalloc;
- spac->bSendAtom_nalloc = over_alloc_dd(nat_tot_specat);
- srenew(spac->bSendAtom, spac->bSendAtom_nalloc);
- for (i = nalloc_old; i < spac->bSendAtom_nalloc; i++)
- {
- spac->bSendAtom[i] = FALSE;
- }
- }
- spas = &spac->spas[d][dir];
- n0 = spac->nreq[d][dir][0];
- nr = spac->nreq[d][dir][1];
- if (debug)
- {
- fprintf(debug, "dim=%d, dir=%d, searching for %d atoms\n",
- d, dir, nr);
- }
- start = nlast - nr;
- spas->nsend = 0;
- nsend[0] = 0;
- for (i = 0; i < nr; i++)
- {
- indr = ireq->ind[start+i];
- ind = -1;
- /* Check if this is a home atom and if so ind will be set */
- if (!ga2la_get_home(dd->ga2la, indr, &ind))
- {
- /* Search in the communicated atoms */
- ind = gmx_hash_get_minone(ga2la_specat, indr);
- }
- if (ind >= 0)
- {
- if (i < n0 || !spac->bSendAtom[ind])
- {
- if (spas->nsend+1 > spas->a_nalloc)
- {
- spas->a_nalloc = over_alloc_large(spas->nsend+1);
- srenew(spas->a, spas->a_nalloc);
- }
- /* Store the local index so we know which coordinates
- * to send out later.
- */
- spas->a[spas->nsend] = ind;
- spac->bSendAtom[ind] = TRUE;
- if (spas->nsend+1 > spac->ibuf_nalloc)
- {
- spac->ibuf_nalloc = over_alloc_large(spas->nsend+1);
- srenew(spac->ibuf, spac->ibuf_nalloc);
- }
- /* Store the global index so we can send it now */
- spac->ibuf[spas->nsend] = indr;
- if (i < n0)
- {
- nsend[0]++;
- }
- spas->nsend++;
- }
- }
- }
- nlast = start;
- /* Clear the local flags */
- for (i = 0; i < spas->nsend; i++)
- {
- spac->bSendAtom[spas->a[i]] = FALSE;
- }
- /* Send and receive the number of indices to communicate */
- nsend[1] = spas->nsend;
- dd_sendrecv_int(dd, d, dir == 0 ? dddirBackward : dddirForward,
- nsend, 2, buf, 2);
- if (debug)
- {
- fprintf(debug, "Send to rank %d, %d (%d) indices, "
- "receive from rank %d, %d (%d) indices\n",
- dd->neighbor[d][1-dir], nsend[1], nsend[0],
- dd->neighbor[d][dir], buf[1], buf[0]);
- if (gmx_debug_at)
- {
- for (i = 0; i < spas->nsend; i++)
- {
- fprintf(debug, " %d", spac->ibuf[i]+1);
- }
- fprintf(debug, "\n");
- }
- }
- nrecv_local += buf[0];
- spas->nrecv = buf[1];
- if (nat_tot_specat + spas->nrecv > dd->gatindex_nalloc)
- {
- dd->gatindex_nalloc =
- over_alloc_dd(nat_tot_specat + spas->nrecv);
- srenew(dd->gatindex, dd->gatindex_nalloc);
- }
- /* Send and receive the indices */
- dd_sendrecv_int(dd, d, dir == 0 ? dddirBackward : dddirForward,
- spac->ibuf, spas->nsend,
- dd->gatindex+nat_tot_specat, spas->nrecv);
- nat_tot_specat += spas->nrecv;
- }
-
- /* Allocate the x/f communication buffers */
- ns = spac->spas[d][0].nsend;
- nr = spac->spas[d][0].nrecv;
- if (ndir == 2)
- {
- ns += spac->spas[d][1].nsend;
- nr += spac->spas[d][1].nrecv;
- }
- if (vbuf_fac*ns > spac->vbuf_nalloc)
- {
- spac->vbuf_nalloc = over_alloc_dd(vbuf_fac*ns);
- srenew(spac->vbuf, spac->vbuf_nalloc);
- }
- if (vbuf_fac == 2 && vbuf_fac*nr > spac->vbuf2_nalloc)
- {
- spac->vbuf2_nalloc = over_alloc_dd(vbuf_fac*nr);
- srenew(spac->vbuf2, spac->vbuf2_nalloc);
- }
-
- /* Make a global to local index for the communication atoms */
- for (i = nat_tot_prev; i < nat_tot_specat; i++)
- {
- gmx_hash_change_or_set(ga2la_specat, dd->gatindex[i], i);
- }
- }
-
- /* Check that in the end we got the number of atoms we asked for */
- if (nrecv_local != ireq->n)
- {
- if (debug)
- {
- fprintf(debug, "Requested %d, received %d (tot recv %d)\n",
- ireq->n, nrecv_local, nat_tot_specat-at_start);
- if (gmx_debug_at)
- {
- for (i = 0; i < ireq->n; i++)
- {
- ind = gmx_hash_get_minone(ga2la_specat, ireq->ind[i]);
- fprintf(debug, " %s%d",
- (ind >= 0) ? "" : "!",
- ireq->ind[i]+1);
- }
- fprintf(debug, "\n");
- }
- }
- fprintf(stderr, "\nDD cell %d %d %d: Neighboring cells do not have atoms:",
- dd->ci[XX], dd->ci[YY], dd->ci[ZZ]);
- for (i = 0; i < ireq->n; i++)
- {
- if (gmx_hash_get_minone(ga2la_specat, ireq->ind[i]) < 0)
- {
- fprintf(stderr, " %d", ireq->ind[i]+1);
- }
- }
- fprintf(stderr, "\n");
- gmx_fatal(FARGS, "DD cell %d %d %d could only obtain %d of the %d atoms that are connected via %ss from the neighboring cells. This probably means your %s lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells%s%s.",
- dd->ci[XX], dd->ci[YY], dd->ci[ZZ],
- nrecv_local, ireq->n, specat_type,
- specat_type, add_err,
- dd->bGridJump ? " or use the -rcon option of mdrun" : "");
- }
-
- spac->at_start = at_start;
- spac->at_end = nat_tot_specat;
-
- if (debug)
- {
- fprintf(debug, "Done setup_specat_communication\n");
- }
-
- return nat_tot_specat;
-}
-
-static void walk_out(int con, int con_offset, int a, int offset, int nrec,
- int ncon1, const t_iatom *ia1, const t_iatom *ia2,
- const t_blocka *at2con,
- const gmx_ga2la_t ga2la, gmx_bool bHomeConnect,
- gmx_domdec_constraints_t *dc,
- gmx_domdec_specat_comm_t *dcc,
- t_ilist *il_local,
- ind_req_t *ireq)
-{
- int a1_gl, a2_gl, a_loc, i, coni, b;
- const t_iatom *iap;
-
- if (dc->gc_req[con_offset+con] == 0)
- {
- /* Add this non-home constraint to the list */
- if (dc->ncon+1 > dc->con_nalloc)
- {
- dc->con_nalloc = over_alloc_large(dc->ncon+1);
- srenew(dc->con_gl, dc->con_nalloc);
- srenew(dc->con_nlocat, dc->con_nalloc);
- }
- dc->con_gl[dc->ncon] = con_offset + con;
- dc->con_nlocat[dc->ncon] = (bHomeConnect ? 1 : 0);
- dc->gc_req[con_offset+con] = 1;
- if (il_local->nr + 3 > il_local->nalloc)
- {
- il_local->nalloc = over_alloc_dd(il_local->nr+3);
- srenew(il_local->iatoms, il_local->nalloc);
- }
- iap = constr_iatomptr(ncon1, ia1, ia2, con);
- il_local->iatoms[il_local->nr++] = iap[0];
- a1_gl = offset + iap[1];
- a2_gl = offset + iap[2];
- /* The following indexing code can probably be optizimed */
- if (ga2la_get_home(ga2la, a1_gl, &a_loc))
- {
- il_local->iatoms[il_local->nr++] = a_loc;
- }
- else
- {
- /* We set this index later */
- il_local->iatoms[il_local->nr++] = -a1_gl - 1;
- }
- if (ga2la_get_home(ga2la, a2_gl, &a_loc))
- {
- il_local->iatoms[il_local->nr++] = a_loc;
- }
- else
- {
- /* We set this index later */
- il_local->iatoms[il_local->nr++] = -a2_gl - 1;
- }
- dc->ncon++;
- }
- /* Check to not ask for the same atom more than once */
- if (gmx_hash_get_minone(dc->ga2la, offset+a) == -1)
- {
- assert(dcc);
- /* Add this non-home atom to the list */
- if (ireq->n+1 > ireq->nalloc)
- {
- ireq->nalloc = over_alloc_large(ireq->n+1);
- srenew(ireq->ind, ireq->nalloc);
- }
- ireq->ind[ireq->n++] = offset + a;
- /* Temporarily mark with -2, we get the index later */
- gmx_hash_set(dc->ga2la, offset+a, -2);
- }
-
- if (nrec > 0)
- {
- for (i = at2con->index[a]; i < at2con->index[a+1]; i++)
- {
- coni = at2con->a[i];
- if (coni != con)
- {
- /* Walk further */
- iap = constr_iatomptr(ncon1, ia1, ia2, coni);
- if (a == iap[1])
- {
- b = iap[2];
- }
- else
- {
- b = iap[1];
- }
- if (!ga2la_get_home(ga2la, offset+b, &a_loc))
- {
- walk_out(coni, con_offset, b, offset, nrec-1,
- ncon1, ia1, ia2, at2con,
- ga2la, FALSE, dc, dcc, il_local, ireq);
- }
- }
- }
- }
-}
-
-static void atoms_to_settles(gmx_domdec_t *dd,
- const gmx_mtop_t *mtop,
- const int *cginfo,
- const int **at2settle_mt,
- int cg_start, int cg_end,
- t_ilist *ils_local,
- ind_req_t *ireq)
-{
- gmx_ga2la_t ga2la;
- gmx_mtop_atomlookup_t alook;
- int settle;
- int nral, sa;
- int cg, a, a_gl, a_glsa, a_gls[3], a_locs[3];
- int mb, molnr, a_mol, offset;
- const gmx_molblock_t *molb;
- const t_iatom *ia1;
- gmx_bool a_home[3];
- int nlocal;
- gmx_bool bAssign;
-
- ga2la = dd->ga2la;
-
- alook = gmx_mtop_atomlookup_settle_init(mtop);
-
- nral = NRAL(F_SETTLE);
-
- for (cg = cg_start; cg < cg_end; cg++)
- {
- if (GET_CGINFO_SETTLE(cginfo[cg]))
- {
- for (a = dd->cgindex[cg]; a < dd->cgindex[cg+1]; a++)
- {
- a_gl = dd->gatindex[a];
-
- gmx_mtop_atomnr_to_molblock_ind(alook, a_gl, &mb, &molnr, &a_mol);
- molb = &mtop->molblock[mb];
-
- settle = at2settle_mt[molb->type][a_mol];
-
- if (settle >= 0)
- {
- offset = a_gl - a_mol;
-
- ia1 = mtop->moltype[molb->type].ilist[F_SETTLE].iatoms;
-
- bAssign = FALSE;
- nlocal = 0;
- for (sa = 0; sa < nral; sa++)
- {
- a_glsa = offset + ia1[settle*(1+nral)+1+sa];
- a_gls[sa] = a_glsa;
- a_home[sa] = ga2la_get_home(ga2la, a_glsa, &a_locs[sa]);
- if (a_home[sa])
- {
- if (nlocal == 0 && a_gl == a_glsa)
- {
- bAssign = TRUE;
- }
- nlocal++;
- }
- }
-
- if (bAssign)
- {
- if (ils_local->nr+1+nral > ils_local->nalloc)
- {
- ils_local->nalloc = over_alloc_dd(ils_local->nr+1+nral);
- srenew(ils_local->iatoms, ils_local->nalloc);
- }
-
- ils_local->iatoms[ils_local->nr++] = ia1[settle*4];
-
- for (sa = 0; sa < nral; sa++)
- {
- if (ga2la_get_home(ga2la, a_gls[sa], &a_locs[sa]))
- {
- ils_local->iatoms[ils_local->nr++] = a_locs[sa];
- }
- else
- {
- ils_local->iatoms[ils_local->nr++] = -a_gls[sa] - 1;
- /* Add this non-home atom to the list */
- if (ireq->n+1 > ireq->nalloc)
- {
- ireq->nalloc = over_alloc_large(ireq->n+1);
- srenew(ireq->ind, ireq->nalloc);
- }
- ireq->ind[ireq->n++] = a_gls[sa];
- /* A check on double atom requests is
- * not required for settle.
- */
- }
- }
- }
- }
- }
- }
- }
-
- gmx_mtop_atomlookup_destroy(alook);
-}
-
-static void atoms_to_constraints(gmx_domdec_t *dd,
- const gmx_mtop_t *mtop,
- const int *cginfo,
- const t_blocka *at2con_mt, int nrec,
- t_ilist *ilc_local,
- ind_req_t *ireq)
-{
- const t_blocka *at2con;
- gmx_ga2la_t ga2la;
- gmx_mtop_atomlookup_t alook;
- int ncon1;
- gmx_molblock_t *molb;
- t_iatom *ia1, *ia2, *iap;
- int nhome, cg, a, a_gl, a_mol, a_loc, b_lo, offset, mb, molnr, b_mol, i, con, con_offset;
- gmx_domdec_constraints_t *dc;
- gmx_domdec_specat_comm_t *dcc;
-
- dc = dd->constraints;
- dcc = dd->constraint_comm;
-
- ga2la = dd->ga2la;
-
- alook = gmx_mtop_atomlookup_init(mtop);
-
- nhome = 0;
- for (cg = 0; cg < dd->ncg_home; cg++)
- {
- if (GET_CGINFO_CONSTR(cginfo[cg]))
- {
- for (a = dd->cgindex[cg]; a < dd->cgindex[cg+1]; a++)
- {
- a_gl = dd->gatindex[a];
-
- gmx_mtop_atomnr_to_molblock_ind(alook, a_gl, &mb, &molnr, &a_mol);
- molb = &mtop->molblock[mb];
-
- ncon1 = mtop->moltype[molb->type].ilist[F_CONSTR].nr/NRAL(F_SETTLE);
-
- ia1 = mtop->moltype[molb->type].ilist[F_CONSTR].iatoms;
- ia2 = mtop->moltype[molb->type].ilist[F_CONSTRNC].iatoms;
-
- /* Calculate the global constraint number offset for the molecule.
- * This is only required for the global index to make sure
- * that we use each constraint only once.
- */
- con_offset =
- dc->molb_con_offset[mb] + molnr*dc->molb_ncon_mol[mb];
-
- /* The global atom number offset for this molecule */
- offset = a_gl - a_mol;
- at2con = &at2con_mt[molb->type];
- for (i = at2con->index[a_mol]; i < at2con->index[a_mol+1]; i++)
- {
- con = at2con->a[i];
- iap = constr_iatomptr(ncon1, ia1, ia2, con);
- if (a_mol == iap[1])
- {
- b_mol = iap[2];
- }
- else
- {
- b_mol = iap[1];
- }
- if (ga2la_get_home(ga2la, offset+b_mol, &a_loc))
- {
- /* Add this fully home constraint at the first atom */
- if (a_mol < b_mol)
- {
- if (dc->ncon+1 > dc->con_nalloc)
- {
- dc->con_nalloc = over_alloc_large(dc->ncon+1);
- srenew(dc->con_gl, dc->con_nalloc);
- srenew(dc->con_nlocat, dc->con_nalloc);
- }
- dc->con_gl[dc->ncon] = con_offset + con;
- dc->con_nlocat[dc->ncon] = 2;
- if (ilc_local->nr + 3 > ilc_local->nalloc)
- {
- ilc_local->nalloc = over_alloc_dd(ilc_local->nr + 3);
- srenew(ilc_local->iatoms, ilc_local->nalloc);
- }
- b_lo = a_loc;
- ilc_local->iatoms[ilc_local->nr++] = iap[0];
- ilc_local->iatoms[ilc_local->nr++] = (a_gl == iap[1] ? a : b_lo);
- ilc_local->iatoms[ilc_local->nr++] = (a_gl == iap[1] ? b_lo : a );
- dc->ncon++;
- nhome++;
- }
- }
- else
- {
- /* We need the nrec constraints coupled to this constraint,
- * so we need to walk out of the home cell by nrec+1 atoms,
- * since already atom bg is not locally present.
- * Therefore we call walk_out with nrec recursions to go
- * after this first call.
- */
- walk_out(con, con_offset, b_mol, offset, nrec,
- ncon1, ia1, ia2, at2con,
- dd->ga2la, TRUE, dc, dcc, ilc_local, ireq);
- }
- }
- }
- }
- }
-
- gmx_mtop_atomlookup_destroy(alook);
-
- if (debug)
- {
- fprintf(debug,
- "Constraints: home %3d border %3d atoms: %3d\n",
- nhome, dc->ncon-nhome,
- dd->constraint_comm ? ireq->n : 0);
- }
-}
-
-int dd_make_local_constraints(gmx_domdec_t *dd, int at_start,
- const gmx_mtop_t *mtop,
- const int *cginfo,
- gmx_constr_t constr, int nrec,
- t_ilist *il_local)
-{
- gmx_domdec_constraints_t *dc;
- t_ilist *ilc_local, *ils_local;
- ind_req_t *ireq;
- const t_blocka *at2con_mt;
- const int **at2settle_mt;
- gmx_hash_t ga2la_specat;
- int at_end, i, j;
- t_iatom *iap;
-
- dc = dd->constraints;
-
- ilc_local = &il_local[F_CONSTR];
- ils_local = &il_local[F_SETTLE];
-
- dc->ncon = 0;
- ilc_local->nr = 0;
- if (dd->constraint_comm)
- {
- at2con_mt = atom2constraints_moltype(constr);
- ireq = &dd->constraint_comm->ireq[0];
- ireq->n = 0;
- }
- else
- {
- at2con_mt = NULL;
- ireq = NULL;
- }
-
- if (dd->bInterCGsettles)
- {
- at2settle_mt = atom2settle_moltype(constr);
- ils_local->nr = 0;
- }
- else
- {
- /* Settle works inside charge groups, we assigned them already */
- at2settle_mt = NULL;
- }
-
- if (at2settle_mt == NULL)
- {
- atoms_to_constraints(dd, mtop, cginfo, at2con_mt, nrec,
- ilc_local, ireq);
- }
- else
- {
- int t0_set;
- int thread;
-
- /* Do the constraints, if present, on the first thread.
- * Do the settles on all other threads.
- */
- t0_set = ((at2con_mt != NULL && dc->nthread > 1) ? 1 : 0);
-
-#pragma omp parallel for num_threads(dc->nthread) schedule(static)
- for (thread = 0; thread < dc->nthread; thread++)
- {
- if (at2con_mt && thread == 0)
- {
- atoms_to_constraints(dd, mtop, cginfo, at2con_mt, nrec,
- ilc_local, ireq);
- }
-
- if (thread >= t0_set)
- {
- int cg0, cg1;
- t_ilist *ilst;
- ind_req_t *ireqt;
-
- /* Distribute the settle check+assignments over
- * dc->nthread or dc->nthread-1 threads.
- */
- cg0 = (dd->ncg_home*(thread-t0_set ))/(dc->nthread-t0_set);
- cg1 = (dd->ncg_home*(thread-t0_set+1))/(dc->nthread-t0_set);
-
- if (thread == t0_set)
- {
- ilst = ils_local;
- }
- else
- {
- ilst = &dc->ils[thread];
- }
- ilst->nr = 0;
-
- ireqt = &dd->constraint_comm->ireq[thread];
- if (thread > 0)
- {
- ireqt->n = 0;
- }
-
- atoms_to_settles(dd, mtop, cginfo, at2settle_mt,
- cg0, cg1,
- ilst, ireqt);
- }
- }
-
- /* Combine the generate settles and requested indices */
- for (thread = 1; thread < dc->nthread; thread++)
- {
- t_ilist *ilst;
- ind_req_t *ireqt;
- int ia;
-
- if (thread > t0_set)
- {
- ilst = &dc->ils[thread];
- if (ils_local->nr + ilst->nr > ils_local->nalloc)
- {
- ils_local->nalloc = over_alloc_large(ils_local->nr + ilst->nr);
- srenew(ils_local->iatoms, ils_local->nalloc);
- }
- for (ia = 0; ia < ilst->nr; ia++)
- {
- ils_local->iatoms[ils_local->nr+ia] = ilst->iatoms[ia];
- }
- ils_local->nr += ilst->nr;
- }
-
- ireqt = &dd->constraint_comm->ireq[thread];
- if (ireq->n+ireqt->n > ireq->nalloc)
- {
- ireq->nalloc = over_alloc_large(ireq->n+ireqt->n);
- srenew(ireq->ind, ireq->nalloc);
- }
- for (ia = 0; ia < ireqt->n; ia++)
- {
- ireq->ind[ireq->n+ia] = ireqt->ind[ia];
- }
- ireq->n += ireqt->n;
- }
-
- if (debug)
- {
- fprintf(debug, "Settles: total %3d\n", ils_local->nr/4);
- }
- }
-
- if (dd->constraint_comm)
- {
- int nral1;
-
- at_end =
- setup_specat_communication(dd, ireq, dd->constraint_comm,
- dd->constraints->ga2la,
- at_start, 2,
- "constraint", " or lincs-order");
-
- /* Fill in the missing indices */
- ga2la_specat = dd->constraints->ga2la;
-
- nral1 = 1 + NRAL(F_CONSTR);
- for (i = 0; i < ilc_local->nr; i += nral1)
- {
- iap = ilc_local->iatoms + i;
- for (j = 1; j < nral1; j++)
- {
- if (iap[j] < 0)
- {
- iap[j] = gmx_hash_get_minone(ga2la_specat, -iap[j]-1);
- }
- }
- }
-
- nral1 = 1 + NRAL(F_SETTLE);
- for (i = 0; i < ils_local->nr; i += nral1)
- {
- iap = ils_local->iatoms + i;
- for (j = 1; j < nral1; j++)
- {
- if (iap[j] < 0)
- {
- iap[j] = gmx_hash_get_minone(ga2la_specat, -iap[j]-1);
- }
- }
- }
- }
- else
- {
- at_end = at_start;
- }
-
- return at_end;
-}
-
-int dd_make_local_vsites(gmx_domdec_t *dd, int at_start, t_ilist *lil)
-{
- gmx_domdec_specat_comm_t *spac;
- ind_req_t *ireq;
- gmx_hash_t ga2la_specat;
- int ftype, nral, i, j, gat, a;
- t_ilist *lilf;
- t_iatom *iatoms;
- int at_end;
-
- spac = dd->vsite_comm;
- ireq = &spac->ireq[0];
- ga2la_specat = dd->ga2la_vsite;
-
- ireq->n = 0;
- /* Loop over all the home vsites */
- for (ftype = 0; ftype < F_NRE; ftype++)
- {
- if (interaction_function[ftype].flags & IF_VSITE)
- {
- nral = NRAL(ftype);
- lilf = &lil[ftype];
- for (i = 0; i < lilf->nr; i += 1+nral)
- {
- iatoms = lilf->iatoms + i;
- /* Check if we have the other atoms */
- for (j = 1; j < 1+nral; j++)
- {
- if (iatoms[j] < 0)
- {
- /* This is not a home atom,
- * we need to ask our neighbors.
- */
- a = -iatoms[j] - 1;
- /* Check to not ask for the same atom more than once */
- if (gmx_hash_get_minone(dd->ga2la_vsite, a) == -1)
- {
- /* Add this non-home atom to the list */
- if (ireq->n+1 > ireq->nalloc)
- {
- ireq->nalloc = over_alloc_large(ireq->n+1);
- srenew(ireq->ind, ireq->nalloc);
- }
- ireq->ind[ireq->n++] = a;
- /* Temporarily mark with -2,
- * we get the index later.
- */
- gmx_hash_set(ga2la_specat, a, -2);
- }
- }
- }
- }
- }
- }
-
- at_end = setup_specat_communication(dd, ireq, dd->vsite_comm, ga2la_specat,
- at_start, 1, "vsite", "");
-
- /* Fill in the missing indices */
- for (ftype = 0; ftype < F_NRE; ftype++)
- {
- if (interaction_function[ftype].flags & IF_VSITE)
- {
- nral = NRAL(ftype);
- lilf = &lil[ftype];
- for (i = 0; i < lilf->nr; i += 1+nral)
- {
- iatoms = lilf->iatoms + i;
- for (j = 1; j < 1+nral; j++)
- {
- if (iatoms[j] < 0)
- {
- iatoms[j] = gmx_hash_get_minone(ga2la_specat, -iatoms[j]-1);
- }
- }
- }
- }
- }
-
- return at_end;
-}
-
-static gmx_domdec_specat_comm_t *specat_comm_init(int nthread)
-{
- gmx_domdec_specat_comm_t *spac;
-
- snew(spac, 1);
- spac->nthread = nthread;
- snew(spac->ireq, spac->nthread);
-
- return spac;
-}
-
-void init_domdec_constraints(gmx_domdec_t *dd,
- gmx_mtop_t *mtop)
-{
- gmx_domdec_constraints_t *dc;
- gmx_molblock_t *molb;
- int mb, ncon, c, a;
-
- if (debug)
- {
- fprintf(debug, "Begin init_domdec_constraints\n");
- }
-
- snew(dd->constraints, 1);
- dc = dd->constraints;
-
- snew(dc->molb_con_offset, mtop->nmolblock);
- snew(dc->molb_ncon_mol, mtop->nmolblock);
-
- ncon = 0;
- for (mb = 0; mb < mtop->nmolblock; mb++)
- {
- molb = &mtop->molblock[mb];
- dc->molb_con_offset[mb] = ncon;
- dc->molb_ncon_mol[mb] =
- mtop->moltype[molb->type].ilist[F_CONSTR].nr/3 +
- mtop->moltype[molb->type].ilist[F_CONSTRNC].nr/3;
- ncon += molb->nmol*dc->molb_ncon_mol[mb];
- }
-
- if (ncon > 0)
- {
- snew(dc->gc_req, ncon);
- for (c = 0; c < ncon; c++)
- {
- dc->gc_req[c] = 0;
- }
- }
-
- /* Use a hash table for the global to local index.
- * The number of keys is a rough estimate, it will be optimized later.
- */
- dc->ga2la = gmx_hash_init(min(mtop->natoms/20,
- mtop->natoms/(2*dd->nnodes)));
-
- dc->nthread = gmx_omp_nthreads_get(emntDomdec);
- snew(dc->ils, dc->nthread);
-
- dd->constraint_comm = specat_comm_init(dc->nthread);
-}
-
-void init_domdec_vsites(gmx_domdec_t *dd, int n_intercg_vsite)
-{
- int i;
- gmx_domdec_constraints_t *dc;
-
- if (debug)
- {
- fprintf(debug, "Begin init_domdec_vsites\n");
- }
-
- /* Use a hash table for the global to local index.
- * The number of keys is a rough estimate, it will be optimized later.
- */
- dd->ga2la_vsite = gmx_hash_init(min(n_intercg_vsite/20,
- n_intercg_vsite/(2*dd->nnodes)));
-
- dd->vsite_comm = specat_comm_init(1);
-}
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/ebin.h"
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "gmx_fatal.h"
-#include "ebin.h"
-#include "main.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
-#include "vec.h"
-#include "physics.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
t_ebin *mk_ebin(void)
{
eb->e_sim[i].e = 0;
eb->e_sim[i].eav = 0;
eb->e_sim[i].esum = 0;
- eb->enm[i].name = strdup(enm[i-index]);
+ eb->enm[i].name = gmx_strdup(enm[i-index]);
if (unit != NULL)
{
- eb->enm[i].unit = strdup(unit);
+ eb->enm[i].unit = gmx_strdup(unit);
}
else
{
}
}
}
- eb->enm[i].unit = strdup(u);
+ eb->enm[i].unit = gmx_strdup(u);
}
}
{
e[i] = i;
sprintf(buf, "e%d", i);
- ce[i] = strdup(buf);
+ ce[i] = gmx_strdup(buf);
}
ie = get_ebin_space(eb, NE, ce);
add_ebin(eb, ie, NE, e, 0);
{
s[i] = i;
sprintf(buf, "s%d", i);
- cs[i] = strdup(buf);
+ cs[i] = gmx_strdup(buf);
}
is = get_ebin_space(eb, NS, cs);
add_ebin(eb, is, NS, s, 0);
{
t[i] = i;
sprintf(buf, "t%d", i);
- ct[i] = strdup(buf);
+ ct[i] = gmx_strdup(buf);
}
it = get_ebin_space(eb, NT, ct);
add_ebin(eb, it, NT, t, 0);
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <stdio.h>
#include <math.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "names.h"
-#include "gromacs/fileio/confio.h"
-#include "txtdump.h"
-#include "pbc.h"
-#include "chargegroup.h"
-#include "vec.h"
-#include "nrnb.h"
-#include "mshift.h"
-#include "mdrun.h"
-#include "update.h"
-#include "physics.h"
-#include "main.h"
-#include "mdatoms.h"
-#include "force.h"
-#include "bondf.h"
-#include "pme.h"
-#include "disre.h"
-#include "orires.h"
-#include "network.h"
-#include "calcmu.h"
-#include "constr.h"
-#include "xvgr.h"
-#include "gromacs/random/random.h"
-#include "domdec.h"
-#include "macros.h"
+#include <stdio.h>
+#include "gromacs/domdec/domdec.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/xtcio.h"
+#include "gromacs/legacyheaders/calcmu.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/random/random.h"
#include "gromacs/timing/wallcycle.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
static void init_df_history_weights(df_history_t *dfhist, t_expanded *expand, int nlim)
{
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/force.h"
+
+#include "config.h"
+#include <assert.h>
#include <math.h>
#include <string.h>
-#include <assert.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "physics.h"
-#include "force.h"
-#include "nonbonded.h"
-#include "names.h"
-#include "network.h"
-#include "pbc.h"
-#include "ns.h"
-#include "nrnb.h"
-#include "bondf.h"
-#include "mshift.h"
-#include "txtdump.h"
-#include "coulomb.h"
-#include "pme.h"
-#include "mdrun.h"
-#include "domdec.h"
-#include "qmmm.h"
-#include "gmx_omp_nthreads.h"
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/ewald/ewald.h"
+#include "gromacs/ewald/long-range-correction.h"
+#include "gromacs/ewald/pme.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/listed-forces/listed-forces.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/forcerec-threading.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
void ns(FILE *fp,
t_forcerec *fr,
gmx_bool bFillGrid,
gmx_bool bDoLongRangeNS)
{
- char *ptr;
int nsearch;
int t, i;
int nthreads_loop gmx_unused;
- /* This reduction can run over any number of threads */
+ // cppcheck-suppress unreadVariable
nthreads_loop = gmx_omp_nthreads_get(emntBonded);
+ /* This reduction can run over any number of threads */
#pragma omp parallel for num_threads(nthreads_loop) private(t) schedule(static)
for (i = 0; i < n; i++)
{
}
}
-void gmx_print_sepdvdl(FILE *fplog, const char *s, real v, real dvdlambda)
-{
- fprintf(fplog, " %-30s V %12.5e dVdl %12.5e\n", s, v, dvdlambda);
-}
-
-void do_force_lowlevel(FILE *fplog, gmx_int64_t step,
- t_forcerec *fr, t_inputrec *ir,
+void do_force_lowlevel(t_forcerec *fr, t_inputrec *ir,
t_idef *idef, t_commrec *cr,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
t_mdatoms *md,
t_fcdata *fcd,
gmx_localtop_t *top,
gmx_genborn_t *born,
- t_atomtypes *atype,
gmx_bool bBornRadii,
matrix box,
t_lambda *fepvals,
{
int i, j;
int donb_flags;
- gmx_bool bDoEpot, bSepDVDL, bSB;
+ gmx_bool bSB;
int pme_flags;
matrix boxs;
rvec box_size;
t_pbc pbc;
- char buf[22];
- double clam_i, vlam_i;
- real dvdl_dum[efptNR], dvdl_nb[efptNR], lam_i[efptNR];
- real dvdl_q, dvdl_lj;
+ real dvdl_dum[efptNR], dvdl_nb[efptNR];
#ifdef GMX_MPI
double t0 = 0.0, t1, t2, t3; /* time measurement for coarse load balancing */
#endif
-#define PRINT_SEPDVDL(s, v, dvdlambda) if (bSepDVDL) { gmx_print_sepdvdl(fplog, s, v, dvdlambda); }
-
set_pbc(&pbc, fr->ePBC, box);
/* reset free energy components */
box_size[i] = box[i][i];
}
- bSepDVDL = (fr->bSepDVDL && do_per_step(step, ir->nstlog));
debug_gmx();
/* do QMMM first if requested */
enerd->term[F_EQM] = calculate_QMMM(cr, x, f, fr);
}
- if (bSepDVDL)
- {
- fprintf(fplog, "Step %s: non-bonded V and dVdl for rank %d:\n",
- gmx_step_str(step, buf), cr->nodeid);
- }
-
/* Call the short range functions all in one go. */
#ifdef GMX_MPI
/* foreign lambda component for walls */
real dvdl_walls = do_walls(ir, fr, box, md, x, f, lambda[efptVDW],
enerd->grpp.ener[egLJSR], nrnb);
- PRINT_SEPDVDL("Walls", 0.0, dvdl_walls);
enerd->dvdl_lin[efptVDW] += dvdl_walls;
}
{
for (i = 0; i < enerd->n_lambda; i++)
{
+ real lam_i[efptNR];
+
for (j = 0; j < efptNR; j++)
{
lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
/* MRS: Eventually, many need to include free energy contribution here! */
if (ir->implicit_solvent)
{
- wallcycle_sub_start(wcycle, ewcsBONDED);
+ wallcycle_sub_start(wcycle, ewcsLISTED);
calc_gb_forces(cr, md, born, top, x, f, fr, idef,
ir->gb_algorithm, ir->sa_algorithm, nrnb, &pbc, graph, enerd);
- wallcycle_sub_stop(wcycle, ewcsBONDED);
+ wallcycle_sub_stop(wcycle, ewcsLISTED);
}
#ifdef GMX_MPI
enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
}
- if (bSepDVDL)
- {
- real V_short_range = 0;
- real dvdl_short_range = 0;
-
- for (i = 0; i < enerd->grpp.nener; i++)
- {
- V_short_range +=
- (fr->bBHAM ?
- enerd->grpp.ener[egBHAMSR][i] :
- enerd->grpp.ener[egLJSR][i])
- + enerd->grpp.ener[egCOULSR][i] + enerd->grpp.ener[egGB][i];
- }
- dvdl_short_range = dvdl_nb[efptVDW] + dvdl_nb[efptCOUL];
- PRINT_SEPDVDL("VdW and Coulomb SR particle-p.",
- V_short_range,
- dvdl_short_range);
- }
debug_gmx();
pr_rvecs(debug, 0, "fshift after SR", fr->fshift, SHIFTS);
}
- /* Shift the coordinates. Must be done before bonded forces and PPPM,
+ /* Shift the coordinates. Must be done before listed forces and PPPM,
* but is also necessary for SHAKE and update, therefore it can NOT
- * go when no bonded forces have to be evaluated.
+ * go when no listed forces have to be evaluated.
*/
/* Here sometimes we would not need to shift with NBFonly,
inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
}
}
- /* Check whether we need to do bondeds or correct for exclusions */
+ /* Check whether we need to do listed interactions or correct for exclusions */
if (fr->bMolPBC &&
- ((flags & GMX_FORCE_BONDED)
+ ((flags & GMX_FORCE_LISTED)
|| EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype)))
{
/* Since all atoms are in the rectangular or triclinic unit-cell,
}
debug_gmx();
- if (flags & GMX_FORCE_BONDED)
- {
- wallcycle_sub_start(wcycle, ewcsBONDED);
- calc_bonds(fplog, cr->ms,
- idef, x, hist, f, fr, &pbc, graph, enerd, nrnb, lambda, md, fcd,
- DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL, atype, born,
- flags,
- fr->bSepDVDL && do_per_step(step, ir->nstlog), step);
-
- /* Check if we have to determine energy differences
- * at foreign lambda's.
- */
- if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) &&
- idef->ilsort != ilsortNO_FE)
- {
- if (idef->ilsort != ilsortFE_SORTED)
- {
- gmx_incons("The bonded interactions are not sorted for free energy");
- }
- for (i = 0; i < enerd->n_lambda; i++)
- {
- reset_foreign_enerdata(enerd);
- for (j = 0; j < efptNR; j++)
- {
- lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
- }
- calc_bonds_lambda(fplog, idef, x, fr, &pbc, graph, &(enerd->foreign_grpp), enerd->foreign_term, nrnb, lam_i, md,
- fcd, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
- sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
- enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
- }
- }
- debug_gmx();
-
- wallcycle_sub_stop(wcycle, ewcsBONDED);
- }
+ do_force_listed(wcycle, box, ir->fepvals, cr->ms,
+ idef, (const rvec *) x, hist, f, fr,
+ &pbc, graph, enerd, nrnb, lambda, md, fcd,
+ DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL,
+ flags);
where();
*cycles_pme = 0;
+ clear_mat(fr->vir_el_recip);
+ clear_mat(fr->vir_lj_recip);
+
+ /* Do long-range electrostatics and/or LJ-PME, including related short-range
+ * corrections.
+ */
if (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype))
{
- real Vlr = 0, Vcorr = 0;
- real dvdl_long_range = 0;
- int status = 0;
+ int status = 0;
+ real Vlr_q = 0, Vlr_lj = 0, Vcorr_q = 0, Vcorr_lj = 0;
+ real dvdl_long_range_q = 0, dvdl_long_range_lj = 0;
bSB = (ir->nwall == 2);
if (bSB)
svmul(ir->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
box_size[ZZ] *= ir->wall_ewald_zfac;
}
- }
-
- /* Do long-range electrostatics and/or LJ-PME, including related short-range
- * corrections.
- */
-
- clear_mat(fr->vir_el_recip);
- clear_mat(fr->vir_lj_recip);
-
- if (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype))
- {
- real Vlr_q = 0, Vlr_lj = 0, Vcorr_q = 0, Vcorr_lj = 0;
- real dvdl_long_range_q = 0, dvdl_long_range_lj = 0;
- int status = 0;
if (EEL_PME_EWALD(fr->eeltype) || EVDW_PME(fr->vdwtype))
{
#pragma omp parallel for num_threads(nthreads) schedule(static)
for (t = 0; t < nthreads; t++)
{
- int s, e, i;
+ int i;
rvec *fnv;
tensor *vir_q, *vir_lj;
real *Vcorrt_q, *Vcorrt_lj, *dvdlt_q, *dvdlt_lj;
fr->vir_el_recip);
}
- PRINT_SEPDVDL("Ewald excl./charge/dip. corr.", Vcorr_q, dvdl_long_range_correction_q);
- PRINT_SEPDVDL("Ewald excl. corr. LJ", Vcorr_lj, dvdl_long_range_correction_lj);
enerd->dvdl_lin[efptCOUL] += dvdl_long_range_correction_q;
enerd->dvdl_lin[efptVDW] += dvdl_long_range_correction_lj;
- }
- if ((EEL_PME(fr->eeltype) || EVDW_PME(fr->vdwtype)))
- {
- if (cr->duty & DUTY_PME)
+ if ((EEL_PME(fr->eeltype) || EVDW_PME(fr->vdwtype)) && (cr->duty & DUTY_PME))
{
/* Do reciprocal PME for Coulomb and/or LJ. */
assert(fr->n_tpi >= 0);
md->chargeA + md->homenr - fr->n_tpi,
&Vlr_q);
}
- PRINT_SEPDVDL("PME mesh", Vlr_q + Vlr_lj, dvdl_long_range_q+dvdl_long_range_lj);
}
}
box_size, cr, md->homenr,
fr->vir_el_recip, fr->ewaldcoeff_q,
lambda[efptCOUL], &dvdl_long_range_q, fr->ewald_table);
- PRINT_SEPDVDL("Ewald long-range", Vlr_q, dvdl_long_range_q);
}
/* Note that with separate PME nodes we get the real energies later */
fr->fshift, &pbc, lambda[efptCOUL], &dvdl_rf_excl);
enerd->dvdl_lin[efptCOUL] += dvdl_rf_excl;
- PRINT_SEPDVDL("RF exclusion correction",
- enerd->term[F_RF_EXCL], dvdl_rf_excl);
}
}
}
fr->t_wait += t3-t2;
if (fr->timesteps == 11)
{
+ char buf[22];
fprintf(stderr, "* PP load balancing info: rank %d, step %s, rel wait time=%3.0f%% , load string value: %7.2f\n",
cr->nodeid, gmx_step_str(fr->timesteps, buf),
100*fr->t_wait/(fr->t_wait+fr->t_fnbf),
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _mvdata_h
-#define _mvdata_h
+#ifndef GMX_MDLIB_FORCEREC_THREADING_H
+#define GMX_MDLIB_FORCEREC_THREADING_H
-#include "typedefs.h"
+#include "gromacs/utility/bitmask.h"
#ifdef __cplusplus
extern "C" {
#endif
-void bcast_ir_mtop(const t_commrec *cr,
- t_inputrec *inputrec, gmx_mtop_t *mtop);
-/* Broadcasts ir and mtop from the master to all nodes in cr->mpi_comm_mygroup.
- */
-
-void bcast_state(const t_commrec *cr, t_state *state);
-/* Broadcasts state from the master to all nodes in cr->mpi_comm_mygroup.
- */
+struct f_thread_t {
+ rvec *f;
+ int f_nalloc;
+ gmx_bitmask_t red_mask; /* Mask for marking which parts of f are filled */
+ rvec *fshift;
+ real ener[F_NRE];
+ gmx_grppairener_t grpp;
+ real Vcorr_q;
+ real Vcorr_lj;
+ real dvdl[efptNR];
+ tensor vir_q;
+ tensor vir_lj;
+};
#ifdef __cplusplus
}
#endif
-#endif /* _mvdata_h */
+#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
+#include <assert.h>
#include <math.h>
#include <string.h>
-#include <assert.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "vec.h"
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/ewald/ewald.h"
+#include "gromacs/gmxlib/cuda_tools/pmalloc_cuda.h"
+#include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/gmx_detect_hardware.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/inputrec.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/tables.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
+#include "gromacs/math/calculate-ewald-splitting-coefficient.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "physics.h"
-#include "force.h"
-#include "tables.h"
-#include "nonbonded.h"
-#include "invblock.h"
-#include "names.h"
-#include "network.h"
-#include "pbc.h"
-#include "ns.h"
-#include "mshift.h"
-#include "txtdump.h"
-#include "coulomb.h"
-#include "md_support.h"
-#include "md_logging.h"
-#include "domdec.h"
-#include "qmmm.h"
-#include "copyrite.h"
-#include "mtop_util.h"
-#include "nbnxn_simd.h"
-#include "nbnxn_search.h"
-#include "nbnxn_atomdata.h"
-#include "nbnxn_consts.h"
-#include "gmx_omp_nthreads.h"
-#include "gmx_detect_hardware.h"
-#include "inputrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/forcerec-threading.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_atomdata.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/mdlib/nbnxn_simd.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/simd/simd.h"
-
-#include "types/nbnxn_cuda_types_ext.h"
-#include "gpu_utils.h"
-#include "nbnxn_cuda_data_mgmt.h"
-#include "pmalloc_cuda.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
t_forcerec *mk_forcerec(void)
{
static real *make_ljpme_c6grid(const gmx_ffparams_t *idef, t_forcerec *fr)
{
- int i, j, k, atnr;
- real c6, c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
- real *grid;
+ int i, j, k, atnr;
+ real c6, c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
+ real *grid;
+ const real oneOverSix = 1.0 / 6.0;
/* For LJ-PME simulations, we correct the energies with the reciprocal space
* inside of the cut-off. To do this the non-bonded kernels needs to have
if (fr->ljpme_combination_rule == eljpmeLB
&& !gmx_numzero(c6) && !gmx_numzero(c12i) && !gmx_numzero(c12j))
{
- sigmai = pow(c12i / c6i, 1.0/6.0);
- sigmaj = pow(c12j / c6j, 1.0/6.0);
+ sigmai = pow(c12i / c6i, oneOverSix);
+ sigmaj = pow(c12j / c6j, oneOverSix);
epsi = c6i * c6i / c12i;
epsj = c6j * c6j / c12j;
c6 = sqrt(epsi * epsj) * pow(0.5*(sigmai+sigmaj), 6);
static real *mk_nbfp_combination_rule(const gmx_ffparams_t *idef, int comb_rule)
{
- real *nbfp;
- int i, j, k, atnr;
- real c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
- real c6, c12;
+ real *nbfp;
+ int i, j, atnr;
+ real c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
+ real c6, c12;
+ const real oneOverSix = 1.0 / 6.0;
atnr = idef->atnr;
snew(nbfp, 2*atnr*atnr);
if (comb_rule == eCOMB_ARITHMETIC
&& !gmx_numzero(c6) && !gmx_numzero(c12))
{
- sigmai = pow(c12i / c6i, 1.0/6.0);
- sigmaj = pow(c12j / c6j, 1.0/6.0);
+ sigmai = pow(c12i / c6i, oneOverSix);
+ sigmaj = pow(c12j / c6j, oneOverSix);
epsi = c6i * c6i / c12i;
epsj = c6j * c6j / c12j;
c6 = sqrt(epsi * epsj) * pow(0.5*(sigmai+sigmaj), 6);
int cginfo,
int *cg_sp)
{
- const t_blocka *excl;
t_atom *atom;
int j, k;
int j0, j1, nj;
cginfo_mb_t *cginfo_mb)
{
const t_block * cgs;
- const t_block * mols;
const gmx_moltype_t *molt;
- int mb, mol, cg_mol, at_offset, cg_offset, am, cgm, i, nmol_ch, nmol;
+ int mb, mol, cg_mol, at_offset, am, cgm, i, nmol_ch, nmol;
int n_solvent_parameters;
solvent_parameters_t *solvent_parameters;
int **cg_sp;
fprintf(debug, "Going to determine what solvent types we have.\n");
}
- mols = &mtop->mols;
-
n_solvent_parameters = 0;
solvent_parameters = NULL;
/* Allocate temporary array for solvent type */
snew(cg_sp, mtop->nmolblock);
- cg_offset = 0;
at_offset = 0;
for (mb = 0; mb < mtop->nmolblock; mb++)
{
&cg_sp[mb][cgm+cg_mol]);
}
}
- cg_offset += cgs->nr;
at_offset += cgs->index[cgs->nr];
}
bestsol = esolNO;
}
-#ifdef DISABLE_WATER_NLIST
- bestsol = esolNO;
-#endif
-
fr->nWatMol = 0;
for (mb = 0; mb < mtop->nmolblock; mb++)
{
cginfo_mb_t *cginfo_mb;
gmx_bool *type_VDW;
int *cginfo;
- int cg_offset, a_offset, cgm, am;
- int mb, m, ncg_tot, cg, a0, a1, gid, ai, j, aj, excl_nalloc;
+ int cg_offset, a_offset;
+ int mb, m, cg, a0, a1, gid, ai, j, aj, excl_nalloc;
int *a_con;
int ftype;
int ia;
gmx_bool bId, *bExcl, bExclIntraAll, bExclInter, bHaveVDW, bHaveQ, bHavePerturbedAtoms;
- ncg_tot = ncg_mtop(mtop);
snew(cginfo_mb, mtop->nmolblock);
snew(type_VDW, fr->ntype);
* Otherwise we make an array of #mol times #cgs per molecule.
*/
bId = TRUE;
- am = 0;
for (m = 0; m < molb->nmol; m++)
{
- am = m*cgs->index[cgs->nr];
+ int am = m*cgs->index[cgs->nr];
for (cg = 0; cg < cgs->nr; cg++)
{
a0 = cgs->index[cg];
for (m = 0; m < (bId ? 1 : molb->nmol); m++)
{
- cgm = m*cgs->nr;
- am = m*cgs->index[cgs->nr];
+ int cgm = m*cgs->nr;
+ int am = m*cgs->index[cgs->nr];
for (cg = 0; cg < cgs->nr; cg++)
{
a0 = cgs->index[cg];
{
const t_atoms *atoms, *atoms_tpi;
const t_blocka *excl;
- int mb, nmol, nmolc, i, j, tpi, tpj, j1, j2, k, n, nexcl, q;
+ int mb, nmol, nmolc, i, j, tpi, tpj, j1, j2, k, nexcl, q;
gmx_int64_t npair, npair_ij, tmpi, tmpj;
double csix, ctwelve;
int ntp, *typecount;
}
}
-static void pick_nbnxn_resources(const t_commrec *cr,
+static void pick_nbnxn_resources(FILE *fp,
+ const t_commrec *cr,
const gmx_hw_info_t *hwinfo,
gmx_bool bDoNonbonded,
gmx_bool *bUseGPU,
{
/* Each PP node will use the intra-node id-th device from the
* list of detected/selected GPUs. */
- if (!init_gpu(cr->rank_pp_intranode, gpu_err_str,
+ if (!init_gpu(fp, cr->rank_pp_intranode, gpu_err_str,
&hwinfo->gpu_info, gpu_opt))
{
/* At this point the init should never fail as we made sure that
gmx_bool bUsesSimpleTables,
real rtab)
{
- real spacing;
-
if (ic->eeltype == eelEWALD || EEL_PME(ic->eeltype) || EVDW_PME(ic->vdwtype))
{
init_ewald_f_table(ic, bUsesSimpleTables, rtab);
{
interaction_const_t *ic;
gmx_bool bUsesSimpleTables = TRUE;
+ const real minusSix = -6.0;
+ const real minusTwelve = -12.0;
snew(ic, 1);
{
case eintmodPOTSHIFT:
/* Only shift the potential, don't touch the force */
- ic->dispersion_shift.cpot = -pow(ic->rvdw, -6.0);
- ic->repulsion_shift.cpot = -pow(ic->rvdw, -12.0);
+ ic->dispersion_shift.cpot = -pow(ic->rvdw, minusSix);
+ ic->repulsion_shift.cpot = -pow(ic->rvdw, minusTwelve);
if (EVDW_PME(ic->vdwtype))
{
real crc2;
crc2 = sqr(ic->ewaldcoeff_lj*ic->rvdw);
- ic->sh_lj_ewald = (exp(-crc2)*(1 + crc2 + 0.5*crc2*crc2) - 1)*pow(ic->rvdw, -6.0);
+ ic->sh_lj_ewald = (exp(-crc2)*(1 + crc2 + 0.5*crc2*crc2) - 1)*pow(ic->rvdw, minusSix);
}
break;
case eintmodFORCESWITCH:
snew(nbv, 1);
- pick_nbnxn_resources(cr, fr->hwinfo,
+ pick_nbnxn_resources(fp, cr, fr->hwinfo,
fr->bNonbonded,
&nbv->bUseGPU,
&bEmulateGPU,
}
}
+gmx_bool usingGpu(nonbonded_verlet_t *nbv)
+{
+ return nbv != NULL && nbv->bUseGPU;
+}
+
void init_forcerec(FILE *fp,
const output_env_t oenv,
t_forcerec *fr,
gmx_bool bNoSolvOpt,
real print_force)
{
- int i, j, m, natoms, ngrp, negp_pp, negptable, egi, egj;
+ int i, m, negp_pp, negptable, egi, egj;
real rtab;
char *env;
double dbl;
gmx_bool bGenericKernelOnly;
gmx_bool bMakeTables, bMakeSeparate14Table, bSomeNormalNbListsAreInUse;
gmx_bool bFEP_NonBonded;
- t_nblists *nbl;
int *nm_ind, egp_flags;
if (fr->hwinfo == NULL)
fr->bDomDec = DOMAINDECOMP(cr);
- natoms = mtop->natoms;
-
if (check_box(ir->ePBC, box))
{
gmx_fatal(FARGS, check_box(ir->ePBC, box));
if (env != NULL)
{
dbl = 0;
- sscanf(env, "%lf", &dbl);
+ sscanf(env, "%20lf", &dbl);
fr->sc_sigma6_min = pow(dbl, 6);
if (fp)
{
egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
if ((egp_flags & EGP_TABLE) && !(egp_flags & EGP_EXCL))
{
- nbl = &(fr->nblists[m]);
if (fr->nnblists > 1)
{
fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = m;
fr->excl_load[t] = i;
}
}
+
+/* Frees GPU memory and destroys the CUDA context.
+ *
+ * Note that this function needs to be called even if GPUs are not used
+ * in this run because the PME ranks have no knowledge of whether GPUs
+ * are used or not, but all ranks need to enter the barrier below.
+ */
+void free_gpu_resources(const t_forcerec *fr,
+ const t_commrec *cr,
+ const gmx_gpu_info_t *gpu_info,
+ const gmx_gpu_opt_t *gpu_opt)
+{
+ gmx_bool bIsPPrankUsingGPU;
+ char gpu_err_str[STRLEN];
+
+ bIsPPrankUsingGPU = (cr->duty & DUTY_PP) && fr && fr->nbv && fr->nbv->bUseGPU;
+
+ if (bIsPPrankUsingGPU)
+ {
+ /* free nbnxn data in GPU memory */
+ nbnxn_cuda_free(fr->nbv->cu_nbv);
+
+ /* With tMPI we need to wait for all ranks to finish deallocation before
+ * destroying the context in free_gpu() as some ranks may be sharing
+ * GPU and context.
+ * Note: as only PP ranks need to free GPU resources, so it is safe to
+ * not call the barrier on PME ranks.
+ */
+#ifdef GMX_THREAD_MPI
+ if (PAR(cr))
+ {
+ gmx_barrier(cr);
+ }
+#endif /* GMX_THREAD_MPI */
+
+ /* uninitialize GPU (by destroying the context) */
+ if (!free_gpu(cr->rank_pp_intranode, gpu_err_str, gpu_info, gpu_opt))
+ {
+ gmx_warning("On rank %d failed to free GPU #%d: %s",
+ cr->nodeid, get_current_gpu_device_id(), gpu_err_str);
+ }
+ }
+}
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/genborn.h"
#include <math.h>
#include <string.h>
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "genborn.h"
-#include "vec.h"
+#include "gromacs/domdec/domdec.h"
#include "gromacs/fileio/pdbio.h"
-#include "names.h"
-#include "physics.h"
-#include "domdec.h"
-#include "network.h"
-#include "gmx_fatal.h"
-#include "mtop_util.h"
-#include "pbc.h"
-#include "nrnb.h"
-#include "bondf.h"
-
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
#ifdef GMX_SIMD_X86_SSE2_OR_HIGHER
# ifdef GMX_DOUBLE
-# include "genborn_sse2_double.h"
-# include "genborn_allvsall_sse2_double.h"
+# include "gromacs/mdlib/genborn_allvsall_sse2_double.h"
+# include "gromacs/mdlib/genborn_sse2_double.h"
# else
-# include "genborn_sse2_single.h"
-# include "genborn_allvsall_sse2_single.h"
+# include "gromacs/mdlib/genborn_allvsall_sse2_single.h"
+# include "gromacs/mdlib/genborn_sse2_single.h"
# endif /* GMX_DOUBLE */
#endif /* SSE or AVX present */
-#include "genborn_allvsall.h"
+#include "gromacs/mdlib/genborn_allvsall.h"
/*#define DISABLE_SSE*/
int list_nalloc;
} t_gbtmpnbls;
-/* This function is exactly the same as the one in bondfree.c. The reason
+/* This function is exactly the same as the one in listed-forces/bonded.cpp. The reason
* it is copied here is that the bonded gb-interactions are evaluated
* not in calc_bonds, but rather in calc_gb_forces
*/
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "genborn_allvsall.h"
#include <math.h>
-#include "types/simple.h"
-#include "vec.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
#include "gromacs/utility/smalloc.h"
-#include "network.h"
-#include "physics.h"
-#include "genborn.h"
-#include "genborn_allvsall.h"
-
typedef struct
{
#ifndef _GENBORN_ALLVSALL_H
#define _GENBORN_ALLVSALL_H
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "types/simple.h"
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
int
genborn_allvsall_calc_still_radii(t_forcerec * fr,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "types/simple.h"
-#include "vec.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/genborn_allvsall.h"
#include "gromacs/utility/smalloc.h"
-#include "network.h"
-#include "physics.h"
-#include "genborn.h"
-#include "genborn_allvsall.h"
-
#if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2009, The GROMACS Development Team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _GENBORN_ALLVSALL_SSE2_DOUBLE_H
#define _GENBORN_ALLVSALL_SSE2_DOUBLE_H
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "types/simple.h"
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
int
genborn_allvsall_calc_still_radii_sse2_double(t_forcerec * fr,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "types/simple.h"
-#include "vec.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/genborn_allvsall.h"
#include "gromacs/utility/smalloc.h"
-#include "network.h"
-#include "physics.h"
-#include "genborn.h"
-#include "genborn_allvsall.h"
-
#if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
#include <gmx_sse2_single.h>
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2009, The GROMACS Development Team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _GENBORN_ALLVSALL_SSE2_SINGLE_H
#define _GENBORN_ALLVSALL_SSE2_SINGLE_H
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "types/simple.h"
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
int
genborn_allvsall_calc_still_radii_sse2_single(t_forcerec * fr,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "genborn.h"
-#include "vec.h"
+#include "gromacs/domdec/domdec.h"
#include "gromacs/fileio/pdbio.h"
-#include "names.h"
-#include "physics.h"
-#include "domdec.h"
-#include "network.h"
-#include "gmx_fatal.h"
-#include "mtop_util.h"
-#include "genborn.h"
-
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
/* Only compile this file if SSE2 intrinsics are available */
#if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
-#include <gmx_sse2_double.h>
-#include <emmintrin.h>
-
#include "genborn_sse2_double.h"
+#include <emmintrin.h>
+#include <gmx_sse2_double.h>
+
int
calc_gb_rad_still_sse2_double(t_commrec *cr, t_forcerec *fr,
int natoms, gmx_localtop_t *top,
#ifndef _genborn_sse2_double_h
#define _genborn_sse2_double_h
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
int
calc_gb_rad_still_sse2_double(t_commrec *cr, t_forcerec *fr, int natoms, gmx_localtop_t *top,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "genborn.h"
-#include "vec.h"
+#include "gromacs/domdec/domdec.h"
#include "gromacs/fileio/pdbio.h"
-#include "names.h"
-#include "physics.h"
-#include "domdec.h"
-#include "network.h"
-#include "gmx_fatal.h"
-#include "mtop_util.h"
-#include "genborn.h"
-
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
/* Only compile this file if SSE intrinsics are available */
#if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
-#include <gmx_sse2_single.h>
-#include <emmintrin.h>
-
#include "genborn_sse2_single.h"
+#include <emmintrin.h>
+#include <gmx_sse2_single.h>
+
int
calc_gb_rad_still_sse2_single(t_commrec *cr, t_forcerec *fr,
#ifndef _genborn_sse_h
#define _genborn_sse_h
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
float
calc_gb_chainrule_sse2_single(int natoms, t_nblist *nl, float *dadx, float *dvda,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
+#include "gmxpre.h"
#include "groupcoord.h"
-#include "network.h"
-#include "pbc.h"
-#include "vec.h"
+
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_ga2la.h"
#define MIN(a, b) (((a) < (b)) ? (a) : (b))
* \inlibraryapi
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
#include <stdio.h>
-#include "typedefs.h"
-#include "types/commrec.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
/*! \brief Select local atoms of a group.
*
* (collective) array such that it can be gmx_summed
* in the communicate_group_positions routine.
*/
+
extern void dd_make_local_group_indices(gmx_ga2la_t ga2la,
const int nr, int anrs[], int *nr_loc,
int *anrs_loc[], int *nalloc_loc,
*
*/
extern void rotate_x(rvec x[], const int nr, matrix rmat);
+
+#ifdef __cplusplus
+}
+#endif
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <stdio.h>
-#include "typedefs.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "main.h"
-#include "mvdata.h"
-#include "gmx_fatal.h"
-#include "symtab.h"
-#include "txtdump.h"
-#include "mdatoms.h"
-#include "mdrun.h"
-#include "names.h"
-#include "calcgrid.h"
-#include "update.h"
-#include "mdebin.h"
-
-#define BUFSIZE 256
-
-#define NOT_FINISHED(l1, l2) \
- printf("not finished yet: lines %d .. %d in %s\n", l1, l2, __FILE__)
-
-void set_state_entries(t_state *state, const t_inputrec *ir)
-{
- int nnhpres;
-
- /* The entries in the state in the tpx file might not correspond
- * with what is needed, so we correct this here.
- */
- state->flags = 0;
- if (ir->efep != efepNO || ir->bExpanded)
- {
- state->flags |= (1<<estLAMBDA);
- state->flags |= (1<<estFEPSTATE);
- }
- state->flags |= (1<<estX);
- if (state->lambda == NULL)
- {
- snew(state->lambda, efptNR);
- }
- if (state->x == NULL)
- {
- snew(state->x, state->nalloc);
- }
- if (EI_DYNAMICS(ir->eI))
- {
- state->flags |= (1<<estV);
- if (state->v == NULL)
- {
- snew(state->v, state->nalloc);
- }
- }
- if (ir->eI == eiSD2)
- {
- state->flags |= (1<<estSDX);
- if (state->sd_X == NULL)
- {
- /* sd_X is not stored in the tpx file, so we need to allocate it */
- snew(state->sd_X, state->nalloc);
- }
- }
- if (ir->eI == eiCG)
- {
- state->flags |= (1<<estCGP);
- if (state->cg_p == NULL)
- {
- /* cg_p is not stored in the tpx file, so we need to allocate it */
- snew(state->cg_p, state->nalloc);
- }
- }
-
- state->nnhpres = 0;
- if (ir->ePBC != epbcNONE)
- {
- state->flags |= (1<<estBOX);
- if (PRESERVE_SHAPE(*ir))
- {
- state->flags |= (1<<estBOX_REL);
- }
- if ((ir->epc == epcPARRINELLORAHMAN) || (ir->epc == epcMTTK))
- {
- state->flags |= (1<<estBOXV);
- }
- if (ir->epc != epcNO)
- {
- if (IR_NPT_TROTTER(ir) || (IR_NPH_TROTTER(ir)))
- {
- state->nnhpres = 1;
- state->flags |= (1<<estNHPRES_XI);
- state->flags |= (1<<estNHPRES_VXI);
- state->flags |= (1<<estSVIR_PREV);
- state->flags |= (1<<estFVIR_PREV);
- state->flags |= (1<<estVETA);
- state->flags |= (1<<estVOL0);
- }
- else
- {
- state->flags |= (1<<estPRES_PREV);
- }
- }
- }
-
- if (ir->etc == etcNOSEHOOVER)
- {
- state->flags |= (1<<estNH_XI);
- state->flags |= (1<<estNH_VXI);
- }
-
- if (ir->etc == etcVRESCALE)
- {
- state->flags |= (1<<estTC_INT);
- }
-
- init_gtc_state(state, state->ngtc, state->nnhpres, ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
- init_ekinstate(&state->ekinstate, ir);
-
- init_energyhistory(&state->enerhist);
- init_df_history(&state->dfhist, ir->fepvals->n_lambda);
- state->swapstate.eSwapCoords = ir->eSwapCoords;
-}
-
-
-void init_parallel(t_commrec *cr, t_inputrec *inputrec,
- gmx_mtop_t *mtop)
-{
- bcast_ir_mtop(cr, inputrec, mtop);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-#include "typedefs.h"
-#include "gmx_fatal.h"
-#include "mdrun.h"
-#include "md_support.h"
-#include "md_logging.h"
-#include "types/iteratedconstraints.h"
-
-#ifdef GMX_DOUBLE
-#define CONVERGEITER 0.000000001
-#define CLOSE_ENOUGH 0.000001000
-#else
-#define CONVERGEITER 0.0001
-#define CLOSE_ENOUGH 0.0050
-#endif
-
-/* we want to keep track of the close calls. If there are too many, there might be some other issues.
- so we make sure that it's either less than some predetermined number, or if more than that number,
- only some small fraction of the total. */
-#define MAX_NUMBER_CLOSE 50
-#define FRACTION_CLOSE 0.001
-
-/* maximum length of cyclic traps to check, emerging from limited numerical precision */
-#define CYCLEMAX 20
-
-void gmx_iterate_init(gmx_iterate_t *iterate, gmx_bool bSetIterationActive)
-{
- int i;
-
- iterate->iter_i = 0;
- iterate->bIterationActive = bSetIterationActive;
- iterate->num_close = 0;
- for (i = 0; i < MAXITERCONST+2; i++)
- {
- iterate->allrelerr[i] = 0;
- }
-}
-
-gmx_bool done_iterating(const t_commrec *cr, FILE *fplog, int nsteps, gmx_iterate_t *iterate, gmx_bool bFirstIterate, real fom, real *newf)
-{
- /* monitor convergence, and use a secant search to propose new
- values.
- x_{i} - x_{i-1}
- The secant method computes x_{i+1} = x_{i} - f(x_{i}) * ---------------------
- f(x_{i}) - f(x_{i-1})
-
- The function we are trying to zero is fom-x, where fom is the
- "figure of merit" which is the pressure (or the veta value) we
- would get by putting in an old value of the pressure or veta into
- the incrementor function for the step or half step. I have
- verified that this gives the same answer as self consistent
- iteration, usually in many fewer steps, especially for small tau_p.
-
- We could possibly eliminate an iteration with proper use
- of the value from the previous step, but that would take a bit
- more bookkeeping, especially for veta, since tests indicate the
- function of veta on the last step is not sufficiently close to
- guarantee convergence this step. This is
- good enough for now. On my tests, I could use tau_p down to
- 0.02, which is smaller that would ever be necessary in
- practice. Generally, 3-5 iterations will be sufficient */
-
- real relerr, err, xmin;
- int i;
- gmx_bool incycle;
-
- if (bFirstIterate)
- {
- iterate->x = fom;
- iterate->f = fom-iterate->x;
- iterate->xprev = 0;
- iterate->fprev = 0;
- *newf = fom;
- }
- else
- {
- iterate->f = fom-iterate->x; /* we want to zero this difference */
- if ((iterate->iter_i > 1) && (iterate->iter_i < MAXITERCONST))
- {
- if (iterate->f == iterate->fprev)
- {
- *newf = iterate->f;
- }
- else
- {
- *newf = iterate->x - (iterate->x-iterate->xprev)*(iterate->f)/(iterate->f-iterate->fprev);
- }
- }
- else
- {
- /* just use self-consistent iteration the first step to initialize, or
- if it's not converging (which happens occasionally -- need to investigate why) */
- *newf = fom;
- }
- }
- /* Consider a slight shortcut allowing us to exit one sooner -- we check the
- difference between the closest of x and xprev to the new
- value. To be 100% certain, we should check the difference between
- the last result, and the previous result, or
-
- relerr = (fabs((x-xprev)/fom));
-
- but this is pretty much never necessary under typical conditions.
- Checking numerically, it seems to lead to almost exactly the same
- trajectories, but there are small differences out a few decimal
- places in the pressure, and eventually in the v_eta, but it could
- save an interation.
-
- if (fabs(*newf-x) < fabs(*newf - xprev)) { xmin = x;} else { xmin = xprev;}
- relerr = (fabs((*newf-xmin) / *newf));
- */
-
- err = fabs((iterate->f-iterate->fprev));
- relerr = fabs(err/fom);
-
- iterate->allrelerr[iterate->iter_i] = relerr;
-
- if (iterate->iter_i > 0)
- {
- if (debug)
- {
- fprintf(debug, "Iterating NPT constraints: %6i %20.12f%14.6g%20.12f\n",
- iterate->iter_i, fom, relerr, *newf);
- }
-
- if ((relerr < CONVERGEITER) || (err < CONVERGEITER) || (fom == 0) || ((iterate->x == iterate->xprev) && iterate->iter_i > 1))
- {
- iterate->bIterationActive = FALSE;
- if (debug)
- {
- fprintf(debug, "Iterating NPT constraints: CONVERGED\n");
- }
- return TRUE;
- }
- if (iterate->iter_i > MAXITERCONST)
- {
- if (relerr < CLOSE_ENOUGH)
- {
- incycle = FALSE;
- for (i = 1; i < CYCLEMAX; i++)
- {
- if ((iterate->allrelerr[iterate->iter_i-(1+i)] == iterate->allrelerr[iterate->iter_i-1]) &&
- (iterate->allrelerr[iterate->iter_i-(1+i)] == iterate->allrelerr[iterate->iter_i-(1+2*i)]))
- {
- incycle = TRUE;
- if (debug)
- {
- fprintf(debug, "Exiting from an NPT iterating cycle of length %d\n", i);
- }
- break;
- }
- }
-
- if (incycle)
- {
- /* step 1: trapped in a numerical attractor */
- /* we are trapped in a numerical attractor, and can't converge any more, and are close to the final result.
- Better to give up convergence here than have the simulation die.
- */
- iterate->num_close++;
- iterate->bIterationActive = FALSE;
- return TRUE;
- }
- else
- {
- /* Step #2: test if we are reasonably close for other reasons, then monitor the number. If not, die */
-
- /* how many close calls have we had? If less than a few, we're OK */
- if (iterate->num_close < MAX_NUMBER_CLOSE)
- {
- md_print_warn(cr, fplog, "Slight numerical convergence deviation with NPT at step %d, relative error only %10.5g, likely not a problem, continuing\n", nsteps, relerr);
- iterate->num_close++;
- iterate->bIterationActive = FALSE;
- return TRUE;
- /* if more than a few, check the total fraction. If too high, die. */
- }
- else if (iterate->num_close/(double)nsteps > FRACTION_CLOSE)
- {
- gmx_fatal(FARGS, "Could not converge NPT constraints, too many exceptions (%d%%\n", iterate->num_close/(double)nsteps);
- }
- }
- }
- else
- {
- gmx_fatal(FARGS, "Could not converge NPT constraints\n");
- }
- }
- }
-
- iterate->xprev = iterate->x;
- iterate->x = *newf;
- iterate->fprev = iterate->f;
- iterate->iter_i++;
-
- return FALSE;
-}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include "typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "mdrun.h"
-#include "domdec.h"
-#include "mtop_util.h"
-#include "vcm.h"
-#include "nrnb.h"
-#include "macros.h"
-#include "md_logging.h"
-#include "md_support.h"
-#include "names.h"
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/md_support.h"
+
+#include <algorithm>
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vcm.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
#include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/snprintf.h"
/* Is the signal in one simulation independent of other simulations? */
-gmx_bool gs_simlocal[eglsNR] = { TRUE, FALSE, FALSE, TRUE };
+gmx_bool gs_simlocal[eglsNR] = { FALSE, FALSE, TRUE };
/* check which of the multisim simulations has the shortest number of
steps and return that number of nsteps */
if (steps_out >= 0 && steps_out < nsteps)
{
char strbuf[255];
- snprintf(strbuf, 255, "Will stop simulation %%d after %s steps (another simulation will end then).\n", "%"GMX_PRId64);
+ snprintf(strbuf, 255, "Will stop simulation %%d after %s steps (another simulation will end then).\n", "%" GMX_PRId64);
fprintf(stderr, strbuf, cr->ms->sim, steps_out);
}
}
{
if (bEqual)
{
- nmin = min(nmin, buf[0]);
+ nmin = std::min(nmin, buf[0]);
}
else
{
int i, gsi;
real gs_buf[eglsNR];
tensor corr_vir, corr_pres;
- gmx_bool bEner, bPres, bTemp, bVV;
- gmx_bool bRerunMD, bStopCM, bGStat, bIterate,
- bFirstIterate, bReadEkin, bEkinAveVel, bScaleEkin, bConstrain;
- real ekin, temp, prescorr, enercorr, dvdlcorr, dvdl_ekin;
+ gmx_bool bEner, bPres, bTemp;
+ gmx_bool bStopCM, bGStat,
+ bReadEkin, bEkinAveVel, bScaleEkin, bConstrain;
+ real prescorr, enercorr, dvdlcorr, dvdl_ekin;
/* translate CGLO flags to gmx_booleans */
- bRerunMD = flags & CGLO_RERUNMD;
- bStopCM = flags & CGLO_STOPCM;
- bGStat = flags & CGLO_GSTAT;
-
+ bStopCM = flags & CGLO_STOPCM;
+ bGStat = flags & CGLO_GSTAT;
bReadEkin = (flags & CGLO_READEKIN);
bScaleEkin = (flags & CGLO_SCALEEKIN);
bEner = flags & CGLO_ENERGY;
bTemp = flags & CGLO_TEMPERATURE;
bPres = (flags & CGLO_PRESSURE);
bConstrain = (flags & CGLO_CONSTRAINT);
- bIterate = (flags & CGLO_ITERATE);
- bFirstIterate = (flags & CGLO_FIRSTITERATE);
/* we calculate a full state kinetic energy either with full-step velocity verlet
or half step where we need the pressure */
}
else
{
-
- calc_ke_part(state, &(ir->opts), mdatoms, ekind, nrnb, bEkinAveVel, bIterate);
+ calc_ke_part(state, &(ir->opts), mdatoms, ekind, nrnb, bEkinAveVel);
}
debug_gmx();
Leap with AveVel is not supported; it's not clear that it will actually work.
bEkinAveVel: If TRUE, we simply multiply ekin by ekinscale to get a full step kinetic energy.
If FALSE, we average ekinh_old and ekinh*ekinscale_nhc to get an averaged half step kinetic energy.
- bSaveEkinOld: If TRUE (in the case of iteration = bIterate is TRUE), we don't reset the ekinscale_nhc.
- If FALSE, we go ahead and erase over it.
*/
enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, &dvdl_ekin,
bEkinAveVel, bScaleEkin);
if (bEner || bPres || bConstrain)
{
- calc_dispcorr(fplog, ir, fr, 0, top_global->natoms, box, state->lambda[efptVDW],
+ calc_dispcorr(ir, fr, top_global->natoms, box, state->lambda[efptVDW],
corr_pres, corr_vir, &prescorr, &enercorr, &dvdlcorr);
}
- if (bEner && bFirstIterate)
+ if (bEner)
{
enerd->term[F_DISPCORR] = enercorr;
enerd->term[F_EPOT] += enercorr;
{
/* find out between which two value of lambda we should be */
frac = (step*fepvals->delta_lambda);
- fep_state = floor(frac*fepvals->n_lambda);
+ fep_state = static_cast<int>(floor(frac*fepvals->n_lambda));
/* interpolate between this state and the next */
/* this assumes that the initial lambda corresponds to lambda==0, which is verified in grompp */
frac = (frac*fepvals->n_lambda)-fep_state;
frac = (step*fepvals->delta_lambda);
if (fepvals->n_lambda > 0)
{
- fep_state = floor(frac*fepvals->n_lambda);
+ fep_state = static_cast<int>(floor(frac*fepvals->n_lambda));
/* interpolate between this state and the next */
/* this assumes that the initial lambda corresponds to lambda==0, which is verified in grompp */
frac = (frac*fepvals->n_lambda)-fep_state;
void rerun_parallel_comm(t_commrec *cr, t_trxframe *fr,
gmx_bool *bNotLastFrame)
{
- gmx_bool bAlloc;
rvec *xp, *vp;
- bAlloc = (fr->natoms == 0);
-
if (MASTER(cr) && !*bNotLastFrame)
{
fr->natoms = -1;
*bNotLastFrame = (fr->natoms >= 0);
}
+
+void set_state_entries(t_state *state, const t_inputrec *ir)
+{
+ /* The entries in the state in the tpx file might not correspond
+ * with what is needed, so we correct this here.
+ */
+ state->flags = 0;
+ if (ir->efep != efepNO || ir->bExpanded)
+ {
+ state->flags |= (1<<estLAMBDA);
+ state->flags |= (1<<estFEPSTATE);
+ }
+ state->flags |= (1<<estX);
+ if (state->lambda == NULL)
+ {
+ snew(state->lambda, efptNR);
+ }
+ if (state->x == NULL)
+ {
+ snew(state->x, state->nalloc);
+ }
+ if (EI_DYNAMICS(ir->eI))
+ {
+ state->flags |= (1<<estV);
+ if (state->v == NULL)
+ {
+ snew(state->v, state->nalloc);
+ }
+ }
+ if (ir->eI == eiSD2)
+ {
+ state->flags |= (1<<estSDX);
+ if (state->sd_X == NULL)
+ {
+ /* sd_X is not stored in the tpx file, so we need to allocate it */
+ snew(state->sd_X, state->nalloc);
+ }
+ }
+ if (ir->eI == eiCG)
+ {
+ state->flags |= (1<<estCGP);
+ if (state->cg_p == NULL)
+ {
+ /* cg_p is not stored in the tpx file, so we need to allocate it */
+ snew(state->cg_p, state->nalloc);
+ }
+ }
+
+ state->nnhpres = 0;
+ if (ir->ePBC != epbcNONE)
+ {
+ state->flags |= (1<<estBOX);
+ if (PRESERVE_SHAPE(*ir))
+ {
+ state->flags |= (1<<estBOX_REL);
+ }
+ if ((ir->epc == epcPARRINELLORAHMAN) || (ir->epc == epcMTTK))
+ {
+ state->flags |= (1<<estBOXV);
+ }
+ if (ir->epc != epcNO)
+ {
+ if (IR_NPT_TROTTER(ir) || (IR_NPH_TROTTER(ir)))
+ {
+ state->nnhpres = 1;
+ state->flags |= (1<<estNHPRES_XI);
+ state->flags |= (1<<estNHPRES_VXI);
+ state->flags |= (1<<estSVIR_PREV);
+ state->flags |= (1<<estFVIR_PREV);
+ state->flags |= (1<<estVETA);
+ state->flags |= (1<<estVOL0);
+ }
+ else
+ {
+ state->flags |= (1<<estPRES_PREV);
+ }
+ }
+ }
+
+ if (ir->etc == etcNOSEHOOVER)
+ {
+ state->flags |= (1<<estNH_XI);
+ state->flags |= (1<<estNH_VXI);
+ }
+
+ if (ir->etc == etcVRESCALE)
+ {
+ state->flags |= (1<<estTC_INT);
+ }
+
+ init_gtc_state(state, state->ngtc, state->nnhpres, ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
+ init_ekinstate(&state->ekinstate, ir);
+
+ init_energyhistory(&state->enerhist);
+ init_df_history(&state->dfhist, ir->fepvals->n_lambda);
+ state->swapstate.eSwapCoords = ir->eSwapCoords;
+}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "typedefs.h"
-#include "mdatoms.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/smalloc.h"
-#include "main.h"
-#include "qmmm.h"
-#include "mtop_util.h"
-#include "gmx_omp_nthreads.h"
#define ALMOST_ZERO 1e-30
t_mdatoms *init_mdatoms(FILE *fp, gmx_mtop_t *mtop, gmx_bool bFreeEnergy)
{
- int mb, a, g, nmol;
+ int a;
double tmA, tmB;
t_atom *atom;
t_mdatoms *md;
gmx_mtop_atomloop_all_t aloop;
- t_ilist *ilist;
snew(md, 1);
int i;
t_grpopts *opts;
gmx_groups_t *groups;
- gmx_molblock_t *molblock;
int nthreads gmx_unused;
+ const real oneOverSix = 1.0 / 6.0;
bLJPME = EVDW_PME(ir->vdwtype);
groups = &mtop->groups;
- molblock = mtop->molblock;
-
/* Index==NULL indicates no DD (unless we have a DD node with no
* atoms), so also check for homenr. This should be
* signaled properly with an extra parameter or nindex==-1.
alook = gmx_mtop_atomlookup_init(mtop);
+ // cppcheck-suppress unreadVariable
nthreads = gmx_omp_nthreads_get(emntDefault);
#pragma omp parallel for num_threads(nthreads) schedule(static)
for (i = 0; i < md->nr; i++)
{
- int g, ag, molb;
+ int g, ag;
real mA, mB, fac;
real c6, c12;
t_atom *atom;
}
else
{
- md->sigmaA[i] = pow(c12/c6, 1.0/6.0);
+ md->sigmaA[i] = pow(c12/c6, oneOverSix);
}
md->sigma3A[i] = 1/(md->sigmaA[i]*md->sigmaA[i]*md->sigmaA[i]);
}
}
else
{
- md->sigmaB[i] = pow(c12/c6, 1.0/6.0);
+ md->sigmaB[i] = pow(c12/c6, oneOverSix);
}
md->sigma3B[i] = 1/(md->sigmaB[i]*md->sigmaB[i]*md->sigmaB[i]);
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/mdebin.h"
-#include <string.h>
#include <float.h>
-#include "typedefs.h"
-#include "mdebin.h"
-#include "gromacs/utility/smalloc.h"
-#include "physics.h"
+#include <stdlib.h>
+#include <string.h>
+
#include "gromacs/fileio/enxio.h"
-#include "vec.h"
-#include "disre.h"
-#include "main.h"
-#include "network.h"
-#include "names.h"
-#include "orires.h"
-#include "constr.h"
-#include "mtop_util.h"
-#include "xvgr.h"
#include "gromacs/fileio/gmxfio.h"
-#include "macros.h"
-#include "mdrun.h"
-#include "mdebin_bar.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/mdebin_bar.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/smalloc.h"
static const char *conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
{
ni = groups->grps[egcTC].nm_ind[i];
sprintf(buf, "T-%s", *(groups->grpname[ni]));
- grpnms[i] = strdup(buf);
+ grpnms[i] = gmx_strdup(buf);
}
md->itemp = get_ebin_space(md->ebin, md->nTC, (const char **)grpnms,
unit_temp_K);
for (j = 0; (j < md->nNHC); j++)
{
sprintf(buf, "Xi-%d-%s", j, bufi);
- grpnms[2*(i*md->nNHC+j)] = strdup(buf);
+ grpnms[2*(i*md->nNHC+j)] = gmx_strdup(buf);
sprintf(buf, "vXi-%d-%s", j, bufi);
- grpnms[2*(i*md->nNHC+j)+1] = strdup(buf);
+ grpnms[2*(i*md->nNHC+j)+1] = gmx_strdup(buf);
}
}
md->itc = get_ebin_space(md->ebin, md->mde_n,
for (j = 0; (j < md->nNHC); j++)
{
sprintf(buf, "Xi-%d-%s", j, bufi);
- grpnms[2*(i*md->nNHC+j)] = strdup(buf);
+ grpnms[2*(i*md->nNHC+j)] = gmx_strdup(buf);
sprintf(buf, "vXi-%d-%s", j, bufi);
- grpnms[2*(i*md->nNHC+j)+1] = strdup(buf);
+ grpnms[2*(i*md->nNHC+j)+1] = gmx_strdup(buf);
}
}
md->itcb = get_ebin_space(md->ebin, md->mdeb_n,
ni = groups->grps[egcTC].nm_ind[i];
bufi = *(groups->grpname[ni]);
sprintf(buf, "Xi-%s", bufi);
- grpnms[2*i] = strdup(buf);
+ grpnms[2*i] = gmx_strdup(buf);
sprintf(buf, "vXi-%s", bufi);
- grpnms[2*i+1] = strdup(buf);
+ grpnms[2*i+1] = gmx_strdup(buf);
}
md->itc = get_ebin_space(md->ebin, md->mde_n,
(const char **)grpnms, unit_invtime);
{
ni = groups->grps[egcTC].nm_ind[i];
sprintf(buf, "Lamb-%s", *(groups->grpname[ni]));
- grpnms[i] = strdup(buf);
+ grpnms[i] = gmx_strdup(buf);
}
md->itc = get_ebin_space(md->ebin, md->mde_n, (const char **)grpnms, "");
}
{
ni = groups->grps[egcACC].nm_ind[i];
sprintf(buf, "Ux-%s", *(groups->grpname[ni]));
- grpnms[3*i+XX] = strdup(buf);
+ grpnms[3*i+XX] = gmx_strdup(buf);
sprintf(buf, "Uy-%s", *(groups->grpname[ni]));
- grpnms[3*i+YY] = strdup(buf);
+ grpnms[3*i+YY] = gmx_strdup(buf);
sprintf(buf, "Uz-%s", *(groups->grpname[ni]));
- grpnms[3*i+ZZ] = strdup(buf);
+ grpnms[3*i+ZZ] = gmx_strdup(buf);
}
md->iu = get_ebin_space(md->ebin, 3*md->nU, (const char **)grpnms, unit_vel);
sfree(grpnms);
if (Nsep > 1)
{
/* and add the closing parenthesis */
- str += sprintf(str, ")");
+ sprintf(str, ")");
}
}
{
/* state for the fep_vals, if we have alchemical sampling */
sprintf(buf, "%s", "Thermodynamic state");
- setname[s] = strdup(buf);
+ setname[s] = gmx_strdup(buf);
s += 1;
}
default:
sprintf(buf, "%s (%s)", "Total Energy", unit_energy);
}
- setname[s] = strdup(buf);
+ setname[s] = gmx_strdup(buf);
s += 1;
}
sprintf(buf, "%s %s = %.4f", dhdl, efpt_singular_names[i],
lam);
}
- setname[s] = strdup(buf);
+ setname[s] = gmx_strdup(buf);
s += 1;
}
}
ir->simtempvals->temperatures[s-(nsetsbegin)],
unit_temp_K);
}
- setname[s] = strdup(buf);
+ setname[s] = gmx_strdup(buf);
s++;
}
if (write_pV)
{
np = sprintf(buf, "pV (%s)", unit_energy);
- setname[nsetsextend-1] = strdup(buf); /* the first entry after
- nsets */
+ setname[nsetsextend-1] = gmx_strdup(buf); /* the first entry after
+ nsets */
}
xvgr_legend(fp, nsetsextend, (const char **)setname, oenv);
nj = groups->grps[egcENER].nm_ind[j];
sprintf(buf, "%s-%s", *(groups->grpname[ni]),
*(groups->grpname[nj]));
- md->print_grpnms[n++] = strdup(buf);
+ md->print_grpnms[n++] = gmx_strdup(buf);
}
}
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "mdebin_bar.h"
-#include <string.h>
#include <float.h>
#include <math.h>
-#include "typedefs.h"
-#include "gmx_fatal.h"
-#include "mdebin.h"
-#include "gromacs/utility/smalloc.h"
+#include <string.h>
+
#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/gmxfio.h"
-#include "mdebin_bar.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* reset the delta_h list to prepare it for new values */
static void mde_delta_h_reset(t_mde_delta_h *dh)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _mdebin_bar_h
#define _mdebin_bar_h
+#include "gromacs/legacyheaders/mdebin.h"
+
#ifdef __cplusplus
extern "C" {
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
+#include <math.h>
#include <string.h>
#include <time.h>
-#include <math.h>
-#include "sysstuff.h"
-#include "gromacs/utility/cstringutil.h"
-#include "network.h"
-#include "gromacs/utility/smalloc.h"
-#include "nrnb.h"
-#include "main.h"
-#include "force.h"
-#include "macros.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "update.h"
-#include "constr.h"
-#include "vec.h"
-#include "tgroup.h"
-#include "mdebin.h"
-#include "vsite.h"
-#include "force.h"
-#include "mdrun.h"
-#include "md_support.h"
-#include "sim_util.h"
-#include "domdec.h"
-#include "mdatoms.h"
-#include "ns.h"
-#include "mtop_util.h"
-#include "pme.h"
-#include "bondf.h"
-#include "gmx_omp_nthreads.h"
-#include "md_logging.h"
+#include <algorithm>
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/ewald/pme.h"
#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/mtxio.h"
#include "gromacs/fileio/trajectory_writing.h"
-#include "gromacs/linearalgebra/mtxio.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/listed-forces/manage-threading.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
-#include "gromacs/imd/imd.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
t_state s;
real *fnorm, real *fmax, int *a_fmax)
{
double fnorm2, *sum;
- real fmax2, fmax2_0, fam;
+ real fmax2, fam;
int la_max, a_max, start, end, i, m, gf;
/* This routine finds the largest force and returns it.
fnorm2 = 0;
fmax2 = 0;
la_max = -1;
- gf = 0;
start = 0;
end = mdatoms->homenr;
if (mdatoms->cFREEZE)
/* Constrain the starting coordinates */
dvdl_constr = 0;
constrain(PAR(cr) ? NULL : fplog, TRUE, TRUE, constr, &(*top)->idef,
- ir, NULL, cr, -1, 0, 1.0, mdatoms,
+ ir, cr, -1, 0, 1.0, mdatoms,
ems->s.x, ems->s.x, NULL, fr->bMolPBC, ems->s.box,
ems->s.lambda[efptFEP], &dvdl_constr,
- NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
+ NULL, NULL, nrnb, econqCoord);
}
}
{
*gstat = global_stat_init(ir);
}
+ else
+ {
+ *gstat = NULL;
+ }
*outf = init_mdoutf(fplog, nfile, fnm, 0, cr, ir, top_global, NULL, wcycle);
x1 = s1->x;
x2 = s2->x;
+ // cppcheck-suppress unreadVariable
nthreads = gmx_omp_nthreads_get(emntUpdate);
#pragma omp parallel num_threads(nthreads)
{
wallcycle_start(wcycle, ewcCONSTR);
dvdl_constr = 0;
constrain(NULL, TRUE, TRUE, constr, &top->idef,
- ir, NULL, cr, count, 0, 1.0, md,
+ ir, cr, count, 0, 1.0, md,
s1->x, s2->x, NULL, bMolPBC, s2->box,
s2->lambda[efptBONDED], &dvdl_constr,
- NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
+ NULL, NULL, nrnb, econqCoord);
wallcycle_stop(wcycle, ewcCONSTR);
}
}
{
real t;
gmx_bool bNS;
- int nabnsb;
tensor force_vir, shake_vir, ekin;
real dvdl_constr, prescorr, enercorr, dvdlcorr;
real terminate = 0;
{
bNS = TRUE;
}
- else if (inputrec->nstlist == -1)
- {
- nabnsb = natoms_beyond_ns_buffer(inputrec, fr, &top->cgs, NULL, ems->s.x);
- if (PAR(cr))
- {
- gmx_sumi(1, &nabnsb, cr);
- }
- bNS = (nabnsb > 0);
- }
}
if (vsite)
top_global, &ems->s, FALSE,
CGLO_ENERGY |
CGLO_PRESSURE |
- CGLO_CONSTRAINT |
- CGLO_FIRSTITERATE);
+ CGLO_CONSTRAINT);
wallcycle_stop(wcycle, ewcMoveE);
}
/* Calculate long range corrections to pressure and energy */
- calc_dispcorr(fplog, inputrec, fr, count, top_global->natoms, ems->s.box, ems->s.lambda[efptVDW],
+ calc_dispcorr(inputrec, fr, top_global->natoms, ems->s.box, ems->s.lambda[efptVDW],
pres, force_vir, &prescorr, &enercorr, &dvdlcorr);
enerd->term[F_DISPCORR] = enercorr;
enerd->term[F_EPOT] += enercorr;
wallcycle_start(wcycle, ewcCONSTR);
dvdl_constr = 0;
constrain(NULL, FALSE, FALSE, constr, &top->idef,
- inputrec, NULL, cr, count, 0, 1.0, mdatoms,
+ inputrec, cr, count, 0, 1.0, mdatoms,
ems->s.x, ems->f, ems->f, fr->bMolPBC, ems->s.box,
ems->s.lambda[efptBONDED], &dvdl_constr,
- NULL, &shake_vir, nrnb, econqForceDispl, FALSE, 0, 0);
- if (fr->bSepDVDL && fplog)
- {
- gmx_print_sepdvdl(fplog, "Constraints", t, dvdl_constr);
- }
+ NULL, &shake_vir, nrnb, econqForceDispl);
enerd->term[F_DVDL_CONSTR] += dvdl_constr;
m_add(force_vir, shake_vir, vir);
wallcycle_stop(wcycle, ewcCONSTR);
rvec *f;
gmx_global_stat_t gstat;
t_graph *graph;
- rvec *f_global, *p, *sf, *sfm;
- double gpa, gpb, gpc, tmp, sum[2], minstep;
+ rvec *f_global, *p, *sf;
+ double gpa, gpb, gpc, tmp, minstep;
real fnormn;
real stepsize;
real a, b, c, beta = 0.0;
int number_steps, neval = 0, nstcg = inputrec->nstcgsteep;
gmx_mdoutf_t outf;
int i, m, gf, step, nminstep;
- real terminate = 0;
step = 0;
if (MASTER(cr))
{
+ double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
fprintf(stderr, " F-max = %12.5e on atom %d\n",
s_min->fmax, s_min->a_fmax+1);
fprintf(stderr, " F-Norm = %12.5e\n",
- s_min->fnorm/sqrt(state_global->natoms));
+ s_min->fnorm/sqrtNumAtoms);
fprintf(stderr, "\n");
/* and copy to the log file too... */
fprintf(fplog, " F-max = %12.5e on atom %d\n",
s_min->fmax, s_min->a_fmax+1);
fprintf(fplog, " F-Norm = %12.5e\n",
- s_min->fnorm/sqrt(state_global->natoms));
+ s_min->fnorm/sqrtNumAtoms);
fprintf(fplog, "\n");
}
/* Start the loop over CG steps.
* the line minimum. We try to interpolate based on the derivative at the endpoints,
* and only continue until we find a lower value. In most cases this means 1-2 iterations.
*
- * I also have a safeguard for potentially really patological functions so we never
+ * I also have a safeguard for potentially really pathological functions so we never
* take more than 20 steps before we give up ...
*
* If we already found a lower value we just skip this step and continue to the update.
}
swap_em_state(s_b, s_c);
gpb = gpc;
- b = c;
}
else
{
}
swap_em_state(s_b, s_a);
gpb = gpa;
- b = a;
}
}
}
swap_em_state(s_b, s_c);
gpb = gpc;
- b = c;
}
/* new search direction */
{
if (bVerbose)
{
+ double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
- step, s_min->epot, s_min->fnorm/sqrt(state_global->natoms),
+ step, s_min->epot, s_min->fnorm/sqrtNumAtoms,
s_min->fmax, s_min->a_fmax+1);
}
/* Store the new (lower) energies */
top_global, inputrec, step,
s_min, state_global, f_global);
- fnormn = s_min->fnorm/sqrt(state_global->natoms);
if (MASTER(cr))
{
+ double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
+ fnormn = s_min->fnorm/sqrtNumAtoms;
print_converged(stderr, CG, inputrec->em_tol, step, converged, number_steps,
s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
print_converged(fplog, CG, inputrec->em_tol, step, converged, number_steps,
t_graph *graph;
rvec *f_global;
int ncorr, nmaxcorr, point, cp, neval, nminstep;
- double stepsize, gpa, gpb, gpc, tmp, minstep;
+ double stepsize, step_taken, gpa, gpb, gpc, tmp, minstep;
real *rho, *alpha, *ff, *xx, *p, *s, *lastx, *lastf, **dx, **dg;
real *xa, *xb, *xc, *fa, *fb, *fc, *xtmp, *ftmp;
real a, b, c, maxdelta, delta;
real diag, Epot0, Epot, EpotA, EpotB, EpotC;
real dgdx, dgdg, sq, yr, beta;
t_mdebin *mdebin;
- gmx_bool converged, first;
+ gmx_bool converged;
rvec mu_tot;
real fnorm, fmax;
gmx_bool do_log, do_ene, do_x, do_f, foundlower, *frozen;
gmx_mdoutf_t outf;
int i, k, m, n, nfmax, gf, step;
int mdof_flags;
- /* not used */
- real terminate;
if (PAR(cr))
{
if (MASTER(cr))
{
+ double sqrtNumAtoms = sqrt(static_cast<double>(state->natoms));
fprintf(stderr, "Using %d BFGS correction steps.\n\n", nmaxcorr);
fprintf(stderr, " F-max = %12.5e on atom %d\n", fmax, nfmax+1);
- fprintf(stderr, " F-Norm = %12.5e\n", fnorm/sqrt(state->natoms));
+ fprintf(stderr, " F-Norm = %12.5e\n", fnorm/sqrtNumAtoms);
fprintf(stderr, "\n");
/* and copy to the log file too... */
fprintf(fplog, "Using %d BFGS correction steps.\n\n", nmaxcorr);
fprintf(fplog, " F-max = %12.5e on atom %d\n", fmax, nfmax+1);
- fprintf(fplog, " F-Norm = %12.5e\n", fnorm/sqrt(state->natoms));
+ fprintf(fplog, " F-Norm = %12.5e\n", fnorm/sqrtNumAtoms);
fprintf(fplog, "\n");
}
+ // Point is an index to the memory of search directions, where 0 is the first one.
point = 0;
+
+ // Set initial search direction to the force (-gradient), or 0 for frozen particles.
for (i = 0; i < n; i++)
{
if (!frozen[i])
}
}
+ // Stepsize will be modified during the search, and actually it is not critical
+ // (the main efficiency in the algorithm comes from changing directions), but
+ // we still need an initial value, so estimate it as the inverse of the norm
+ // so we take small steps where the potential fluctuates a lot.
stepsize = 1.0/fnorm;
- converged = FALSE;
/* Start the loop over BFGS steps.
* Each successful step is counted, and we continue until
/* Do the linesearching in the direction dx[point][0..(n-1)] */
- /* pointer to current direction - point=0 first time here */
+ /* make s a pointer to current search direction - point=0 first time we get here */
s = dx[point];
- /* calculate line gradient */
+ // calculate line gradient in position A
for (gpa = 0, i = 0; i < n; i++)
{
gpa -= s[i]*ff[i];
}
- /* Calculate minimum allowed stepsize, before the average (norm)
+ /* Calculate minimum allowed stepsize along the line, before the average (norm)
* relative change in coordinate is smaller than precision
*/
for (minstep = 0, i = 0; i < n; i++)
break;
}
- /* Store old forces and coordinates */
+ // Before taking any steps along the line, store the old position
for (i = 0; i < n; i++)
{
lastx[i] = xx[i];
}
Epot0 = Epot;
- first = TRUE;
-
for (i = 0; i < n; i++)
{
xa[i] = xx[i];
}
/* Take a step downhill.
- * In theory, we should minimize the function along this direction.
+ * In theory, we should find the actual minimum of the function in this
+ * direction, somewhere along the line.
* That is quite possible, but it turns out to take 5-10 function evaluations
* for each line. However, we dont really need to find the exact minimum -
* it is much better to start a new BFGS step in a modified direction as soon
*
* In practice, we just try to take a single step.
* If it worked (i.e. lowered the energy), we increase the stepsize but
- * the continue straight to the next BFGS step without trying to find any minimum.
+ * continue straight to the next BFGS step without trying to find any minimum,
+ * i.e. we change the search direction too. If the line was smooth, it is
+ * likely we are in a smooth region, and then it makes sense to take longer
+ * steps in the modified search direction too.
+ *
* If it didn't work (higher energy), there must be a minimum somewhere between
- * the old position and the new one.
+ * the old position and the new one. Then we need to start by finding a lower
+ * value before we change search direction. Since the energy was apparently
+ * quite rough, we need to decrease the step size.
*
* Due to the finite numerical accuracy, it turns out that it is a good idea
- * to even accept a SMALL increase in energy, if the derivative is still downhill.
+ * to accept a SMALL increase in energy, if the derivative is still downhill.
* This leads to lower final energies in the tests I've done. / Erik
*/
- foundlower = FALSE;
+
+ // State "A" is the first position along the line.
+ // reference position along line is initially zero
EpotA = Epot0;
a = 0.0;
- c = a + stepsize; /* reference position along line is zero */
- /* Check stepsize first. We do not allow displacements
- * larger than emstep.
- */
+ // Check stepsize first. We do not allow displacements
+ // larger than emstep.
+ //
do
{
+ // Pick a new position C by adding stepsize to A.
c = a + stepsize;
+
+ // Calculate what the largest change in any individual coordinate
+ // would be (translation along line * gradient along line)
maxdelta = 0;
for (i = 0; i < n; i++)
{
maxdelta = delta;
}
}
+ // If any displacement is larger than the stepsize limit, reduce the step
if (maxdelta > inputrec->em_stepsize)
{
stepsize *= 0.1;
}
while (maxdelta > inputrec->em_stepsize);
- /* Take a trial step */
+ // Take a trial step and move the coordinate array xc[] to position C
for (i = 0; i < n; i++)
{
xc[i] = lastx[i] + c*s[i];
}
neval++;
- /* Calculate energy for the trial step */
+ // Calculate energy for the trial step in position C
ems.s.x = (rvec *)xc;
ems.f = (rvec *)fc;
evaluate_energy(fplog, cr,
mu_tot, enerd, vir, pres, step, FALSE);
EpotC = ems.epot;
- /* Calc derivative along line */
+ // Calc line gradient in position C
for (gpc = 0, i = 0; i < n; i++)
{
gpc -= s[i]*fc[i]; /* f is negative gradient, thus the sign */
gmx_sumd(1, &gpc, cr);
}
- /* This is the max amount of increase in energy we tolerate */
+ // This is the max amount of increase in energy we tolerate.
+ // By allowing VERY small changes (close to numerical precision) we
+ // frequently find even better (lower) final energies.
tmp = sqrt(GMX_REAL_EPS)*fabs(EpotA);
- /* Accept the step if the energy is lower, or if it is not significantly higher
- * and the line derivative is still negative.
- */
+ // Accept the step if the energy is lower in the new position C (compared to A),
+ // or if it is not significantly higher and the line derivative is still negative.
if (EpotC < EpotA || (gpc < 0 && EpotC < (EpotA+tmp)))
{
+ // Great, we found a better energy. We no longer try to alter the
+ // stepsize, but simply accept this new better position. The we select a new
+ // search direction instead, which will be much more efficient than continuing
+ // to take smaller steps along a line. Set fnorm based on the new C position,
+ // which will be used to update the stepsize to 1/fnorm further down.
foundlower = TRUE;
- /* Great, we found a better energy. Increase step for next iteration
- * if we are still going down, decrease it otherwise
- */
- if (gpc < 0)
- {
- stepsize *= 1.618034; /* The golden section */
- }
- else
- {
- stepsize *= 0.618034; /* 1/golden section */
- }
+ fnorm = ems.fnorm;
}
else
{
- /* New energy is the same or higher. We will have to do some work
- * to find a smaller value in the interval. Take smaller step next time!
- */
+ // If we got here, the energy is NOT lower in point C, i.e. it will be the same
+ // or higher than in point A. In this case it is pointless to move to point C,
+ // so we will have to do more iterations along the same line to find a smaller
+ // value in the interval [A=0.0,C].
+ // Here, A is still 0.0, but that will change when we do a search in the interval
+ // [0.0,C] below. That search we will do by interpolation or bisection rather
+ // than with the stepsize, so no need to modify it. For the next search direction
+ // it will be reset to 1/fnorm anyway.
foundlower = FALSE;
- stepsize *= 0.618034;
}
- /* OK, if we didn't find a lower value we will have to locate one now - there must
- * be one in the interval [a=0,c].
- * The same thing is valid here, though: Don't spend dozens of iterations to find
- * the line minimum. We try to interpolate based on the derivative at the endpoints,
- * and only continue until we find a lower value. In most cases this means 1-2 iterations.
- *
- * I also have a safeguard for potentially really patological functions so we never
- * take more than 20 steps before we give up ...
- *
- * If we already found a lower value we just skip this step and continue to the update.
- */
-
if (!foundlower)
{
-
+ // OK, if we didn't find a lower value we will have to locate one now - there must
+ // be one in the interval [a,c].
+ // The same thing is valid here, though: Don't spend dozens of iterations to find
+ // the line minimum. We try to interpolate based on the derivative at the endpoints,
+ // and only continue until we find a lower value. In most cases this means 1-2 iterations.
+ // I also have a safeguard for potentially really pathological functions so we never
+ // take more than 20 steps before we give up.
+ // If we already found a lower value we just skip this step and continue to the update.
nminstep = 0;
do
{
- /* Select a new trial point.
- * If the derivatives at points a & c have different sign we interpolate to zero,
- * otherwise just do a bisection.
- */
-
+ // Select a new trial point B in the interval [A,C].
+ // If the derivatives at points a & c have different sign we interpolate to zero,
+ // otherwise just do a bisection since there might be multiple minima/maxima
+ // inside the interval.
if (gpa < 0 && gpc > 0)
{
b = a + gpa*(a-c)/(gpc-gpa);
b = 0.5*(a+c);
}
- /* Take a trial step */
+ // Take a trial step to point B
for (i = 0; i < n; i++)
{
xb[i] = lastx[i] + b*s[i];
}
neval++;
- /* Calculate energy for the trial step */
+ // Calculate energy for the trial step in point B
ems.s.x = (rvec *)xb;
ems.f = (rvec *)fb;
evaluate_energy(fplog, cr,
vsite, constr, fcd, graph, mdatoms, fr,
mu_tot, enerd, vir, pres, step, FALSE);
EpotB = ems.epot;
-
fnorm = ems.fnorm;
+ // Calculate gradient in point B
for (gpb = 0, i = 0; i < n; i++)
{
gpb -= s[i]*fb[i]; /* f is negative gradient, thus the sign */
gmx_sumd(1, &gpb, cr);
}
- /* Keep one of the intervals based on the value of the derivative at the new point */
+ // Keep one of the intervals [A,B] or [B,C] based on the value of the derivative
+ // at the new point B, and rename the endpoints of this new interval A and C.
if (gpb > 0)
{
/* Replace c endpoint with b */
xx[i] = xc[i];
ff[i] = fc[i];
}
- stepsize = c;
+ step_taken = c;
}
else
{
xx[i] = xa[i];
ff[i] = fa[i];
}
- stepsize = a;
+ step_taken = a;
}
}
xx[i] = xc[i];
ff[i] = fc[i];
}
- stepsize = c;
+ step_taken = c;
}
/* Update the memory information, and calculate a new
for (i = 0; i < n; i++)
{
dg[point][i] = lastf[i]-ff[i];
- dx[point][i] *= stepsize;
+ dx[point][i] *= step_taken;
}
dgdg = 0;
}
}
- stepsize = 1.0;
-
/* Test whether the convergence criterion is met */
get_f_norm_max(cr, &(inputrec->opts), mdatoms, f, &fnorm, &fmax, &nfmax);
{
if (bVerbose)
{
+ double sqrtNumAtoms = sqrt(static_cast<double>(state->natoms));
fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
- step, Epot, fnorm/sqrt(state->natoms), fmax, nfmax+1);
+ step, Epot, fnorm/sqrtNumAtoms, fmax, nfmax+1);
}
/* Store the new (lower) energies */
upd_mdebin(mdebin, FALSE, FALSE, (double)step,
IMD_send_positions(inputrec->imd);
}
+ // Reset stepsize in we are doing more iterations
+ stepsize = 1.0/fnorm;
+
/* Stop when the maximum force lies below tolerance.
* If we have reached machine precision, converged is already set to true.
*/
-
converged = converged || (fmax < inputrec->em_tol);
} /* End of the loop */
if (MASTER(cr))
{
+ double sqrtNumAtoms = sqrt(static_cast<double>(state->natoms));
print_converged(stderr, LBFGS, inputrec->em_tol, step, converged,
- number_steps, Epot, fmax, nfmax, fnorm/sqrt(state->natoms));
+ number_steps, Epot, fmax, nfmax, fnorm/sqrtNumAtoms);
print_converged(fplog, LBFGS, inputrec->em_tol, step, converged,
- number_steps, Epot, fmax, nfmax, fnorm/sqrt(state->natoms));
+ number_steps, Epot, fmax, nfmax, fnorm/sqrtNumAtoms);
fprintf(fplog, "\nPerformed %d energy evaluations in total.\n", neval);
}
rvec *f;
gmx_global_stat_t gstat;
t_graph *graph;
- real stepsize, constepsize;
+ real stepsize;
real ustep, fnormn;
gmx_mdoutf_t outf;
t_mdebin *mdebin;
int nsteps;
int count = 0;
int steps_accepted = 0;
- /* not used */
- real terminate = 0;
s_min = init_em_state();
s_try = init_em_state();
if (count == 0)
{
- s_min->epot = s_try->epot + 1;
+ s_min->epot = s_try->epot;
}
/* Print it if necessary */
{
fprintf(stderr, "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",
count, ustep, s_try->epot, s_try->fmax, s_try->a_fmax+1,
- (s_try->epot < s_min->epot) ? '\n' : '\r');
+ ( (count == 0) || (s_try->epot < s_min->epot) ) ? '\n' : '\r');
}
- if (s_try->epot < s_min->epot)
+ if ( (count == 0) || (s_try->epot < s_min->epot) )
{
/* Store the new (lower) energies */
upd_mdebin(mdebin, FALSE, FALSE, (double)count,
top_global, inputrec, count,
s_min, state_global, f_global);
- fnormn = s_min->fnorm/sqrt(state_global->natoms);
-
if (MASTER(cr))
{
+ double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
+ fnormn = s_min->fnorm/sqrtNumAtoms;
+
print_converged(stderr, SD, inputrec->em_tol, count, bDone, nsteps,
s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
print_converged(fplog, SD, inputrec->em_tol, count, bDone, nsteps,
rvec *f;
gmx_global_stat_t gstat;
t_graph *graph;
- real t, t0, lambda, lam0;
- gmx_bool bNS;
tensor vir, pres;
rvec mu_tot;
rvec *fneg, *dfdx;
int i, j, k, row, col;
real der_range = 10.0*sqrt(GMX_REAL_EPS);
real x_min;
- real fnorm, fmax;
+ bool bIsMaster = MASTER(cr);
if (constr != NULL)
{
snew(dfdx, natoms);
#ifndef GMX_DOUBLE
- if (MASTER(cr))
+ if (bIsMaster)
{
fprintf(stderr,
"NOTE: This version of Gromacs has been compiled in single precision,\n"
bSparse = TRUE;
}
- if (MASTER(cr))
+ if (bIsMaster)
{
sz = DIM*top_global->natoms;
}
}
- /* Initial values */
- t0 = inputrec->init_t;
- lam0 = inputrec->fepvals->init_lambda;
- t = t0;
- lambda = lam0;
-
init_nrnb(nrnb);
where();
/* fudge nr of steps to nr of atoms */
inputrec->nsteps = natoms*2;
- if (MASTER(cr))
+ if (bIsMaster)
{
fprintf(stderr, "starting normal mode calculation '%s'\n%d steps.\n\n",
*(top_global->name), (int)inputrec->nsteps);
}
}
- if (!MASTER(cr))
+ if (!bIsMaster)
{
#ifdef GMX_MPI
#ifdef GMX_DOUBLE
}
}
/* write progress */
- if (MASTER(cr) && bVerbose)
+ if (bIsMaster && bVerbose)
{
fprintf(stderr, "\rFinished step %d out of %d",
- min(atom+nnodes, natoms), natoms);
+ std::min(atom+nnodes, natoms), natoms);
fflush(stderr);
}
}
- if (MASTER(cr))
+ if (bIsMaster)
{
fprintf(stderr, "\n\nWriting Hessian...\n");
gmx_mtxio_write(ftp2fn(efMTX, nfile, fnm), sz, sz, full_matrix, sparse_matrix);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef NB_VERLET_H
#define NB_VERLET_H
-#include "nbnxn_pairlist.h"
-#include "nbnxn_cuda_types_ext.h"
+#include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
#ifdef __cplusplus
extern "C" {
#endif
-/*! Nonbonded NxN kernel types: plain C, CPU SIMD, GPU CUDA, GPU emulation */
+/** Nonbonded NxN kernel types: plain C, CPU SIMD, GPU CUDA, GPU emulation */
typedef enum
{
nbnxnkNotSet = 0,
nbnxnkNR
} nbnxn_kernel_type;
-/*! Return a string indentifying the kernel type */
+/** Return a string indentifying the kernel type */
const char *lookup_nbnxn_kernel_name(int kernel_type);
enum {
enbvClearFNo, enbvClearFYes
};
-typedef struct {
+typedef struct nonbonded_verlet_group_t {
nbnxn_pairlist_set_t nbl_lists; /* pair list(s) */
nbnxn_atomdata_t *nbat; /* atom data */
int kernel_type; /* non-bonded kernel - see enum above */
} nonbonded_verlet_group_t;
/* non-bonded data structure with Verlet-type cut-off */
-typedef struct {
+typedef struct nonbonded_verlet_t {
nbnxn_search_t nbs; /* n vs n atom pair searching data */
int ngrp; /* number of interaction groups */
nonbonded_verlet_group_t grp[2]; /* local and non-local interaction group */
used for the 8x8x8 CUDA kernels */
} nonbonded_verlet_t;
+/*! \brief Getter for bUseGPU */
+gmx_bool
+usingGpu(nonbonded_verlet_t *nbv);
+
#ifdef __cplusplus
}
#endif
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "nbnxn_atomdata.h"
+
+#include "config.h"
+#include <assert.h>
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include <assert.h>
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "nbnxn_consts.h"
-#include "nbnxn_internal.h"
-#include "nbnxn_atomdata.h"
-#include "nbnxn_search.h"
-#include "gromacs/utility/gmxomp.h"
-#include "gmx_omp_nthreads.h"
+
#include "thread_mpi/atomic.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_internal.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
+
/* Default nbnxn allocation routine, allocates NBNXN_MEM_ALIGN byte aligned */
void nbnxn_alloc_aligned(void **ptr, size_t nbytes)
{
i0 = b *NBNXN_BUFFERFLAG_SIZE*nbat->fstride;
i1 = (b+1)*NBNXN_BUFFERFLAG_SIZE*nbat->fstride;
- if ((flags->flag[b] & (1ULL<<index[1])) || group_size > 2)
+ if (bitmask_is_set(flags->flag[b], index[1]) || group_size > 2)
{
#ifdef GMX_NBNXN_SIMD
nbnxn_atomdata_reduce_reals_simd
nbnxn_atomdata_reduce_reals
#endif
(nbat->out[index[0]].f,
- (flags->flag[b] & (1ULL<<index[0])) || group_size > 2,
+ bitmask_is_set(flags->flag[b], index[0]) || group_size > 2,
&(nbat->out[index[1]].f), 1, i0, i1);
}
- else if (!(flags->flag[b] & (1ULL<<index[0])))
+ else if (!bitmask_is_set(flags->flag[b], index[0]))
{
nbnxn_atomdata_clear_reals(nbat->out[index[0]].f,
i0, i1);
nfptr = 0;
for (out = 1; out < nbat->nout; out++)
{
- if (flags->flag[b] & (1U<<out))
+ if (bitmask_is_set(flags->flag[b], out))
{
fptr[nfptr++] = nbat->out[out].f;
}
nbnxn_atomdata_reduce_reals
#endif
(nbat->out[0].f,
- flags->flag[b] & (1U<<0),
+ bitmask_is_set(flags->flag[b], 0),
fptr, nfptr,
i0, i1);
}
- else if (!(flags->flag[b] & (1U<<0)))
+ else if (!bitmask_is_set(flags->flag[b], 0))
{
nbnxn_atomdata_clear_reals(nbat->out[0].f,
i0, i1);
#ifndef _nbnxn_atomdata_h
#define _nbnxn_atomdata_h
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
#ifdef __cplusplus
extern "C" {
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014 by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define NBNXN_GPU_CLUSTER_SIZE 8
/* With GPU kernels we group cluster pairs in 4 to optimize memory usage.
- * To change this, also change nbnxn_cj4_t in include/types/nbnxn_pairlist.h.
+ * To change this, also change nbnxn_cj4_t in gromacs/mdlib/nbnxn_pairlist.h.
*/
#define NBNXN_GPU_JGROUP_SIZE 4
#define NBNXN_GPU_JGROUP_SIZE_2LOG 2
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
if(GMX_GPU)
file(GLOB CUDA_NB_SOURCES *.cu)
- CUDA_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
- CUDA_ADD_LIBRARY(nbnxn_cuda STATIC ${CUDA_NB_SOURCES}
- OPTIONS
- RELWITHDEBINFO -g
- DEBUG -g -D_DEBUG_=1)
- target_link_libraries(nbnxn_cuda cuda_tools)
+ set(MDLIB_SOURCES ${MDLIB_SOURCES} ${CUDA_NB_SOURCES} PARENT_SCOPE)
endif()
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "nbnxn_cuda.h"
+
+#include "config.h"
-#include <stdlib.h>
#include <assert.h>
+#include <stdlib.h>
#if defined(_MSVC)
#include <limits>
#include <cuda.h>
-#include "types/simple.h"
-#include "types/nbnxn_pairlist.h"
-#include "types/nb_verlet.h"
-#include "types/ishift.h"
-#include "types/force_flags.h"
-#include "../nbnxn_consts.h"
-
#ifdef TMPI_ATOMICS
#include "thread_mpi/atomic.h"
#endif
+#include "gromacs/gmxlib/cuda_tools/cudautils.cuh"
+#include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/utility/cstringutil.h"
+
#include "nbnxn_cuda_types.h"
-#include "../../gmxlib/cuda_tools/cudautils.cuh"
-#include "nbnxn_cuda.h"
-#include "nbnxn_cuda_data_mgmt.h"
#if defined TEXOBJ_SUPPORTED && __CUDA_ARCH__ >= 300
#define USE_TEXOBJ
#define NCL_PER_SUPERCL (NBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER)
#define CL_SIZE (NBNXN_GPU_CLUSTER_SIZE)
+/* NTHREAD_Z controls the number of j-clusters processed concurrently on NTHREAD_Z
+ * warp-pairs per block.
+ *
+ * - On CC 2.0-3.5, 5.0, and 5.2, NTHREAD_Z == 1, translating to 64 th/block with 16
+ * blocks/multiproc, is the fastest even though this setup gives low occupancy.
+ * NTHREAD_Z > 1 results in excessive register spilling unless the minimum blocks
+ * per multiprocessor is reduced proportionally to get the original number of max
+ * threads in flight (and slightly lower performance).
+ * - On CC 3.7 there are enough registers to double the number of threads; using
+ * NTHREADS_Z == 2 is fastest with 16 blocks (TODO: test with RF and other kernels
+ * with low-register use).
+ *
+ * Note that the current kernel implementation only supports NTHREAD_Z > 1 with
+ * shuffle-based reduction, hence CC >= 3.0.
+ */
+
+/* Kernel launch bounds as function of NTHREAD_Z.
+ * - CC 3.5/5.2: NTHREAD_Z=1, (64, 16) bounds
+ * - CC 3.7: NTHREAD_Z=2, (128, 16) bounds
+ */
+#if __CUDA_ARCH__ == 370
+#define NTHREAD_Z (2)
+#define MIN_BLOCKS_PER_MP (16)
+#else
+#define NTHREAD_Z (1)
+#define MIN_BLOCKS_PER_MP (16)
+#endif
+#define THREADS_PER_BLOCK (CL_SIZE*CL_SIZE*NTHREAD_Z)
+
+
/***** The kernels come here *****/
-#include "nbnxn_cuda_kernel_utils.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh"
/* Top-level kernel generation: will generate through multiple inclusion the
* following flavors for all kernels:
* - force and energy output with pair list pruning.
*/
/** Force only **/
-#include "nbnxn_cuda_kernels.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh"
/** Force & energy **/
#define CALC_ENERGIES
-#include "nbnxn_cuda_kernels.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh"
#undef CALC_ENERGIES
/*** Pair-list pruning kernels ***/
/** Force only **/
#define PRUNE_NBL
-#include "nbnxn_cuda_kernels.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh"
/** Force & energy **/
#define CALC_ENERGIES
-#include "nbnxn_cuda_kernels.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh"
#undef CALC_ENERGIES
#undef PRUNE_NBL
}
/*! Calculates the amount of shared memory required by the CUDA kernel in use. */
-static inline int calc_shmem_required()
+static inline int calc_shmem_required(const int num_threads_z)
{
int shmem;
/* NOTE: with the default kernel on sm3.0 we need shmem only for pre-loading */
/* i-atom x+q in shared memory */
shmem = NCL_PER_SUPERCL * CL_SIZE * sizeof(float4);
- /* cj in shared memory, for both warps separately */
- shmem += 2 * NBNXN_GPU_JGROUP_SIZE * sizeof(int);
+ /* cj in shared memory, for each warp separately */
+ shmem += num_threads_z * 2 * NBNXN_GPU_JGROUP_SIZE * sizeof(int);
#ifdef IATYPE_SHMEM
/* i-atom types in shared memory */
shmem += NCL_PER_SUPERCL * CL_SIZE * sizeof(int);
bCalcEner,
plist->bDoPrune || always_prune);
- /* kernel launch config */
+ /* Kernel launch config:
+ * - The thread block dimensions match the size of i-clusters, j-clusters,
+ * and j-cluster concurrency, in x, y, and z, respectively.
+ * - The 1D block-grid contains as many blocks as super-clusters.
+ */
+ int num_threads_z = 1;
+ if (cu_nb->dev_info->prop.major == 3 && cu_nb->dev_info->prop.minor == 7)
+ {
+ num_threads_z = 2;
+ }
nblock = calc_nb_kernel_nblock(plist->nsci, cu_nb->dev_info);
- dim_block = dim3(CL_SIZE, CL_SIZE, 1);
+ dim_block = dim3(CL_SIZE, CL_SIZE, num_threads_z);
dim_grid = dim3(nblock, 1, 1);
- shmem = calc_shmem_required();
+ shmem = calc_shmem_required(num_threads_z);
if (debug)
{
fprintf(debug, "GPU launch configuration:\n\tThread block: %dx%dx%d\n\t"
- "Grid: %dx%d\n\t#Super-clusters/clusters: %d/%d (%d)\n",
+ "\tGrid: %dx%d\n\t#Super-clusters/clusters: %d/%d (%d)\n"
+ "\tShMem: %d\n",
dim_block.x, dim_block.y, dim_block.z,
dim_grid.x, dim_grid.y, plist->nsci*NCL_PER_SUPERCL,
- NCL_PER_SUPERCL, plist->na_c);
+ NCL_PER_SUPERCL, plist->na_c,
+ shmem);
}
nb_kernel<<< dim_grid, dim_block, shmem, stream>>> (*adat, *nbp, *plist, bCalcFshift);
if (devinfo->prop.major >= 3)
{
/* Default kernel on sm 3.x 48/16 kB Shared/L1 */
- stat = cudaFuncSetCacheConfig(nb_kfunc_ener_prune_ptr[i][j], cudaFuncCachePreferShared);
- stat = cudaFuncSetCacheConfig(nb_kfunc_ener_noprune_ptr[i][j], cudaFuncCachePreferShared);
- stat = cudaFuncSetCacheConfig(nb_kfunc_noener_prune_ptr[i][j], cudaFuncCachePreferShared);
+ cudaFuncSetCacheConfig(nb_kfunc_ener_prune_ptr[i][j], cudaFuncCachePreferShared);
+ cudaFuncSetCacheConfig(nb_kfunc_ener_noprune_ptr[i][j], cudaFuncCachePreferShared);
+ cudaFuncSetCacheConfig(nb_kfunc_noener_prune_ptr[i][j], cudaFuncCachePreferShared);
stat = cudaFuncSetCacheConfig(nb_kfunc_noener_noprune_ptr[i][j], cudaFuncCachePreferShared);
}
else
{
/* On Fermi prefer L1 gives 2% higher performance */
/* Default kernel on sm_2.x 16/48 kB Shared/L1 */
- stat = cudaFuncSetCacheConfig(nb_kfunc_ener_prune_ptr[i][j], cudaFuncCachePreferL1);
- stat = cudaFuncSetCacheConfig(nb_kfunc_ener_noprune_ptr[i][j], cudaFuncCachePreferL1);
- stat = cudaFuncSetCacheConfig(nb_kfunc_noener_prune_ptr[i][j], cudaFuncCachePreferL1);
+ cudaFuncSetCacheConfig(nb_kfunc_ener_prune_ptr[i][j], cudaFuncCachePreferL1);
+ cudaFuncSetCacheConfig(nb_kfunc_ener_noprune_ptr[i][j], cudaFuncCachePreferL1);
+ cudaFuncSetCacheConfig(nb_kfunc_noener_prune_ptr[i][j], cudaFuncCachePreferL1);
stat = cudaFuncSetCacheConfig(nb_kfunc_noener_noprune_ptr[i][j], cudaFuncCachePreferL1);
}
CU_RET_ERR(stat, "cudaFuncSetCacheConfig failed");
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
#ifndef NBNXN_CUDA_H
#define NBNXN_CUDA_H
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "config.h"
-#include "types/nbnxn_cuda_types_ext.h"
-#include "types/simple.h"
+#include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef GMX_GPU
#define FUNC_TERM ;
extern "C" {
#endif
-/*! Launch asynchronously the nonbonded force calculations.
+struct nbnxn_atomdata_t;
+
+/*! \brief
+ * Launch asynchronously the nonbonded force calculations.
+ *
* This consists of the following (async) steps launched:
* - upload x and q;
* - upload shift vector;
* The local and non-local interaction calculations are launched in two
* separate streams.
*/
-void nbnxn_cuda_launch_kernel(nbnxn_cuda_ptr_t gmx_unused cu_nb,
- const nbnxn_atomdata_t gmx_unused *nbdata,
- int gmx_unused flags,
- int gmx_unused iloc) FUNC_TERM
+void nbnxn_cuda_launch_kernel(nbnxn_cuda_ptr_t gmx_unused cu_nb,
+ const struct nbnxn_atomdata_t gmx_unused *nbdata,
+ int gmx_unused flags,
+ int gmx_unused iloc) FUNC_TERM
-/*! Launch asynchronously the download of nonbonded forces from the GPU
- * (and energies/shift forces if required).
+/*! \brief
+ * Launch asynchronously the download of nonbonded forces from the GPU
+ * (and energies/shift forces if required).
*/
-void nbnxn_cuda_launch_cpyback(nbnxn_cuda_ptr_t gmx_unused cu_nb,
- const nbnxn_atomdata_t gmx_unused *nbatom,
- int gmx_unused flags,
- int gmx_unused aloc) FUNC_TERM
+void nbnxn_cuda_launch_cpyback(nbnxn_cuda_ptr_t gmx_unused cu_nb,
+ const struct nbnxn_atomdata_t gmx_unused *nbatom,
+ int gmx_unused flags,
+ int gmx_unused aloc) FUNC_TERM
-/*! Wait for the asynchronously launched nonbonded calculations and data
- * transfers to finish.
+/*! \brief
+ * Wait for the asynchronously launched nonbonded calculations and data
+ * transfers to finish.
*/
-void nbnxn_cuda_wait_gpu(nbnxn_cuda_ptr_t gmx_unused cu_nb,
- const nbnxn_atomdata_t gmx_unused *nbatom,
- int gmx_unused flags,
- int gmx_unused aloc,
- real gmx_unused *e_lj,
- real gmx_unused *e_el,
- rvec gmx_unused *fshift) FUNC_TERM
+void nbnxn_cuda_wait_gpu(nbnxn_cuda_ptr_t gmx_unused cu_nb,
+ const struct nbnxn_atomdata_t gmx_unused *nbatom,
+ int gmx_unused flags,
+ int gmx_unused aloc,
+ real gmx_unused *e_lj,
+ real gmx_unused *e_el,
+ rvec gmx_unused *fshift) FUNC_TERM
#ifdef __cplusplus
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "nbnxn_cuda_data_mgmt.h"
+
+#include "config.h"
#include <assert.h>
#include <stdarg.h>
-#include <stdlib.h>
#include <stdio.h>
+#include <stdlib.h>
#include <cuda.h>
-
-#include "gmx_fatal.h"
+#include <cuda_profiler_api.h>
+
+#include "gromacs/gmxlib/cuda_tools/cudautils.cuh"
+#include "gromacs/gmxlib/cuda_tools/pmalloc_cuda.h"
+#include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
+#include "gromacs/legacyheaders/gmx_detect_hardware.h"
+#include "gromacs/legacyheaders/tables.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "tables.h"
-#include "typedefs.h"
-#include "types/enums.h"
-#include "types/nb_verlet.h"
-#include "types/interaction_const.h"
-#include "types/force_flags.h"
-#include "../nbnxn_consts.h"
-#include "gmx_detect_hardware.h"
#include "nbnxn_cuda_types.h"
-#include "../../gmxlib/cuda_tools/cudautils.cuh"
-#include "nbnxn_cuda_data_mgmt.h"
-#include "pmalloc_cuda.h"
-#include "gpu_utils.h"
-
-// Hack for release-5-0 only to avoid a common.h dependency in CUDA code,
-// which causes issues with some nvcc/boost combinations.
-// Solved with a larger-scale header refactoring in master.
-#ifndef GMX_UNUSED_VALUE
-#define GMX_UNUSED_VALUE(value) (void)value
-#endif
static bool bUseCudaEventBlockingSync = false; /* makes the CPU thread block */
/*! Re-generate the GPU Ewald force table, resets rlist, and update the
* electrostatic type switching to twin cut-off (or back) if needed. */
-void nbnxn_cuda_pme_loadbal_update_param(nbnxn_cuda_ptr_t cu_nb,
- const interaction_const_t *ic)
+void nbnxn_cuda_pme_loadbal_update_param(const nonbonded_verlet_t *nbv,
+ const interaction_const_t *ic)
{
- cu_nbparam_t *nbp = cu_nb->nbparam;
+ if (!nbv || nbv->grp[0].kernel_type != nbnxnk8x8x8_CUDA)
+ {
+ return;
+ }
+ nbnxn_cuda_ptr_t cu_nb = nbv->cu_nbv;
+ cu_nbparam_t *nbp = cu_nb->nbparam;
set_cutoff_parameters(nbp, ic);
cu_plist_t *plist, *plist_nl;
cu_timers_t *timers;
+ /* Stopping the nvidia profiler here allows us to eliminate the subsequent
+ uninitialization API calls from the trace. */
+ if (getenv("NVPROF_ID") != NULL)
+ {
+ stat = cudaProfilerStop();
+ CU_RET_ERR(stat, "cudaProfilerStop failed");
+ }
+
if (cu_nb == NULL)
{
return;
return (cu_nb != NULL && cu_nb->bDoTime) ? cu_nb->timings : NULL;
}
-void nbnxn_cuda_reset_timings(nbnxn_cuda_ptr_t cu_nb)
+void nbnxn_cuda_reset_timings(nonbonded_verlet_t* nbv)
{
- if (cu_nb->bDoTime)
+ /* The NVPROF_ID environment variable is set by nvprof and indicates that
+ mdrun is executed in the CUDA profiler.
+ If nvprof was run is with "--profile-from-start off", the profiler will
+ be started here. This way we can avoid tracing the CUDA events from the
+ first part of the run. Starting the profiler again does nothing.
+ */
+ if (getenv("NVPROF_ID") != NULL)
+ {
+ cudaError_t stat;
+ stat = cudaProfilerStart();
+ CU_RET_ERR(stat, "cudaProfilerStart failed");
+ }
+
+ if (nbv->cu_nbv && nbv->cu_nbv->bDoTime)
{
- init_timings(cu_nb->timings);
+ init_timings(nbv->cu_nbv->timings);
}
}
#ifndef NBNXN_CUDA_DATA_MGMT_H
#define NBNXN_CUDA_DATA_MGMT_H
-#include "types/simple.h"
-#include "types/interaction_const.h"
-#include "types/nbnxn_cuda_types_ext.h"
-#include "types/hw_info.h"
-#include "types/nb_verlet.h"
+#include "config.h"
+
+#include "gromacs/legacyheaders/types/hw_info.h"
+#include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef GMX_GPU
#define FUNC_TERM ;
extern "C" {
#endif
-/*! Initializes the data structures related to CUDA nonbonded calculations. */
+struct nonbonded_verlet_group_t;
+struct nbnxn_pairlist_t;
+struct nbnxn_atomdata_t;
+
+/** Initializes the data structures related to CUDA nonbonded calculations. */
FUNC_QUALIFIER
void nbnxn_cuda_init(FILE gmx_unused *fplog,
nbnxn_cuda_ptr_t gmx_unused *p_cu_nb,
/* true of both local and non-local are don on GPU */
gmx_bool gmx_unused bLocalAndNonlocal) FUNC_TERM
-/*! Initializes simulation constant data. */
+/** Initializes simulation constant data. */
FUNC_QUALIFIER
-void nbnxn_cuda_init_const(nbnxn_cuda_ptr_t gmx_unused cu_nb,
- const interaction_const_t gmx_unused *ic,
- const nonbonded_verlet_group_t gmx_unused *nbv_group) FUNC_TERM
+void nbnxn_cuda_init_const(nbnxn_cuda_ptr_t gmx_unused cu_nb,
+ const interaction_const_t gmx_unused *ic,
+ const struct nonbonded_verlet_group_t gmx_unused *nbv_group) FUNC_TERM
-/*! Initializes pair-list data for GPU, called at every pair search step. */
+/** Initializes pair-list data for GPU, called at every pair search step. */
FUNC_QUALIFIER
-void nbnxn_cuda_init_pairlist(nbnxn_cuda_ptr_t gmx_unused cu_nb,
- const nbnxn_pairlist_t gmx_unused *h_nblist,
- int gmx_unused iloc) FUNC_TERM
+void nbnxn_cuda_init_pairlist(nbnxn_cuda_ptr_t gmx_unused cu_nb,
+ const struct nbnxn_pairlist_t gmx_unused *h_nblist,
+ int gmx_unused iloc) FUNC_TERM
-/*! Initializes atom-data on the GPU, called at every pair search step. */
+/** Initializes atom-data on the GPU, called at every pair search step. */
FUNC_QUALIFIER
-void nbnxn_cuda_init_atomdata(nbnxn_cuda_ptr_t gmx_unused cu_nb,
- const nbnxn_atomdata_t gmx_unused *atomdata) FUNC_TERM
+void nbnxn_cuda_init_atomdata(const nbnxn_cuda_ptr_t gmx_unused cu_nb,
+ const struct nbnxn_atomdata_t gmx_unused *atomdata) FUNC_TERM
/*! \brief Update parameters during PP-PME load balancing. */
FUNC_QUALIFIER
-void nbnxn_cuda_pme_loadbal_update_param(nbnxn_cuda_ptr_t gmx_unused cu_nb,
- const interaction_const_t gmx_unused *ic) FUNC_TERM
+void nbnxn_cuda_pme_loadbal_update_param(const struct nonbonded_verlet_t gmx_unused *nbv,
+ const interaction_const_t gmx_unused *ic) FUNC_TERM
-/*! Uploads shift vector to the GPU if the box is dynamic (otherwise just returns). */
+/** Uploads shift vector to the GPU if the box is dynamic (otherwise just returns). */
FUNC_QUALIFIER
-void nbnxn_cuda_upload_shiftvec(nbnxn_cuda_ptr_t gmx_unused cu_nb,
- const nbnxn_atomdata_t gmx_unused *nbatom) FUNC_TERM
+void nbnxn_cuda_upload_shiftvec(nbnxn_cuda_ptr_t gmx_unused cu_nb,
+ const struct nbnxn_atomdata_t gmx_unused *nbatom) FUNC_TERM
-/*! Clears GPU outputs: nonbonded force, shift force and energy. */
+/** Clears GPU outputs: nonbonded force, shift force and energy. */
FUNC_QUALIFIER
void nbnxn_cuda_clear_outputs(nbnxn_cuda_ptr_t gmx_unused cu_nb,
int gmx_unused flags) FUNC_TERM
-/*! Frees all GPU resources used for the nonbonded calculations. */
+/** Frees all GPU resources used for the nonbonded calculations. */
FUNC_QUALIFIER
void nbnxn_cuda_free(nbnxn_cuda_ptr_t gmx_unused cu_nb) FUNC_TERM
-/*! Returns the GPU timings structure or NULL if GPU is not used or timing is off. */
+/** Returns the GPU timings structure or NULL if GPU is not used or timing is off. */
FUNC_QUALIFIER
wallclock_gpu_t * nbnxn_cuda_get_timings(nbnxn_cuda_ptr_t gmx_unused cu_nb)
#ifdef GMX_GPU
}
#endif
-/*! Resets nonbonded GPU timings. */
+/** Resets nonbonded GPU timings. */
FUNC_QUALIFIER
-void nbnxn_cuda_reset_timings(nbnxn_cuda_ptr_t gmx_unused cu_nb) FUNC_TERM
+void nbnxn_cuda_reset_timings(struct nonbonded_verlet_t gmx_unused *nbv) FUNC_TERM
-/*! Calculates the minimum size of proximity lists to improve SM load balance
- with CUDA non-bonded kernels. */
+/** Calculates the minimum size of proximity lists to improve SM load balance
+ * with CUDA non-bonded kernels. */
FUNC_QUALIFIER
int nbnxn_cuda_min_ci_balanced(nbnxn_cuda_ptr_t gmx_unused cu_nb)
#ifdef GMX_GPU
}
#endif
-/*! Returns if analytical Ewald CUDA kernels are used. */
+/** Returns if analytical Ewald CUDA kernels are used. */
FUNC_QUALIFIER
gmx_bool nbnxn_cuda_is_kernel_ewald_analytical(const nbnxn_cuda_ptr_t gmx_unused cu_nb)
#ifdef GMX_GPU
*/
#include "gromacs/math/utilities.h"
+#include "gromacs/pbcutil/ishift.h"
/* Note that floating-point constants in CUDA code should be suffixed
* with f (e.g. 0.5f), to stop the compiler producing intermediate
* code that is in double precision.
/*
Kernel launch parameters:
- #blocks = #pair lists, blockId = pair list Id
- - #threads = CL_SIZE^2
- - shmem = CL_SIZE^2 * sizeof(float)
+ - #threads = NTHREAD_Z * CL_SIZE^2
+ - shmem = see nbnxn_cuda.cu:calc_shmem_required()
Each thread calculates an i force-component taking one pair of i-j atoms.
*/
+
#if __CUDA_ARCH__ >= 350
-__launch_bounds__(64, 16)
+__launch_bounds__(THREADS_PER_BLOCK, MIN_BLOCKS_PER_MP)
+#else
+__launch_bounds__(THREADS_PER_BLOCK)
#endif
#ifdef PRUNE_NBL
#ifdef CALC_ENERGIES
unsigned int tidxi = threadIdx.x;
unsigned int tidxj = threadIdx.y;
unsigned int tidx = threadIdx.y * blockDim.x + threadIdx.x;
+ unsigned int tidxz = threadIdx.z;
unsigned int bidx = blockIdx.x;
unsigned int widx = tidx / WARP_SIZE; /* warp index */
/* shmem buffer for i x+q pre-loading */
extern __shared__ float4 xqib[];
- /* shmem buffer for cj, for both warps separately */
- int *cjs = (int *)(xqib + NCL_PER_SUPERCL * CL_SIZE);
+ /* shmem buffer for cj, for each warp separately */
+ int *cjs = ((int *)(xqib + NCL_PER_SUPERCL * CL_SIZE)) + tidxz * 2 * NBNXN_GPU_JGROUP_SIZE;
#ifdef IATYPE_SHMEM
/* shmem buffer for i atom-type pre-loading */
- int *atib = (int *)(cjs + 2 * NBNXN_GPU_JGROUP_SIZE);
+ int *atib = ((int *)(xqib + NCL_PER_SUPERCL * CL_SIZE)) + NTHREAD_Z * 2 * NBNXN_GPU_JGROUP_SIZE;
#endif
#ifndef REDUCE_SHUFFLE
#ifdef IATYPE_SHMEM
float *f_buf = (float *)(atib + NCL_PER_SUPERCL * CL_SIZE);
#else
- float *f_buf = (float *)(cjs + 2 * NBNXN_GPU_JGROUP_SIZE);
+ float *f_buf = (float *)(cjs + NTHREAD_Z * 2 * NBNXN_GPU_JGROUP_SIZE);
#endif
#endif
cij4_start = nb_sci.cj4_ind_start; /* first ...*/
cij4_end = nb_sci.cj4_ind_end; /* and last index of j clusters */
- /* Pre-load i-atom x and q into shared memory */
- ci = sci * NCL_PER_SUPERCL + tidxj;
- ai = ci * CL_SIZE + tidxi;
- xqib[tidxj * CL_SIZE + tidxi] = xq[ai] + shift_vec[nb_sci.shift];
+ if (tidxz == 0)
+ {
+ /* Pre-load i-atom x and q into shared memory */
+ ci = sci * NCL_PER_SUPERCL + tidxj;
+ ai = ci * CL_SIZE + tidxi;
+ xqib[tidxj * CL_SIZE + tidxi] = xq[ai] + shift_vec[nb_sci.shift];
#ifdef IATYPE_SHMEM
- /* Pre-load the i-atom types into shared memory */
- atib[tidxj * CL_SIZE + tidxi] = atom_types[ai];
+ /* Pre-load the i-atom types into shared memory */
+ atib[tidxj * CL_SIZE + tidxi] = atom_types[ai];
#endif
+ }
__syncthreads();
for (ci_offset = 0; ci_offset < NCL_PER_SUPERCL; ci_offset++)
/* divide the self term(s) equally over the j-threads, then multiply with the coefficients. */
#ifdef LJ_EWALD
- E_lj /= CL_SIZE;
+ E_lj /= CL_SIZE*NTHREAD_Z;
E_lj *= 0.5f*ONE_SIXTH_F*lje_coeff6_6;
#endif /* LJ_EWALD */
#if defined EL_EWALD_ANY || defined EL_RF || defined EL_CUTOFF
- E_el /= CL_SIZE;
+ E_el /= CL_SIZE*NTHREAD_Z;
#if defined EL_RF || defined EL_CUTOFF
E_el *= -nbparam.epsfac*0.5f*c_rf;
#else
fshift_buf = make_float3(0.0f);
/* loop over the j clusters = seen by any of the atoms in the current super-cluster */
- for (j4 = cij4_start; j4 < cij4_end; j4++)
+ for (j4 = cij4_start + tidxz; j4 < cij4_end; j4 += NTHREAD_Z)
{
wexcl_idx = pl_cj4[j4].imei[widx].excl_ind;
imask = pl_cj4[j4].imei[widx].imask;
* code that is in double precision.
*/
-#include "../../gmxlib/cuda_tools/vectype_ops.cuh"
+#include "gromacs/gmxlib/cuda_tools/vectype_ops.cuh"
#ifndef NBNXN_CUDA_KERNEL_UTILS_CUH
#define NBNXN_CUDA_KERNEL_UTILS_CUH
/* cut-off + V shift LJ */
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecCut_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef NB_KERNEL_FUNC_NAME
/* LJ-Ewald w geometric combination rules */
#define LJ_EWALD_COMB_GEOM
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecCut_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_EWALD_COMB_GEOM
#undef NB_KERNEL_FUNC_NAME
/* LJ-Ewald w LB combination rules */
#define LJ_EWALD_COMB_LB
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecCut_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_EWALD_COMB_LB
#undef NB_KERNEL_FUNC_NAME
/* F switch LJ */
#define LJ_FORCE_SWITCH
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecCut_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_FORCE_SWITCH
#undef NB_KERNEL_FUNC_NAME
/* V switch LJ */
#define LJ_POT_SWITCH
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecCut_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_POT_SWITCH
#undef NB_KERNEL_FUNC_NAME
/* cut-off + V shift LJ */
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecRF_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef NB_KERNEL_FUNC_NAME
/* LJ-Ewald w geometric combination rules */
#define LJ_EWALD_COMB_GEOM
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecRF_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_EWALD_COMB_GEOM
#undef NB_KERNEL_FUNC_NAME
/* LJ-Ewald w LB combination rules */
#define LJ_EWALD_COMB_LB
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecRF_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_EWALD_COMB_LB
#undef NB_KERNEL_FUNC_NAME
/* F switch LJ */
#define LJ_FORCE_SWITCH
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecRF_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_FORCE_SWITCH
#undef NB_KERNEL_FUNC_NAME
/* V switch LJ */
#define LJ_POT_SWITCH
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecRF_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_POT_SWITCH
#undef NB_KERNEL_FUNC_NAME
/* cut-off + V shift LJ */
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEw_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef NB_KERNEL_FUNC_NAME
/* LJ-Ewald w geometric combination rules */
#define LJ_EWALD_COMB_GEOM
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEw_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_EWALD_COMB_GEOM
#undef NB_KERNEL_FUNC_NAME
/* LJ-Ewald w LB combination rules */
#define LJ_EWALD_COMB_LB
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEw_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_EWALD_COMB_LB
#undef NB_KERNEL_FUNC_NAME
/* F switch LJ */
#define LJ_FORCE_SWITCH
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEw_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_FORCE_SWITCH
#undef NB_KERNEL_FUNC_NAME
/* V switch LJ */
#define LJ_POT_SWITCH
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEw_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_POT_SWITCH
#undef NB_KERNEL_FUNC_NAME
/* cut-off + V shift LJ */
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwTwinCut_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef NB_KERNEL_FUNC_NAME
/* LJ-Ewald w geometric combination rules */
#define LJ_EWALD_COMB_GEOM
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwTwinCut_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_EWALD_COMB_GEOM
#undef NB_KERNEL_FUNC_NAME
/* LJ-Ewald w LB combination rules */
#define LJ_EWALD_COMB_LB
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwTwinCut_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_EWALD_COMB_LB
#undef NB_KERNEL_FUNC_NAME
/* F switch LJ */
#define LJ_FORCE_SWITCH
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwTwinCut_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_FORCE_SWITCH
#undef NB_KERNEL_FUNC_NAME
/* V switch LJ */
#define LJ_POT_SWITCH
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwTwinCut_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_POT_SWITCH
#undef NB_KERNEL_FUNC_NAME
/* cut-off + V shift LJ */
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTab_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef NB_KERNEL_FUNC_NAME
/* LJ-Ewald w geometric combination rules */
#define LJ_EWALD_COMB_GEOM
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTab_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_EWALD_COMB_GEOM
#undef NB_KERNEL_FUNC_NAME
/* LJ-Ewald w LB combination rules */
#define LJ_EWALD_COMB_LB
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTab_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_EWALD_COMB_LB
#undef NB_KERNEL_FUNC_NAME
/* F switch LJ */
#define LJ_FORCE_SWITCH
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTab_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_FORCE_SWITCH
#undef NB_KERNEL_FUNC_NAME
/* V switch LJ */
#define LJ_POT_SWITCH
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTab_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_POT_SWITCH
#undef NB_KERNEL_FUNC_NAME
/* cut-off + V shift LJ */
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTabTwinCut_VdwLJ ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef NB_KERNEL_FUNC_NAME
/* LJ-Ewald w geometric combination rules */
#define LJ_EWALD_COMB_GEOM
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTabTwinCut_VdwLJEwCombGeom ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_EWALD_COMB_GEOM
#undef NB_KERNEL_FUNC_NAME
/* LJ-Ewald w LB combination rules */
#define LJ_EWALD_COMB_LB
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTabTwinCut_VdwLJEwCombLB ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_EWALD_COMB_LB
#undef NB_KERNEL_FUNC_NAME
/* F switch LJ */
#define LJ_FORCE_SWITCH
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTabTwinCut_VdwLJFsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_FORCE_SWITCH
#undef NB_KERNEL_FUNC_NAME
/* V switch LJ */
#define LJ_POT_SWITCH
#define NB_KERNEL_FUNC_NAME(x, ...) x ## _ElecEwQSTabTwinCut_VdwLJPsw ## __VA_ARGS__
-#include "nbnxn_cuda_kernel.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#undef LJ_POT_SWITCH
#undef NB_KERNEL_FUNC_NAME
#ifndef NBNXN_CUDA_TYPES_H
#define NBNXN_CUDA_TYPES_H
-#include "types/interaction_const.h"
-#include "types/nbnxn_pairlist.h"
-#include "types/nbnxn_cuda_types_ext.h"
-#include "../../gmxlib/cuda_tools/cudautils.cuh"
+#include "gromacs/gmxlib/cuda_tools/cudautils.cuh"
+#include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
/* CUDA versions from 5.0 above support texture objects. */
#if CUDA_VERSION >= 5000
#ifndef _nbnxn_internal_h
#define _nbnxn_internal_h
-#include "typedefs.h"
-#include "nbnxn_simd.h"
-#include "domdec.h"
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
+#include "gromacs/mdlib/nbnxn_simd.h"
#include "gromacs/timing/cyclecounter.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include "nbnxn_kernel_common.h"
+#include "gromacs/pbcutil/ishift.h"
+
static void
clear_f_all(const nbnxn_atomdata_t *nbat, real *f)
{
clear_f_flagged(const nbnxn_atomdata_t *nbat, int output_index, real *f)
{
const nbnxn_buffer_flags_t *flags;
- unsigned our_flag;
+ gmx_bitmask_t our_flag;
int g, b, a0, a1, i;
flags = &nbat->buffer_flags;
- our_flag = (1U << output_index);
+ bitmask_init_bit(&our_flag, output_index);
for (b = 0; b < flags->nflag; b++)
{
- if (flags->flag[b] & our_flag)
+ if (!bitmask_is_disjoint(flags->flag[b], our_flag))
{
a0 = b*NBNXN_BUFFERFLAG_SIZE;
a1 = a0 + NBNXN_BUFFERFLAG_SIZE;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _nbnxn_kernel_common_h
#define _nbnxn_kernel_common_h
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
#ifdef __cplusplus
extern "C" {
import re
import sys
import os
+os.chdir(os.path.dirname(os.path.abspath(__file__)))
import collections # Requires Python 2.7
sys.path.append('../../../../../admin')
from copyright import create_copyright_header
KernelNamePrefix = 'nbnxn_kernel'
KernelsName = "{0}_simd_{1}".format(KernelNamePrefix,type)
KernelsHeaderFileName = "{0}.h".format(KernelsName,type)
+ KernelsHeaderPathName = "gromacs/mdlib/nbnxn_kernels/simd_{0}/{1}".format(type,KernelsHeaderFileName)
KernelFunctionLookupTable = {}
KernelDeclarations = ''
KernelTemplate = read_kernel_template("{0}_kernel.c.pre".format(KernelsName))
ElectrostaticsDict[elec]['define'],
VdwTreatmentDict[ljtreat]['define'],
EnergiesComputationDict[ener]['define'],
- KernelsHeaderFileName,
+ KernelsHeaderPathName,
KernelName,
" " * (len(KernelName) + 1),
VerletKernelTypeDict[type]['UnrollSize'],
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* {0}, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE {7}
#include "{4}"
{3}
#ifdef {0}
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* {0} */
#ifdef CALC_ENERGIES
{6}real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef {0}
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* {0} */
{{
/* No need to call gmx_incons() here, because the only function
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* {0}, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE {7}
#include "{4}"
{3}
#ifdef {0}
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* {0} */
#ifdef CALC_ENERGIES
{6}real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef {0}
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* {0} */
{{
/* No need to call gmx_incons() here, because the only function
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "typedefs.h"
+#include "config.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/nb_verlet.h"
#include "gromacs/mdlib/nbnxn_simd.h"
#ifdef {0}
{2}
#define GMX_SIMD_J_UNROLL_SIZE {3}
#include "{4}"
-#include "../nbnxn_kernel_common.h"
-#include "gmx_omp_nthreads.h"
-#include "types/force_flags.h"
-#include "gmx_fatal.h"
+
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
+#include "gromacs/utility/fatalerror.h"
/*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels
*/
#else /* {0} */
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#endif /* {0} */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "typedefs.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
#include "gromacs/mdlib/nbnxn_simd.h"
#ifdef __cplusplus
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "nbnxn_kernel_gpu_ref.h"
+
+#include "config.h"
#include <math.h>
-#include "types/simple.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
#include "gromacs/math/utilities.h"
-#include "vec.h"
-#include "typedefs.h"
-#include "force.h"
-#include "nbnxn_kernel_gpu_ref.h"
-#include "../nbnxn_consts.h"
-#include "nbnxn_kernel_common.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
+#include "gromacs/pbcutil/ishift.h"
#define NCL_PER_SUPERCL (NBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER)
#define CL_SIZE (NBNXN_GPU_CLUSTER_SIZE)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _nbnxn_kernel_gpu_ref_h
#define _nbnxn_kernel_gpu_ref_h
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "nbnxn_kernel_ref.h"
+
+#include "config.h"
-#include <math.h>
#include <assert.h>
+#include <math.h>
-#include "typedefs.h"
-#include "vec.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
+#include "gromacs/pbcutil/ishift.h"
#include "gromacs/utility/smalloc.h"
-#include "force.h"
-#include "gmx_omp_nthreads.h"
-#include "nbnxn_kernel_ref.h"
-#include "../nbnxn_consts.h"
-#include "nbnxn_kernel_common.h"
/*! \brief Typedefs for declaring lookup tables of kernel functions.
*/
/* Analytical reaction-field kernels */
#define CALC_COUL_RF
#define LJ_CUT
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
#undef LJ_CUT
#define LJ_FORCE_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
#undef LJ_FORCE_SWITCH
#define LJ_POT_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
#undef LJ_POT_SWITCH
#define LJ_EWALD
#define LJ_CUT
#define LJ_EWALD_COMB_GEOM
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
#undef LJ_EWALD_COMB_GEOM
#define LJ_EWALD_COMB_LB
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
#undef LJ_EWALD_COMB_LB
#undef LJ_CUT
#undef LJ_EWALD
/* Tabulated exclusion interaction electrostatics kernels */
#define CALC_COUL_TAB
#define LJ_CUT
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
#undef LJ_CUT
#define LJ_FORCE_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
#undef LJ_FORCE_SWITCH
#define LJ_POT_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
#undef LJ_POT_SWITCH
#define LJ_EWALD
#define LJ_CUT
#define LJ_EWALD_COMB_GEOM
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
#undef LJ_EWALD_COMB_GEOM
#define LJ_EWALD_COMB_LB
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
#undef LJ_EWALD_COMB_LB
#undef LJ_CUT
#undef LJ_EWALD
/* Twin-range cut-off kernels */
#define VDW_CUTOFF_CHECK
#define LJ_CUT
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
#undef LJ_CUT
#define LJ_FORCE_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
#undef LJ_FORCE_SWITCH
#define LJ_POT_SWITCH
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
#undef LJ_POT_SWITCH
#define LJ_EWALD
#define LJ_CUT
#define LJ_EWALD_COMB_GEOM
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
#undef LJ_EWALD_COMB_GEOM
#define LJ_EWALD_COMB_LB
-#include "nbnxn_kernel_ref_includes.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_includes.h"
#undef LJ_EWALD_COMB_LB
#undef LJ_CUT
#undef LJ_EWALD
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _nbnxn_kernel_ref_h
#define _nbnxn_kernel_ref_h
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
#ifdef __cplusplus
extern "C" {
*/
/* Include the force only kernels */
-#include "nbnxn_kernel_ref_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h"
/* Include the force+energy kernels */
#define CALC_ENERGIES
-#include "nbnxn_kernel_ref_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h"
#undef CALC_ENERGIES
/* Include the force+energygroups kernels */
#define CALC_ENERGIES
#define ENERGY_GROUPS
-#include "nbnxn_kernel_ref_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h"
#undef ENERGY_GROUPS
#undef CALC_ENERGIES
{
#define CALC_COULOMB
#define HALF_LJ
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
#undef HALF_LJ
#undef CALC_COULOMB
}
- /* cppcheck-suppress duplicateBranch */
else if (do_coul)
{
#define CALC_COULOMB
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
#undef CALC_COULOMB
}
else
{
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
}
#undef CHECK_EXCLS
cjind++;
{
#define CALC_COULOMB
#define HALF_LJ
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
#undef HALF_LJ
#undef CALC_COULOMB
}
- /* cppcheck-suppress duplicateBranch */
else if (do_coul)
{
#define CALC_COULOMB
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
#undef CALC_COULOMB
}
else
{
-#include "nbnxn_kernel_ref_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h"
}
}
ninner += cjind1 - cjind0;
#ifndef _nbnxn_kernel_simd_utils_h_
#define _nbnxn_kernel_simd_utils_h_
+#include "config.h"
+
#include "gromacs/legacyheaders/types/simple.h"
/*! \brief Provides hardware-specific utility routines for the SIMD kernels.
return NULL;
}
-#include "nbnxn_kernel_simd_utils_ref.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_ref.h"
#else /* GMX_SIMD_REFERENCE */
-#if defined GMX_TARGET_X86 && !defined __MIC__
+#if defined GMX_TARGET_X86 && !defined GMX_SIMD_X86_MIC
/* Include x86 SSE2 compatible SIMD functions */
/* Set the stride for the lookup of the two LJ parameters from their
#ifdef GMX_DOUBLE
#if GMX_SIMD_REAL_WIDTH == 2
-#include "nbnxn_kernel_simd_utils_x86_128d.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_128d.h"
#else
-#include "nbnxn_kernel_simd_utils_x86_256d.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_256d.h"
#endif
#else /* GMX_DOUBLE */
/* In single precision aligned FDV0 table loads are optimal */
#define TAB_FDV0
#if GMX_SIMD_REAL_WIDTH == 4
-#include "nbnxn_kernel_simd_utils_x86_128s.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_128s.h"
#else
-#include "nbnxn_kernel_simd_utils_x86_256s.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_256s.h"
#endif
#endif /* GMX_DOUBLE */
-#else /* GMX_TARGET_X86 && !__MIC__ */
+#else /* GMX_TARGET_X86 && !GMX_SIMD_X86_MIC */
#if GMX_SIMD_REAL_WIDTH > 4
/* For width>4 we use unaligned loads. And thus we can use the minimal stride */
#endif
#ifdef GMX_SIMD_IBM_QPX
-#include "nbnxn_kernel_simd_utils_ibm_qpx.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_ibm_qpx.h"
#endif /* GMX_SIMD_IBM_QPX */
-#ifdef __MIC__
-#include "nbnxn_kernel_simd_utils_x86_mic.h"
+#ifdef GMX_SIMD_X86_MIC
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_mic.h"
#endif
-#endif /* GMX_TARGET_X86 && !__MIC__ */
+#endif /* GMX_TARGET_X86 && !GMX_SIMD_X86_MIC */
#endif /* GMX_SIMD_REFERENCE */
#ifndef _nbnxn_kernel_simd_utils_x86_128s_h_
#define _nbnxn_kernel_simd_utils_x86_128s_h_
+#include "config.h"
+
#include "gromacs/legacyheaders/types/simple.h"
/* This files contains all functions/macros for the SIMD kernels
#ifndef _nbnxn_kernel_simd_utils_x86_256s_h_
#define _nbnxn_kernel_simd_utils_x86_256s_h_
+#include "config.h"
+
/* This files contains all functions/macros for the SIMD kernels
* which have explicit dependencies on the j-cluster size and/or SIMD-width.
* The functionality which depends on the j-cluster size is:
static gmx_inline gmx_exclfilter gmx_simdcall
gmx_load_exclusion_filter(const unsigned *i)
{
+ /* cppcheck-suppress invalidPointerCast */
return gmx_simd_load_r((real *) (i));
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _nbnxn_kernel_x86_simd128_h
#define _nbnxn_kernel_x86_simd128_h
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _nbnxn_kernel_x86_simd256_h
#define _nbnxn_kernel_x86_simd256_h
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_FORCE_SWITCH
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_FORCE_SWITCH
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_FORCE_SWITCH
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_POT_SWITCH
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_POT_SWITCH
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_POT_SWITCH
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_FORCE_SWITCH
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_FORCE_SWITCH
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_FORCE_SWITCH
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_POT_SWITCH
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_POT_SWITCH
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_POT_SWITCH
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_TAB
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_FORCE_SWITCH
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_FORCE_SWITCH
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_FORCE_SWITCH
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_POT_SWITCH
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_POT_SWITCH
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_POT_SWITCH
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_2XNN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
#define CALC_COUL_RF
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_kernel_simd_2xnn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h"
#else /* GMX_NBNXN_SIMD_2XNN */
{
/* No need to call gmx_incons() here, because the only function
* kernel type 2xnn.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "typedefs.h"
+#include "config.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/nb_verlet.h"
#include "gromacs/mdlib/nbnxn_simd.h"
#ifdef GMX_NBNXN_SIMD_2XNN
#define GMX_SIMD_J_UNROLL_SIZE 2
#include "nbnxn_kernel_simd_2xnn.h"
-#include "../nbnxn_kernel_common.h"
-#include "gmx_omp_nthreads.h"
-#include "types/force_flags.h"
-#include "gmx_fatal.h"
+
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
+#include "gromacs/utility/fatalerror.h"
/*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels
*/
#else /* GMX_NBNXN_SIMD_2XNN */
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#endif /* GMX_NBNXN_SIMD_2XNN */
* kernel type 2xnn.
*/
-#include "typedefs.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
#include "gromacs/mdlib/nbnxn_simd.h"
#ifdef __cplusplus
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/pbcutil/ishift.h"
#include "gromacs/simd/simd.h"
#include "gromacs/simd/simd_math.h"
#include "gromacs/simd/vector_operations.h"
-#include "../../nbnxn_consts.h"
#ifdef CALC_COUL_EWALD
#include "gromacs/math/utilities.h"
#endif
#define UNROLLJ (GMX_SIMD_REAL_WIDTH/GMX_SIMD_J_UNROLL_SIZE)
/* The stride of all the atom data arrays is equal to half the SIMD width */
-#define STRIDE (GMX_SIMD_REAL_WIDTH/GMX_SIMD_J_UNROLL_SIZE)
+#define STRIDE UNROLLJ
-#include "../nbnxn_kernel_simd_utils.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h"
static gmx_inline void gmx_simdcall
gmx_load_simd_2xnn_interactions(int excl,
/* Atom indices (of the first atom in the cluster) */
aj = cj*UNROLLJ;
#if defined CALC_LJ && (defined LJ_COMB_GEOM || defined LJ_COMB_LB || defined LJ_EWALD_GEOM)
-#if UNROLLJ == STRIDE
aj2 = aj*2;
-#else
- aj2 = (cj>>1)*2*STRIDE + (cj & 1)*UNROLLJ;
-#endif
#endif
-#if UNROLLJ == STRIDE
ajx = aj*DIM;
-#else
- ajx = (cj>>1)*DIM*STRIDE + (cj & 1)*UNROLLJ;
-#endif
ajy = ajx + STRIDE;
ajz = ajy + STRIDE;
#define CHECK_EXCLS
while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
{
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
cjind++;
}
#undef CHECK_EXCLS
for (; (cjind < cjind1); cjind++)
{
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
}
#undef HALF_LJ
#undef CALC_COULOMB
#define CHECK_EXCLS
while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
{
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
cjind++;
}
#undef CHECK_EXCLS
for (; (cjind < cjind1); cjind++)
{
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
}
#undef CALC_COULOMB
}
#define CHECK_EXCLS
while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
{
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
cjind++;
}
#undef CHECK_EXCLS
for (; (cjind < cjind1); cjind++)
{
-#include "nbnxn_kernel_simd_2xnn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h"
}
}
#undef CALC_LJ
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_FORCE_SWITCH
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_FORCE_SWITCH
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_FORCE_SWITCH
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_POT_SWITCH
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_POT_SWITCH
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_POT_SWITCH
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_EWALD
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define VDW_CUTOFF_CHECK /* Use twin-range cut-off */
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_FORCE_SWITCH
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_FORCE_SWITCH
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_FORCE_SWITCH
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_POT_SWITCH
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_POT_SWITCH
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_POT_SWITCH
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_TAB
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_FORCE_SWITCH
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_FORCE_SWITCH
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_FORCE_SWITCH
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_POT_SWITCH
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_POT_SWITCH
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_POT_SWITCH
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_CUT
/* Will not calculate energies */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_CUT
#define CALC_ENERGIES
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* GMX_NBNXN_SIMD_4XN, so that this file reduces to a stub
* function definition when the kernel will never be called.
*/
+#include "gmxpre.h"
+
#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#define CALC_COUL_RF
#define LJ_CUT
#define ENERGY_GROUPS
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_common.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
#endif /* GMX_NBNXN_SIMD_4XN */
#ifdef CALC_ENERGIES
real gmx_unused *fshift)
#endif /* CALC_ENERGIES */
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_kernel_simd_4xn_outer.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_outer.h"
#else /* GMX_NBNXN_SIMD_4XN */
{
/* No need to call gmx_incons() here, because the only function
* kernel type 4xn.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "typedefs.h"
+#include "config.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/nb_verlet.h"
#include "gromacs/mdlib/nbnxn_simd.h"
#ifdef GMX_NBNXN_SIMD_4XN
#define GMX_SIMD_J_UNROLL_SIZE 1
#include "nbnxn_kernel_simd_4xn.h"
-#include "../nbnxn_kernel_common.h"
-#include "gmx_omp_nthreads.h"
-#include "types/force_flags.h"
-#include "gmx_fatal.h"
+
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
+#include "gromacs/utility/fatalerror.h"
/*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels
*/
#else /* GMX_NBNXN_SIMD_4XN */
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
#endif /* GMX_NBNXN_SIMD_4XN */
* kernel type 4xn.
*/
-#include "typedefs.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
#include "gromacs/mdlib/nbnxn_simd.h"
#ifdef __cplusplus
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/pbcutil/ishift.h"
#include "gromacs/simd/simd.h"
#include "gromacs/simd/simd_math.h"
#include "gromacs/simd/vector_operations.h"
-#include "../../nbnxn_consts.h"
#ifdef CALC_COUL_EWALD
#include "gromacs/math/utilities.h"
#endif
+#include "config.h"
+
#ifndef GMX_SIMD_J_UNROLL_SIZE
#error "Need to define GMX_SIMD_J_UNROLL_SIZE before including the 4xn kernel common header file"
#endif
#define STRIDE (UNROLLI)
#endif
-#include "../nbnxn_kernel_simd_utils.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h"
static gmx_inline void gmx_simdcall
gmx_load_simd_4xn_interactions(int excl,
#define CHECK_EXCLS
while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
{
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
cjind++;
}
#undef CHECK_EXCLS
for (; (cjind < cjind1); cjind++)
{
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
}
#undef HALF_LJ
#undef CALC_COULOMB
#define CHECK_EXCLS
while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
{
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
cjind++;
}
#undef CHECK_EXCLS
for (; (cjind < cjind1); cjind++)
{
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
}
#undef CALC_COULOMB
}
#define CHECK_EXCLS
while (cjind < cjind1 && nbl->cj[cjind].excl != NBNXN_INTERACTION_MASK_ALL)
{
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
cjind++;
}
#undef CHECK_EXCLS
for (; (cjind < cjind1); cjind++)
{
-#include "nbnxn_kernel_simd_4xn_inner.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h"
}
}
#undef CALC_LJ
#ifndef _nbnxn_pairlist_h
#define _nbnxn_pairlist_h
-#include "nblist.h"
+#include <stddef.h>
+
+#include "thread_mpi/atomic.h"
+
+#include "gromacs/legacyheaders/types/nblist.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/bitmask.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
*/
} nbnxn_excl_t;
-typedef struct {
+typedef struct nbnxn_pairlist_t {
gmx_cache_protect_t cp0;
nbnxn_alloc_t *alloc;
#define NBNXN_BUFFERFLAG_SIZE 16
#endif
-/* We currently store the reduction flags as bits in an unsigned int.
- * In most cases this limits the number of flags to 32.
- * The reduction will automatically disable the flagging and do a full
- * reduction when the flags won't fit, but this will lead to very slow
- * reduction. As we anyhow don't expect reasonable performance with
- * more than 32 threads, we put in this hard limit.
- * You can increase this number, but the reduction will be very slow.
+/* We store the reduction flags as gmx_bitmask_t.
+ * This limits the number of flags to BITMASK_SIZE.
*/
-#define NBNXN_BUFFERFLAG_MAX_THREADS 32
+#define NBNXN_BUFFERFLAG_MAX_THREADS (BITMASK_SIZE)
/* Flags for telling if threads write to force output buffers */
typedef struct {
- int nflag; /* The number of flag blocks */
- unsigned int *flag; /* Bit i is set when thread i writes to a cell-block */
- int flag_nalloc; /* Allocation size of cxy_flag */
+ int nflag; /* The number of flag blocks */
+ gmx_bitmask_t *flag; /* Bit i is set when thread i writes to a cell-block */
+ int flag_nalloc; /* Allocation size of cxy_flag */
} nbnxn_buffer_flags_t;
/* LJ combination rules: geometric, Lorentz-Berthelot, none */
ljcrGEOM, ljcrLB, ljcrNONE, ljcrNR
};
-/* TODO: Remove need for forward declare */
-struct tMPI_Atomic;
-
-typedef struct {
+typedef struct nbnxn_atomdata_t {
nbnxn_alloc_t *alloc;
nbnxn_free_t *free;
int ntype; /* The number of different atom types */
gmx_bool bUseBufferFlags; /* Use the flags or operate on all atoms */
nbnxn_buffer_flags_t buffer_flags; /* Flags for buffer zeroing+reduc. */
gmx_bool bUseTreeReduce; /* Use tree for force reduction */
- struct tMPI_Atomic *syncStep; /* Synchronization step for tree reduce */
+ tMPI_Atomic_t *syncStep; /* Synchronization step for tree reduce */
} nbnxn_atomdata_t;
#ifdef __cplusplus
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "nbnxn_search.h"
+#include <assert.h>
#include <math.h>
#include <string.h>
-#include <assert.h>
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "types/commrec.h"
-#include "macros.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/math/utilities.h"
-#include "vec.h"
-#include "pbc.h"
-#include "nbnxn_consts.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_atomdata.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/smalloc.h"
+
/* nbnxn_internal.h included gromacs/simd/macros.h */
-#include "nbnxn_internal.h"
-#ifdef GMX_NBNXN_SIMD
+#include "gromacs/mdlib/nbnxn_internal.h"
+#ifdef GMX_SIMD
#include "gromacs/simd/vector_operations.h"
#endif
-#include "nbnxn_atomdata.h"
-#include "nbnxn_search.h"
-#include "gmx_omp_nthreads.h"
-#include "nrnb.h"
-#include "ns.h"
-
-#include "gromacs/fileio/gmxfio.h"
#ifdef NBNXN_SEARCH_BB_SIMD4
/* Always use 4-wide SIMD for bounding box calculations */
int cxy_start, int cxy_end,
int *sort_work)
{
- int cxy;
- int cx, cy, cz = -1, c = -1, ncz;
- int na, ash, na_c, ind, a;
- int subdiv_z, sub_z, na_z, ash_z;
- int subdiv_y, sub_y, na_y, ash_y;
- int subdiv_x, sub_x, na_x, ash_x;
+ int cxy;
+ int cx, cy, cz = -1, c = -1, ncz;
+ int na, ash, na_c, ind, a;
+ int subdiv_z, sub_z, na_z, ash_z;
+ int subdiv_y, sub_y, na_y, ash_y;
+ int subdiv_x, sub_x, na_x, ash_x;
- /* cppcheck-suppress unassignedVariable */
nbnxn_bb_t bb_work_array[2], *bb_work_aligned;
bb_work_aligned = (nbnxn_bb_t *)(((size_t)(bb_work_array+1)) & (~((size_t)15)));
}
for (b = 0; b < flags->nflag; b++)
{
- flags->flag[b] = 0;
+ bitmask_clear(&(flags->flag[b]));
}
}
}
#ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_search_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_search_simd_4xn.h"
#endif
#ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_search_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_search_simd_2xnn.h"
#endif
/* Plain C or SIMD4 code for making a pair list of super-cell sci vs scj.
grid = &nbs->grid[0];
+ if (min_ci_balanced <= 0 || grid->nc >= min_ci_balanced || grid->nc == 0)
+ {
+ /* We don't need to worry */
+ return -1;
+ }
+
ls[XX] = (grid->c1[XX] - grid->c0[XX])/(grid->ncx*GPU_NSUBCELL_X);
ls[YY] = (grid->c1[YY] - grid->c0[YY])/(grid->ncy*GPU_NSUBCELL_Y);
ls[ZZ] = (grid->c1[ZZ] - grid->c0[ZZ])*grid->ncx*grid->ncy/(grid->nc*GPU_NSUBCELL_Z);
nsp_est = nsp_est_nl;
}
- if (min_ci_balanced <= 0 || grid->nc >= min_ci_balanced || grid->nc == 0)
- {
- /* We don't need to worry */
- nsubpair_max = -1;
- }
- else
- {
- /* Thus the (average) maximum j-list size should be as follows */
- nsubpair_max = max(1, (int)(nsp_est/min_ci_balanced+0.5));
+ /* Thus the (average) maximum j-list size should be as follows */
+ nsubpair_max = max(1, (int)(nsp_est/min_ci_balanced+0.5));
- /* Since the target value is a maximum (this avoids high outliers,
- * which lead to load imbalance), not average, we add half the
- * number of pairs in a cj4 block to get the average about right.
- */
- nsubpair_max += GPU_NSUBCELL*NBNXN_GPU_JGROUP_SIZE/2;
- }
+ /* Since the target value is a maximum (this avoids high outliers,
+ * which lead to load imbalance), not average, we add half the
+ * number of pairs in a cj4 block to get the average about right.
+ */
+ nsubpair_max += GPU_NSUBCELL*NBNXN_GPU_JGROUP_SIZE/2;
if (debug)
{
int ndistc;
int ncpcheck;
int gridi_flag_shift = 0, gridj_flag_shift = 0;
- unsigned int *gridj_flag = NULL;
+ gmx_bitmask_t *gridj_flag = NULL;
int ncj_old_i, ncj_old_j;
nbs_cycle_start(&work->cc[enbsCCsearch]);
cbl = nbl->cj[nbl->ncj-1].cj >> gridj_flag_shift;
for (cb = cbf; cb <= cbl; cb++)
{
- gridj_flag[cb] = 1U<<th;
+ bitmask_init_bit(&gridj_flag[cb], th);
}
}
}
if (bFBufferFlag && nbl->ncj > ncj_old_i)
{
- work->buffer_flags.flag[(gridi->cell0+ci)>>gridi_flag_shift] = 1U<<th;
+ bitmask_init_bit(&(work->buffer_flags.flag[(gridi->cell0+ci)>>gridi_flag_shift]), th);
}
}
int nsrc,
const nbnxn_buffer_flags_t *dest)
{
- int s, b;
- const unsigned int *flag;
+ int s, b;
+ gmx_bitmask_t *flag;
for (s = 0; s < nsrc; s++)
{
for (b = 0; b < dest->nflag; b++)
{
- dest->flag[b] |= flag[b];
+ bitmask_union(&(dest->flag[b]), flag[b]);
}
}
}
static void print_reduction_cost(const nbnxn_buffer_flags_t *flags, int nout)
{
- int nelem, nkeep, ncopy, nred, b, c, out;
+ int nelem, nkeep, ncopy, nred, b, c, out;
+ gmx_bitmask_t mask_0;
nelem = 0;
nkeep = 0;
ncopy = 0;
nred = 0;
+ bitmask_init_bit(&mask_0, 0);
for (b = 0; b < flags->nflag; b++)
{
- if (flags->flag[b] == 1)
+ if (bitmask_is_equal(flags->flag[b], mask_0))
{
/* Only flag 0 is set, no copy of reduction required */
nelem++;
nkeep++;
}
- else if (flags->flag[b] > 0)
+ else if (!bitmask_is_zero(flags->flag[b]))
{
c = 0;
for (out = 0; out < nout; out++)
{
- if (flags->flag[b] & (1U<<out))
+ if (bitmask_is_set(flags->flag[b], out))
{
c++;
}
#ifndef _nbnxn_search_h
#define _nbnxn_search_h
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
#ifdef __cplusplus
extern "C" {
*/
/* Get the half-width SIMD stuff from the kernel utils files */
-#include "nbnxn_kernels/nbnxn_kernel_simd_utils.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h"
#if GMX_SIMD_REAL_WIDTH >= 2*NBNXN_CPU_CLUSTER_I_SIZE
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
#if GMX_SIMD_REAL_WIDTH >= NBNXN_CPU_CLUSTER_I_SIZE
#define STRIDE_S (GMX_SIMD_REAL_WIDTH)
#else
float d2;
int xind_f, xind_l, cj;
+ /* cppcheck-suppress selfAssignment . selfAssignment for width 4.*/
cjf = CI_TO_CJ_SIMD_4XN(cjf);
cjl = CI_TO_CJ_SIMD_4XN(cjl+1) - 1;
#ifndef _nbnxn_simd_h
#define _nbnxn_simd_h
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "config.h"
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
/* Include SIMD, below we select kernels based on the SIMD width */
#include "gromacs/simd/simd.h"
/* MIC for double is implemented in the SIMD module but so far missing in
mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils_x86_mic.h */
-#if defined __MIC__ && !defined GMX_DOUBLE
+#if defined GMX_SIMD_X86_MIC && !defined GMX_DOUBLE
#define GMX_NBNXN_SIMD
#endif
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "typedefs.h"
-#include "types/nlistheuristics.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-
-void reset_nlistheuristics(gmx_nlheur_t *nlh, gmx_int64_t step)
-{
- nlh->lt_runav = 0;
- nlh->lt_runav2 = 0;
- nlh->step_nscheck = step;
-}
-
-void init_nlistheuristics(gmx_nlheur_t *nlh,
- gmx_bool bGStatEveryStep, gmx_int64_t step)
-{
- nlh->bGStatEveryStep = bGStatEveryStep;
- nlh->nns = 0;
- nlh->nabnsb = 0;
- nlh->s1 = 0;
- nlh->s2 = 0;
- nlh->ab = 0;
-
- reset_nlistheuristics(nlh, step);
-}
-
-void update_nliststatistics(gmx_nlheur_t *nlh, gmx_int64_t step)
-{
- gmx_int64_t nl_lt;
- char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
-
- /* Determine the neighbor list life time */
- nl_lt = step - nlh->step_ns;
- if (debug)
- {
- fprintf(debug, "%d atoms beyond ns buffer, updating neighbor list after %s steps\n", nlh->nabnsb, gmx_step_str(nl_lt, sbuf));
- }
- nlh->nns++;
- nlh->s1 += nl_lt;
- nlh->s2 += nl_lt*nl_lt;
- nlh->ab += nlh->nabnsb;
- if (nlh->lt_runav == 0)
- {
- nlh->lt_runav = nl_lt;
- /* Initialize the fluctuation average
- * such that at startup we check after 0 steps.
- */
- nlh->lt_runav2 = sqr(nl_lt/2.0);
- }
- /* Running average with 0.9 gives an exp. history of 9.5 */
- nlh->lt_runav2 = 0.9*nlh->lt_runav2 + 0.1*sqr(nlh->lt_runav - nl_lt);
- nlh->lt_runav = 0.9*nlh->lt_runav + 0.1*nl_lt;
- if (nlh->bGStatEveryStep)
- {
- /* Always check the nlist validity */
- nlh->step_nscheck = step;
- }
- else
- {
- /* We check after: <life time> - 2*sigma
- * The factor 2 is quite conservative,
- * but we assume that with nstlist=-1 the user
- * prefers exact integration over performance.
- */
- nlh->step_nscheck = step
- + (int)(nlh->lt_runav - 2.0*sqrt(nlh->lt_runav2)) - 1;
- }
- if (debug)
- {
- fprintf(debug, "nlist life time %s run av. %4.1f sig %3.1f check %s check with -gcom %d\n",
- gmx_step_str(nl_lt, sbuf), nlh->lt_runav, sqrt(nlh->lt_runav2),
- gmx_step_str(nlh->step_nscheck-step+1, sbuf2),
- (int)(nlh->lt_runav - 2.0*sqrt(nlh->lt_runav2)));
- }
-}
-
-void set_nlistheuristics(gmx_nlheur_t *nlh, gmx_bool bReset, gmx_int64_t step)
-{
- int d;
-
- if (bReset)
- {
- reset_nlistheuristics(nlh, step);
- }
- else
- {
- update_nliststatistics(nlh, step);
- }
-
- nlh->step_ns = step;
- /* Initialize the cumulative coordinate scaling matrix */
- clear_mat(nlh->scale_tot);
- for (d = 0; d < DIM; d++)
- {
- nlh->scale_tot[d][d] = 1.0;
- }
-}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/ns.h"
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/nsgrid.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/math/utilities.h"
-#include "vec.h"
-#include "types/commrec.h"
-#include "network.h"
-#include "nsgrid.h"
-#include "force.h"
-#include "nonbonded.h"
-#include "ns.h"
-#include "pbc.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "nrnb.h"
-#include "txtdump.h"
-#include "mtop_util.h"
-
-#include "domdec.h"
-#include "adress.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+#include "adress.h"
/*
* E X C L U S I O N H A N D L I N G
/* Did we get the solvent loops so we can use optimized water kernels? */
if (nbl->nlist_sr[eNL_VDWQQ_WATER].kernelptr_vf == NULL
|| nbl->nlist_sr[eNL_QQ_WATER].kernelptr_vf == NULL
-#ifndef DISABLE_WATERWATER_NLIST
|| nbl->nlist_sr[eNL_VDWQQ_WATERWATER].kernelptr_vf == NULL
- || nbl->nlist_sr[eNL_QQ_WATERWATER].kernelptr_vf == NULL
-#endif
- )
+ || nbl->nlist_sr[eNL_QQ_WATERWATER].kernelptr_vf == NULL)
{
fr->solvent_opt = esolNO;
if (log != NULL)
if (iwater != esolNO)
{
- vdwc = &nlist[eNL_VDWQQ_WATER];
- vdw = &nlist[eNL_VDW];
- coul = &nlist[eNL_QQ_WATER];
-#ifndef DISABLE_WATERWATER_NLIST
+ vdwc = &nlist[eNL_VDWQQ_WATER];
+ vdw = &nlist[eNL_VDW];
+ coul = &nlist[eNL_QQ_WATER];
vdwc_ww = &nlist[eNL_VDWQQ_WATERWATER];
coul_ww = &nlist[eNL_QQ_WATERWATER];
-#endif
}
else
{
if (bDoCoul && bDoVdW)
{
new_i_nblist(vdwc, i_atom, shift, gid);
-#ifndef DISABLE_WATERWATER_NLIST
new_i_nblist(vdwc_ww, i_atom, shift, gid);
-#endif
}
if (bDoVdW)
{
if (bDoCoul)
{
new_i_nblist(coul, i_atom, shift, gid);
-#ifndef DISABLE_WATERWATER_NLIST
new_i_nblist(coul_ww, i_atom, shift, gid);
-#endif
}
/* Loop over the j charge groups */
for (j = 0; (j < nj); j++)
}
else
{
-#ifdef DISABLE_WATERWATER_NLIST
- /* Add entries for the three atoms - only do VdW if we need to */
- if (!bDoVdW)
- {
- add_j_to_nblist(coul, jj0, bLR);
- }
- else
- {
- add_j_to_nblist(vdwc, jj0, bLR);
- }
- add_j_to_nblist(coul, jj0+1, bLR);
- add_j_to_nblist(coul, jj0+2, bLR);
-#else
/* One entry for the entire water-water interaction */
if (!bDoVdW)
{
{
add_j_to_nblist(vdwc_ww, jj0, bLR);
}
-#endif
}
}
else if (iwater == esolTIP4P && jwater == esolTIP4P)
}
else
{
-#ifdef DISABLE_WATERWATER_NLIST
- /* Add entries for the four atoms - only do VdW if we need to */
- if (bDoVdW)
- {
- add_j_to_nblist(vdw, jj0, bLR);
- }
- add_j_to_nblist(coul, jj0+1, bLR);
- add_j_to_nblist(coul, jj0+2, bLR);
- add_j_to_nblist(coul, jj0+3, bLR);
-#else
/* One entry for the entire water-water interaction */
if (!bDoVdW)
{
{
add_j_to_nblist(vdwc_ww, jj0, bLR);
}
-#endif
}
}
else
close_i_nblist(vdw);
close_i_nblist(coul);
close_i_nblist(vdwc);
-#ifndef DISABLE_WATERWATER_NLIST
close_i_nblist(coul_ww);
close_i_nblist(vdwc_ww);
-#endif
}
else
{
gmx_ns_t *ns;
atom_id **nl_lr_ljc, **nl_lr_one, **nl_sr;
int *nlr_ljc, *nlr_one, *nsr;
- gmx_domdec_t *dd = NULL;
+ gmx_domdec_t *dd;
t_block *cgs = &(top->cgs);
int *cginfo = fr->cginfo;
/* atom_id *i_atoms,*cgsindex=cgs->index; */
ns = &fr->ns;
bDomDec = DOMAINDECOMP(cr);
- if (bDomDec)
- {
- dd = cr->dd;
- }
+ dd = cr->dd;
bTriclinicX = ((YY < grid->npbcdim &&
(!bDomDec || dd->nc[YY] == 1) && box[YY][XX] != 0) ||
return nsearch;
}
-
-int natoms_beyond_ns_buffer(t_inputrec *ir, t_forcerec *fr, t_block *cgs,
- matrix scale_tot, rvec *x)
-{
- int cg0, cg1, cg, a0, a1, a, i, j;
- real rint, hbuf2, scale;
- rvec *cg_cm, cgsc;
- gmx_bool bIsotropic;
- int nBeyond;
-
- nBeyond = 0;
-
- rint = max(ir->rcoulomb, ir->rvdw);
- if (ir->rlist < rint)
- {
- gmx_fatal(FARGS, "The neighbor search buffer has negative size: %f nm",
- ir->rlist - rint);
- }
- cg_cm = fr->cg_cm;
-
- cg0 = fr->cg0;
- cg1 = fr->hcg;
-
- if (!EI_DYNAMICS(ir->eI) || !DYNAMIC_BOX(*ir))
- {
- hbuf2 = sqr(0.5*(ir->rlist - rint));
- for (cg = cg0; cg < cg1; cg++)
- {
- a0 = cgs->index[cg];
- a1 = cgs->index[cg+1];
- for (a = a0; a < a1; a++)
- {
- if (distance2(cg_cm[cg], x[a]) > hbuf2)
- {
- nBeyond++;
- }
- }
- }
- }
- else
- {
- bIsotropic = TRUE;
- scale = scale_tot[0][0];
- for (i = 1; i < DIM; i++)
- {
- /* With anisotropic scaling, the original spherical ns volumes become
- * ellipsoids. To avoid costly transformations we use the minimum
- * eigenvalue of the scaling matrix for determining the buffer size.
- * Since the lower half is 0, the eigenvalues are the diagonal elements.
- */
- scale = min(scale, scale_tot[i][i]);
- if (scale_tot[i][i] != scale_tot[i-1][i-1])
- {
- bIsotropic = FALSE;
- }
- for (j = 0; j < i; j++)
- {
- if (scale_tot[i][j] != 0)
- {
- bIsotropic = FALSE;
- }
- }
- }
- hbuf2 = sqr(0.5*(scale*ir->rlist - rint));
- if (bIsotropic)
- {
- for (cg = cg0; cg < cg1; cg++)
- {
- svmul(scale, cg_cm[cg], cgsc);
- a0 = cgs->index[cg];
- a1 = cgs->index[cg+1];
- for (a = a0; a < a1; a++)
- {
- if (distance2(cgsc, x[a]) > hbuf2)
- {
- nBeyond++;
- }
- }
- }
- }
- else
- {
- /* Anistropic scaling */
- for (cg = cg0; cg < cg1; cg++)
- {
- /* Since scale_tot contains the transpose of the scaling matrix,
- * we need to multiply with the transpose.
- */
- tmvmul_ur0(scale_tot, cg_cm[cg], cgsc);
- a0 = cgs->index[cg];
- a1 = cgs->index[cg+1];
- for (a = a0; a < a1; a++)
- {
- if (distance2(cgsc, x[a]) > hbuf2)
- {
- nBeyond++;
- }
- }
- }
- }
- }
-
- return nBeyond;
-}
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <stdlib.h>
+#include "gromacs/legacyheaders/nsgrid.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "nsgrid.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "network.h"
-#include "domdec.h"
-#include "pbc.h"
#include <stdio.h>
-#include "gromacs/fileio/futil.h"
+#include <stdlib.h>
+
+#include "gromacs/domdec/domdec.h"
#include "gromacs/fileio/pdbio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
/***********************************
* Grid Routines
*/
/* Determine the shift for the corners of the triclinic box */
add_tric = izones_size[j]*box[j][i]/box[j][j];
- if (dd && dd->ndim == 1 && j == ZZ)
+ if (dd->ndim == 1 && j == ZZ)
{
/* With 1D domain decomposition the cg's are not in
* the triclinic box, but trilinic x-y and rectangular y-z.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <math.h>
+#include "gromacs/legacyheaders/perf_est.h"
-#include "perf_est.h"
-#include "physics.h"
-#include "vec.h"
-#include "mtop_util.h"
-#include "types/commrec.h"
-#include "nbnxn_search.h"
-#include "nbnxn_consts.h"
+#include <math.h>
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/fatalerror.h"
/* Computational cost of bonded, non-bonded and PME calculations.
* This will be machine dependent.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#ifdef GMX_QMMM_GAMESS
#include <math.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "physics.h"
-#include "macros.h"
-#include "vec.h"
-#include "force.h"
-#include "invblock.h"
-#include "gromacs/fileio/confio.h"
-#include "names.h"
-#include "network.h"
-#include "pbc.h"
-#include "ns.h"
-#include "nrnb.h"
-#include "bondf.h"
-#include "mshift.h"
-#include "txtdump.h"
-#include "qmmm.h"
#include <stdio.h>
-#include <string.h>
-#include "gmx_fatal.h"
-#include "typedefs.h"
#include <stdlib.h>
+#include <string.h>
+
+#include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* QMMM sub routines */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#ifdef GMX_QMMM_GAUSSIAN
#include <math.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "physics.h"
-#include "macros.h"
-#include "vec.h"
-#include "force.h"
-#include "invblock.h"
-#include "gromacs/fileio/confio.h"
-#include "names.h"
-#include "network.h"
-#include "pbc.h"
-#include "ns.h"
-#include "nrnb.h"
-#include "bondf.h"
-#include "mshift.h"
-#include "txtdump.h"
-#include "qmmm.h"
#include <stdio.h>
-#include <string.h>
-#include "gmx_fatal.h"
-#include "typedefs.h"
#include <stdlib.h>
+#include <string.h>
+
+#include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* TODO: this should be made thread-safe */
if (buf)
{
- qm->gauss_dir = strdup(buf);
+ qm->gauss_dir = gmx_strdup(buf);
}
else
{
buf = getenv("GMX_QM_GAUSS_EXE");
if (buf)
{
- qm->gauss_exe = strdup(buf);
+ qm->gauss_exe = gmx_strdup(buf);
}
else
{
buf = getenv("GMX_QM_MODIFIED_LINKS_DIR");
if (buf)
{
- qm->devel_dir = strdup (buf);
+ qm->devel_dir = gmx_strdup (buf);
}
else
{
"input.log");
}
fprintf(stderr, "Calling '%s'\n", buf);
-#ifdef GMX_NO_SYSTEM
- printf("Warning-- No calls to system(3) supported on this platform.");
- gmx_fatal(FARGS, "Call to '%s' failed\n", buf);
-#else
if (system(buf) != 0)
{
gmx_fatal(FARGS, "Call to '%s' failed\n", buf);
}
-#endif
}
real call_gaussian(t_commrec *cr, t_forcerec *fr,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#ifdef GMX_QMMM_MOPAC
#include <math.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "physics.h"
-#include "macros.h"
-#include "vec.h"
-#include "force.h"
-#include "invblock.h"
-#include "gromacs/fileio/confio.h"
-#include "names.h"
-#include "network.h"
-#include "pbc.h"
-#include "ns.h"
-#include "nrnb.h"
-#include "bondf.h"
-#include "mshift.h"
-#include "txtdump.h"
-#include "qmmm.h"
#include <stdio.h>
-#include <string.h>
-#include "gmx_fatal.h"
-#include "typedefs.h"
#include <stdlib.h>
+#include <string.h>
+
+#include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* mopac interface routines */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "physics.h"
-#include "macros.h"
-#include "vec.h"
-#include "force.h"
-#include "invblock.h"
-#include "gromacs/fileio/confio.h"
-#include "names.h"
-#include "network.h"
-#include "pbc.h"
-#include "ns.h"
-#include "nrnb.h"
-#include "bondf.h"
-#include "mshift.h"
-#include "txtdump.h"
-#include "qmmm.h"
#include <stdio.h>
-#include <string.h>
-#include "gmx_fatal.h"
-#include "typedefs.h"
#include <stdlib.h>
+#include <string.h>
+
+#include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* ORCA interface routines */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/qmmm.h"
+
+#include "config.h"
#include <math.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "physics.h"
-#include "macros.h"
-#include "vec.h"
-#include "force.h"
-#include "invblock.h"
-#include "gromacs/fileio/confio.h"
-#include "names.h"
-#include "network.h"
-#include "pbc.h"
-#include "ns.h"
-#include "nrnb.h"
-#include "bondf.h"
-#include "mshift.h"
-#include "txtdump.h"
-#include "qmmm.h"
#include <stdio.h>
-#include <string.h>
-#include "gmx_fatal.h"
-#include "typedefs.h"
#include <stdlib.h>
-#include "mtop_util.h"
+#include <string.h>
+#include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* declarations of the interfaces to the QM packages. The _SH indicate
* the QM interfaces can be used for Surface Hopping simulations
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "force.h"
-#include "names.h"
-#include "vec.h"
-#include "physics.h"
-#include "copyrite.h"
-#include "pbc.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
real RF_excl_correction(const t_forcerec *fr, t_graph *g,
const t_mdatoms *mdatoms, const t_blocka *excl,
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "pbc.h"
-#include "txtdump.h"
-#include "vec.h"
-#include "nrnb.h"
-#include "constr.h"
-
-typedef struct gmx_shakedata
-{
- rvec *rij;
- real *M2;
- real *tt;
- real *dist2;
- int nalloc;
- /* SOR stuff */
- real delta;
- real omega;
- real gamma;
-} t_gmx_shakedata;
-
-gmx_shakedata_t shake_init()
-{
- gmx_shakedata_t d;
-
- snew(d, 1);
-
- d->nalloc = 0;
- d->rij = NULL;
- d->M2 = NULL;
- d->tt = NULL;
- d->dist2 = NULL;
-
- /* SOR initialization */
- d->delta = 0.1;
- d->omega = 1.0;
- d->gamma = 1000000;
-
- return d;
-}
-
-static void pv(FILE *log, char *s, rvec x)
-{
- int m;
-
- fprintf(log, "%5s:", s);
- for (m = 0; (m < DIM); m++)
- {
- fprintf(log, " %10.3f", x[m]);
- }
- fprintf(log, "\n");
- fflush(log);
-}
-
-void cshake(atom_id iatom[], int ncon, int *nnit, int maxnit,
- real dist2[], real xp[], real rij[], real m2[], real omega,
- real invmass[], real tt[], real lagr[], int *nerror)
-{
- /*
- * r.c. van schaik and w.f. van gunsteren
- * eth zuerich
- * june 1992
- * Adapted for use with Gromacs by David van der Spoel november 92 and later.
- */
- /* default should be increased! MRS 8/4/2009 */
- const real mytol = 1e-10;
-
- int ll, i, j, i3, j3, l3;
- int ix, iy, iz, jx, jy, jz;
- real toler, rpij2, rrpr, tx, ty, tz, diff, acor, im, jm;
- real xh, yh, zh, rijx, rijy, rijz;
- real tix, tiy, tiz;
- real tjx, tjy, tjz;
- int nit, error, nconv;
- real iconvf;
-
- error = 0;
- nconv = 1;
- for (nit = 0; (nit < maxnit) && (nconv != 0) && (error == 0); nit++)
- {
- nconv = 0;
- for (ll = 0; (ll < ncon) && (error == 0); ll++)
- {
- l3 = 3*ll;
- rijx = rij[l3+XX];
- rijy = rij[l3+YY];
- rijz = rij[l3+ZZ];
- i = iatom[l3+1];
- j = iatom[l3+2];
- i3 = 3*i;
- j3 = 3*j;
- ix = i3+XX;
- iy = i3+YY;
- iz = i3+ZZ;
- jx = j3+XX;
- jy = j3+YY;
- jz = j3+ZZ;
-
- tx = xp[ix]-xp[jx];
- ty = xp[iy]-xp[jy];
- tz = xp[iz]-xp[jz];
- rpij2 = tx*tx+ty*ty+tz*tz;
- toler = dist2[ll];
- diff = toler-rpij2;
-
- /* iconvf is less than 1 when the error is smaller than a bound */
- /* But if tt is too big, then it will result in looping in iconv */
-
- iconvf = fabs(diff)*tt[ll];
-
- if (iconvf > 1)
- {
- nconv = iconvf;
- rrpr = rijx*tx+rijy*ty+rijz*tz;
-
- if (rrpr < toler*mytol)
- {
- error = ll+1;
- }
- else
- {
- acor = omega*diff*m2[ll]/rrpr;
- lagr[ll] += acor;
- xh = rijx*acor;
- yh = rijy*acor;
- zh = rijz*acor;
- im = invmass[i];
- jm = invmass[j];
- xp[ix] += xh*im;
- xp[iy] += yh*im;
- xp[iz] += zh*im;
- xp[jx] -= xh*jm;
- xp[jy] -= yh*jm;
- xp[jz] -= zh*jm;
- }
- }
- }
- }
- *nnit = nit;
- *nerror = error;
-}
-
-int vec_shakef(FILE *fplog, gmx_shakedata_t shaked,
- real invmass[], int ncon,
- t_iparams ip[], t_iatom *iatom,
- real tol, rvec x[], rvec prime[], real omega,
- gmx_bool bFEP, real lambda, real lagr[],
- real invdt, rvec *v,
- gmx_bool bCalcVir, tensor vir_r_m_dr, int econq,
- t_vetavars *vetavar)
-{
- rvec *rij;
- real *M2, *tt, *dist2;
- int maxnit = 1000;
- int nit = 0, ll, i, j, type;
- t_iatom *ia;
- real L1, tol2, toler;
- real mm = 0., tmp;
- int error = 0;
- real g, vscale, rscale, rvscale;
-
- if (ncon > shaked->nalloc)
- {
- shaked->nalloc = over_alloc_dd(ncon);
- srenew(shaked->rij, shaked->nalloc);
- srenew(shaked->M2, shaked->nalloc);
- srenew(shaked->tt, shaked->nalloc);
- srenew(shaked->dist2, shaked->nalloc);
- }
- rij = shaked->rij;
- M2 = shaked->M2;
- tt = shaked->tt;
- dist2 = shaked->dist2;
-
- L1 = 1.0-lambda;
- tol2 = 2.0*tol;
- ia = iatom;
- for (ll = 0; (ll < ncon); ll++, ia += 3)
- {
- type = ia[0];
- i = ia[1];
- j = ia[2];
-
- mm = 2*(invmass[i]+invmass[j]);
- rij[ll][XX] = x[i][XX]-x[j][XX];
- rij[ll][YY] = x[i][YY]-x[j][YY];
- rij[ll][ZZ] = x[i][ZZ]-x[j][ZZ];
- M2[ll] = 1.0/mm;
- if (bFEP)
- {
- toler = sqr(L1*ip[type].constr.dA + lambda*ip[type].constr.dB);
- }
- else
- {
- toler = sqr(ip[type].constr.dA);
- }
- dist2[ll] = toler;
- tt[ll] = 1.0/(toler*tol2);
- }
-
- switch (econq)
- {
- case econqCoord:
- cshake(iatom, ncon, &nit, maxnit, dist2, prime[0], rij[0], M2, omega, invmass, tt, lagr, &error);
- break;
- case econqVeloc:
- crattle(iatom, ncon, &nit, maxnit, dist2, prime[0], rij[0], M2, omega, invmass, tt, lagr, &error, invdt, vetavar);
- break;
- }
-
- if (nit >= maxnit)
- {
- if (fplog)
- {
- fprintf(fplog, "Shake did not converge in %d steps\n", maxnit);
- }
- fprintf(stderr, "Shake did not converge in %d steps\n", maxnit);
- nit = 0;
- }
- else if (error != 0)
- {
- if (fplog)
- {
- fprintf(fplog, "Inner product between old and new vector <= 0.0!\n"
- "constraint #%d atoms %u and %u\n",
- error-1, iatom[3*(error-1)+1]+1, iatom[3*(error-1)+2]+1);
- }
- fprintf(stderr, "Inner product between old and new vector <= 0.0!\n"
- "constraint #%d atoms %u and %u\n",
- error-1, iatom[3*(error-1)+1]+1, iatom[3*(error-1)+2]+1);
- nit = 0;
- }
-
- /* Constraint virial and correct the lagrange multipliers for the length */
-
- ia = iatom;
-
- for (ll = 0; (ll < ncon); ll++, ia += 3)
- {
-
- if ((econq == econqCoord) && v != NULL)
- {
- /* Correct the velocities */
- mm = lagr[ll]*invmass[ia[1]]*invdt/vetavar->rscale;
- for (i = 0; i < DIM; i++)
- {
- v[ia[1]][i] += mm*rij[ll][i];
- }
- mm = lagr[ll]*invmass[ia[2]]*invdt/vetavar->rscale;
- for (i = 0; i < DIM; i++)
- {
- v[ia[2]][i] -= mm*rij[ll][i];
- }
- /* 16 flops */
- }
-
- /* constraint virial */
- if (bCalcVir)
- {
- if (econq == econqCoord)
- {
- mm = lagr[ll]/vetavar->rvscale;
- }
- if (econq == econqVeloc)
- {
- mm = lagr[ll]/(vetavar->vscale*vetavar->vscale_nhc[0]);
- }
- for (i = 0; i < DIM; i++)
- {
- tmp = mm*rij[ll][i];
- for (j = 0; j < DIM; j++)
- {
- vir_r_m_dr[i][j] -= tmp*rij[ll][j];
- }
- }
- /* 21 flops */
- }
-
- /* Correct the lagrange multipliers for the length */
- /* (more details would be useful here . . . )*/
-
- type = ia[0];
- if (bFEP)
- {
- toler = L1*ip[type].constr.dA + lambda*ip[type].constr.dB;
- }
- else
- {
- toler = ip[type].constr.dA;
- lagr[ll] *= toler;
- }
- }
-
- return nit;
-}
-
-static void check_cons(FILE *log, int nc, rvec x[], rvec prime[], rvec v[],
- t_iparams ip[], t_iatom *iatom,
- real invmass[], int econq)
-{
- t_iatom *ia;
- int ai, aj;
- int i;
- real d, dp;
- rvec dx, dv;
-
- fprintf(log,
- " i mi j mj before after should be\n");
- ia = iatom;
- for (i = 0; (i < nc); i++, ia += 3)
- {
- ai = ia[1];
- aj = ia[2];
- rvec_sub(x[ai], x[aj], dx);
- d = norm(dx);
-
- switch (econq)
- {
- case econqCoord:
- rvec_sub(prime[ai], prime[aj], dx);
- dp = norm(dx);
- fprintf(log, "%5d %5.2f %5d %5.2f %10.5f %10.5f %10.5f\n",
- ai+1, 1.0/invmass[ai],
- aj+1, 1.0/invmass[aj], d, dp, ip[ia[0]].constr.dA);
- break;
- case econqVeloc:
- rvec_sub(v[ai], v[aj], dv);
- d = iprod(dx, dv);
- rvec_sub(prime[ai], prime[aj], dv);
- dp = iprod(dx, dv);
- fprintf(log, "%5d %5.2f %5d %5.2f %10.5f %10.5f %10.5f\n",
- ai+1, 1.0/invmass[ai],
- aj+1, 1.0/invmass[aj], d, dp, 0.);
- break;
- }
- }
-}
-
-gmx_bool bshakef(FILE *log, gmx_shakedata_t shaked,
- real invmass[], int nblocks, int sblock[],
- t_idef *idef, t_inputrec *ir, rvec x_s[], rvec prime[],
- t_nrnb *nrnb, real *lagr, real lambda, real *dvdlambda,
- real invdt, rvec *v, gmx_bool bCalcVir, tensor vir_r_m_dr,
- gmx_bool bDumpOnError, int econq, t_vetavars *vetavar)
-{
- t_iatom *iatoms;
- real *lam, dt_2, dvdl;
- int i, n0, ncons, blen, type;
- int tnit = 0, trij = 0;
-
-#ifdef DEBUG
- fprintf(log, "nblocks=%d, sblock[0]=%d\n", nblocks, sblock[0]);
-#endif
-
- ncons = idef->il[F_CONSTR].nr/3;
-
- for (i = 0; i < ncons; i++)
- {
- lagr[i] = 0;
- }
-
- iatoms = &(idef->il[F_CONSTR].iatoms[sblock[0]]);
- lam = lagr;
- for (i = 0; (i < nblocks); )
- {
- blen = (sblock[i+1]-sblock[i]);
- blen /= 3;
- n0 = vec_shakef(log, shaked, invmass, blen, idef->iparams,
- iatoms, ir->shake_tol, x_s, prime, shaked->omega,
- ir->efep != efepNO, lambda, lam, invdt, v, bCalcVir, vir_r_m_dr,
- econq, vetavar);
-
-#ifdef DEBUGSHAKE
- check_cons(log, blen, x_s, prime, v, idef->iparams, iatoms, invmass, econq);
-#endif
-
- if (n0 == 0)
- {
- if (bDumpOnError && log)
- {
- {
- check_cons(log, blen, x_s, prime, v, idef->iparams, iatoms, invmass, econq);
- }
- }
- return FALSE;
- }
- tnit += n0*blen;
- trij += blen;
- iatoms += 3*blen; /* Increment pointer! */
- lam += blen;
- i++;
- }
- /* only for position part? */
- if (econq == econqCoord)
- {
- if (ir->efep != efepNO)
- {
- real bondA, bondB;
- dt_2 = 1/sqr(ir->delta_t);
- dvdl = 0;
- for (i = 0; i < ncons; i++)
- {
- type = idef->il[F_CONSTR].iatoms[3*i];
-
- /* dh/dl contribution from constraint force is dh/dr (constraint force) dot dr/dl */
- /* constraint force is -\sum_i lagr_i* d(constraint)/dr, with constrant = r^2-d^2 */
- /* constraint force is -\sum_i lagr_i* 2 r */
- /* so dh/dl = -\sum_i lagr_i* 2 r * dr/dl */
- /* However, by comparison with lincs and with
- comparison with a full thermodynamics cycle (see
- redmine issue #1255), this is off by a factor of
- two -- the 2r should apparently just be r. Further
- investigation should be done at some point to
- understand why and see if there is something deeper
- we are missing */
-
- bondA = idef->iparams[type].constr.dA;
- bondB = idef->iparams[type].constr.dB;
- dvdl += lagr[i] * dt_2 * ((1.0-lambda)*bondA + lambda*bondB) * (bondB-bondA);
- }
- *dvdlambda += dvdl;
- }
- }
-#ifdef DEBUG
- fprintf(log, "tnit: %5d omega: %10.5f\n", tnit, omega);
-#endif
- if (ir->bShakeSOR)
- {
- if (tnit > shaked->gamma)
- {
- shaked->delta *= -0.5;
- }
- shaked->omega += shaked->delta;
- shaked->gamma = tnit;
- }
- inc_nrnb(nrnb, eNR_SHAKE, tnit);
- inc_nrnb(nrnb, eNR_SHAKE_RIJ, trij);
- if (v)
- {
- inc_nrnb(nrnb, eNR_CONSTR_V, trij*2);
- }
- if (bCalcVir)
- {
- inc_nrnb(nrnb, eNR_CONSTR_VIR, trij);
- }
-
- return TRUE;
-}
-
-void crattle(atom_id iatom[], int ncon, int *nnit, int maxnit,
- real dist2[], real vp[], real rij[], real m2[], real omega,
- real invmass[], real tt[], real lagr[], int *nerror, real invdt, t_vetavars *vetavar)
-{
- /*
- * r.c. van schaik and w.f. van gunsteren
- * eth zuerich
- * june 1992
- * Adapted for use with Gromacs by David van der Spoel november 92 and later.
- * rattle added by M.R. Shirts, April 2004, from code written by Jay Ponder in TINKER
- * second part of rattle algorithm
- */
-
- const real mytol = 1e-10;
-
- int ll, i, j, i3, j3, l3, ii;
- int ix, iy, iz, jx, jy, jz;
- real toler, rijd, vpijd, vx, vy, vz, diff, acor, xdotd, fac, im, jm, imdt, jmdt;
- real xh, yh, zh, rijx, rijy, rijz;
- real tix, tiy, tiz;
- real tjx, tjy, tjz;
- int nit, error, nconv;
- real veta, vscale_nhc, iconvf;
-
- veta = vetavar->veta;
- vscale_nhc = vetavar->vscale_nhc[0]; /* for now, just use the first state */
-
- error = 0;
- nconv = 1;
- for (nit = 0; (nit < maxnit) && (nconv != 0) && (error == 0); nit++)
- {
- nconv = 0;
- for (ll = 0; (ll < ncon) && (error == 0); ll++)
- {
- l3 = 3*ll;
- rijx = rij[l3+XX];
- rijy = rij[l3+YY];
- rijz = rij[l3+ZZ];
- i = iatom[l3+1];
- j = iatom[l3+2];
- i3 = 3*i;
- j3 = 3*j;
- ix = i3+XX;
- iy = i3+YY;
- iz = i3+ZZ;
- jx = j3+XX;
- jy = j3+YY;
- jz = j3+ZZ;
- vx = vp[ix]-vp[jx];
- vy = vp[iy]-vp[jy];
- vz = vp[iz]-vp[jz];
-
- vpijd = vx*rijx+vy*rijy+vz*rijz;
- toler = dist2[ll];
- /* this is r(t+dt) \dotproduct \dot{r}(t+dt) */
- xdotd = vpijd*vscale_nhc + veta*toler;
-
- /* iconv is zero when the error is smaller than a bound */
- iconvf = fabs(xdotd)*(tt[ll]/invdt);
-
- if (iconvf > 1)
- {
- nconv = iconvf;
- fac = omega*2.0*m2[ll]/toler;
- acor = -fac*xdotd;
- lagr[ll] += acor;
-
- xh = rijx*acor;
- yh = rijy*acor;
- zh = rijz*acor;
-
- im = invmass[i]/vscale_nhc;
- jm = invmass[j]/vscale_nhc;
-
- vp[ix] += xh*im;
- vp[iy] += yh*im;
- vp[iz] += zh*im;
- vp[jx] -= xh*jm;
- vp[jy] -= yh*jm;
- vp[jz] -= zh*jm;
- }
- }
- }
- *nnit = nit;
- *nerror = error;
-}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include <math.h>
+
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/smalloc.h"
+
+typedef struct gmx_shakedata
+{
+ rvec *rij;
+ real *half_of_reduced_mass;
+ real *distance_squared_tolerance;
+ real *constraint_distance_squared;
+ int nalloc;
+ /* SOR stuff */
+ real delta;
+ real omega;
+ real gamma;
+} t_gmx_shakedata;
+
+gmx_shakedata_t shake_init()
+{
+ gmx_shakedata_t d;
+
+ snew(d, 1);
+
+ d->nalloc = 0;
+ d->rij = NULL;
+ d->half_of_reduced_mass = NULL;
+ d->distance_squared_tolerance = NULL;
+ d->constraint_distance_squared = NULL;
+
+ /* SOR initialization */
+ d->delta = 0.1;
+ d->omega = 1.0;
+ d->gamma = 1000000;
+
+ return d;
+}
+
+static void pv(FILE *log, char *s, rvec x)
+{
+ int m;
+
+ fprintf(log, "%5s:", s);
+ for (m = 0; (m < DIM); m++)
+ {
+ fprintf(log, " %10.3f", x[m]);
+ }
+ fprintf(log, "\n");
+ fflush(log);
+}
+
+/*! \brief Inner kernel for SHAKE constraints
+ *
+ * Original implementation from R.C. van Schaik and W.F. van Gunsteren
+ * (ETH Zuerich, June 1992), adapted for GROMACS by David van der
+ * Spoel November 1992.
+ *
+ * The algorithm here is based section five of Ryckaert, Ciccotti and
+ * Berendsen, J Comp Phys, 23, 327, 1977.
+ *
+ * \param[in] iatom Mini-topology of triples of constraint type (unused in this
+ * function) and indices of the two atoms involved
+ * \param[in] ncon Number of constraints
+ * \param[out] nnit Number of iterations performed
+ * \param[in] maxnit Maximum number of iterations permitted
+ * \param[in] constraint_distance_squared The objective value for each constraint
+ * \param[inout] positions The initial (and final) values of the positions of all atoms
+ * \param[in] initial_displacements The initial displacements of each constraint
+ * \param[in] half_of_reduced_mass Half of the reduced mass for each constraint
+ * \param[in] omega SHAKE over-relaxation factor (set non-1.0 by
+ * using shake-sor=yes in the .mdp, but there is no documentation anywhere)
+ * \param[in] invmass Inverse mass of each atom
+ * \param[in] distance_squared_tolerance Multiplicative tolerance on the difference in the
+ * square of the constrained distance (see code)
+ * \param[out] scaled_lagrange_multiplier Scaled Lagrange multiplier for each constraint (-2 * eta from p. 336
+ * of the paper, divided by the constraint distance)
+ * \param[out] nerror Zero upon success, returns one more than the index of the
+ * problematic constraint if the input was malformed
+ *
+ * \todo Make SHAKE use better data structures, in particular for iatom. */
+void cshake(const atom_id iatom[], int ncon, int *nnit, int maxnit,
+ const real constraint_distance_squared[], real positions[],
+ const real initial_displacements[], const real half_of_reduced_mass[], real omega,
+ const real invmass[], const real distance_squared_tolerance[],
+ real scaled_lagrange_multiplier[], int *nerror)
+{
+ /* default should be increased! MRS 8/4/2009 */
+ const real mytol = 1e-10;
+
+ int ll, i, j, i3, j3, l3;
+ int ix, iy, iz, jx, jy, jz;
+ real r_dot_r_prime;
+ real constraint_distance_squared_ll;
+ real r_prime_squared;
+ real scaled_lagrange_multiplier_ll;
+ real r_prime_x, r_prime_y, r_prime_z, diff, im, jm;
+ real xh, yh, zh, rijx, rijy, rijz;
+ int nit, error, nconv;
+ real iconvf;
+
+ // TODO nconv is used solely as a boolean, so we should write the
+ // code like that
+ error = 0;
+ nconv = 1;
+ for (nit = 0; (nit < maxnit) && (nconv != 0) && (error == 0); nit++)
+ {
+ nconv = 0;
+ for (ll = 0; (ll < ncon) && (error == 0); ll++)
+ {
+ l3 = 3*ll;
+ rijx = initial_displacements[l3+XX];
+ rijy = initial_displacements[l3+YY];
+ rijz = initial_displacements[l3+ZZ];
+ i = iatom[l3+1];
+ j = iatom[l3+2];
+ i3 = 3*i;
+ j3 = 3*j;
+ ix = i3+XX;
+ iy = i3+YY;
+ iz = i3+ZZ;
+ jx = j3+XX;
+ jy = j3+YY;
+ jz = j3+ZZ;
+
+ /* Compute r prime between atoms i and j, which is the
+ displacement *before* this update stage */
+ r_prime_x = positions[ix]-positions[jx];
+ r_prime_y = positions[iy]-positions[jy];
+ r_prime_z = positions[iz]-positions[jz];
+ r_prime_squared = (r_prime_x * r_prime_x +
+ r_prime_y * r_prime_y +
+ r_prime_z * r_prime_z);
+ constraint_distance_squared_ll = constraint_distance_squared[ll];
+ diff = constraint_distance_squared_ll - r_prime_squared;
+
+ /* iconvf is less than 1 when the error is smaller than a bound */
+ iconvf = fabs(diff) * distance_squared_tolerance[ll];
+
+ if (iconvf > 1.0)
+ {
+ nconv = static_cast<int>(iconvf);
+ r_dot_r_prime = (rijx * r_prime_x +
+ rijy * r_prime_y +
+ rijz * r_prime_z);
+
+ if (r_dot_r_prime < constraint_distance_squared_ll * mytol)
+ {
+ error = ll+1;
+ }
+ else
+ {
+ /* The next line solves equation 5.6 (neglecting
+ the term in g^2), for g */
+ scaled_lagrange_multiplier_ll = omega*diff*half_of_reduced_mass[ll]/r_dot_r_prime;
+ scaled_lagrange_multiplier[ll] += scaled_lagrange_multiplier_ll;
+ xh = rijx * scaled_lagrange_multiplier_ll;
+ yh = rijy * scaled_lagrange_multiplier_ll;
+ zh = rijz * scaled_lagrange_multiplier_ll;
+ im = invmass[i];
+ jm = invmass[j];
+ positions[ix] += xh*im;
+ positions[iy] += yh*im;
+ positions[iz] += zh*im;
+ positions[jx] -= xh*jm;
+ positions[jy] -= yh*jm;
+ positions[jz] -= zh*jm;
+ }
+ }
+ }
+ }
+ *nnit = nit;
+ *nerror = error;
+}
+
+int vec_shakef(FILE *fplog, gmx_shakedata_t shaked,
+ real invmass[], int ncon,
+ t_iparams ip[], t_iatom *iatom,
+ real tol, rvec x[], rvec prime[], real omega,
+ gmx_bool bFEP, real lambda, real scaled_lagrange_multiplier[],
+ real invdt, rvec *v,
+ gmx_bool bCalcVir, tensor vir_r_m_dr, int econq)
+{
+ rvec *rij;
+ real *half_of_reduced_mass, *distance_squared_tolerance, *constraint_distance_squared;
+ int maxnit = 1000;
+ int nit = 0, ll, i, j, d, d2, type;
+ t_iatom *ia;
+ real L1;
+ real mm = 0., tmp;
+ int error = 0;
+ real constraint_distance;
+
+ if (ncon > shaked->nalloc)
+ {
+ shaked->nalloc = over_alloc_dd(ncon);
+ srenew(shaked->rij, shaked->nalloc);
+ srenew(shaked->half_of_reduced_mass, shaked->nalloc);
+ srenew(shaked->distance_squared_tolerance, shaked->nalloc);
+ srenew(shaked->constraint_distance_squared, shaked->nalloc);
+ }
+ rij = shaked->rij;
+ half_of_reduced_mass = shaked->half_of_reduced_mass;
+ distance_squared_tolerance = shaked->distance_squared_tolerance;
+ constraint_distance_squared = shaked->constraint_distance_squared;
+
+ L1 = 1.0-lambda;
+ ia = iatom;
+ for (ll = 0; (ll < ncon); ll++, ia += 3)
+ {
+ type = ia[0];
+ i = ia[1];
+ j = ia[2];
+
+ mm = 2.0*(invmass[i]+invmass[j]);
+ rij[ll][XX] = x[i][XX]-x[j][XX];
+ rij[ll][YY] = x[i][YY]-x[j][YY];
+ rij[ll][ZZ] = x[i][ZZ]-x[j][ZZ];
+ half_of_reduced_mass[ll] = 1.0/mm;
+ if (bFEP)
+ {
+ constraint_distance = L1*ip[type].constr.dA + lambda*ip[type].constr.dB;
+ }
+ else
+ {
+ constraint_distance = ip[type].constr.dA;
+ }
+ constraint_distance_squared[ll] = sqr(constraint_distance);
+ distance_squared_tolerance[ll] = 0.5/(constraint_distance_squared[ll]*tol);
+ }
+
+ switch (econq)
+ {
+ case econqCoord:
+ cshake(iatom, ncon, &nit, maxnit, constraint_distance_squared, prime[0], rij[0], half_of_reduced_mass, omega, invmass, distance_squared_tolerance, scaled_lagrange_multiplier, &error);
+ break;
+ case econqVeloc:
+ crattle(iatom, ncon, &nit, maxnit, constraint_distance_squared, prime[0], rij[0], half_of_reduced_mass, omega, invmass, distance_squared_tolerance, scaled_lagrange_multiplier, &error, invdt);
+ break;
+ }
+
+ if (nit >= maxnit)
+ {
+ if (fplog)
+ {
+ fprintf(fplog, "Shake did not converge in %d steps\n", maxnit);
+ }
+ fprintf(stderr, "Shake did not converge in %d steps\n", maxnit);
+ nit = 0;
+ }
+ else if (error != 0)
+ {
+ if (fplog)
+ {
+ fprintf(fplog, "Inner product between old and new vector <= 0.0!\n"
+ "constraint #%d atoms %d and %d\n",
+ error-1, iatom[3*(error-1)+1]+1, iatom[3*(error-1)+2]+1);
+ }
+ fprintf(stderr, "Inner product between old and new vector <= 0.0!\n"
+ "constraint #%d atoms %d and %d\n",
+ error-1, iatom[3*(error-1)+1]+1, iatom[3*(error-1)+2]+1);
+ nit = 0;
+ }
+
+ /* Constraint virial and correct the Lagrange multipliers for the length */
+
+ ia = iatom;
+
+ for (ll = 0; (ll < ncon); ll++, ia += 3)
+ {
+ type = ia[0];
+ i = ia[1];
+ j = ia[2];
+
+ if ((econq == econqCoord) && v != NULL)
+ {
+ /* Correct the velocities */
+ mm = scaled_lagrange_multiplier[ll]*invmass[i]*invdt;
+ for (d = 0; d < DIM; d++)
+ {
+ v[ia[1]][d] += mm*rij[ll][d];
+ }
+ mm = scaled_lagrange_multiplier[ll]*invmass[j]*invdt;
+ for (d = 0; d < DIM; d++)
+ {
+ v[ia[2]][d] -= mm*rij[ll][d];
+ }
+ /* 16 flops */
+ }
+
+ /* constraint virial */
+ if (bCalcVir)
+ {
+ mm = scaled_lagrange_multiplier[ll];
+ for (d = 0; d < DIM; d++)
+ {
+ tmp = mm*rij[ll][d];
+ for (d2 = 0; d2 < DIM; d2++)
+ {
+ vir_r_m_dr[d][d2] -= tmp*rij[ll][d2];
+ }
+ }
+ /* 21 flops */
+ }
+
+ /* cshake and crattle produce Lagrange multipliers scaled by
+ the reciprocal of the constraint length, so fix that */
+ if (bFEP)
+ {
+ constraint_distance = L1*ip[type].constr.dA + lambda*ip[type].constr.dB;
+ }
+ else
+ {
+ constraint_distance = ip[type].constr.dA;
+ }
+ scaled_lagrange_multiplier[ll] *= constraint_distance;
+ }
+
+ return nit;
+}
+
+static void check_cons(FILE *log, int nc, rvec x[], rvec prime[], rvec v[],
+ t_iparams ip[], t_iatom *iatom,
+ real invmass[], int econq)
+{
+ t_iatom *ia;
+ int ai, aj;
+ int i;
+ real d, dp;
+ rvec dx, dv;
+
+ fprintf(log,
+ " i mi j mj before after should be\n");
+ ia = iatom;
+ for (i = 0; (i < nc); i++, ia += 3)
+ {
+ ai = ia[1];
+ aj = ia[2];
+ rvec_sub(x[ai], x[aj], dx);
+ d = norm(dx);
+
+ switch (econq)
+ {
+ case econqCoord:
+ rvec_sub(prime[ai], prime[aj], dx);
+ dp = norm(dx);
+ fprintf(log, "%5d %5.2f %5d %5.2f %10.5f %10.5f %10.5f\n",
+ ai+1, 1.0/invmass[ai],
+ aj+1, 1.0/invmass[aj], d, dp, ip[ia[0]].constr.dA);
+ break;
+ case econqVeloc:
+ rvec_sub(v[ai], v[aj], dv);
+ d = iprod(dx, dv);
+ rvec_sub(prime[ai], prime[aj], dv);
+ dp = iprod(dx, dv);
+ fprintf(log, "%5d %5.2f %5d %5.2f %10.5f %10.5f %10.5f\n",
+ ai+1, 1.0/invmass[ai],
+ aj+1, 1.0/invmass[aj], d, dp, 0.);
+ break;
+ }
+ }
+}
+
+gmx_bool bshakef(FILE *log, gmx_shakedata_t shaked,
+ real invmass[], int nblocks, int sblock[],
+ t_idef *idef, t_inputrec *ir, rvec x_s[], rvec prime[],
+ t_nrnb *nrnb, real *scaled_lagrange_multiplier, real lambda, real *dvdlambda,
+ real invdt, rvec *v, gmx_bool bCalcVir, tensor vir_r_m_dr,
+ gmx_bool bDumpOnError, int econq)
+{
+ t_iatom *iatoms;
+ real dt_2, dvdl;
+ int i, n0, ncon, blen, type, ll;
+ int tnit = 0, trij = 0;
+
+#ifdef DEBUG
+ fprintf(log, "nblocks=%d, sblock[0]=%d\n", nblocks, sblock[0]);
+#endif
+
+ ncon = idef->il[F_CONSTR].nr/3;
+
+ for (ll = 0; ll < ncon; ll++)
+ {
+ scaled_lagrange_multiplier[ll] = 0;
+ }
+
+ iatoms = &(idef->il[F_CONSTR].iatoms[sblock[0]]);
+ for (i = 0; (i < nblocks); )
+ {
+ blen = (sblock[i+1]-sblock[i]);
+ blen /= 3;
+ n0 = vec_shakef(log, shaked, invmass, blen, idef->iparams,
+ iatoms, ir->shake_tol, x_s, prime, shaked->omega,
+ ir->efep != efepNO, lambda, scaled_lagrange_multiplier, invdt, v, bCalcVir, vir_r_m_dr,
+ econq);
+
+#ifdef DEBUGSHAKE
+ check_cons(log, blen, x_s, prime, v, idef->iparams, iatoms, invmass, econq);
+#endif
+
+ if (n0 == 0)
+ {
+ if (bDumpOnError && log)
+ {
+ {
+ check_cons(log, blen, x_s, prime, v, idef->iparams, iatoms, invmass, econq);
+ }
+ }
+ return FALSE;
+ }
+ tnit += n0*blen;
+ trij += blen;
+ iatoms += 3*blen; /* Increment pointer! */
+ scaled_lagrange_multiplier += blen;
+ i++;
+ }
+ /* only for position part? */
+ if (econq == econqCoord)
+ {
+ if (ir->efep != efepNO)
+ {
+ real bondA, bondB;
+ /* TODO This should probably use invdt, so that sd integrator scaling works properly */
+ dt_2 = 1/sqr(ir->delta_t);
+ dvdl = 0;
+ for (ll = 0; ll < ncon; ll++)
+ {
+ type = idef->il[F_CONSTR].iatoms[3*ll];
+
+ /* Per equations in the manual, dv/dl = -2 \sum_ll lagrangian_ll * r_ll * (d_B - d_A) */
+ /* The vector scaled_lagrange_multiplier[ll] contains the value -2 r_ll eta_ll (eta_ll is the
+ estimate of the Langrangian, definition on page 336 of Ryckaert et al 1977),
+ so the pre-factors are already present. */
+ bondA = idef->iparams[type].constr.dA;
+ bondB = idef->iparams[type].constr.dB;
+ dvdl += scaled_lagrange_multiplier[ll] * dt_2 * (bondB - bondA);
+ }
+ *dvdlambda += dvdl;
+ }
+ }
+#ifdef DEBUG
+ fprintf(log, "tnit: %5d omega: %10.5f\n", tnit, omega);
+#endif
+ if (ir->bShakeSOR)
+ {
+ if (tnit > shaked->gamma)
+ {
+ shaked->delta *= -0.5;
+ }
+ shaked->omega += shaked->delta;
+ shaked->gamma = tnit;
+ }
+ inc_nrnb(nrnb, eNR_SHAKE, tnit);
+ inc_nrnb(nrnb, eNR_SHAKE_RIJ, trij);
+ if (v)
+ {
+ inc_nrnb(nrnb, eNR_CONSTR_V, trij*2);
+ }
+ if (bCalcVir)
+ {
+ inc_nrnb(nrnb, eNR_CONSTR_VIR, trij);
+ }
+
+ return TRUE;
+}
+
+void crattle(atom_id iatom[], int ncon, int *nnit, int maxnit,
+ real constraint_distance_squared[], real vp[], real rij[], real m2[], real omega,
+ real invmass[], real distance_squared_tolerance[], real scaled_lagrange_multiplier[],
+ int *nerror, real invdt)
+{
+ /*
+ * r.c. van schaik and w.f. van gunsteren
+ * eth zuerich
+ * june 1992
+ * Adapted for use with Gromacs by David van der Spoel november 92 and later.
+ * rattle added by M.R. Shirts, April 2004, from code written by Jay Ponder in TINKER
+ * second part of rattle algorithm
+ */
+
+ int ll, i, j, i3, j3, l3;
+ int ix, iy, iz, jx, jy, jz;
+ real constraint_distance_squared_ll;
+ real vpijd, vx, vy, vz, acor, fac, im, jm;
+ real xh, yh, zh, rijx, rijy, rijz;
+ int nit, error, nconv;
+ real iconvf;
+
+ // TODO nconv is used solely as a boolean, so we should write the
+ // code like that
+ error = 0;
+ nconv = 1;
+ for (nit = 0; (nit < maxnit) && (nconv != 0) && (error == 0); nit++)
+ {
+ nconv = 0;
+ for (ll = 0; (ll < ncon) && (error == 0); ll++)
+ {
+ l3 = 3*ll;
+ rijx = rij[l3+XX];
+ rijy = rij[l3+YY];
+ rijz = rij[l3+ZZ];
+ i = iatom[l3+1];
+ j = iatom[l3+2];
+ i3 = 3*i;
+ j3 = 3*j;
+ ix = i3+XX;
+ iy = i3+YY;
+ iz = i3+ZZ;
+ jx = j3+XX;
+ jy = j3+YY;
+ jz = j3+ZZ;
+ vx = vp[ix]-vp[jx];
+ vy = vp[iy]-vp[jy];
+ vz = vp[iz]-vp[jz];
+
+ vpijd = vx*rijx+vy*rijy+vz*rijz;
+ constraint_distance_squared_ll = constraint_distance_squared[ll];
+
+ /* iconv is zero when the error is smaller than a bound */
+ iconvf = fabs(vpijd)*(distance_squared_tolerance[ll]/invdt);
+
+ if (iconvf > 1)
+ {
+ nconv = static_cast<int>(iconvf);
+ fac = omega*2.0*m2[ll]/constraint_distance_squared_ll;
+ acor = -fac*vpijd;
+ scaled_lagrange_multiplier[ll] += acor;
+ xh = rijx*acor;
+ yh = rijy*acor;
+ zh = rijz*acor;
+
+ im = invmass[i];
+ jm = invmass[j];
+
+ vp[ix] += xh*im;
+ vp[iy] += yh*im;
+ vp[iz] += zh*im;
+ vp[jx] -= xh*jm;
+ vp[jy] -= yh*jm;
+ vp[jz] -= zh*jm;
+ }
+ }
+ }
+ *nnit = nit;
+ *nerror = error;
+}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/shellfc.h"
+#include <stdlib.h>
#include <string.h>
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "txtdump.h"
-#include "force.h"
-#include "mdrun.h"
-#include "mdatoms.h"
-#include "vsite.h"
-#include "network.h"
-#include "names.h"
-#include "constr.h"
-#include "domdec.h"
-#include "physics.h"
-#include "shellfc.h"
-#include "mtop_util.h"
-#include "chargegroup.h"
-#include "macros.h"
+#include <algorithm>
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
int nnucl;
real mass[], gmx_mtop_t *mtop, gmx_bool bInit)
{
int i, m, s1, n1, n2, n3;
- real dt_1, dt_2, dt_3, fudge, tm, m1, m2, m3;
+ real dt_1, fudge, tm, m1, m2, m3;
rvec *ptr;
gmx_mtop_atomlookup_t alook = NULL;
t_atom *atom;
else
{
/* Not the correct masses with FE, but it is just a prediction... */
- m1 = atom[n1].m;
- m2 = atom[n2].m;
+ gmx_mtop_atomnr_to_atom(alook, n1, &atom);
+ m1 = atom->m;
+ gmx_mtop_atomnr_to_atom(alook, n2, &atom);
+ m2 = atom->m;
}
tm = dt_1/(m1+m2);
for (m = 0; (m < DIM); m++)
int *shell_index = NULL, *at2cg;
t_atom *atom;
int n[eptNR], ns, nshell, nsi;
- int i, j, nmol, type, mb, mt, a_offset, cg, mol, ftype, nra;
+ int i, j, nmol, type, mb, a_offset, cg, mol, ftype, nra;
real qS, alpha;
int aS, aN = 0; /* Shell and nucleus */
int bondtypes[] = { F_BONDS, F_HARMONIC, F_CUBICBONDS, F_POLARIZATION, F_ANHARM_POL, F_WATER_POL };
step_scale_increment = 0.2,
step_scale_max = 1.2,
step_scale_multiple = (step_scale_max - step_scale_min) / step_scale_increment;
- int i, shell, d;
- real dx, df, k_est;
+ int i, shell, d;
+ real dx, df, k_est;
+ const real zero = 0;
#ifdef PRINT_STEP
- real step_min, step_max;
+ real step_min, step_max;
step_min = 1e30;
step_max = 0;
{
s[i].step[d] = s[i].k_1;
#ifdef PRINT_STEP
- step_min = min(step_min, s[i].step[d]);
- step_max = max(step_max, s[i].step[d]);
+ step_min = std::min(step_min, s[i].step[d]);
+ step_max = std::max(step_max, s[i].step[d]);
#endif
}
}
* step_scale_multiple * s[i].step[d] */
s[i].step[d] =
step_scale_min * s[i].step[d] +
- step_scale_increment * min(step_scale_multiple * s[i].step[d], max(k_est, 0));
+ step_scale_increment * std::min(step_scale_multiple * s[i].step[d], std::max(k_est, zero));
}
else
{
}
}
#ifdef PRINT_STEP
- step_min = min(step_min, s[i].step[d]);
- step_max = max(step_max, s[i].step[d]);
+ step_min = std::min(step_min, s[i].step[d]);
+ step_max = std::max(step_max, s[i].step[d]);
#endif
}
}
{
rvec *xnold, *xnew;
double w_dt;
- int gf, ga, gt;
- real dt, scale;
+ real dt;
int n, d;
unsigned short *ptype;
- rvec p, dx;
if (DOMAINDECOMP(cr))
{
}
}
}
- constrain(log, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, 1.0, md,
+ constrain(log, FALSE, FALSE, constr, idef, ir, cr, step, 0, 1.0, md,
x, xnold-start, NULL, bMolPBC, box,
lambda[efptBONDED], &(dvdlambda[efptBONDED]),
- NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
- constrain(log, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, 1.0, md,
+ NULL, NULL, nrnb, econqCoord);
+ constrain(log, FALSE, FALSE, constr, idef, ir, cr, step, 0, 1.0, md,
x, xnew-start, NULL, bMolPBC, box,
lambda[efptBONDED], &(dvdlambda[efptBONDED]),
- NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
+ NULL, NULL, nrnb, econqCoord);
for (n = start; n < end; n++)
{
}
/* Project the acceleration on the old bond directions */
- constrain(log, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, 1.0, md,
+ constrain(log, FALSE, FALSE, constr, idef, ir, cr, step, 0, 1.0, md,
x_old, xnew-start, acc_dir, bMolPBC, box,
lambda[efptBONDED], &(dvdlambda[efptBONDED]),
- NULL, NULL, nrnb, econqDeriv_FlexCon, FALSE, 0, 0);
+ NULL, NULL, nrnb, econqDeriv_FlexCon);
}
int relax_shell_flexcon(FILE *fplog, t_commrec *cr, gmx_bool bVerbose,
t_idef *idef;
rvec *pos[2], *force[2], *acc_dir = NULL, *x_old = NULL;
real Epot[2], df[2];
- rvec dx;
real sf_dir, invdt;
- real ftol, xiH, xiS, dum = 0;
+ real ftol, dum = 0;
char sbuf[22];
gmx_bool bCont, bInit;
int nat, dd_ac0, dd_ac1 = 0, i;
int start = 0, homenr = md->homenr, end = start+homenr, cg0, cg1;
- int nflexcon, g, number_steps, d, Min = 0, count = 0;
+ int nflexcon, number_steps, d, Min = 0, count = 0;
#define Try (1-Min) /* At start Try = 1 */
bCont = (mdstep == inputrec->init_step) && inputrec->bContinuation;
if (nflexcon > 0)
{
dd_get_constraint_range(cr->dd, &dd_ac0, &dd_ac1);
- nat = max(nat, dd_ac1);
+ nat = std::max(nat, dd_ac1);
}
}
else
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/sim_util.h"
+
+#include "config.h"
#include <assert.h>
#include <math.h>
#include <stdio.h>
#include <string.h>
-#ifdef HAVE_SYS_TIME_H
-#include <sys/time.h>
-#endif
-#include "typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "names.h"
-#include "txtdump.h"
-#include "pbc.h"
-#include "chargegroup.h"
-#include "vec.h"
-#include "nrnb.h"
-#include "mshift.h"
-#include "mdrun.h"
-#include "sim_util.h"
-#include "update.h"
-#include "physics.h"
-#include "main.h"
-#include "mdatoms.h"
-#include "force.h"
-#include "bondf.h"
-#include "pme.h"
-#include "disre.h"
-#include "orires.h"
-#include "network.h"
-#include "calcmu.h"
-#include "constr.h"
-#include "xvgr.h"
-#include "copyrite.h"
-#include "domdec.h"
-#include "genborn.h"
-#include "nbnxn_atomdata.h"
-#include "nbnxn_search.h"
-#include "nbnxn_kernels/nbnxn_kernel_ref.h"
-#include "nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
-#include "nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
-#include "nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
-#include "nonbonded.h"
-#include "../gmxlib/nonbonded/nb_kernel.h"
-#include "../gmxlib/nonbonded/nb_free_energy.h"
-
-#include "gromacs/timing/wallcycle.h"
-#include "gromacs/timing/walltime_accounting.h"
-#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/domdec/domdec.h"
#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/ewald/pme.h"
+#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/calcmu.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_atomdata.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/pulling/pull_rotation.h"
-#include "gromacs/imd/imd.h"
-#include "adress.h"
-#include "qmmm.h"
-
-#include "gmx_omp_nthreads.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/sysinfo.h"
-#include "nbnxn_cuda_data_mgmt.h"
-#include "nbnxn_cuda/nbnxn_cuda.h"
+#include "adress.h"
void print_time(FILE *out,
gmx_walltime_accounting_t walltime_accounting,
tensor vir_part, t_graph *graph, matrix box,
t_nrnb *nrnb, const t_forcerec *fr, int ePBC)
{
- int i, j;
- tensor virtest;
+ int i;
/* The short-range virial from surrounding boxes */
clear_mat(vir_part);
}
}
-static void posres_wrapper(FILE *fplog,
- int flags,
- gmx_bool bSepDVDL,
- t_inputrec *ir,
- t_nrnb *nrnb,
- gmx_localtop_t *top,
- matrix box, rvec x[],
- gmx_enerdata_t *enerd,
- real *lambda,
- t_forcerec *fr)
-{
- t_pbc pbc;
- real v, dvdl;
- int i;
-
- /* Position restraints always require full pbc */
- set_pbc(&pbc, ir->ePBC, box);
- dvdl = 0;
- v = posres(top->idef.il[F_POSRES].nr, top->idef.il[F_POSRES].iatoms,
- top->idef.iparams_posres,
- (const rvec*)x, fr->f_novirsum, fr->vir_diag_posres,
- ir->ePBC == epbcNONE ? NULL : &pbc,
- lambda[efptRESTRAINT], &dvdl,
- fr->rc_scaling, fr->ePBC, fr->posres_com, fr->posres_comB);
- if (bSepDVDL)
- {
- gmx_print_sepdvdl(fplog, interaction_function[F_POSRES].longname, v, dvdl);
- }
- enerd->term[F_POSRES] += v;
- /* If just the force constant changes, the FEP term is linear,
- * but if k changes, it is not.
- */
- enerd->dvdl_nonlin[efptRESTRAINT] += dvdl;
- inc_nrnb(nrnb, eNR_POSRES, top->idef.il[F_POSRES].nr/2);
-
- if ((ir->fepvals->n_lambda > 0) && (flags & GMX_FORCE_DHDL))
- {
- for (i = 0; i < enerd->n_lambda; i++)
- {
- real dvdl_dum, lambda_dum;
-
- lambda_dum = (i == 0 ? lambda[efptRESTRAINT] : ir->fepvals->all_lambda[efptRESTRAINT][i-1]);
- v = posres(top->idef.il[F_POSRES].nr, top->idef.il[F_POSRES].iatoms,
- top->idef.iparams_posres,
- (const rvec*)x, NULL, NULL,
- ir->ePBC == epbcNONE ? NULL : &pbc, lambda_dum, &dvdl,
- fr->rc_scaling, fr->ePBC, fr->posres_com, fr->posres_comB);
- enerd->enerpart_lambda[i] += v;
- }
- }
-}
-
-static void fbposres_wrapper(t_inputrec *ir,
- t_nrnb *nrnb,
- gmx_localtop_t *top,
- matrix box, rvec x[],
- gmx_enerdata_t *enerd,
- t_forcerec *fr)
-{
- t_pbc pbc;
- real v;
-
- /* Flat-bottomed position restraints always require full pbc */
- set_pbc(&pbc, ir->ePBC, box);
- v = fbposres(top->idef.il[F_FBPOSRES].nr, top->idef.il[F_FBPOSRES].iatoms,
- top->idef.iparams_fbposres,
- (const rvec*)x, fr->f_novirsum, fr->vir_diag_posres,
- ir->ePBC == epbcNONE ? NULL : &pbc,
- fr->rc_scaling, fr->ePBC, fr->posres_com);
- enerd->term[F_FBPOSRES] += v;
- inc_nrnb(nrnb, eNR_FBPOSRES, top->idef.il[F_FBPOSRES].nr/2);
-}
-
-static void pull_potential_wrapper(FILE *fplog,
- gmx_bool bSepDVDL,
- t_commrec *cr,
+static void pull_potential_wrapper(t_commrec *cr,
t_inputrec *ir,
matrix box, rvec x[],
rvec f[],
enerd->term[F_COM_PULL] +=
pull_potential(ir->ePull, ir->pull, mdatoms, &pbc,
cr, t, lambda[efptRESTRAINT], x, f, vir_force, &dvdl);
- if (bSepDVDL)
- {
- gmx_print_sepdvdl(fplog, "Com pull", enerd->term[F_COM_PULL], dvdl);
- }
enerd->dvdl_lin[efptRESTRAINT] += dvdl;
wallcycle_stop(wcycle, ewcPULLPOT);
}
-static void pme_receive_force_ener(FILE *fplog,
- gmx_bool bSepDVDL,
- t_commrec *cr,
+static void pme_receive_force_ener(t_commrec *cr,
gmx_wallcycle_t wcycle,
gmx_enerdata_t *enerd,
t_forcerec *fr)
{
- real e_q, e_lj, v, dvdl_q, dvdl_lj;
+ real e_q, e_lj, dvdl_q, dvdl_lj;
float cycles_ppdpme, cycles_seppme;
cycles_ppdpme = wallcycle_stop(wcycle, ewcPPDURINGPME);
gmx_pme_receive_f(cr, fr->f_novirsum, fr->vir_el_recip, &e_q,
fr->vir_lj_recip, &e_lj, &dvdl_q, &dvdl_lj,
&cycles_seppme);
- if (bSepDVDL)
- {
- gmx_print_sepdvdl(fplog, "Electrostatic PME mesh", e_q, dvdl_q);
- gmx_print_sepdvdl(fplog, "Lennard-Jones PME mesh", e_lj, dvdl_lj);
- }
enerd->term[F_COUL_RECIP] += e_q;
enerd->term[F_LJ_RECIP] += e_lj;
enerd->dvdl_lin[efptCOUL] += dvdl_q;
t_nrnb *nrnb,
gmx_wallcycle_t wcycle)
{
- int nnbl, kernel_type, enr_nbnxn_kernel_ljc, enr_nbnxn_kernel_lj;
- char *env;
+ int enr_nbnxn_kernel_ljc, enr_nbnxn_kernel_lj;
nonbonded_verlet_group_t *nbvg;
gmx_bool bCUDA;
wallcycle_sub_stop(wcycle, ewcsNONBONDED);
}
+gmx_bool use_GPU(const nonbonded_verlet_t *nbv)
+{
+ return nbv != NULL && nbv->bUseGPU;
+}
+
void do_force_cutsVERLET(FILE *fplog, t_commrec *cr,
t_inputrec *inputrec,
gmx_int64_t step, t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_bool bBornRadii,
int flags)
{
- int cg0, cg1, i, j;
+ int cg1, i, j;
int start, homenr;
- int nb_kernel_type;
double mu[2*DIM];
- gmx_bool bSepDVDL, bStateChanged, bNS, bFillGrid, bCalcCGCM, bBS;
+ gmx_bool bStateChanged, bNS, bFillGrid, bCalcCGCM;
gmx_bool bDoLongRange, bDoForces, bSepLRF, bUseGPU, bUseOrEmulGPU;
gmx_bool bDiffKernels = FALSE;
- matrix boxs;
rvec vzero, box_diag;
- real e, v, dvdl;
float cycles_pme, cycles_force, cycles_wait_gpu;
nonbonded_verlet_t *nbv;
cycles_force = 0;
cycles_wait_gpu = 0;
nbv = fr->nbv;
- nb_kernel_type = fr->nbv->grp[0].kernel_type;
start = 0;
homenr = mdatoms->homenr;
- bSepDVDL = (fr->bSepDVDL && do_per_step(step, inputrec->nstlog));
-
clear_mat(vir_force);
- cg0 = 0;
if (DOMAINDECOMP(cr))
{
cg1 = cr->dd->ncg_tot;
#ifdef GMX_MPI
if (!(cr->duty & DUTY_PME))
{
+ gmx_bool bBS;
+ matrix boxs;
+
/* Send particle coordinates to the pme nodes.
* Since this is only implemented for domain decomposition
* and domain decomposition does not use the graph,
}
/* We calculate the non-bonded forces, when done on the CPU, here.
- * We do this before calling do_force_lowlevel, as in there bondeds
- * forces are calculated before PME, which does communication.
- * With this order, non-bonded and bonded force calculation imbalance
- * can be balanced out by the domain decomposition load balancing.
+ * We do this before calling do_force_lowlevel, because in that
+ * function, the listed forces are calculated before PME, which
+ * does communication. With this order, non-bonded and listed
+ * force calculation imbalance can be balanced out by the domain
+ * decomposition load balancing.
*/
if (!bUseOrEmulGPU)
update_QMMMrec(cr, fr, x, mdatoms, box, top);
}
- if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0)
- {
- posres_wrapper(fplog, flags, bSepDVDL, inputrec, nrnb, top, box, x,
- enerd, lambda, fr);
- }
-
- if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_FBPOSRES].nr > 0)
- {
- fbposres_wrapper(inputrec, nrnb, top, box, x, enerd, fr);
- }
-
/* Compute the bonded and non-bonded energies and optionally forces */
- do_force_lowlevel(fplog, step, fr, inputrec, &(top->idef),
+ do_force_lowlevel(fr, inputrec, &(top->idef),
cr, nrnb, wcycle, mdatoms,
x, hist, f, bSepLRF ? fr->f_twin : f, enerd, fcd, top, fr->born,
- &(top->atomtypes), bBornRadii, box,
+ bBornRadii, box,
inputrec->fepvals, lambda, graph, &(top->excls), fr->mu_tot,
flags, &cycles_pme);
/* Since the COM pulling is always done mass-weighted, no forces are
* applied to vsites and this call can be done after vsite spreading.
*/
- pull_potential_wrapper(fplog, bSepDVDL, cr, inputrec, box, x,
+ pull_potential_wrapper(cr, inputrec, box, x,
f, vir_force, mdatoms, enerd, lambda, t,
wcycle);
}
/* In case of node-splitting, the PP nodes receive the long-range
* forces, virial and energy from the PME nodes here.
*/
- pme_receive_force_ener(fplog, bSepDVDL, cr, wcycle, enerd, fr);
+ pme_receive_force_ener(cr, wcycle, enerd, fr);
}
if (bDoForces)
int cg0, cg1, i, j;
int start, homenr;
double mu[2*DIM];
- gmx_bool bSepDVDL, bStateChanged, bNS, bFillGrid, bCalcCGCM, bBS;
- gmx_bool bDoLongRangeNS, bDoForces, bDoPotential, bSepLRF;
+ gmx_bool bStateChanged, bNS, bFillGrid, bCalcCGCM;
+ gmx_bool bDoLongRangeNS, bDoForces, bSepLRF;
gmx_bool bDoAdressWF;
- matrix boxs;
- rvec vzero, box_diag;
- real e, v, dvdlambda[efptNR];
t_pbc pbc;
float cycles_pme, cycles_force;
start = 0;
homenr = mdatoms->homenr;
- bSepDVDL = (fr->bSepDVDL && do_per_step(step, inputrec->nstlog));
-
clear_mat(vir_force);
cg0 = 0;
bFillGrid = (bNS && bStateChanged);
bCalcCGCM = (bFillGrid && !DOMAINDECOMP(cr));
bDoForces = (flags & GMX_FORCE_FORCES);
- bDoPotential = (flags & GMX_FORCE_ENERGY);
bSepLRF = ((inputrec->nstcalclr > 1) && bDoForces &&
(flags & GMX_FORCE_SEPLRF) && (flags & GMX_FORCE_DO_LR));
#ifdef GMX_MPI
if (!(cr->duty & DUTY_PME))
{
+ gmx_bool bBS;
+ matrix boxs;
+
/* Send particle coordinates to the pme nodes.
* Since this is only implemented for domain decomposition
* and domain decomposition does not use the graph,
update_QMMMrec(cr, fr, x, mdatoms, box, top);
}
- if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0)
- {
- posres_wrapper(fplog, flags, bSepDVDL, inputrec, nrnb, top, box, x,
- enerd, lambda, fr);
- }
-
- if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_FBPOSRES].nr > 0)
- {
- fbposres_wrapper(inputrec, nrnb, top, box, x, enerd, fr);
- }
-
/* Compute the bonded and non-bonded energies and optionally forces */
- do_force_lowlevel(fplog, step, fr, inputrec, &(top->idef),
+ do_force_lowlevel(fr, inputrec, &(top->idef),
cr, nrnb, wcycle, mdatoms,
x, hist, f, bSepLRF ? fr->f_twin : f, enerd, fcd, top, fr->born,
- &(top->atomtypes), bBornRadii, box,
+ bBornRadii, box,
inputrec->fepvals, lambda,
graph, &(top->excls), fr->mu_tot,
flags,
if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F)
{
- pull_potential_wrapper(fplog, bSepDVDL, cr, inputrec, box, x,
+ pull_potential_wrapper(cr, inputrec, box, x,
f, vir_force, mdatoms, enerd, lambda, t,
wcycle);
}
/* In case of node-splitting, the PP nodes receive the long-range
* forces, virial and energy from the PME nodes here.
*/
- pme_receive_force_ener(fplog, bSepDVDL, cr, wcycle, enerd, fr);
+ pme_receive_force_ener(cr, wcycle, enerd, fr);
}
if (bDoForces)
/* constrain the current position */
constrain(NULL, TRUE, FALSE, constr, &(top->idef),
- ir, NULL, cr, step, 0, 1.0, md,
+ ir, cr, step, 0, 1.0, md,
state->x, state->x, NULL,
fr->bMolPBC, state->box,
state->lambda[efptBONDED], &dvdl_dum,
- NULL, NULL, nrnb, econqCoord,
- ir->epc == epcMTTK, state->veta, state->veta);
+ NULL, NULL, nrnb, econqCoord);
if (EI_VV(ir->eI))
{
/* constrain the inital velocity, and save it */
/* also may be useful if we need the ekin from the halfstep for velocity verlet */
- /* might not yet treat veta correctly */
constrain(NULL, TRUE, FALSE, constr, &(top->idef),
- ir, NULL, cr, step, 0, 1.0, md,
+ ir, cr, step, 0, 1.0, md,
state->x, state->v, state->v,
fr->bMolPBC, state->box,
state->lambda[efptBONDED], &dvdl_dum,
- NULL, NULL, nrnb, econqVeloc,
- ir->epc == epcMTTK, state->veta, state->veta);
+ NULL, NULL, nrnb, econqVeloc);
}
/* constrain the inital velocities at t-dt/2 */
if (EI_STATE_VELOCITY(ir->eI) && ir->eI != eiVV)
}
dvdl_dum = 0;
constrain(NULL, TRUE, FALSE, constr, &(top->idef),
- ir, NULL, cr, step, -1, 1.0, md,
+ ir, cr, step, -1, 1.0, md,
state->x, savex, NULL,
fr->bMolPBC, state->box,
state->lambda[efptBONDED], &dvdl_dum,
- state->v, NULL, nrnb, econqCoord,
- ir->epc == epcMTTK, state->veta, state->veta);
+ state->v, NULL, nrnb, econqCoord);
for (i = start; i < end; i++)
{
double invscale, invscale2, invscale3;
double r, ea, eb, ec, pa, pb, pc, pd;
double y0, f, g, h;
- int ri, offset, tabfactor;
+ int ri, offset;
+ double tabfactor;
invscale = 1.0/scale;
invscale2 = invscale*invscale;
void calc_enervirdiff(FILE *fplog, int eDispCorr, t_forcerec *fr)
{
- double eners[2], virs[2], enersum, virsum, y0, f, g, h;
- double r0, r1, r, rc3, rc9, ea, eb, ec, pa, pb, pc, pd;
- double invscale, invscale2, invscale3;
- int ri0, ri1, ri, i, offstart, offset;
- real scale, *vdwtab, tabfactor, tmp;
+ double eners[2], virs[2], enersum, virsum;
+ double r0, rc3, rc9;
+ int ri0, ri1, i;
+ real scale, *vdwtab;
fr->enershiftsix = 0;
fr->enershifttwelve = 0;
vdwtab = fr->nblists[0].table_vdw.data;
/* Round the cut-offs to exact table values for precision */
- ri0 = floor(fr->rvdw_switch*scale);
- ri1 = ceil(fr->rvdw*scale);
+ ri0 = static_cast<int>(floor(fr->rvdw_switch*scale));
+ ri1 = static_cast<int>(ceil(fr->rvdw*scale));
/* The code below has some support for handling force-switching, i.e.
* when the force (instead of potential) is switched over a limited
ri0 = (fr->vdw_modifier == eintmodPOTSHIFT) ? ri1 : ri0;
r0 = ri0/scale;
- r1 = ri1/scale;
rc3 = r0*r0*r0;
rc9 = rc3*rc3*rc3;
}
}
-void calc_dispcorr(FILE *fplog, t_inputrec *ir, t_forcerec *fr,
- gmx_int64_t step, int natoms,
+void calc_dispcorr(t_inputrec *ir, t_forcerec *fr,
+ int natoms,
matrix box, real lambda, tensor pres, tensor virial,
real *prescorr, real *enercorr, real *dvdlcorr)
{
}
}
- if (fr->bSepDVDL && do_per_step(step, ir->nstlog))
- {
- gmx_print_sepdvdl(fplog, "Dispersion correction", *enercorr, dvdlambda);
- }
if (fr->efep != efepNO)
{
*dvdlcorr += dvdlambda;
t_inputrec *inputrec,
t_nrnb nrnb[], gmx_wallcycle_t wcycle,
gmx_walltime_accounting_t walltime_accounting,
- wallclock_gpu_t *gputimes,
+ nonbonded_verlet_t *nbv,
gmx_bool bWriteStat)
{
- int i, j;
t_nrnb *nrnb_tot = NULL;
- real delta_t;
- double nbfs, mflop;
+ double delta_t = 0;
+ double nbfs = 0, mflop = 0;
double elapsed_time,
elapsed_time_over_all_ranks,
elapsed_time_over_all_threads,
if (SIMMASTER(cr))
{
+ wallclock_gpu_t* gputimes = use_GPU(nbv) ?
+ nbnxn_cuda_get_timings(nbv->cu_nbv) : NULL;
wallcycle_print(fplog, cr->nnodes, cr->npmenodes,
elapsed_time_over_all_ranks,
wcycle, gputimes);
{
delta_t = inputrec->delta_t;
}
- else
- {
- delta_t = 0;
- }
if (fplog)
{
gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags,
gmx_wallcycle_t wcycle)
{
- int i, j, n;
- real tmpt, mod;
+ int i;
/* Initial values */
*t = *t0 = ir->init_t;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <string.h>
#include <stdio.h>
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "sysstuff.h"
-#include "gmx_fatal.h"
-#include "network.h"
-#include "txtdump.h"
-#include "names.h"
-#include "physics.h"
-#include "vec.h"
-#include "gromacs/math/utilities.h"
-#include "main.h"
-#include "force.h"
-#include "vcm.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
-#include "network.h"
-#include "rbin.h"
-#include "tgroup.h"
-#include "gromacs/fileio/xtcio.h"
+#include <string.h>
+
+#include "gromacs/domdec/domdec.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/trnio.h"
-#include "domdec.h"
-#include "constr.h"
-#include "checkpoint.h"
-#include "xvgr.h"
-#include "md_support.h"
-#include "mdrun.h"
-#include "sim_util.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/rbin.h"
+#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vcm.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
typedef struct gmx_global_stat
{
int nener, j;
real *rmsd_data = NULL;
double nb;
- gmx_bool bVV, bTemp, bEner, bPres, bConstrVir, bEkinAveVel, bFirstIterate, bReadEkin;
+ gmx_bool bVV, bTemp, bEner, bPres, bConstrVir, bEkinAveVel, bReadEkin;
bVV = EI_VV(inputrec->eI);
bTemp = flags & CGLO_TEMPERATURE;
bEner = flags & CGLO_ENERGY;
bPres = (flags & CGLO_PRESSURE);
bConstrVir = (flags & CGLO_CONSTRAINT);
- bFirstIterate = (flags & CGLO_FIRSTITERATE);
bEkinAveVel = (inputrec->eI == eiVV || (inputrec->eI == eiVVAK && bPres));
bReadEkin = (flags & CGLO_READEKIN);
}
where();
- if ((bPres || !bVV) && bFirstIterate)
+ if (bPres || !bVV)
{
ifv = add_binr(rb, DIM*DIM, fvir[0]);
}
if (bEner)
{
where();
- if (bFirstIterate)
- {
- ie = add_binr(rb, nener, copyenerd);
- }
+ ie = add_binr(rb, nener, copyenerd);
where();
if (constr)
{
where();
}
- if (bFirstIterate)
+ for (j = 0; (j < egNR); j++)
{
- for (j = 0; (j < egNR); j++)
+ inn[j] = add_binr(rb, enerd->grpp.nener, enerd->grpp.ener[j]);
+ }
+ where();
+ if (inputrec->efep != efepNO)
+ {
+ idvdll = add_bind(rb, efptNR, enerd->dvdl_lin);
+ idvdlnl = add_bind(rb, efptNR, enerd->dvdl_nonlin);
+ if (enerd->n_lambda > 0)
{
- inn[j] = add_binr(rb, enerd->grpp.nener, enerd->grpp.ener[j]);
- }
- where();
- if (inputrec->efep != efepNO)
- {
- idvdll = add_bind(rb, efptNR, enerd->dvdl_lin);
- idvdlnl = add_bind(rb, efptNR, enerd->dvdl_nonlin);
- if (enerd->n_lambda > 0)
- {
- iepl = add_bind(rb, enerd->n_lambda, enerd->enerpart_lambda);
- }
+ iepl = add_bind(rb, enerd->n_lambda, enerd->enerpart_lambda);
}
}
}
where();
}
}
- if ((bPres || !bVV) && bFirstIterate)
+ if (bPres || !bVV)
{
extract_binr(rb, ifv, DIM*DIM, fvir[0]);
}
if (bEner)
{
- if (bFirstIterate)
+ extract_binr(rb, ie, nener, copyenerd);
+ if (rmsd_data)
{
- extract_binr(rb, ie, nener, copyenerd);
- if (rmsd_data)
- {
- extract_binr(rb, irmsd, inputrec->eI == eiSD2 ? 3 : 2, rmsd_data);
- }
- if (!NEED_MUTOT(*inputrec))
- {
- extract_binr(rb, imu, DIM, mu_tot);
- }
+ extract_binr(rb, irmsd, inputrec->eI == eiSD2 ? 3 : 2, rmsd_data);
+ }
+ if (!NEED_MUTOT(*inputrec))
+ {
+ extract_binr(rb, imu, DIM, mu_tot);
+ }
- for (j = 0; (j < egNR); j++)
+ for (j = 0; (j < egNR); j++)
+ {
+ extract_binr(rb, inn[j], enerd->grpp.nener, enerd->grpp.ener[j]);
+ }
+ if (inputrec->efep != efepNO)
+ {
+ extract_bind(rb, idvdll, efptNR, enerd->dvdl_lin);
+ extract_bind(rb, idvdlnl, efptNR, enerd->dvdl_nonlin);
+ if (enerd->n_lambda > 0)
{
- extract_binr(rb, inn[j], enerd->grpp.nener, enerd->grpp.ener[j]);
+ extract_bind(rb, iepl, enerd->n_lambda, enerd->enerpart_lambda);
}
- if (inputrec->efep != efepNO)
- {
- extract_bind(rb, idvdll, efptNR, enerd->dvdl_lin);
- extract_bind(rb, idvdlnl, efptNR, enerd->dvdl_nonlin);
- if (enerd->n_lambda > 0)
- {
- extract_bind(rb, iepl, enerd->n_lambda, enerd->enerpart_lambda);
- }
- }
- if (DOMAINDECOMP(cr))
+ }
+ if (DOMAINDECOMP(cr))
+ {
+ extract_bind(rb, inb, 1, &nb);
+ if ((int)(nb + 0.5) != cr->dd->nbonded_global)
{
- extract_bind(rb, inb, 1, &nb);
- if ((int)(nb + 0.5) != cr->dd->nbonded_global)
- {
- dd_print_missing_interactions(fplog, cr, (int)(nb + 0.5), top_global, state_local);
- }
+ dd_print_missing_interactions(fplog, cr, (int)(nb + 0.5), top_global, state_local);
}
- where();
-
- filter_enerdterm(copyenerd, FALSE, enerd->term, bTemp, bPres, bEner);
}
+ where();
+
+ filter_enerdterm(copyenerd, FALSE, enerd->term, bTemp, bPres, bEner);
}
if (vcm)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/tables.h"
#include <math.h>
+
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
-#include "typedefs.h"
-#include "names.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
-#include "xvgr.h"
-#include "vec.h"
-#include "main.h"
-#include "network.h"
-#include "physics.h"
-#include "force.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "macros.h"
-#include "tables.h"
/* All the possible (implemented) table functions */
enum {
}
#ifdef DEBUG_SWITCH
- gmx_fio_fclose(fp);
+ xvgrclose(fp);
#endif
}
evaluate_table(table.data, 4*k, 12, table.scale, x0, &y0, &yp);
fprintf(fp, "%15.10e %15.10e %15.10e\n", x0, y0, yp);
}
- gmx_fio_fclose(fp);
+ xvgrclose(fp);
}
done_tabledata(&(td[k]));
}
fprintf(fp, "%15.10e %15.10e %15.10e\n", x0, y0, yp);
}
- gmx_fio_fclose(fp);
+ xvgrclose(fp);
}
/*
fprintf(fp, "%15.10e %15.10e %15.10e\n", x0, y0, yp);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
done_tabledata(&(td[0]));
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+gmx_add_unit_test(MdlibUnitTest mdlib-test
+ shake.cpp)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include <assert.h>
+
+#include <vector>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/types/simple.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+namespace
+{
+
+/*! \brief Stride of the vector of atom_id used to describe each SHAKE
+ * constraint
+ *
+ * Like other such code, SHAKE is hard-wired to use t_ilist.iatoms as
+ * a flat vector of tuples of general data. Here, they are triples
+ * containing the index of the constraint type, and then the indices
+ * of the two atoms involved. So for each constraint, we must stride
+ * this vector by three to get access to its information. */
+const int constraintStride = 3;
+
+/*! \brief Compute the displacements between pairs of constrained
+ * atoms described in the iatom "topology". */
+std::vector<real>
+computeDisplacements(const std::vector<atom_id> &iatom,
+ const std::vector<real> &positions)
+{
+ assert(0 == iatom.size() % constraintStride);
+ int numConstraints = iatom.size() / constraintStride;
+ std::vector<real> displacements;
+
+ for (int ll = 0; ll != numConstraints; ++ll)
+ {
+ int atom_i = iatom[ll*constraintStride + 1];
+ int atom_j = iatom[ll*constraintStride + 2];
+
+ for (int d = 0; d != DIM; d++)
+ {
+ displacements.push_back(positions[atom_i*DIM + d] - positions[atom_j*DIM + d]);
+ }
+ }
+
+ return displacements;
+}
+
+/*! \brief Compute half of the reduced mass of each pair of constrained
+ * atoms in the iatom "topology".
+ *
+ * The reduced mass is m = 1/(1/m_i + 1/m_j)) */
+std::vector<real>
+computeHalfOfReducedMasses(const std::vector<atom_id> &iatom,
+ const std::vector<real> &inverseMasses)
+{
+ int numConstraints = iatom.size() / constraintStride;
+ std::vector<real> halfOfReducedMasses;
+
+ for (int ll = 0; ll != numConstraints; ++ll)
+ {
+ int atom_i = iatom[ll*constraintStride + 1];
+ int atom_j = iatom[ll*constraintStride + 2];
+
+ halfOfReducedMasses.push_back(0.5 / (inverseMasses[atom_i] + inverseMasses[atom_j]));
+ }
+
+ return halfOfReducedMasses;
+}
+
+/*! \brief Compute the distances corresponding to the vector of displacements components */
+std::vector<real>
+computeDistancesSquared(const std::vector<real> &displacements)
+{
+ assert(0 == displacements.size() % DIM);
+ int numDistancesSquared = displacements.size() / DIM;
+ std::vector<real> distanceSquared;
+
+ for (int i = 0; i != numDistancesSquared; ++i)
+ {
+ distanceSquared.push_back(0.0);
+ for (int d = 0; d != DIM; ++d)
+ {
+ real displacement = displacements[i*DIM + d];
+ distanceSquared.back() += displacement * displacement;
+ }
+ }
+
+ return distanceSquared;
+}
+
+/*! \brief Test fixture for testing SHAKE */
+class ShakeTest : public ::testing::Test
+{
+ public:
+ /*! \brief Set up data for test cases to use when constructing
+ their input */
+ void SetUp()
+ {
+ inverseMassesDatabase_.push_back(2.0);
+ inverseMassesDatabase_.push_back(3.0);
+ inverseMassesDatabase_.push_back(4.0);
+ inverseMassesDatabase_.push_back(1.0);
+
+ positionsDatabase_.push_back(2.5);
+ positionsDatabase_.push_back(-3.1);
+ positionsDatabase_.push_back(15.7);
+
+ positionsDatabase_.push_back(0.51);
+ positionsDatabase_.push_back(-3.02);
+ positionsDatabase_.push_back(15.55);
+
+ positionsDatabase_.push_back(-0.5);
+ positionsDatabase_.push_back(-3.0);
+ positionsDatabase_.push_back(15.2);
+
+ positionsDatabase_.push_back(-1.51);
+ positionsDatabase_.push_back(-2.95);
+ positionsDatabase_.push_back(15.05);
+ }
+
+ //! Run the test
+ void runTest(size_t gmx_unused numAtoms,
+ size_t numConstraints,
+ const std::vector<atom_id> &iatom,
+ const std::vector<real> &constrainedDistances,
+ const std::vector<real> &inverseMasses,
+ const std::vector<real> &positions)
+ {
+ // Check the test input is consistent
+ assert(numConstraints * constraintStride == iatom.size());
+ assert(numConstraints == constrainedDistances.size());
+ assert(numAtoms == inverseMasses.size());
+ assert(numAtoms * DIM == positions.size());
+ for (size_t i = 0; i != numConstraints; ++i)
+ {
+ for (size_t j = 1; j < 3; j++)
+ {
+ // Check that the topology refers to atoms that have masses and positions
+ assert(iatom[i*constraintStride + j] >= 0);
+ assert(iatom[i*constraintStride + j] < static_cast<atom_id>(numAtoms));
+ }
+ }
+ std::vector<real> distanceSquaredTolerances;
+ std::vector<real> lagrangianValues;
+ std::vector<real> constrainedDistancesSquared;
+
+ for (size_t i = 0; i != numConstraints; ++i)
+ {
+ constrainedDistancesSquared.push_back(constrainedDistances[i] * constrainedDistances[i]);
+ distanceSquaredTolerances.push_back(1.0 / (constrainedDistancesSquared.back() * ShakeTest::tolerance_));
+ lagrangianValues.push_back(0.0);
+ }
+ std::vector<real> halfOfReducedMasses = computeHalfOfReducedMasses(iatom, inverseMasses);
+ std::vector<real> initialDisplacements = computeDisplacements(iatom, positions);
+
+ std::vector<real> finalPositions = positions;
+ int numIterations = 0;
+ int numErrors = 0;
+
+ cshake(&iatom[0], numConstraints, &numIterations,
+ ShakeTest::maxNumIterations_, &constrainedDistancesSquared[0],
+ &finalPositions[0], &initialDisplacements[0], &halfOfReducedMasses[0],
+ omega_, &inverseMasses[0],
+ &distanceSquaredTolerances[0],
+ &lagrangianValues[0],
+ &numErrors);
+
+ std::vector<real> finalDisplacements = computeDisplacements(iatom, finalPositions);
+ std::vector<real> finalDistancesSquared = computeDistancesSquared(finalDisplacements);
+ assert(numConstraints == finalDistancesSquared.size());
+
+ EXPECT_EQ(0, numErrors);
+ EXPECT_GT(numIterations, 1);
+ EXPECT_LT(numIterations, ShakeTest::maxNumIterations_);
+ // TODO wrap this in a Google Mock matcher if there's
+ // other tests like it some time?
+ for (size_t i = 0; i != numConstraints; ++i)
+ {
+ gmx::test::FloatingPointTolerance constraintTolerance =
+ gmx::test::relativeToleranceAsFloatingPoint(constrainedDistancesSquared[i],
+ ShakeTest::tolerance_);
+ // Assert that the constrained distances are within the required tolerance
+ EXPECT_FLOAT_EQ_TOL(constrainedDistancesSquared[i],
+ finalDistancesSquared[i],
+ constraintTolerance);
+ }
+ }
+
+ //! Tolerance for SHAKE conversion (ie. shake-tol .mdp setting)
+ static const real tolerance_;
+ //! Maximum number of iterations permitted in these tests
+ static const int maxNumIterations_;
+ //! SHAKE over-relaxation (SOR) factor
+ static const real omega_;
+ //! Database of inverse masses of atoms in the topology
+ std::vector<real> inverseMassesDatabase_;
+ //! Database of atom positions (three reals per atom)
+ std::vector<real> positionsDatabase_;
+};
+
+const real ShakeTest::tolerance_ = 1e-5;
+const int ShakeTest::maxNumIterations_ = 30;
+const real ShakeTest::omega_ = 1.0;
+
+TEST_F(ShakeTest, ConstrainsOneBond)
+{
+ int numAtoms = 2;
+ int numConstraints = 1;
+
+ std::vector<atom_id> iatom;
+ iatom.push_back(-1); // unused
+ iatom.push_back(0); // i atom index
+ iatom.push_back(1); // j atom index
+
+ std::vector<real> constrainedDistances;
+ constrainedDistances.push_back(2.0);
+
+ std::vector<real> inverseMasses(inverseMassesDatabase_.begin(),
+ inverseMassesDatabase_.begin() + numAtoms);
+ std::vector<real> positions(positionsDatabase_.begin(),
+ positionsDatabase_.begin() + numAtoms * DIM);
+
+ runTest(numAtoms, numConstraints, iatom, constrainedDistances, inverseMasses, positions);
+}
+
+TEST_F(ShakeTest, ConstrainsTwoDisjointBonds)
+{
+ int numAtoms = 4;
+ int numConstraints = 2;
+
+ std::vector<atom_id> iatom;
+ iatom.push_back(-1); // unused
+ iatom.push_back(0); // i atom index
+ iatom.push_back(1); // j atom index
+
+ iatom.push_back(-1); // unused
+ iatom.push_back(2); // i atom index
+ iatom.push_back(3); // j atom index
+
+ std::vector<real> constrainedDistances;
+ constrainedDistances.push_back(2.0);
+ constrainedDistances.push_back(1.0);
+
+ std::vector<real> inverseMasses(inverseMassesDatabase_.begin(),
+ inverseMassesDatabase_.begin() + numAtoms);
+ std::vector<real> positions(positionsDatabase_.begin(),
+ positionsDatabase_.begin() + numAtoms * DIM);
+
+ runTest(numAtoms, numConstraints, iatom, constrainedDistances, inverseMasses, positions);
+}
+
+TEST_F(ShakeTest, ConstrainsTwoBondsWithACommonAtom)
+{
+ int numAtoms = 3;
+ int numConstraints = 2;
+
+ std::vector<atom_id> iatom;
+ iatom.push_back(-1); // unused
+ iatom.push_back(0); // i atom index
+ iatom.push_back(1); // j atom index
+
+ iatom.push_back(-1); // unused
+ iatom.push_back(1); // i atom index
+ iatom.push_back(2); // j atom index
+
+ std::vector<real> constrainedDistances;
+ constrainedDistances.push_back(2.0);
+ constrainedDistances.push_back(1.0);
+
+ std::vector<real> inverseMasses(inverseMassesDatabase_.begin(),
+ inverseMassesDatabase_.begin() + numAtoms);
+ std::vector<real> positions(positionsDatabase_.begin(),
+ positionsDatabase_.begin() + numAtoms * DIM);
+
+ runTest(numAtoms, numConstraints, iatom, constrainedDistances, inverseMasses, positions);
+}
+
+TEST_F(ShakeTest, ConstrainsThreeBondsWithCommonAtoms)
+{
+ int numAtoms = 4;
+ int numConstraints = 3;
+
+ std::vector<atom_id> iatom;
+ iatom.push_back(-1); // unused
+ iatom.push_back(0); // i atom index
+ iatom.push_back(1); // j atom index
+
+ iatom.push_back(-1); // unused
+ iatom.push_back(1); // i atom index
+ iatom.push_back(2); // j atom index
+
+ iatom.push_back(-1); // unused
+ iatom.push_back(2); // i atom index
+ iatom.push_back(3); // j atom index
+
+ std::vector<real> constrainedDistances;
+ constrainedDistances.push_back(2.0);
+ constrainedDistances.push_back(1.0);
+ constrainedDistances.push_back(1.0);
+
+ std::vector<real> inverseMasses(inverseMassesDatabase_.begin(),
+ inverseMassesDatabase_.begin() + numAtoms);
+ std::vector<real> positions(positionsDatabase_.begin(),
+ positionsDatabase_.begin() + numAtoms * DIM);
+
+ runTest(numAtoms, numConstraints, iatom, constrainedDistances, inverseMasses, positions);
+}
+
+} // namespace
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "gromacs/legacyheaders/tgroup.h"
#include <math.h>
-#include "macros.h"
-#include "main.h"
+
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/rbin.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
-#include "tgroup.h"
-#include "vec.h"
-#include "network.h"
-#include "update.h"
-#include "rbin.h"
-#include "mtop_util.h"
-#include "gmx_omp_nthreads.h"
static void init_grptcstat(int ngtc, t_grp_tcstat tcstat[])
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015 by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include <math.h>
+#include <stdlib.h>
#include <string.h>
#include <time.h>
-#include <math.h>
-#include "sysstuff.h"
-#include "network.h"
-#include "gromacs/utility/smalloc.h"
-#include "nrnb.h"
-#include "main.h"
-#include "chargegroup.h"
-#include "force.h"
-#include "macros.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "update.h"
-#include "constr.h"
-#include "vec.h"
-#include "tgroup.h"
-#include "mdebin.h"
-#include "vsite.h"
-#include "force.h"
-#include "mdrun.h"
-#include "domdec.h"
-#include "gromacs/random/random.h"
-#include "physics.h"
-#include "xvgr.h"
-#include "mdatoms.h"
-#include "ns.h"
-#include "mtop_util.h"
-#include "pme.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
-#include "gromacs/simd/simd.h"
+#include <algorithm>
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/ewald/pme.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/random/random.h"
+#include "gromacs/simd/simd.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static void global_max(t_commrec *cr, int *n)
{
gmx_sumi(cr->nnodes, sum, cr);
for (i = 0; i < cr->nnodes; i++)
{
- *n = max(*n, sum[i]);
+ *n = std::max(*n, sum[i]);
}
sfree(sum);
unsigned long gmx_unused Flags,
gmx_walltime_accounting_t walltime_accounting)
{
- const char *TPI = "Test Particle Insertion";
gmx_localtop_t *top;
gmx_groups_t *groups;
gmx_enerdata_t *enerd;
gmx_int64_t rnd_count_stride, rnd_count;
gmx_int64_t seed;
double rnd[4];
- int i, start, end;
+ int i;
FILE *fp_tpi = NULL;
char *ptr, *dump_pdb, **leg, str[STRLEN], str2[STRLEN];
double dbl, dump_ener;
real *mass_cavity = NULL, mass_tot;
int nbin;
double invbinw, *bin, refvolshift, logV, bUlogV;
- real dvdl, prescorr, enercorr, dvdlcorr;
+ real prescorr, enercorr, dvdlcorr;
gmx_bool bEnergyOutOfBounds;
const char *tpid_leg[2] = {"direct", "reweighted"};
* The center of mass of the last atoms is then used for TPIC.
*/
nat_cavity = 0;
- while (sscanf(ptr, "%lf%n", &dbl, &i) > 0)
+ while (sscanf(ptr, "%20lf%n", &dbl, &i) > 0)
{
srenew(mass_cavity, nat_cavity+1);
mass_cavity[nat_cavity] = dbl;
dump_ener = 0;
if (dump_pdb)
{
- sscanf(dump_pdb, "%lf", &dump_ener);
+ sscanf(dump_pdb, "%20lf", &dump_ener);
}
atoms2md(top_global, inputrec, 0, NULL, top_global->natoms, mdatoms);
snew(leg, 4+nener);
e = 0;
sprintf(str, "-kT log(<Ve\\S-\\betaU\\N>/<V>)");
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
sprintf(str, "f. -kT log<e\\S-\\betaU\\N>");
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
sprintf(str, "f. <e\\S-\\betaU\\N>");
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
sprintf(str, "f. V");
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
sprintf(str, "f. <Ue\\S-\\betaU\\N>");
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
for (i = 0; i < ngid; i++)
{
sprintf(str, "f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>",
*(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
}
if (bDispCorr)
{
sprintf(str, "f. <U\\sdisp c\\Ne\\S-\\betaU\\N>");
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
}
if (bCharge)
{
{
sprintf(str, "f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>",
*(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
}
if (bRFExcl)
{
sprintf(str, "f. <U\\sRF excl\\Ne\\S-\\betaU\\N>");
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
}
if (EEL_FULL(fr->eeltype))
{
sprintf(str, "f. <U\\sCoul recip\\Ne\\S-\\betaU\\N>");
- leg[e++] = strdup(str);
+ leg[e++] = gmx_strdup(str);
}
}
xvgr_legend(fp_tpi, 4+nener, (const char**)leg, oenv);
bNS = FALSE;
/* Calculate long range corrections to pressure and energy */
- calc_dispcorr(fplog, inputrec, fr, step, top_global->natoms, state->box,
+ calc_dispcorr(inputrec, fr, top_global->natoms, state->box,
lambda, pres, vir, &prescorr, &enercorr, &dvdlcorr);
/* figure out how to rearrange the next 4 lines MRS 8/4/2009 */
enerd->term[F_DISPCORR] = enercorr;
if (fp_tpi != NULL)
{
- gmx_fio_fclose(fp_tpi);
+ xvgrclose(fp_tpi);
}
if (fplog != NULL)
(int)(bin[i]+0.5),
bin[i]*exp(-bUlogV)*V_all/VembU_all);
}
- gmx_fio_fclose(fp_tpi);
+ xvgrclose(fp_tpi);
}
sfree(bin);
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "gromacs/legacyheaders/update.h"
-#include <stdio.h>
#include <math.h>
+#include <stdio.h>
-#include "types/commrec.h"
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "nrnb.h"
-#include "physics.h"
-#include "macros.h"
-#include "vec.h"
-#include "main.h"
-#include "update.h"
-#include "gromacs/random/random.h"
-#include "mshift.h"
-#include "tgroup.h"
-#include "force.h"
-#include "names.h"
-#include "txtdump.h"
-#include "mdrun.h"
-#include "constr.h"
-#include "disre.h"
-#include "orires.h"
-#include "gmx_omp_nthreads.h"
+#include <algorithm>
#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/random/random.h"
#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxomp.h"
-#include "gromacs/pulling/pull.h"
+#include "gromacs/utility/smalloc.h"
/*For debugging, start at v(-dt/2) for velolcity verlet -- uncomment next line */
/*#define STARTFROMDT2*/
unsigned short cACC[], rvec v[], rvec f[],
gmx_bool bExtended, real veta, real alpha)
{
- double imass, w_dt;
+ double w_dt;
int gf = 0, ga = 0;
- rvec vrel;
- real u, vn, vv, va, vb, vnrel;
int n, d;
double g, mv1, mv2;
rvec x[], rvec xprime[], rvec v[],
gmx_bool bExtended, real veta)
{
- double imass, w_dt;
int gf = 0;
int n, d;
double g, mr1, mr2;
}
for (d = 0; d < DIM; d++)
{
- vn = v[n][d];
-
if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
{
vn = (lg*vrel[d] + dt*(imass*f[n][d] - 0.5*vxi*vrel[d]
{
gmx_stochd_t *sd;
gmx_sd_const_t *sdc;
- int ngtc, n, th;
+ int ngtc, n;
real y;
snew(sd, 1);
for (n = 0; n < ngtc; n++)
{
- reft = max(0.0, opts->ref_t[n]);
+ reft = std::max<real>(0, opts->ref_t[n]);
if ((opts->tau_t[n] > 0) && (reft > 0)) /* tau_t or ref_t = 0 means that no randomization is done */
{
sd->randomize_group[n] = TRUE;
{
ga = cACC[n];
}
- if (cTC)
- {
- gt = cTC[n];
- }
for (d = 0; d < DIM; d++)
{
{
gf = cFREEZE[n];
}
- if (cACC)
- {
- ga = cACC[n];
- }
if (cTC)
{
gt = cTC[n];
* half of the update, needs to be remembered for the second half.
*/
rvec *sd_V;
- real kT;
int gf = 0, ga = 0, gt = 0;
real vn = 0, Vmh, Xmh;
real ism;
}
static void calc_ke_part_normal(rvec v[], t_grpopts *opts, t_mdatoms *md,
- gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel,
- gmx_bool bSaveEkinOld)
+ gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel)
{
int g;
t_grp_tcstat *tcstat = ekind->tcstat;
int nthread, thread;
/* three main: VV with AveVel, vv with AveEkin, leap with AveEkin. Leap with AveVel is also
- an option, but not supported now. Additionally, if we are doing iterations.
+ an option, but not supported now.
bEkinAveVel: If TRUE, we sum into ekin, if FALSE, into ekinh.
- bSavEkinOld: If TRUE (in the case of iteration = bIterate is TRUE), we don't copy over the ekinh_old.
- If FALSE, we overrwrite it.
*/
/* group velocities are calculated in update_ekindata and
*/
for (g = 0; (g < opts->ngtc); g++)
{
-
- if (!bSaveEkinOld)
- {
- copy_mat(tcstat[g].ekinh, tcstat[g].ekinh_old);
- }
+ copy_mat(tcstat[g].ekinh, tcstat[g].ekinh_old);
if (bEkinAveVel)
{
clear_mat(tcstat[g].ekinf);
+ tcstat[g].ekinscalef_nhc = 1.0; /* need to clear this -- logic is complicated! */
}
else
{
clear_mat(tcstat[g].ekinh);
}
- if (bEkinAveVel)
- {
- tcstat[g].ekinscalef_nhc = 1.0; /* need to clear this -- logic is complicated! */
- }
}
ekind->dekindl_old = ekind->dekindl;
-
- nthread = gmx_omp_nthreads_get(emntUpdate);
+ nthread = gmx_omp_nthreads_get(emntUpdate);
#pragma omp parallel for num_threads(nthread) schedule(static)
for (thread = 0; thread < nthread; thread++)
}
void calc_ke_part(t_state *state, t_grpopts *opts, t_mdatoms *md,
- gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel, gmx_bool bSaveEkinOld)
+ gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel)
{
if (ekind->cosacc.cos_accel == 0)
{
- calc_ke_part_normal(state->v, opts, md, ekind, nrnb, bEkinAveVel, bSaveEkinOld);
+ calc_ke_part_normal(state->v, opts, md, ekind, nrnb, bEkinAveVel);
}
else
{
}
static void deform(gmx_update_t upd,
- int start, int homenr, rvec x[], matrix box, matrix *scale_tot,
+ int start, int homenr, rvec x[], matrix box,
const t_inputrec *ir, gmx_int64_t step)
{
matrix bnew, invbox, mu;
x[i][YY] = mu[YY][YY]*x[i][YY]+mu[ZZ][YY]*x[i][ZZ];
x[i][ZZ] = mu[ZZ][ZZ]*x[i][ZZ];
}
- if (scale_tot != NULL)
- {
- /* The transposes of the scaling matrices are stored,
- * so we need to do matrix multiplication in the inverse order.
- */
- mmul_ur0(*scale_tot, mu, *scale_tot);
- }
}
void update_tcouple(gmx_int64_t step,
{
gmx_bool bTCouple = FALSE;
real dttc;
- int i, start, end, homenr, offset;
+ int i, offset;
/* if using vv with trotter decomposition methods, we do this elsewhere in the code */
if (inputrec->etc != etcNO &&
}
}
}
- constrain(NULL, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, 1.0, md,
+ constrain(NULL, FALSE, FALSE, constr, idef, ir, cr, step, 0, 1.0, md,
state->x, xp, xp, bMolPBC, state->box, state->lambda[efptBONDED], NULL,
- NULL, vir_lr_constr, nrnb, econqCoord, ir->epc == epcMTTK, state->veta, state->veta);
+ NULL, vir_lr_constr, nrnb, econqForce);
}
/* Add nstcalclr-1 times the LR force to the sum of both forces
gmx_int64_t step,
real *dvdlambda, /* the contribution to be added to the bonded interactions */
t_inputrec *inputrec, /* input record and box stuff */
- gmx_ekindata_t *ekind,
t_mdatoms *md,
t_state *state,
gmx_bool bMolPBC,
gmx_update_t upd,
gmx_constr_t constr,
gmx_bool bFirstHalf,
- gmx_bool bCalcVir,
- real vetanew)
+ gmx_bool bCalcVir)
{
- gmx_bool bExtended, bLastStep, bLog = FALSE, bEner = FALSE, bDoConstr = FALSE;
+ gmx_bool bLastStep, bLog = FALSE, bEner = FALSE, bDoConstr = FALSE;
double dt;
- real dt_1;
- int start, homenr, nrend, i, n, m, g, d;
+ int start, homenr, nrend, i, m;
tensor vir_con;
- rvec *vbuf, *xprime = NULL;
+ rvec *xprime = NULL;
int nth, th;
if (constr)
nrend = start+homenr;
dt = inputrec->delta_t;
- dt_1 = 1.0/dt;
/*
* Steps (7C, 8C)
if (EI_VV(inputrec->eI) && bFirstHalf)
{
constrain(NULL, bLog, bEner, constr, idef,
- inputrec, ekind, cr, step, 1, 1.0, md,
+ inputrec, cr, step, 1, 1.0, md,
state->x, state->v, state->v,
bMolPBC, state->box,
state->lambda[efptBONDED], dvdlambda,
- NULL, bCalcVir ? &vir_con : NULL, nrnb, econqVeloc,
- inputrec->epc == epcMTTK, state->veta, vetanew);
+ NULL, bCalcVir ? &vir_con : NULL, nrnb, econqVeloc);
}
else
{
constrain(NULL, bLog, bEner, constr, idef,
- inputrec, ekind, cr, step, 1, 1.0, md,
+ inputrec, cr, step, 1, 1.0, md,
state->x, xprime, NULL,
bMolPBC, state->box,
state->lambda[efptBONDED], dvdlambda,
- state->v, bCalcVir ? &vir_con : NULL, nrnb, econqCoord,
- inputrec->epc == epcMTTK, state->veta, state->veta);
+ state->v, bCalcVir ? &vir_con : NULL, nrnb, econqCoord);
}
wallcycle_stop(wcycle, ewcCONSTR);
wallcycle_start(wcycle, ewcCONSTR);
constrain(NULL, bLog, bEner, constr, idef,
- inputrec, NULL, cr, step, 1, 0.5, md,
+ inputrec, cr, step, 1, 0.5, md,
state->x, xprime, NULL,
bMolPBC, state->box,
state->lambda[efptBONDED], dvdlambda,
- state->v, NULL, nrnb, econqCoord, FALSE, 0, 0);
+ state->v, NULL, nrnb, econqCoord);
wallcycle_stop(wcycle, ewcCONSTR);
}
/* Constrain the coordinates xprime */
wallcycle_start(wcycle, ewcCONSTR);
constrain(NULL, bLog, bEner, constr, idef,
- inputrec, NULL, cr, step, 1, 1.0, md,
+ inputrec, cr, step, 1, 1.0, md,
state->x, xprime, NULL,
bMolPBC, state->box,
state->lambda[efptBONDED], dvdlambda,
- NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
+ NULL, NULL, nrnb, econqCoord);
wallcycle_stop(wcycle, ewcCONSTR);
}
}
}
else
{
+#ifndef __clang_analyzer__
+ // cppcheck-suppress unreadVariable
nth = gmx_omp_nthreads_get(emntUpdate);
-
+#endif
#pragma omp parallel for num_threads(nth) schedule(static)
for (i = start; i < nrend; i++)
{
t_mdatoms *md,
t_state *state,
rvec force[], /* forces on home particles */
- matrix *scale_tot,
matrix pcoupl_mu,
t_nrnb *nrnb,
gmx_update_t upd)
{
- gmx_bool bExtended, bLastStep, bLog = FALSE, bEner = FALSE;
double dt;
- real dt_1;
- int start, homenr, nrend, i, n, m, g;
- tensor vir_con;
+ int start, homenr, i, n, m;
start = 0;
homenr = md->homenr;
- nrend = start+homenr;
-
- bExtended =
- (inputrec->etc == etcNOSEHOOVER) ||
- (inputrec->epc == epcPARRINELLORAHMAN) ||
- (inputrec->epc == epcMTTK);
dt = inputrec->delta_t;
break;
}
- if ((!(IR_NPT_TROTTER(inputrec) || IR_NPH_TROTTER(inputrec))) && scale_tot)
- {
- /* The transposes of the scaling matrices are stored,
- * therefore we need to reverse the order in the multiplication.
- */
- mmul_ur0(*scale_tot, pcoupl_mu, *scale_tot);
- }
-
if (DEFORM(*inputrec))
{
- deform(upd, start, homenr, state->x, state->box, scale_tot, inputrec, step);
+ deform(upd, start, homenr, state->x, state->box, inputrec, step);
}
where();
dump_it_all(fplog, "After update",
gmx_constr_t constr,
t_idef *idef)
{
- gmx_bool bNH, bPR, bLastStep, bLog = FALSE, bEner = FALSE, bDoConstr = FALSE;
+ gmx_bool bNH, bPR, bDoConstr = FALSE;
double dt, alpha;
- real *imass, *imassin;
rvec *force;
- real dt_1;
- int start, homenr, nrend, i, j, d, n, m, g;
- int blen0, blen1, iatom, jatom, nshake, nsettle, nconstr, nexpand;
- int *icom = NULL;
- tensor vir_con;
- rvec *vcom, *xcom, *vall, *xall, *xin, *vin, *forcein, *fall, *xpall, *xprimein, *xprime;
+ int start, homenr, nrend;
+ rvec *xprime;
int nth, th;
bDoConstr = (NULL != constr);
xprime = get_xprime(state, upd);
dt = inputrec->delta_t;
- dt_1 = 1.0/dt;
/* We need to update the NMR restraint history when time averaging is used */
if (state->flags & (1<<estDISRE_RM3TAV))
t_mdatoms *md, t_state *state, gmx_update_t upd, gmx_constr_t constr)
{
- int i;
real rate = (ir->delta_t)/ir->opts.tau_t[0];
if (ir->etc == etcANDERSEN && constr != NULL)
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "macros.h"
-#include "vcm.h"
-#include "vec.h"
+#include "gromacs/legacyheaders/vcm.h"
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/smalloc.h"
-#include "names.h"
-#include "txtdump.h"
-#include "network.h"
-#include "pbc.h"
t_vcm *init_vcm(FILE *fp, gmx_groups_t *groups, t_inputrec *ir)
{
rvec x[], rvec v[], t_vcm *vcm)
{
int i, g, m;
- real m0, xx, xy, xz, yy, yz, zz;
+ real m0;
rvec j0;
if (vcm->mode != ecmNO)
void do_stopcm_grp(int start, int homenr, unsigned short *group_id,
rvec x[], rvec v[], t_vcm *vcm)
{
- int i, g, m;
- real tm, tm_1;
+ int i, g;
rvec dv, dx;
if (vcm->mode != ecmNO)
int m, g;
real ekcm, ekrot, tm, tm_1, Temp_cm;
rvec jcm;
- tensor Icm, Tcm;
+ tensor Icm;
/* First analyse the total results */
if (vcm->mode != ecmNO)
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/vsite.h"
#include <stdio.h>
-#include "typedefs.h"
-#include "vsite.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "nrnb.h"
-#include "vec.h"
-#include "network.h"
-#include "mshift.h"
-#include "pbc.h"
-#include "domdec.h"
-#include "mtop_util.h"
-#include "gmx_omp_nthreads.h"
+#include <algorithm>
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
/* Routines to send/recieve coordinates and force
* of constructing atoms.
static int constr_vsiten(t_iatom *ia, t_iparams ip[],
rvec *x, t_pbc *pbc)
{
- rvec xs, x1, dx;
+ rvec x1, dx;
dvec dsum;
int n3, av, ai, i;
real a;
gmx_bool bPBCAll;
rvec xpbc, xv, vv, dx;
real a1, b1, c1, inv_dt;
- int i, inc, ii, nra, nr, tp, ftype;
+ int i, inc, nra, nr, tp, ftype;
t_iatom avsite, ai, aj, ak, al, pbc_atom;
t_iatom *ia;
t_pbc *pbc_null2;
int *vsite_pbc, ishift;
- rvec reftmp, vtmp, rtmp;
if (v != NULL)
{
{
t_pbc pbc, *pbc_null;
gmx_bool bDomDec;
- int nthreads;
bDomDec = cr && DOMAINDECOMP(cr);
rvec fi, fj, dx;
t_iatom av, ai, aj;
ivec di;
- real b;
int siv, sij;
av = ia[1];
gmx_bool VirCorr, matrix dxdf,
t_pbc *pbc, t_graph *g)
{
- real fx, fy, fz, c, invl, fproj, a1;
+ real c, invl, fproj, a1;
rvec xvi, xij, xjk, xix, fv, temp;
t_iatom av, ai, aj, ak;
- int svi, sji, skj, d;
+ int svi, sji, skj;
ivec di;
av = ia[1];
{
gmx_bool bPBCAll;
real a1, b1, c1;
- int i, inc, m, nra, nr, tp, ftype;
+ int i, inc, nra, nr, tp, ftype;
t_iatom *ia;
t_pbc *pbc_null2;
int *vsite_pbc;
static int count_intercg_vsite(gmx_mtop_t *mtop,
gmx_bool *bHaveChargeGroups)
{
- int mb, mt, ftype, nral, i, cg, a;
+ int mb, ftype, nral, i, cg, a;
gmx_molblock_t *molb;
gmx_moltype_t *molt;
int *a2cg;
t_atom *atom, t_mdatoms *md,
t_block *cgs, int *a2cg)
{
- int ftype, nral, i, j, vsi, vsite, cg_v, cg_c, a, nc3 = 0;
+ int ftype, nral, i, j, vsi, vsite, cg_v, a, nc3 = 0;
t_ilist *il;
t_iatom *ia;
int **vsite_pbc, *vsite_pbc_f;
gmx_bool bSerial_NoPBC)
{
int nvsite, i;
- int *a2cg, cg;
+ int *a2cg;
gmx_vsite_t *vsite;
int mt;
gmx_moltype_t *molt;
- int nthreads;
/* check if there are vsites */
nvsite = 0;
{
for (j = i + 1; j < i + nral1; j++)
{
- vsite_atom_range = max(vsite_atom_range, iat[j]);
+ vsite_atom_range = std::max(vsite_atom_range, iat[j]);
}
}
}
/* The 3 below is from 1+NRAL(ftype)=3 */
vs_ind_end = i + ip[iat[i]].vsiten.n*3;
- vsite_atom_range = max(vsite_atom_range, iat[i+1]);
+ vsite_atom_range = std::max(vsite_atom_range, iat[i+1]);
while (i < vs_ind_end)
{
- vsite_atom_range = max(vsite_atom_range, iat[i+2]);
+ vsite_atom_range = std::max(vsite_atom_range, iat[i+2]);
i += 3;
}
}
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
+
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/math/utilities.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
-#include "force.h"
-#include "gromacs/fileio/filenm.h"
-#include "nrnb.h"
-#include "vec.h"
void make_wall_tables(FILE *fplog, const output_env_t oenv,
const t_inputrec *ir, const char *tabfn,
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <stdio.h>
#include <string.h>
-#include "force.h"
-#include "gromacs/utility/smalloc.h"
-#include "types/commrec.h"
-#include "ns.h"
-#include "nrnb.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-#include "gromacs/fileio/futil.h"
-#include "names.h"
-#include "domdec.h"
+
+#include "gromacs/domdec/domdec.h"
#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define header "Neighborlist:"
file(GLOB ONLINEHELP_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${ONLINEHELP_SOURCES} PARENT_SCOPE)
-set(ONLINEHELP_PUBLIC_HEADERS
- helptopicinterface.h)
-gmx_install_headers(onlinehelp ${ONLINEHELP_PUBLIC_HEADERS})
-
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_onlinehelp
*/
+#include "gmxpre.h"
+
#include "helpformat.h"
#include <algorithm>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
-#include "../utility/common.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_onlinehelp
*/
+#include "gmxpre.h"
+
#include "helpmanager.h"
#include <string>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
-#include "../utility/common.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_onlinehelp
*/
+#include "gmxpre.h"
+
#include "helptopic.h"
#include <map>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_ONLINEHELP_HELPTOPIC_H
#define GMX_ONLINEHELP_HELPTOPIC_H
-#include "../utility/common.h"
-#include "../utility/stringutil.h"
-#include "../utility/uniqueptr.h"
-
-#include "helptopicinterface.h"
+#include "gromacs/onlinehelp/helptopicinterface.h"
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/uniqueptr.h"
namespace gmx
{
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/*! \file
+/*! \libinternal \defgroup module_onlinehelp Help Formatting for Online Help (onlinehelp)
+ * \ingroup group_utilitymodules
+ * \brief
+ * Provides functionality for formatting help text for console and other
+ * formats.
+ *
+ * This module provides helper functions and classes for formatting console
+ * help, as well as man pages and HTML help from the source code. It should
+ * not be necessary to call any methods in this module outside the \Gromacs
+ * library.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ */
+/*! \libinternal \file
* \brief
* Declares gmx::HelpTopicInterface.
*
#ifndef GMX_ONLINEHELP_HELPTOPICINTERFACE_H
#define GMX_ONLINEHELP_HELPTOPICINTERFACE_H
-#include "../utility/uniqueptr.h"
+#include "gromacs/utility/uniqueptr.h"
namespace gmx
{
class HelpWriterContext;
-/*! \brief
+/*! \libinternal \brief
* Provides a single online help topic.
*
- * \if libapi
* Implementations of these methods should not throw, except that writeHelp()
* is allowed to throw on out-of-memory or I/O errors since those it cannot
* avoid.
*
* Header helptopic.h contains classes that implement this interface and make
* it simple to write concrete help topic classes.
- * \endif
- *
- * This class is in a public header, and exposed through HelpTopicPointer, but
- * it is not intended to be used outside the library. To access a help topic
- * with public API methods, use HelpManager.
*
* \inlibraryapi
* \ingroup module_onlinehelp
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_onlinehelp
*/
+#include "gmxpre.h"
+
#include "helpwritercontext.h"
#include <cctype>
namespace
{
-//! \addtogroup module_onlinehelp
+//! \internal \addtogroup module_onlinehelp
//! \{
struct t_sandr
#include <string>
#include <vector>
-#include "../utility/common.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_onlinehelp
*/
-#include <gtest/gtest.h>
+#include "gmxpre.h"
#include "gromacs/onlinehelp/helpformat.h"
+#include <gtest/gtest.h>
+
#include "testutils/stringtest.h"
namespace
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_onlinehelp
*/
+#include "gmxpre.h"
+
#include "gromacs/onlinehelp/helpmanager.h"
#include <string>
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_onlinehelp
*/
+#include "gmxpre.h"
+
#include "mock_helptopic.h"
#include <gmock/gmock.h>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_OPTIONS_H
#define GMX_OPTIONS_H
-#include "options/basicoptions.h"
-#include "options/filenameoption.h"
-#include "options/options.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/filenameoptionmanager.h"
+#include "gromacs/options/options.h"
#endif
file(GLOB OPTIONS_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${OPTIONS_SOURCES} PARENT_SCOPE)
-set(OPTIONS_PUBLIC_HEADERS
+gmx_install_headers(
abstractoption.h
basicoptions.h
filenameoption.h
+ filenameoptionmanager.h
optionfiletype.h
optionflags.h
options.h
- timeunitmanager.h)
-gmx_install_headers(options ${OPTIONS_PUBLIC_HEADERS})
+ timeunitmanager.h
+ )
if (BUILD_TESTING)
add_subdirectory(tests)
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_options
*/
-#include "gromacs/options/abstractoption.h"
+#include "gmxpre.h"
+
+#include "abstractoption.h"
#include "gromacs/options/abstractoptionstorage.h"
#include "gromacs/options/optionflags.h"
#include <string>
#include <vector>
-#include "../utility/common.h"
-#include "../utility/uniqueptr.h"
-
-#include "optionflags.h"
+#include "gromacs/options/optionflags.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
class AbstractOptionStorage;
template <typename T> class OptionStorageTemplate;
+class OptionManagerContainer;
class Options;
-//! Smart pointer for managing an AbstractOptionStorage object.
-typedef gmx_unique_ptr<AbstractOptionStorage>::type
- AbstractOptionStoragePointer;
-
/*! \brief
* Abstract base class for specifying option properties.
*
/*! \brief
* Creates a default storage object for the option.
*
- * \returns The created storage object.
- * \throws APIError if invalid option settings have been provided.
+ * \param[in] managers Manager container (unused if the option does
+ * not use a manager).
+ * \returns The created storage object.
+ * \throws APIError if invalid option settings have been provided.
*
* This method is called by Options::addOption() when initializing an
* option from the settings.
* They should also throw APIError if they detect problems.
*
* Should only be called by Options::addOption().
+ *
+ * The ownership of the return value is passed, but is not using a
+ * smart pointer to avoid introducing such a dependency in an installed
+ * header. The implementation will always consist of a single `new`
+ * call and returning that value, and the caller always immediately
+ * wraps the pointer in a smart pointer, so there is not exception
+ * safety issue.
*/
- virtual AbstractOptionStoragePointer createStorage() const = 0;
+ virtual AbstractOptionStorage *createStorage(
+ const OptionManagerContainer &managers) const = 0;
//! Sets the description for the option.
void setDescription(const char *descr) { descr_ = descr; }
#include <string>
-#include "../utility/common.h"
-
-#include "optionflags.h"
+#include "gromacs/options/optionflags.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_options
*/
+#include "gmxpre.h"
+
#include "basicoptions.h"
-#include "basicoptionstorage.h"
#include <cerrno>
#include <cstdio>
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/stringutil.h"
+#include "basicoptionstorage.h"
+
namespace
{
* BooleanOption
*/
-AbstractOptionStoragePointer BooleanOption::createStorage() const
+AbstractOptionStorage *
+BooleanOption::createStorage(const OptionManagerContainer & /*managers*/) const
{
- return AbstractOptionStoragePointer(new BooleanOptionStorage(*this));
+ return new BooleanOptionStorage(*this);
}
* IntegerOption
*/
-AbstractOptionStoragePointer IntegerOption::createStorage() const
+AbstractOptionStorage *
+IntegerOption::createStorage(const OptionManagerContainer & /*managers*/) const
{
- return AbstractOptionStoragePointer(new IntegerOptionStorage(*this));
+ return new IntegerOptionStorage(*this);
}
* Int64Option
*/
-AbstractOptionStoragePointer Int64Option::createStorage() const
+AbstractOptionStorage *
+Int64Option::createStorage(const OptionManagerContainer & /*managers*/) const
{
- return AbstractOptionStoragePointer(new Int64OptionStorage(*this));
+ return new Int64OptionStorage(*this);
}
* DoubleOption
*/
-AbstractOptionStoragePointer DoubleOption::createStorage() const
+AbstractOptionStorage *
+DoubleOption::createStorage(const OptionManagerContainer & /*managers*/) const
{
- return AbstractOptionStoragePointer(new DoubleOptionStorage(*this));
+ return new DoubleOptionStorage(*this);
}
* FloatOption
*/
-AbstractOptionStoragePointer FloatOption::createStorage() const
+AbstractOptionStorage *
+FloatOption::createStorage(const OptionManagerContainer & /*managers*/) const
{
- return AbstractOptionStoragePointer(new FloatOptionStorage(*this));
+ return new FloatOptionStorage(*this);
}
GMX_THROW(APIError("Conflicting default values"));
}
}
- // If there is no default value, match is still -1.
- if (enumIndexStore_ != NULL)
- {
- *enumIndexStore_ = match;
- }
}
if (settings.defaultEnumIndex_ >= 0)
{
addValue(allowed_[settings.defaultEnumIndex_]);
commitValues();
}
+ // Somewhat subtly, this does not update the stored enum index if the
+ // caller has not provided store() or storeVector(), because values()
+ // will be empty in such a case. This leads to (desired) behavior of
+ // preserving the existing value in the enum index store variable in such
+ // cases.
+ refreshEnumIndexStore();
}
std::string StringOptionStorage::formatExtraDescription() const
void StringOptionStorage::refreshValues()
{
MyBase::refreshValues();
+ refreshEnumIndexStore();
+}
+
+void StringOptionStorage::refreshEnumIndexStore()
+{
if (enumIndexStore_ != NULL)
{
for (size_t i = 0; i < values().size(); ++i)
{
- ValueList::const_iterator match =
- std::find(allowed_.begin(), allowed_.end(), values()[i]);
- GMX_ASSERT(match != allowed_.end(),
- "Enum value not found (internal error)");
- enumIndexStore_[i] = static_cast<int>(match - allowed_.begin());
+ if (values()[i].empty())
+ {
+ enumIndexStore_[i] = -1;
+ }
+ else
+ {
+ ValueList::const_iterator match =
+ std::find(allowed_.begin(), allowed_.end(), values()[i]);
+ GMX_ASSERT(match != allowed_.end(),
+ "Enum value not found (internal error)");
+ enumIndexStore_[i] = static_cast<int>(match - allowed_.begin());
+ }
}
}
}
* StringOption
*/
-AbstractOptionStoragePointer StringOption::createStorage() const
+AbstractOptionStorage *
+StringOption::createStorage(const OptionManagerContainer & /*managers*/) const
{
- return AbstractOptionStoragePointer(new StringOptionStorage(*this));
+ return new StringOptionStorage(*this);
}
} // namespace gmx
#include <string>
-#include "../legacyheaders/types/simple.h"
-#include "../utility/gmxassert.h"
-
-#include "abstractoption.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/gmxassert.h"
namespace gmx
{
private:
//! Creates a BooleanOptionStorage object.
- virtual AbstractOptionStoragePointer createStorage() const;
+ virtual AbstractOptionStorage *createStorage(
+ const OptionManagerContainer &managers) const;
};
/*! \brief
private:
//! Creates an IntegerOptionStorage object.
- virtual AbstractOptionStoragePointer createStorage() const;
+ virtual AbstractOptionStorage *createStorage(
+ const OptionManagerContainer &managers) const;
/*! \brief
* Needed to initialize IntegerOptionStorage from this class without
private:
//! Creates an Int64OptionStorage object.
- virtual AbstractOptionStoragePointer createStorage() const;
+ virtual AbstractOptionStorage *createStorage(
+ const OptionManagerContainer &managers) const;
/*! \brief
* Needed to initialize Int64OptionStorage from this class without
private:
//! Creates a DoubleOptionStorage object.
- virtual AbstractOptionStoragePointer createStorage() const;
+ virtual AbstractOptionStorage *createStorage(
+ const OptionManagerContainer &managers) const;
bool bTime_;
private:
//! Creates a FloatOptionStorage object.
- virtual AbstractOptionStoragePointer createStorage() const;
+ virtual AbstractOptionStorage *createStorage(
+ const OptionManagerContainer &managers) const;
bool bTime_;
* The index (zero-based) of the selected value in the array \p values
* provided to enumValues() is written into \p *store after the
* option gets its value. If the option has not been provided,
- * and there is no default value, -1 is stored.
+ * and there is no default value, -1 is stored. If store(),
+ * storeVector() or defaultEnumIndex() is not present, the value in
+ * \p *store is kept as a default value, otherwise it is always
+ * overwritten.
*
* Cannot be specified without enumValue().
*
private:
//! Creates a StringOptionStorage object.
- virtual AbstractOptionStoragePointer createStorage() const;
+ virtual AbstractOptionStorage *createStorage(
+ const OptionManagerContainer &managers) const;
const char *const *enumValues_;
int enumValuesCount_;
#include <string>
#include <vector>
-#include "basicoptions.h"
-#include "optionstoragetemplate.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/optionstoragetemplate.h"
namespace gmx
{
virtual void convertValue(const std::string &value);
virtual void refreshValues();
+ void refreshEnumIndexStore();
+
StringOptionInfo info_;
ValueList allowed_;
int *enumIndexStore_;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_options
*/
+#include "gmxpre.h"
+
#include "filenameoption.h"
-#include "filenameoptionstorage.h"
+
+#include <cstring>
#include <string>
#include <vector>
#include "gromacs/fileio/filenm.h"
-
+#include "gromacs/options/filenameoptionmanager.h"
+#include "gromacs/options/optionmanagercontainer.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/file.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/stringutil.h"
+#include "filenameoptionstorage.h"
+
namespace gmx
{
namespace
{
-class FileTypeRegistry;
-
//! \addtogroup module_options
//! \{
-//! Shorthand for a list of file extensions.
-typedef std::vector<const char *> ExtensionList;
+/*! \brief
+ * Mapping from OptionFileType to a file type in filenm.h.
+ */
+struct FileTypeMapping
+{
+ //! OptionFileType value to map.
+ OptionFileType optionType;
+ //! Corresponding file type from filenm.h.
+ int fileType;
+};
+
+//! Mappings from OptionFileType to file types in filenm.h.
+const FileTypeMapping c_fileTypeMapping[] =
+{
+ { eftTopology, efTPS },
+ { eftTrajectory, efTRX },
+ { eftPDB, efPDB },
+ { eftIndex, efNDX },
+ { eftPlot, efXVG },
+ { eftGenericData, efDAT }
+};
/********************************************************************
* FileTypeHandler
*/
-/*! \internal \brief
+/*! \internal
+ * \brief
* Handles a single file type known to FileNameOptionStorage.
+ *
+ * Methods in this class do not throw, except for a possible std::bad_alloc
+ * when constructing std::string return values.
*/
class FileTypeHandler
{
public:
- //! Returns the list of extensions for this file type.
- const ExtensionList &extensions() const { return extensions_; }
-
- //! Returns whether \p filename has a valid extension for this type.
- bool hasKnownExtension(const std::string &filename) const;
- //! Adds a default extension for this type to \p filename.
- std::string addExtension(const std::string &filename) const;
/*! \brief
- * Adds an extension to \p filename if it results in an existing file.
+ * Returns a handler for a single file type.
*
- * Tries to add each extension for this file type to \p filename and
- * checks whether this results in an existing file.
- * The first match is returned.
- * Returns an empty string if no existing file is found.
+ * \param[in] fileType File type (from filenm.h) to use.
*/
- std::string findFileWithExtension(const std::string &filename) const;
+ explicit FileTypeHandler(int fileType);
- private:
- //! Possible extensions for this file type.
- ExtensionList extensions_;
+ //! Returns the number of acceptable extensions for this file type.
+ int extensionCount() const;
+ //! Returns the extension with the given index.
+ const char *extension(int i) const;
+
+ //! Returns whether \p fileType (from filenm.h) is accepted for this type.
+ bool isValidType(int fileType) const;
+ private:
/*! \brief
- * Needed for initialization; all initialization is handled by
- * FileTypeRegistry.
+ * File type (from filenm.h) represented by this handler.
+ *
+ * -1 represents an unknown file type.
*/
- friend class FileTypeRegistry;
+ int fileType_;
+ //! Number of different extensions this type supports.
+ int extensionCount_;
+ /*! \brief
+ * List of simple file types that are included in this type.
+ *
+ * If `fileType_` represents a generic type in filenm.h, i.e., a type
+ * that accepts multiple different types of files, then this is an
+ * array of `extensionCount_` elements, each element specifying one
+ * non-generic file type that this option accepts.
+ * `NULL` for single-extension types.
+ */
+ const int *genericTypes_;
};
-bool
-FileTypeHandler::hasKnownExtension(const std::string &filename) const
+FileTypeHandler::FileTypeHandler(int fileType)
+ : fileType_(fileType), extensionCount_(0), genericTypes_(NULL)
{
- for (size_t i = 0; i < extensions_.size(); ++i)
+ if (fileType_ >= 0)
{
- if (endsWith(filename, extensions_[i]))
+ const int genericTypeCount = ftp2generic_count(fileType_);
+ if (genericTypeCount > 0)
{
- return true;
+ extensionCount_ = genericTypeCount;
+ genericTypes_ = ftp2generic_list(fileType_);
}
- }
- return false;
-}
-
-std::string
-FileTypeHandler::addExtension(const std::string &filename) const
-{
- if (extensions_.empty())
- {
- return filename;
- }
- return filename + extensions_[0];
-}
-
-std::string
-FileTypeHandler::findFileWithExtension(const std::string &filename) const
-{
- for (size_t i = 0; i < extensions_.size(); ++i)
- {
- std::string testFilename(filename + extensions_[i]);
- if (File::exists(testFilename))
+ else if (ftp2ext_with_dot(fileType_)[0] != '\0')
{
- return testFilename;
+ extensionCount_ = 1;
}
}
- return std::string();
}
-/********************************************************************
- * FileTypeRegistry
- */
-
-/*! \internal \brief
- * Singleton for managing static file type info for FileNameOptionStorage.
- */
-class FileTypeRegistry
+int FileTypeHandler::extensionCount() const
{
- public:
- //! Returns a singleton instance of this class.
- static const FileTypeRegistry &instance();
- //! Returns a handler for a single file type.
- const FileTypeHandler &
- handlerForType(OptionFileType type, int legacyType) const;
-
- private:
- //! Initializes the file type registry.
- FileTypeRegistry();
-
- //! Registers a file type that corresponds to a ftp in filenm.h.
- void registerType(int type, int ftp);
- //! Registers a file type with a single extension.
- void registerType(int type, const char *extension);
-
- std::vector<FileTypeHandler> filetypes_;
-};
-
-// static
-const FileTypeRegistry &
-FileTypeRegistry::instance()
-{
- static FileTypeRegistry singleton;
- return singleton;
-}
-
-const FileTypeHandler &
-FileTypeRegistry::handlerForType(OptionFileType type, int legacyType) const
-{
- int index = type;
- if (type == eftUnknown && legacyType >= 0)
- {
- index = eftOptionFileType_NR + legacyType;
- }
- GMX_RELEASE_ASSERT(index >= 0 && static_cast<size_t>(index) < filetypes_.size(),
- "Invalid file type");
- return filetypes_[index];
+ return extensionCount_;
}
-FileTypeRegistry::FileTypeRegistry()
+const char *FileTypeHandler::extension(int i) const
{
- filetypes_.resize(eftOptionFileType_NR + efNR);
- registerType(eftTopology, efTPS);
- registerType(eftTrajectory, efTRX);
- registerType(eftPDB, efPDB);
- registerType(eftIndex, efNDX);
- registerType(eftPlot, efXVG);
- registerType(eftGenericData, efDAT);
- for (int i = 0; i < efNR; ++i)
+ GMX_ASSERT(i >= 0 && i < extensionCount_, "Invalid extension index");
+ if (genericTypes_ != NULL)
{
- registerType(eftOptionFileType_NR + i, i);
+ return ftp2ext_with_dot(genericTypes_[i]);
}
+ return ftp2ext_with_dot(fileType_);
}
-void FileTypeRegistry::registerType(int type, int ftp)
+bool
+FileTypeHandler::isValidType(int fileType) const
{
- GMX_RELEASE_ASSERT(type >= 0 && static_cast<size_t>(type) < filetypes_.size(),
- "Invalid file type");
- const int genericTypeCount = ftp2generic_count(ftp);
- if (genericTypeCount > 0)
+ if (genericTypes_ != NULL)
{
- const int *const genericTypes = ftp2generic_list(ftp);
- filetypes_[type].extensions_.clear();
- filetypes_[type].extensions_.reserve(genericTypeCount);
- for (int i = 0; i < genericTypeCount; ++i)
+ for (int i = 0; i < extensionCount(); ++i)
{
- filetypes_[type].extensions_.push_back(ftp2ext_with_dot(genericTypes[i]));
+ if (fileType == genericTypes_[i])
+ {
+ return true;
+ }
}
+ return false;
}
else
{
- registerType(type, ftp2ext_with_dot(ftp));
- }
-}
-
-void FileTypeRegistry::registerType(int type, const char *extension)
-{
- GMX_RELEASE_ASSERT(type >= 0 && static_cast<size_t>(type) < filetypes_.size(),
- "Invalid file type");
- filetypes_[type].extensions_.assign(1, extension);
-}
-
-/*! \brief
- * Helper method to complete a file name provided to a file name option.
- *
- * \param[in] value Value provided to the file name option.
- * \param[in] filetype File type for the option.
- * \param[in] legacyType If \p filetype is eftUnknown, this gives the type as
- * an enum value from filenm.h.
- * \param[in] bCompleteToExisting
- * Whether to check existing files when completing the extension.
- * \returns \p value with possible extension added.
- */
-std::string completeFileName(const std::string &value, OptionFileType filetype,
- int legacyType, bool bCompleteToExisting)
-{
- if (bCompleteToExisting && File::exists(value))
- {
- // TODO: This may not work as expected if the value is passed to a
- // function that uses fn2ftp() to determine the file type and the input
- // file has an unrecognized extension.
- return value;
- }
- const FileTypeRegistry ®istry = FileTypeRegistry::instance();
- const FileTypeHandler &typeHandler = registry.handlerForType(filetype, legacyType);
- if (typeHandler.hasKnownExtension(value))
- {
- return value;
- }
- if (bCompleteToExisting)
- {
- std::string newValue = typeHandler.findFileWithExtension(value);
- if (!newValue.empty())
- {
- return newValue;
- }
+ return fileType == fileType_;
}
- return typeHandler.addExtension(value);
}
//! \}
* FileNameOptionStorage
*/
-FileNameOptionStorage::FileNameOptionStorage(const FileNameOption &settings)
- : MyBase(settings), info_(this), filetype_(settings.filetype_),
- legacyType_(settings.legacyType_),
- bRead_(settings.bRead_), bWrite_(settings.bWrite_),
- bLibrary_(settings.bLibrary_)
+FileNameOptionStorage::FileNameOptionStorage(const FileNameOption &settings,
+ FileNameOptionManager *manager)
+ : MyBase(settings), info_(this), manager_(manager), fileType_(-1),
+ defaultExtension_(""), bRead_(settings.bRead_), bWrite_(settings.bWrite_),
+ bLibrary_(settings.bLibrary_), bAllowMissing_(settings.bAllowMissing_)
{
+ GMX_RELEASE_ASSERT(!hasFlag(efOption_MultipleTimes),
+ "allowMultiple() is not supported for file name options");
+ if (settings.optionType_ == eftUnknown && settings.legacyType_ >= 0)
+ {
+ fileType_ = settings.legacyType_;
+ }
+ else
+ {
+ ConstArrayRef<FileTypeMapping> map(c_fileTypeMapping);
+ ConstArrayRef<FileTypeMapping>::const_iterator i;
+ for (i = map.begin(); i != map.end(); ++i)
+ {
+ if (i->optionType == settings.optionType_)
+ {
+ fileType_ = i->fileType;
+ break;
+ }
+ }
+ }
+ FileTypeHandler typeHandler(fileType_);
+ if (settings.defaultType_ >= 0 && settings.defaultType_ < efNR)
+ {
+ // This also assures that the default type is not a generic type.
+ GMX_RELEASE_ASSERT(typeHandler.isValidType(settings.defaultType_),
+ "Default type for a file option is not an accepted "
+ "type for the option");
+ FileTypeHandler defaultHandler(settings.defaultType_);
+ defaultExtension_ = defaultHandler.extension(0);
+ }
+ else if (typeHandler.extensionCount() > 0)
+ {
+ defaultExtension_ = typeHandler.extension(0);
+ }
if (settings.defaultBasename_ != NULL)
{
- std::string defaultValue =
- completeFileName(settings.defaultBasename_, filetype_,
- legacyType_, false);
+ std::string defaultValue(settings.defaultBasename_);
+ int type = fn2ftp(settings.defaultBasename_);
+ GMX_RELEASE_ASSERT(type == efNR || type == settings.defaultType_,
+ "Default basename has an extension that does not "
+ "match the default type");
+ if (type == efNR)
+ {
+ defaultValue.append(defaultExtension());
+ }
setDefaultValueIfSet(defaultValue);
- if (isRequired())
+ if (isRequired() || settings.bLegacyOptionalBehavior_)
{
setDefaultValue(defaultValue);
}
std::string FileNameOptionStorage::typeString() const
{
- const FileTypeRegistry ®istry = FileTypeRegistry::instance();
- const FileTypeHandler &typeHandler = registry.handlerForType(filetype_, legacyType_);
- const ExtensionList &extensions = typeHandler.extensions();
- std::string result;
- ExtensionList::const_iterator i;
- int count = 0;
- for (i = extensions.begin(); count < 2 && i != extensions.end(); ++i, ++count)
+ FileTypeHandler typeHandler(fileType_);
+ std::string result;
+ int count;
+ for (count = 0; count < 2 && count < typeHandler.extensionCount(); ++count)
{
- if (i != extensions.begin())
+ if (count > 0)
{
result.append("/");
}
- result.append(*i);
+ result.append(typeHandler.extension(count));
}
- if (i != extensions.end())
+ if (count < typeHandler.extensionCount())
{
result.append("/...");
}
if (result.empty())
{
- if (legacyType_ == efRND)
+ if (isDirectoryOption())
{
result = "dir";
}
std::string FileNameOptionStorage::formatExtraDescription() const
{
- const FileTypeRegistry ®istry = FileTypeRegistry::instance();
- const FileTypeHandler &typeHandler = registry.handlerForType(filetype_, legacyType_);
- const ExtensionList &extensions = typeHandler.extensions();
- std::string result;
- if (extensions.size() > 2)
+ FileTypeHandler typeHandler(fileType_);
+ std::string result;
+ if (typeHandler.extensionCount() > 2)
{
result.append(":");
- ExtensionList::const_iterator i;
- for (i = extensions.begin(); i != extensions.end(); ++i)
+ for (int i = 0; i < typeHandler.extensionCount(); ++i)
{
result.append(" ");
- result.append((*i) + 1);
+ // Skip the dot.
+ result.append(typeHandler.extension(i) + 1);
}
}
return result;
void FileNameOptionStorage::convertValue(const std::string &value)
{
- bool bInput = isInputFile() || isInputOutputFile();
- addValue(completeFileName(value, filetype_, legacyType_, bInput));
+ if (manager_ != NULL)
+ {
+ std::string processedValue = manager_->completeFileName(value, info_);
+ if (!processedValue.empty())
+ {
+ // If the manager returns a value, use it without further checks,
+ // except for sanity checking.
+ if (!isDirectoryOption())
+ {
+ const int fileType = fn2ftp(processedValue.c_str());
+ if (fileType == efNR)
+ {
+ // If the manager returned an invalid file name, assume
+ // that it knows what it is doing. But assert that it
+ // only does that for the only case that it is currently
+ // required for: VMD plugins.
+ GMX_ASSERT(isInputFile() && isTrajectoryOption(),
+ "Manager returned an invalid file name");
+ }
+ else
+ {
+ GMX_ASSERT(isValidType(fileType),
+ "Manager returned an invalid file name");
+ }
+ }
+ addValue(processedValue);
+ return;
+ }
+ }
+ // Currently, directory options are simple, and don't need any
+ // special processing.
+ // TODO: Consider splitting them into a separate DirectoryOption.
+ if (isDirectoryOption())
+ {
+ addValue(value);
+ return;
+ }
+ const int fileType = fn2ftp(value.c_str());
+ if (fileType == efNR)
+ {
+ std::string message
+ = formatString("File '%s' cannot be used by GROMACS because it "
+ "does not have a recognizable extension.\n"
+ "The following extensions are possible for this option:\n %s",
+ value.c_str(), joinStrings(extensions(), ", ").c_str());
+ GMX_THROW(InvalidInputError(message));
+ }
+ else if (!isValidType(fileType))
+ {
+ std::string message
+ = formatString("File name '%s' cannot be used for this option.\n"
+ "Only the following extensions are possible:\n %s",
+ value.c_str(), joinStrings(extensions(), ", ").c_str());
+ GMX_THROW(InvalidInputError(message));
+ }
+ addValue(value);
+}
+
+void FileNameOptionStorage::processAll()
+{
+ if (manager_ != NULL && hasFlag(efOption_HasDefaultValue))
+ {
+ ValueList &valueList = values();
+ GMX_RELEASE_ASSERT(valueList.size() == 1,
+ "There should be only one default value");
+ if (!valueList[0].empty())
+ {
+ const std::string &oldValue = valueList[0];
+ GMX_ASSERT(endsWith(oldValue, defaultExtension()),
+ "Default value does not have the expected extension");
+ const std::string prefix
+ = stripSuffixIfPresent(oldValue, defaultExtension());
+ const std::string newValue
+ = manager_->completeDefaultFileName(prefix, info_);
+ if (!newValue.empty() && newValue != oldValue)
+ {
+ GMX_ASSERT(isValidType(fn2ftp(newValue.c_str())),
+ "Manager returned an invalid default value");
+ valueList[0] = newValue;
+ refreshValues();
+ }
+ }
+ }
}
bool FileNameOptionStorage::isDirectoryOption() const
{
- return legacyType_ == efRND;
+ return fileType_ == efRND;
+}
+
+bool FileNameOptionStorage::isTrajectoryOption() const
+{
+ return fileType_ == efTRX;
+}
+
+const char *FileNameOptionStorage::defaultExtension() const
+{
+ return defaultExtension_;
}
-ConstArrayRef<const char *> FileNameOptionStorage::extensions() const
+std::vector<const char *> FileNameOptionStorage::extensions() const
{
- const FileTypeRegistry ®istry = FileTypeRegistry::instance();
- const FileTypeHandler &typeHandler = registry.handlerForType(filetype_, legacyType_);
- const ExtensionList &extensions = typeHandler.extensions();
- return constArrayRefFromVector<const char *>(extensions.begin(), extensions.end());
+ FileTypeHandler typeHandler(fileType_);
+ std::vector<const char *> result;
+ result.reserve(typeHandler.extensionCount());
+ for (int i = 0; i < typeHandler.extensionCount(); ++i)
+ {
+ result.push_back(typeHandler.extension(i));
+ }
+ return result;
+}
+
+bool FileNameOptionStorage::isValidType(int fileType) const
+{
+ FileTypeHandler typeHandler(fileType_);
+ return typeHandler.isValidType(fileType);
+}
+
+ConstArrayRef<int> FileNameOptionStorage::fileTypes() const
+{
+ if (fileType_ < 0)
+ {
+ return ConstArrayRef<int>();
+ }
+ const int genericTypeCount = ftp2generic_count(fileType_);
+ if (genericTypeCount > 0)
+ {
+ return constArrayRefFromArray<int>(ftp2generic_list(fileType_), genericTypeCount);
+ }
+ return constArrayRefFromArray<int>(&fileType_, 1);
}
/********************************************************************
return option().isLibraryFile();
}
+bool FileNameOptionInfo::allowMissing() const
+{
+ return option().allowMissing();
+}
+
bool FileNameOptionInfo::isDirectoryOption() const
{
return option().isDirectoryOption();
}
+bool FileNameOptionInfo::isTrajectoryOption() const
+{
+ return option().isTrajectoryOption();
+}
+
+const char *FileNameOptionInfo::defaultExtension() const
+{
+ return option().defaultExtension();
+}
+
FileNameOptionInfo::ExtensionList FileNameOptionInfo::extensions() const
{
return option().extensions();
}
+bool FileNameOptionInfo::isValidType(int fileType) const
+{
+ return option().isValidType(fileType);
+}
+
+ConstArrayRef<int> FileNameOptionInfo::fileTypes() const
+{
+ return option().fileTypes();
+}
+
/********************************************************************
* FileNameOption
*/
-AbstractOptionStoragePointer FileNameOption::createStorage() const
+AbstractOptionStorage *
+FileNameOption::createStorage(const OptionManagerContainer &managers) const
{
- return AbstractOptionStoragePointer(new FileNameOptionStorage(*this));
+ return new FileNameOptionStorage(*this, managers.get<FileNameOptionManager>());
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_OPTIONS_FILENAMEOPTION_H
#include <string>
+#include <vector>
-#include "abstractoption.h"
-#include "optionfiletype.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/options/optionfiletype.h"
namespace gmx
{
template <typename T> class ConstArrayRef;
class FileNameOptionInfo;
+class FileNameOptionManager;
class FileNameOptionStorage;
/*! \brief
//! Initializes an option with the given name.
explicit FileNameOption(const char *name)
- : MyBase(name), filetype_(eftUnknown), legacyType_(-1),
- defaultBasename_(NULL),
- bRead_(false), bWrite_(false), bLibrary_(false)
+ : MyBase(name), optionType_(eftUnknown), legacyType_(-1),
+ defaultBasename_(NULL), defaultType_(-1),
+ bLegacyOptionalBehavior_(false),
+ bRead_(false), bWrite_(false), bLibrary_(false),
+ bAllowMissing_(false)
{
}
* Either this attribute or legacyType() must be provided.
*/
MyClass &filetype(OptionFileType type)
- { filetype_ = type; return me(); }
+ { optionType_ = type; return me(); }
/*! \brief
* Sets the type of the file from an enum in filenm.h.
*
*/
MyClass &legacyType(int type)
{ legacyType_ = type; return me(); }
+ /*! \brief
+ * Changes the behavior of optional options to match old t_filenm.
+ *
+ * If this is not set, optional options return an empty string if not
+ * set. If this is set, a non-empty value is always returned.
+ * In the latter case, whether the option is set only affects the
+ * return value of OptionInfo::isSet() and Options::isSet().
+ */
+ MyClass &legacyOptionalBehavior()
+ { bLegacyOptionalBehavior_ = true; return me(); }
//! Tells that the file provided by this option is used for input only.
MyClass &inputFile()
{ bRead_ = true; bWrite_ = false; return me(); }
*/
MyClass &libraryFile(bool bLibrary = true)
{ bLibrary_ = bLibrary; return me(); }
+ /*! \brief
+ * Tells that missing file names explicitly provided by the user are
+ * valid for this input option.
+ *
+ * If this method is not called, an error will be raised if the user
+ * explicitly provides a file name that does not name an existing file,
+ * or if the default value does not resolve to a valid file name for a
+ * required option that the user has not set.
+ *
+ * This method only has effect with input files, and only if a
+ * FileNameOptionManager is being used.
+ */
+ MyClass &allowMissing(bool bAllow = true)
+ { bAllowMissing_ = bAllow; return me(); }
/*! \brief
* Sets a default basename for the file option.
*
* Use this method instead of defaultValue() or defaultValueIfSet() to
* set a default value for a file name option. No extension needs to
- * be provided; it is automatically added based on filetype().
+ * be provided; it is automatically added based on filetype() or
+ * defaultType().
* The behavior is also adjusted based on required(): if the option is
* required, the value given to defaultBasename() is treated as for
* both defaultValue() and defaultValueIfSet(), otherwise it is treated
* as for defaultValueIfSet().
+ *
+ * For input files that accept multiple extensions, the extension is
+ * completed to the default extension on creation of the option or at
+ * time of parsing an option without a value.
+ *
+ * If FileNameOptionManager is used, the extension may change during
+ * Options::finish(), as this is the time when the default names are
+ * checked against the file system to provide an extension that matches
+ * an existing file if that is possible.
+ *
+ * If FileNameOptionManager is used, and
+ * FileNameOptionManager::addDefaultFileNameOption() is used, and the
+ * user provides a global default file name using that option, then the
+ * global default takes precedence over defaultBasename().
*/
MyClass &defaultBasename(const char *basename)
{ defaultBasename_ = basename; return me(); }
+ /*! \brief
+ * Sets a default type/extension for the file option.
+ *
+ * For options that accept multiple types of files (e.g.,
+ * eftTrajectory), this method sets the default extension used
+ * for completing defaultBasename(), as well as the default extension
+ * used by FileNameOptionManager to complete various file names.
+ *
+ * The value should be one of the enumerated `ef*` values from
+ * filenm.h, and be a valid type for the type specified with
+ * filetype().
+ */
+ MyClass &defaultType(int filetype)
+ { defaultType_ = filetype; return me(); }
private:
// Use defaultBasename() instead.
using MyBase::defaultValueIfSet;
//! Creates a FileNameOptionStorage object.
- virtual AbstractOptionStoragePointer createStorage() const;
+ virtual AbstractOptionStorage *createStorage(
+ const OptionManagerContainer &managers) const;
- OptionFileType filetype_;
+ OptionFileType optionType_;
int legacyType_;
const char *defaultBasename_;
+ int defaultType_;
+ bool bLegacyOptionalBehavior_;
bool bRead_;
bool bWrite_;
bool bLibrary_;
+ bool bAllowMissing_;
/*! \brief
* Needed to initialize FileNameOptionStorage from this class without
{
public:
//! Shorthand for a list of extensions.
- typedef ConstArrayRef<const char *> ExtensionList;
+ typedef std::vector<const char *> ExtensionList;
//! Creates an option info object for the given option.
explicit FileNameOptionInfo(FileNameOptionStorage *option);
* \see FileNameOption::libraryFile()
*/
bool isLibraryFile() const;
+ //! Whether the (input) option allows missing files to be provided.
+ bool allowMissing() const;
//! Whether the option specifies directories.
bool isDirectoryOption() const;
+ //! Whether the option specifies a generic trajectory file.
+ bool isTrajectoryOption() const;
+ //! Returns the default extension for this option.
+ const char *defaultExtension() const;
//! Returns the list of extensions this option accepts.
ExtensionList extensions() const;
+ //! Returns whether \p fileType (from filenm.h) is accepted for this option.
+ bool isValidType(int fileType) const;
+ //! Returns the list of file types this option accepts.
+ ConstArrayRef<int> fileTypes() const;
private:
const FileNameOptionStorage &option() const;
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements gmx::FileNameOptionManager.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_options
+ */
+#include "gmxpre.h"
+
+#include "filenameoptionmanager.h"
+
+#include <cstring>
+
+#include <string>
+
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/options.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/file.h"
+#include "gromacs/utility/path.h"
+#include "gromacs/utility/stringutil.h"
+
+namespace gmx
+{
+
+namespace
+{
+
+//! Extensions that are recognized as compressed files.
+const char *const c_compressedExtensions[] =
+{ ".gz", ".Z" };
+
+/********************************************************************
+ * Helper functions
+ */
+
+/*! \brief
+ * Adds an extension to \p prefix if it results in an existing file.
+ *
+ * Tries to add each extension for this file type to \p prefix and
+ * checks whether this results in an existing file.
+ * The first match is returned.
+ * Returns an empty string if no existing file is found.
+ */
+std::string findExistingExtension(const std::string &prefix,
+ const FileNameOptionInfo &option)
+{
+ ConstArrayRef<int> types = option.fileTypes();
+ ConstArrayRef<int>::const_iterator i;
+ for (i = types.begin(); i != types.end(); ++i)
+ {
+ std::string testFilename(prefix + ftp2ext_with_dot(*i));
+ if (File::exists(testFilename))
+ {
+ return testFilename;
+ }
+ }
+ return std::string();
+}
+
+} // namespace
+
+/********************************************************************
+ * FileNameOptionManager::Impl
+ */
+
+/*! \internal \brief
+ * Private implemention class for FileNameOptionManager.
+ *
+ * \ingroup module_options
+ */
+class FileNameOptionManager::Impl
+{
+ public:
+ Impl() : bInputCheckingDisabled_(false) {}
+
+ //! Global default file name, if set.
+ std::string defaultFileName_;
+ //! Whether input option processing has been disabled.
+ bool bInputCheckingDisabled_;
+};
+
+/********************************************************************
+ * FileNameOptionManager
+ */
+
+FileNameOptionManager::FileNameOptionManager()
+ : impl_(new Impl())
+{
+}
+
+FileNameOptionManager::~FileNameOptionManager()
+{
+}
+
+void FileNameOptionManager::disableInputOptionChecking(bool bDisable)
+{
+ impl_->bInputCheckingDisabled_ = bDisable;
+}
+
+void FileNameOptionManager::addDefaultFileNameOption(
+ Options *options, const char *name)
+{
+ options->addOption(
+ StringOption(name).store(&impl_->defaultFileName_)
+ .description("Set the default filename for all file options"));
+}
+
+std::string FileNameOptionManager::completeFileName(
+ const std::string &value, const FileNameOptionInfo &option)
+{
+ const bool bAllowMissing = option.allowMissing();
+ const bool bInput
+ = option.isInputFile() || option.isInputOutputFile();
+ // Currently, directory options are simple, and don't need any
+ // special processing.
+ // TODO: Consider splitting them into a separate DirectoryOption.
+ if (option.isDirectoryOption())
+ {
+ if (!impl_->bInputCheckingDisabled_ && bInput && !bAllowMissing
+ && !Directory::exists(value))
+ {
+ std::string message
+ = formatString("Directory '%s' does not exist or is not accessible.",
+ value.c_str());
+ // TODO: Get actual errno value from the attempt to open the file
+ // to provide better feedback to the user.
+ GMX_THROW(InvalidInputError(message));
+ }
+ return value;
+ }
+ const int fileType = fn2ftp(value.c_str());
+ if (bInput && !impl_->bInputCheckingDisabled_)
+ {
+ if (fileType == efNR && File::exists(value))
+ {
+ ConstArrayRef<const char *> compressedExtensions(c_compressedExtensions);
+ ConstArrayRef<const char *>::const_iterator ext;
+ for (ext = compressedExtensions.begin(); ext != compressedExtensions.end(); ++ext)
+ {
+ if (endsWith(value, *ext))
+ {
+ std::string newValue = value.substr(0, value.length() - std::strlen(*ext));
+ if (option.isValidType(fn2ftp(newValue.c_str())))
+ {
+ return newValue;
+ }
+ else
+ {
+ return std::string();
+ }
+ }
+ }
+ // VMD plugins may be able to read the file.
+ if (option.isInputFile() && option.isTrajectoryOption())
+ {
+ return value;
+ }
+ }
+ else if (fileType == efNR)
+ {
+ std::string processedValue = findExistingExtension(value, option);
+ if (!processedValue.empty())
+ {
+ return processedValue;
+ }
+ if (bAllowMissing)
+ {
+ return value + option.defaultExtension();
+ }
+ else if (option.isLibraryFile())
+ {
+ // TODO: Treat also library files here.
+ return value + option.defaultExtension();
+ }
+ else
+ {
+ std::string message
+ = formatString("File '%s' does not exist or is not accessible.\n"
+ "The following extensions were tried to complete the file name:\n %s",
+ value.c_str(), joinStrings(option.extensions(), ", ").c_str());
+ GMX_THROW(InvalidInputError(message));
+ }
+ }
+ else if (option.isValidType(fileType))
+ {
+ if (option.isLibraryFile())
+ {
+ // TODO: Treat also library files.
+ }
+ else if (!bAllowMissing && !File::exists(value))
+ {
+ std::string message
+ = formatString("File '%s' does not exist or is not accessible.",
+ value.c_str());
+ // TODO: Get actual errno value from the attempt to open the file
+ // to provide better feedback to the user.
+ GMX_THROW(InvalidInputError(message));
+ }
+ return value;
+ }
+ }
+ else // Not an input file
+ {
+ if (fileType == efNR)
+ {
+ return value + option.defaultExtension();
+ }
+ else if (option.isValidType(fileType))
+ {
+ return value;
+ }
+ }
+ return std::string();
+}
+
+std::string FileNameOptionManager::completeDefaultFileName(
+ const std::string &prefix, const FileNameOptionInfo &option)
+{
+ if (option.isDirectoryOption() || impl_->bInputCheckingDisabled_)
+ {
+ return std::string();
+ }
+ const bool bInput = option.isInputFile() || option.isInputOutputFile();
+ const std::string realPrefix
+ = !impl_->defaultFileName_.empty() ? impl_->defaultFileName_ : prefix;
+ const bool bAllowMissing = option.allowMissing();
+ if (bInput)
+ {
+ std::string completedName = findExistingExtension(realPrefix, option);
+ if (!completedName.empty())
+ {
+ return completedName;
+ }
+ if (bAllowMissing)
+ {
+ return realPrefix + option.defaultExtension();
+ }
+ else if (option.isLibraryFile())
+ {
+ // TODO: Treat also library files here.
+ return realPrefix + option.defaultExtension();
+ }
+ else if (option.isSet())
+ {
+ std::string message
+ = formatString("No file name was provided, and the default file "
+ "'%s' does not exist or is not accessible.\n"
+ "The following extensions were tried to complete the file name:\n %s",
+ prefix.c_str(), joinStrings(option.extensions(), ", ").c_str());
+ GMX_THROW(InvalidInputError(message));
+ }
+ else if (option.isRequired())
+ {
+ std::string message
+ = formatString("Required option was not provided, and the default file "
+ "'%s' does not exist or is not accessible.\n"
+ "The following extensions were tried to complete the file name:\n %s",
+ prefix.c_str(), joinStrings(option.extensions(), ", ").c_str());
+ GMX_THROW(InvalidInputError(message));
+ }
+ // We get here with the legacy optional behavior.
+ }
+ return realPrefix + option.defaultExtension();
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Declares gmx::FileNameOptionManager.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inpublicapi
+ * \ingroup module_options
+ */
+#ifndef GMX_OPTIONS_FILENAMEOPTIONMANAGER_H
+#define GMX_OPTIONS_FILENAMEOPTIONMANAGER_H
+
+#include <string>
+
+#include "gromacs/options/options.h"
+#include "gromacs/utility/classhelpers.h"
+
+namespace gmx
+{
+
+class FileNameOptionInfo;
+class Options;
+
+/*! \brief
+ * Handles interaction of file name options with global options.
+ *
+ * This class contains all logic that completes file names based on user input
+ * and file system contents. Additionally, this class implements support for a
+ * global default file name that overrides any option-specific default, as well
+ * as additional control over how the completion is done.
+ *
+ * \todo
+ * Most of the functionality in this class is specific to command line parsing,
+ * so it would be cleaner to replace this with an interface, and have the
+ * actual code in the `commandline` module.
+ *
+ * Adding a FileNameOptionManager for an Options object is optional, even if
+ * the Options contains FileNameOption options. Features from the manager are
+ * not available if the manager is not created, but otherwise the options work:
+ * the values provided to FileNameOption are used as they are, and exceptions
+ * are thrown if they are no valid instead of attempting to complete them.
+ *
+ * \see Options::addManager()
+ *
+ * \inpublicapi
+ * \ingroup module_selection
+ */
+class FileNameOptionManager : public OptionManagerInterface
+{
+ public:
+ FileNameOptionManager();
+ virtual ~FileNameOptionManager();
+
+ /*! \brief
+ * Disables special input file option handling.
+ *
+ * If disabled, this removes all file system calls from the file
+ * name option parsing.
+ * The values returned by FileNameOption for input and input/output
+ * files are handled with the same simple rule as for output files:
+ * the default extension is added if the file does not end in a
+ * recognized extension, and no other checking is done.
+ *
+ * This changes the following behavior:
+ * - Providing non-existent files does not trigger errors.
+ * - Extensions for input files are not completed to an existing file.
+ * - Compressed input files do not work.
+ */
+ void disableInputOptionChecking(bool bDisable);
+
+ /*! \brief
+ * Adds an option for setting the default global file name.
+ *
+ * \param options Options to add the option to.
+ * \param[in] name Name of the option to add.
+ *
+ * If the user sets the option, it affects all file name options that
+ * would normally return a default value: the basename for the returned
+ * value is taken from the value of the default file name option,
+ * instead from an option-specific default
+ * (FileNameOption::defaultBaseName()).
+ */
+ void addDefaultFileNameOption(Options *options, const char *name);
+
+ /*! \brief
+ * Completes file name option values.
+ *
+ * \param[in] value Value provided by the user.
+ * \param[in] option Option for which the value should be completed.
+ * \returns Value for the file name option.
+ * \throws std::bad_alloc if out of memory.
+ * \throws InvalidInputError if the value is not valid for this
+ * option.
+ *
+ * This method is called for each value that the user provides to
+ * a FileNameOption. The return value (if non-empty) is used as the
+ * value of the option instead of the user-provided one.
+ */
+ std::string completeFileName(const std::string &value,
+ const FileNameOptionInfo &option);
+ /*! \brief
+ * Completes default values for file name options.
+ *
+ * \param[in] prefix Default prefix for the file name.
+ * \param[in] option Option for which the value should be completed.
+ * \returns Value for the file name option.
+ * \throws std::bad_alloc if out of memory.
+ * \throws InvalidInputError if the value is not valid for this
+ * option.
+ *
+ * This method is called for each FileNameOption that has a default
+ * value (either a standard default value, or if the user provided the
+ * option without an explicit value). \p prefix is the default value
+ * without the default extension for the option.
+ * If the return value is non-empty, it is used as the default value
+ * for the option instead of \p prefix + default extension.
+ */
+ std::string completeDefaultFileName(const std::string &prefix,
+ const FileNameOptionInfo &option);
+
+ private:
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
+};
+
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_OPTIONS_FILENAMEOPTIONSTORAGE_H
#include <string>
+#include <vector>
-#include "filenameoption.h"
-#include "optionfiletype.h"
-#include "optionstoragetemplate.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/optionfiletype.h"
+#include "gromacs/options/optionstoragetemplate.h"
namespace gmx
{
class FileNameOption;
+class FileNameOptionManager;
/*! \internal \brief
* Converts, validates, and stores file names.
class FileNameOptionStorage : public OptionStorageTemplate<std::string>
{
public:
- //! \copydoc StringOptionStorage::StringOptionStorage()
- explicit FileNameOptionStorage(const FileNameOption &settings);
+ /*! \brief
+ * Initializes the storage from option settings.
+ *
+ * \param[in] settings Storage settings.
+ * \param manager Manager for this object (can be NULL).
+ */
+ FileNameOptionStorage(const FileNameOption &settings,
+ FileNameOptionManager *manager);
virtual OptionInfo &optionInfo() { return info_; }
virtual std::string typeString() const;
bool isInputOutputFile() const { return bRead_ && bWrite_; }
//! \copydoc FileNameOptionInfo::isLibraryFile()
bool isLibraryFile() const { return bLibrary_; }
+ //! \copydoc FileNameOptionInfo::allowMissing()
+ bool allowMissing() const { return bAllowMissing_; }
//! \copydoc FileNameOptionInfo::isDirectoryOption()
bool isDirectoryOption() const;
+ //! \copydoc FileNameOptionInfo::isTrajectoryOption()
+ bool isTrajectoryOption() const;
+ //! \copydoc FileNameOptionInfo::defaultExtension()
+ const char *defaultExtension() const;
//! \copydoc FileNameOptionInfo::extensions()
- ConstArrayRef<const char *> extensions() const;
+ std::vector<const char *> extensions() const;
+ //! \copydoc FileNameOptionInfo::isValidType()
+ bool isValidType(int fileType) const;
+ //! \copydoc FileNameOptionInfo::fileTypes()
+ ConstArrayRef<int> fileTypes() const;
private:
virtual void convertValue(const std::string &value);
+ virtual void processAll();
FileNameOptionInfo info_;
- OptionFileType filetype_;
- int legacyType_;
+ FileNameOptionManager *manager_;
+ int fileType_;
+ const char *defaultExtension_;
bool bRead_;
bool bWrite_;
bool bLibrary_;
+ bool bAllowMissing_;
};
} // namespace gmx
#ifndef GMX_OPTIONS_OPTIONFLAGS_H
#define GMX_OPTIONS_OPTIONFLAGS_H
-#include "../utility/flags.h"
+#include "gromacs/utility/flags.h"
namespace gmx
{
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares gmx::OptionManagerContainer.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_options
+ */
+#ifndef GMX_OPTIONS_OPTIONMANAGERCONTAINER_H
+#define GMX_OPTIONS_OPTIONMANAGERCONTAINER_H
+
+#include <vector>
+
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/gmxassert.h"
+
+namespace gmx
+{
+
+class OptionManagerInterface;
+
+/*! \libinternal
+ * \brief
+ * Container to keep managers added with Options::addManager() and pass them
+ * to options.
+ *
+ * Consistency of the managers (e.g., that there is at most one manager of a
+ * certain type) is only checked when the managers are accessed.
+ *
+ * \inlibraryapi
+ * \ingroup module_options
+ */
+class OptionManagerContainer
+{
+ public:
+ OptionManagerContainer()
+ {
+ }
+
+ //! Returns `true` if there are no managers.
+ bool empty() const { return list_.empty(); }
+
+ //! Adds a manager to the container.
+ void add(OptionManagerInterface *manager)
+ {
+ list_.push_back(manager);
+ }
+ /*! \brief
+ * Retrieves a manager of a certain type.
+ *
+ * \tparam ManagerType Type of manager to retrieve
+ * (should derive from OptionManagerInterface).
+ * \returns The manager, or `NULL` if there is none.
+ *
+ * This method is used in AbstractOption::createStorage() to retrieve
+ * a manager of a certain type for options that use a manager.
+ *
+ * The return value is `NULL` if there is no manager of the given type.
+ * The caller needs to handle this (either by asserting, or by handling
+ * the manager as optional).
+ */
+ template <class ManagerType>
+ ManagerType *get() const
+ {
+ ManagerType *result = NULL;
+ for (ListType::const_iterator i = list_.begin(); i != list_.end(); ++i)
+ {
+ ManagerType *curr = dynamic_cast<ManagerType *>(*i);
+ if (curr != NULL)
+ {
+ GMX_RELEASE_ASSERT(result == NULL,
+ "More than one applicable option manager is set");
+ result = curr;
+ }
+ }
+ return result;
+ }
+
+ private:
+ //! Shorthand for the internal container type.
+ typedef std::vector<OptionManagerInterface *> ListType;
+
+ ListType list_;
+
+ GMX_DISALLOW_COPY_AND_ASSIGN(OptionManagerContainer);
+};
+
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
#include <vector>
-#include "abstractoption.h"
-#include "options.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/options/optionmanagercontainer.h"
+#include "gromacs/options/options.h"
+#include "gromacs/utility/uniqueptr.h"
namespace gmx
{
class Options::Impl
{
public:
+ //! Smart pointer for managing an AbstractOptionStorage object.
+ typedef gmx_unique_ptr<AbstractOptionStorage>::type
+ AbstractOptionStoragePointer;
//! Convenience type for list of sections.
typedef std::vector<Options *> SubSectionList;
//! Convenience type for list of options.
std::string title_;
//! Full description for the Options object.
std::string description_;
+ /*! \brief
+ * Option managers set for this collection.
+ *
+ * This is non-empty only for the top-level Options object.
+ */
+ OptionManagerContainer managers_;
/*! \brief
* List of subsections, in insertion order.
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_options
*/
-#include "gromacs/options/options.h"
+#include "gmxpre.h"
+
+#include "options.h"
#include "gromacs/options/abstractoption.h"
#include "gromacs/options/abstractoptionstorage.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/messagestringcollector.h"
#include "gromacs/utility/stringutil.h"
#include "options-impl.h"
namespace gmx
{
+/********************************************************************
+ * OptionManagerInterface
+ */
+
+OptionManagerInterface::~OptionManagerInterface()
+{
+}
+
/********************************************************************
* Options::Impl
*/
impl_->description_ = concatenateStrings(descArray.data(), descArray.size());
}
+void Options::addManager(OptionManagerInterface *manager)
+{
+ GMX_RELEASE_ASSERT(impl_->parent_ == NULL,
+ "Can only add a manager in a top-level Options object");
+ // This ensures that all options see the same set of managers.
+ GMX_RELEASE_ASSERT(impl_->options_.empty(),
+ "Can only add a manager before options");
+ // This check could be relaxed if we instead checked that the subsections
+ // do not have options.
+ GMX_RELEASE_ASSERT(impl_->subSections_.empty(),
+ "Can only add a manager before subsections");
+ impl_->managers_.add(manager);
+}
+
void Options::addSubSection(Options *section)
{
+ // This is required, because managers are used from the root Options
+ // object, so they are only seen after the subsection has been added.
+ GMX_RELEASE_ASSERT(section->impl_->options_.empty(),
+ "Can only add a subsection before it has any options");
+ GMX_RELEASE_ASSERT(section->impl_->managers_.empty(),
+ "Can only have managers in a top-level Options object");
// Make sure that section is not already inserted somewhere.
GMX_RELEASE_ASSERT(section->impl_->parent_ == NULL,
"Cannot add as subsection twice");
OptionInfo *Options::addOption(const AbstractOption &settings)
{
- AbstractOptionStoragePointer option(settings.createStorage());
+ Options::Impl *root = impl_.get();
+ while (root->parent_ != NULL)
+ {
+ root = root->parent_->impl_.get();
+ }
+ Impl::AbstractOptionStoragePointer option(settings.createStorage(root->managers_));
if (impl_->findOption(option->name().c_str()) != NULL)
{
GMX_THROW(APIError("Duplicate option: " + option->name()));
#include <string>
-#include "../utility/common.h"
-#include "../utility/gmxassert.h"
-
-#include "abstractoption.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/gmxassert.h"
namespace gmx
{
class OptionsAssigner;
class OptionsIterator;
+/*! \brief
+ * Base class for option managers.
+ *
+ * This class is used as a marker for all classes that are used with
+ * Options::addManager(). It doesn't provide any methods, but only supports
+ * transporting these classes through the Options collection into the
+ * individual option implementation classes.
+ *
+ * The virtual destructor is present to make this class polymorphic, such that
+ * `dynamic_cast` can be used when retrieving a manager of a certain type for
+ * the individual options.
+ *
+ * \inlibraryapi
+ * \ingroup module_options
+ */
+class OptionManagerInterface
+{
+ protected:
+ virtual ~OptionManagerInterface();
+};
+
/*! \brief
* Collection of options.
*
*/
void setDescription(const ConstArrayRef<const char *> &descArray);
+ /*! \brief
+ * Adds an option manager.
+ *
+ * \param manager Manager to add.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * Option managers are used by some types of options that require
+ * interaction between different option instances (e.g., selection
+ * options), or need to support globally set properties (e.g., a global
+ * default file prefix). Option objects can retrieve the pointer to
+ * their manager when they are created, and the caller can alter the
+ * behavior of the options through the manager.
+ * See the individual managers for details.
+ *
+ * Caller is responsible for memory management of \p manager.
+ * The Options object (and its contained options) only stores a
+ * reference to the object.
+ *
+ * This method cannot be called after adding options or subsections.
+ */
+ void addManager(OptionManagerInterface *manager);
+
/*! \brief
* Adds an option collection as a subsection of this collection.
*
* subsection. If an attempt is made to add two different subsections
* with the same name, this function asserts.
*
- * For certain functionality to work properly, no options should
- * be added to the subsection after it has been added to another
- * collection.
+ * \p section should not have any options added at the point this
+ * method is called.
*
* Only a pointer to the provided object is stored. The caller is
* responsible that the object exists for the lifetime of the
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_options
*/
-#include "gromacs/options/optionsassigner.h"
+#include "gmxpre.h"
+
+#include "optionsassigner.h"
#include <deque>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
-#include "../utility/common.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
#include <boost/scoped_ptr.hpp>
-#include "../utility/common.h"
-#include "../utility/exceptions.h"
-#include "../utility/gmxassert.h"
-
-#include "abstractoption.h"
-#include "abstractoptionstorage.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/options/abstractoptionstorage.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2012, by the GROMACS development team, led by
+ * Copyright (c) 2010,2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_options
*/
-#include "gromacs/options/optionsvisitor.h"
+#include "gmxpre.h"
+
+#include "optionsvisitor.h"
#include "gromacs/options/abstractoptionstorage.h"
#include "gromacs/options/options.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
-#include "../utility/common.h"
-
-#include "abstractoption.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2011,2012, by the GROMACS development team, led by
+# Copyright (c) 2010,2011,2012,2014, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
gmx_add_unit_test(OptionsUnitTests options-test
abstractoptionstorage.cpp
filenameoption.cpp
+ filenameoptionmanager.cpp
option.cpp
optionsassigner.cpp
timeunitmanager.cpp)
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_options
*/
-#include <vector>
+#include "gmxpre.h"
+
#include <string>
+#include <vector>
#include <gmock/gmock.h>
#include <gtest/gtest.h>
#include "gromacs/options/abstractoption.h"
#include "gromacs/options/options.h"
-#include "gromacs/options/optionstoragetemplate.h"
#include "gromacs/options/optionsassigner.h"
+#include "gromacs/options/optionstoragetemplate.h"
#include "gromacs/utility/exceptions.h"
#include "testutils/testasserts.h"
}
private:
- virtual gmx::AbstractOptionStoragePointer createStorage() const
+ virtual gmx::AbstractOptionStorage *createStorage(
+ const gmx::OptionManagerContainer & /*managers*/) const
{
- return gmx::AbstractOptionStoragePointer(new MockOptionStorage(*this));
+ return new MockOptionStorage(*this);
}
};
*/
/*! \internal \file
* \brief
- * Tests file name option implementation.
+ * Tests basic file name option implementation.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_options
*/
-#include <vector>
+#include "gmxpre.h"
+
+#include "gromacs/options/filenameoption.h"
#include <gtest/gtest.h>
-#include "gromacs/options/filenameoption.h"
+#include "gromacs/fileio/filenm.h"
#include "gromacs/options/options.h"
#include "gromacs/options/optionsassigner.h"
#include "gromacs/utility/exceptions.h"
-#include "gromacs/utility/file.h"
#include "testutils/testasserts.h"
-#include "testutils/testfilemanager.h"
namespace
{
using gmx::FileNameOption;
-using gmx::test::TestFileManager;
-TEST(FileNameOptionTest, AddsMissingExtension)
+TEST(FileNameOptionTest, HandlesRequiredDefaultValueWithoutExtension)
{
gmx::Options options(NULL, NULL);
std::string value;
ASSERT_NO_THROW_GMX(options.addOption(
- FileNameOption("f").store(&value)
- .filetype(gmx::eftTrajectory).outputFile()));
+ FileNameOption("f").store(&value).required()
+ .filetype(gmx::eftGenericData).outputFile()
+ .defaultBasename("testfile")));
+ EXPECT_EQ("testfile.dat", value);
gmx::OptionsAssigner assigner(&options);
EXPECT_NO_THROW_GMX(assigner.start());
- EXPECT_NO_THROW_GMX(assigner.startOption("f"));
- EXPECT_NO_THROW_GMX(assigner.appendValue("testfile"));
- EXPECT_NO_THROW_GMX(assigner.finishOption());
EXPECT_NO_THROW_GMX(assigner.finish());
EXPECT_NO_THROW_GMX(options.finish());
- EXPECT_EQ("testfile.xtc", value);
+ EXPECT_EQ("testfile.dat", value);
}
-TEST(FileNameOptionTest, HandlesRequiredDefaultValueWithoutExtension)
+TEST(FileNameOptionTest, HandlesRequiredOptionWithoutValue)
{
gmx::Options options(NULL, NULL);
std::string value;
gmx::OptionsAssigner assigner(&options);
EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.startOption("f"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
EXPECT_NO_THROW_GMX(assigner.finish());
EXPECT_NO_THROW_GMX(options.finish());
EXPECT_EQ("testfile.dat", value);
}
-TEST(FileNameOptionTest, HandlesRequiredOptionWithoutValue)
+TEST(FileNameOptionTest, HandlesOptionalUnsetOption)
{
gmx::Options options(NULL, NULL);
std::string value;
ASSERT_NO_THROW_GMX(options.addOption(
- FileNameOption("f").store(&value).required()
- .filetype(gmx::eftGenericData).outputFile()
+ FileNameOption("f").store(&value)
+ .filetype(gmx::eftTrajectory).outputFile()
.defaultBasename("testfile")));
+ EXPECT_TRUE(value.empty());
gmx::OptionsAssigner assigner(&options);
EXPECT_NO_THROW_GMX(assigner.start());
- EXPECT_NO_THROW_GMX(assigner.startOption("f"));
- EXPECT_NO_THROW_GMX(assigner.finishOption());
EXPECT_NO_THROW_GMX(assigner.finish());
EXPECT_NO_THROW_GMX(options.finish());
- EXPECT_EQ("testfile.dat", value);
+ EXPECT_TRUE(value.empty());
}
TEST(FileNameOptionTest, HandlesOptionalDefaultValueWithoutExtension)
EXPECT_EQ("testfile.ndx", value);
}
-TEST(FileNameOptionTest, AddsMissingExtensionBasedOnExistingFile)
+TEST(FileNameOptionTest, HandlesRequiredCustomDefaultExtension)
+{
+ gmx::Options options(NULL, NULL);
+ std::string value;
+ ASSERT_NO_THROW_GMX(options.addOption(
+ FileNameOption("f").store(&value).required()
+ .filetype(gmx::eftTrajectory).outputFile()
+ .defaultBasename("testfile")
+ .defaultType(efPDB)));
+ EXPECT_EQ("testfile.pdb", value);
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options.finish());
+
+ EXPECT_EQ("testfile.pdb", value);
+}
+
+TEST(FileNameOptionTest, HandlesOptionalCustomDefaultExtension)
{
gmx::Options options(NULL, NULL);
std::string value;
ASSERT_NO_THROW_GMX(options.addOption(
FileNameOption("f").store(&value)
- .filetype(gmx::eftTrajectory).inputFile()));
- TestFileManager tempFiles;
- std::string filename(tempFiles.getTemporaryFilePath(".trr"));
- gmx::File::writeFileFromString(filename, "Dummy trajectory file");
- std::string inputValue(filename.substr(0, filename.length() - 4));
+ .filetype(gmx::eftTrajectory).outputFile()
+ .defaultBasename("testfile")
+ .defaultType(efPDB)));
+ EXPECT_TRUE(value.empty());
gmx::OptionsAssigner assigner(&options);
EXPECT_NO_THROW_GMX(assigner.start());
EXPECT_NO_THROW_GMX(assigner.startOption("f"));
- EXPECT_NO_THROW_GMX(assigner.appendValue(inputValue));
EXPECT_NO_THROW_GMX(assigner.finishOption());
EXPECT_NO_THROW_GMX(assigner.finish());
EXPECT_NO_THROW_GMX(options.finish());
- EXPECT_EQ(filename, value);
+ EXPECT_EQ("testfile.pdb", value);
+}
+
+TEST(FileNameOptionTest, GivesErrorOnUnknownFileSuffix)
+{
+ gmx::Options options(NULL, NULL);
+ std::string value;
+ ASSERT_NO_THROW_GMX(options.addOption(
+ FileNameOption("f").store(&value)
+ .filetype(gmx::eftIndex).outputFile()));
+ EXPECT_TRUE(value.empty());
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.startOption("f"));
+ EXPECT_THROW_GMX(assigner.appendValue("testfile.foo"), gmx::InvalidInputError);
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options.finish());
+
+ EXPECT_TRUE(value.empty());
+}
+
+TEST(FileNameOptionTest, GivesErrorOnInvalidFileSuffix)
+{
+ gmx::Options options(NULL, NULL);
+ std::string value;
+ ASSERT_NO_THROW_GMX(options.addOption(
+ FileNameOption("f").store(&value)
+ .filetype(gmx::eftTrajectory).outputFile()));
+ EXPECT_TRUE(value.empty());
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.startOption("f"));
+ EXPECT_THROW_GMX(assigner.appendValue("testfile.dat"), gmx::InvalidInputError);
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options.finish());
+
+ EXPECT_TRUE(value.empty());
}
} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests file name option implementation dependent on gmx::FileNameOptionManager.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_options
+ */
+#include "gmxpre.h"
+
+#include "gromacs/options/filenameoptionmanager.h"
+
+#include <gtest/gtest.h>
+
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/options.h"
+#include "gromacs/options/optionsassigner.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/file.h"
+#include "gromacs/utility/path.h"
+
+#include "testutils/testasserts.h"
+#include "testutils/testfilemanager.h"
+
+namespace
+{
+
+using gmx::FileNameOption;
+
+class FileNameOptionManagerTest : public ::testing::Test
+{
+ public:
+ FileNameOptionManagerTest()
+ : options_(NULL, NULL)
+ {
+ options_.addManager(&manager_);
+ }
+
+ std::string createDummyFile(const char *suffix)
+ {
+ std::string filename(tempFiles_.getTemporaryFilePath(suffix));
+ gmx::File::writeFileFromString(filename, "Dummy file");
+ return filename;
+ }
+
+ gmx::FileNameOptionManager manager_;
+ gmx::Options options_;
+ gmx::test::TestFileManager tempFiles_;
+};
+
+/********************************************************************
+ * Actual tests
+ */
+
+TEST_F(FileNameOptionManagerTest, AddsMissingExtension)
+{
+ std::string value;
+ ASSERT_NO_THROW_GMX(options_.addOption(
+ FileNameOption("f").store(&value)
+ .filetype(gmx::eftTrajectory).outputFile()));
+
+ gmx::OptionsAssigner assigner(&options_);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.startOption("f"));
+ EXPECT_NO_THROW_GMX(assigner.appendValue("testfile"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options_.finish());
+
+ EXPECT_EQ("testfile.xtc", value);
+}
+
+TEST_F(FileNameOptionManagerTest, AddsMissingCustomDefaultExtension)
+{
+ std::string value;
+ ASSERT_NO_THROW_GMX(options_.addOption(
+ FileNameOption("f").store(&value)
+ .filetype(gmx::eftTrajectory).outputFile()
+ .defaultType(efPDB)));
+
+ gmx::OptionsAssigner assigner(&options_);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.startOption("f"));
+ EXPECT_NO_THROW_GMX(assigner.appendValue("testfile"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options_.finish());
+
+ EXPECT_EQ("testfile.pdb", value);
+}
+
+TEST_F(FileNameOptionManagerTest, GivesErrorOnMissingInputFile)
+{
+ std::string value;
+ ASSERT_NO_THROW_GMX(options_.addOption(
+ FileNameOption("f").store(&value)
+ .filetype(gmx::eftIndex).inputFile()));
+ EXPECT_TRUE(value.empty());
+
+ gmx::OptionsAssigner assigner(&options_);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.startOption("f"));
+ EXPECT_THROW_GMX(assigner.appendValue("missing.ndx"), gmx::InvalidInputError);
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options_.finish());
+
+ EXPECT_TRUE(value.empty());
+}
+
+TEST_F(FileNameOptionManagerTest, GivesErrorOnMissingGenericInputFile)
+{
+ std::string value;
+ ASSERT_NO_THROW_GMX(options_.addOption(
+ FileNameOption("f").store(&value)
+ .filetype(gmx::eftTrajectory).inputFile()));
+ EXPECT_TRUE(value.empty());
+
+ gmx::OptionsAssigner assigner(&options_);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.startOption("f"));
+ EXPECT_THROW_GMX(assigner.appendValue("missing.trr"), gmx::InvalidInputError);
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options_.finish());
+
+ EXPECT_TRUE(value.empty());
+}
+
+TEST_F(FileNameOptionManagerTest, GivesErrorOnMissingDefaultInputFile)
+{
+ std::string value;
+ ASSERT_NO_THROW_GMX(options_.addOption(
+ FileNameOption("f").store(&value)
+ .filetype(gmx::eftIndex).inputFile()
+ .defaultBasename("missing")));
+
+ gmx::OptionsAssigner assigner(&options_);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.startOption("f"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_THROW_GMX(options_.finish(), gmx::InvalidInputError);
+}
+
+TEST_F(FileNameOptionManagerTest, GivesErrorOnMissingRequiredInputFile)
+{
+ std::string value;
+ ASSERT_NO_THROW_GMX(options_.addOption(
+ FileNameOption("f").store(&value).required()
+ .filetype(gmx::eftIndex).inputFile()
+ .defaultBasename("missing")));
+ EXPECT_EQ("missing.ndx", value);
+
+ gmx::OptionsAssigner assigner(&options_);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_THROW_GMX(options_.finish(), gmx::InvalidInputError);
+}
+
+TEST_F(FileNameOptionManagerTest, AcceptsMissingInputFileIfSpecified)
+{
+ std::string value;
+ ASSERT_NO_THROW_GMX(options_.addOption(
+ FileNameOption("f").store(&value)
+ .filetype(gmx::eftIndex).inputFile()
+ .allowMissing()));
+ EXPECT_TRUE(value.empty());
+
+ gmx::OptionsAssigner assigner(&options_);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.startOption("f"));
+ EXPECT_NO_THROW_GMX(assigner.appendValue("missing.ndx"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options_.finish());
+
+ EXPECT_EQ("missing.ndx", value);
+}
+
+TEST_F(FileNameOptionManagerTest, AcceptsMissingDefaultInputFileIfSpecified)
+{
+ std::string value;
+ ASSERT_NO_THROW_GMX(options_.addOption(
+ FileNameOption("f").store(&value)
+ .filetype(gmx::eftIndex).inputFile()
+ .defaultBasename("missing")
+ .allowMissing()));
+
+ gmx::OptionsAssigner assigner(&options_);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.startOption("f"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options_.finish());
+
+ EXPECT_EQ("missing.ndx", value);
+}
+
+TEST_F(FileNameOptionManagerTest, AcceptsMissingRequiredInputFileIfSpecified)
+{
+ std::string value;
+ ASSERT_NO_THROW_GMX(options_.addOption(
+ FileNameOption("f").store(&value).required()
+ .filetype(gmx::eftIndex).inputFile()
+ .defaultBasename("missing")
+ .allowMissing()));
+ EXPECT_EQ("missing.ndx", value);
+
+ gmx::OptionsAssigner assigner(&options_);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options_.finish());
+
+ EXPECT_EQ("missing.ndx", value);
+}
+
+TEST_F(FileNameOptionManagerTest, AddsMissingExtensionBasedOnExistingFile)
+{
+ std::string filename(createDummyFile(".trr"));
+ std::string inputValue(gmx::Path::stripExtension(filename));
+
+ std::string value;
+ ASSERT_NO_THROW_GMX(options_.addOption(
+ FileNameOption("f").store(&value)
+ .filetype(gmx::eftTrajectory).inputFile()));
+
+ gmx::OptionsAssigner assigner(&options_);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.startOption("f"));
+ EXPECT_NO_THROW_GMX(assigner.appendValue(inputValue));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options_.finish());
+
+ EXPECT_EQ(filename, value);
+}
+
+TEST_F(FileNameOptionManagerTest,
+ AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile)
+{
+ std::string filename(createDummyFile(".trr"));
+ std::string inputValue(gmx::Path::stripExtension(filename));
+
+ std::string value;
+ ASSERT_NO_THROW_GMX(options_.addOption(
+ FileNameOption("f").store(&value).required()
+ .filetype(gmx::eftTrajectory).inputFile()
+ .defaultBasename(inputValue.c_str())));
+ EXPECT_EQ(inputValue + ".xtc", value);
+
+ gmx::OptionsAssigner assigner(&options_);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.startOption("f"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options_.finish());
+
+ EXPECT_EQ(filename, value);
+}
+
+TEST_F(FileNameOptionManagerTest,
+ AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile)
+{
+ std::string filename(createDummyFile(".trr"));
+ std::string inputValue(gmx::Path::stripExtension(filename));
+
+ std::string value;
+ ASSERT_NO_THROW_GMX(options_.addOption(
+ FileNameOption("f").store(&value)
+ .filetype(gmx::eftTrajectory).inputFile()
+ .defaultBasename(inputValue.c_str())));
+
+ gmx::OptionsAssigner assigner(&options_);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.startOption("f"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options_.finish());
+
+ EXPECT_EQ(filename, value);
+}
+
+TEST_F(FileNameOptionManagerTest,
+ AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile)
+{
+ std::string filename(createDummyFile(".trr"));
+ std::string inputValue(gmx::Path::stripExtension(filename));
+
+ std::string value;
+ ASSERT_NO_THROW_GMX(options_.addOption(
+ FileNameOption("f").store(&value).required()
+ .filetype(gmx::eftTrajectory).inputFile()
+ .defaultBasename("foo")));
+ ASSERT_NO_THROW_GMX(manager_.addDefaultFileNameOption(&options_, "deffnm"));
+ EXPECT_EQ("foo.xtc", value);
+
+ gmx::OptionsAssigner assigner(&options_);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.startOption("deffnm"));
+ EXPECT_NO_THROW_GMX(assigner.appendValue(inputValue));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options_.finish());
+
+ EXPECT_EQ(filename, value);
+}
+
+TEST_F(FileNameOptionManagerTest,
+ AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile)
+{
+ std::string filename(createDummyFile(".trr"));
+ std::string inputValue(gmx::Path::stripExtension(filename));
+
+ std::string value;
+ ASSERT_NO_THROW_GMX(options_.addOption(
+ FileNameOption("f").store(&value)
+ .filetype(gmx::eftTrajectory).inputFile()
+ .defaultBasename("foo")));
+ ASSERT_NO_THROW_GMX(manager_.addDefaultFileNameOption(&options_, "deffnm"));
+
+ gmx::OptionsAssigner assigner(&options_);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.startOption("deffnm"));
+ EXPECT_NO_THROW_GMX(assigner.appendValue(inputValue));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.startOption("f"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options_.finish());
+
+ EXPECT_EQ(filename, value);
+}
+
+} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_options
*/
-#include <vector>
+#include "gmxpre.h"
+
#include <string>
+#include <vector>
#include <gtest/gtest.h>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_options
*/
+#include "gmxpre.h"
+
+#include "gromacs/options/optionsassigner.h"
+
#include <limits>
#include <vector>
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
-#include "gromacs/options/optionsassigner.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/stringutil.h"
int value1 = 1;
int value2 = 2;
using gmx::IntegerOption;
+ ASSERT_NO_THROW(options.addSubSection(&sub1));
+ ASSERT_NO_THROW(options.addSubSection(&sub2));
ASSERT_NO_THROW(options.addOption(IntegerOption("p").store(&value)));
ASSERT_NO_THROW(sub1.addOption(IntegerOption("p").store(&value1)));
ASSERT_NO_THROW(sub2.addOption(IntegerOption("p").store(&value2)));
- ASSERT_NO_THROW(options.addSubSection(&sub1));
- ASSERT_NO_THROW(options.addSubSection(&sub2));
gmx::OptionsAssigner assigner(&options);
EXPECT_NO_THROW(assigner.start());
int pvalue2 = 2;
int rvalue = 5;
using gmx::IntegerOption;
+ ASSERT_NO_THROW(options.addSubSection(&sub1));
+ ASSERT_NO_THROW(options.addSubSection(&sub2));
ASSERT_NO_THROW(options.addOption(IntegerOption("p").store(&pvalue)));
ASSERT_NO_THROW(sub1.addOption(IntegerOption("p").store(&pvalue1)));
ASSERT_NO_THROW(sub1.addOption(IntegerOption("q").store(&qvalue)));
ASSERT_NO_THROW(sub2.addOption(IntegerOption("p").store(&pvalue2)));
ASSERT_NO_THROW(sub2.addOption(IntegerOption("r").store(&rvalue)));
- ASSERT_NO_THROW(options.addSubSection(&sub1));
- ASSERT_NO_THROW(options.addSubSection(&sub2));
gmx::OptionsAssigner assigner(&options);
assigner.setNoStrictSectioning(true);
EXPECT_EQ(1, index);
}
+TEST(OptionsAssignerStringTest, HandlesEnumDefaultValueFromVariable)
+{
+ gmx::Options options(NULL, NULL);
+ std::string value("test");
+ const char * const allowed[] = { "none", "test", "value" };
+ int index = -1;
+ using gmx::StringOption;
+ ASSERT_NO_THROW(options.addOption(
+ StringOption("p").store(&value)
+ .enumValue(allowed).storeEnumIndex(&index)));
+ EXPECT_EQ("test", value);
+ EXPECT_EQ(1, index);
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW(assigner.start());
+ EXPECT_NO_THROW(assigner.finish());
+ EXPECT_NO_THROW(options.finish());
+
+ EXPECT_EQ("test", value);
+ EXPECT_EQ(1, index);
+}
+
+TEST(OptionsAssignerStringTest, HandlesEnumDefaultValueFromVector)
+{
+ gmx::Options options(NULL, NULL);
+ std::vector<std::string> value;
+ value.push_back("test");
+ value.push_back("value");
+ const char * const allowed[] = { "none", "test", "value" };
+ int index[2] = {-1, -1};
+ using gmx::StringOption;
+ ASSERT_NO_THROW(options.addOption(
+ StringOption("p").storeVector(&value).valueCount(2)
+ .enumValue(allowed).storeEnumIndex(index)));
+ EXPECT_EQ("test", value[0]);
+ EXPECT_EQ("value", value[1]);
+ EXPECT_EQ(1, index[0]);
+ EXPECT_EQ(2, index[1]);
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW(assigner.start());
+ EXPECT_NO_THROW(assigner.finish());
+ EXPECT_NO_THROW(options.finish());
+
+ EXPECT_EQ("test", value[0]);
+ EXPECT_EQ("value", value[1]);
+ EXPECT_EQ(1, index[0]);
+ EXPECT_EQ(2, index[1]);
+}
+
TEST(OptionsAssignerStringTest, HandlesEnumDefaultIndex)
{
gmx::Options options(NULL, NULL);
EXPECT_EQ(1, index);
}
+TEST(OptionsAssignerStringTest, HandlesEnumDefaultIndexFromVariable)
+{
+ gmx::Options options(NULL, NULL);
+ const char * const allowed[] = { "none", "test", "value" };
+ int index = 1;
+ using gmx::StringOption;
+ ASSERT_NO_THROW(options.addOption(
+ StringOption("p")
+ .enumValue(allowed).storeEnumIndex(&index)));
+ EXPECT_EQ(1, index);
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW(assigner.start());
+ EXPECT_NO_THROW(assigner.finish());
+ EXPECT_NO_THROW(options.finish());
+
+ EXPECT_EQ(1, index);
+}
+
} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_options
*/
+#include "gmxpre.h"
+
+#include "gromacs/options/timeunitmanager.h"
+
#include <gtest/gtest.h>
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
#include "gromacs/options/optionsassigner.h"
-#include "gromacs/options/timeunitmanager.h"
#include "testutils/testasserts.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_options
*/
-#include "gromacs/options/timeunitmanager.h"
+#include "gmxpre.h"
+
+#include "timeunitmanager.h"
+
+#include <cstdlib>
+
+#include <algorithm>
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
#include "gromacs/options/optionsvisitor.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/stringutil.h"
namespace
{
return 1.0 / timeScaleFactor();
}
+void TimeUnitManager::setTimeUnitFromEnvironment()
+{
+ const char *const value = std::getenv("GMXTIMEUNIT");
+ if (value != NULL)
+ {
+ ConstArrayRef<const char *> timeUnits(g_timeUnits);
+ ConstArrayRef<const char *>::const_iterator i =
+ std::find(timeUnits.begin(), timeUnits.end(), std::string(value));
+ if (i == timeUnits.end())
+ {
+ std::string message = formatString(
+ "Time unit provided with environment variable GMXTIMEUNIT=%s "
+ "is not recognized as a valid time unit.\n"
+ "Possible values are: %s",
+ value, joinStrings(timeUnits, ", ").c_str());
+ GMX_THROW(InvalidInputError(message));
+ }
+ timeUnit_ = i - timeUnits.begin();
+ }
+}
+
void TimeUnitManager::addTimeUnitOption(Options *options, const char *name)
{
options->addOption(StringOption(name).enumValue(g_timeUnits)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_OPTIONS_TIMEUNITMANAGER_H
#define GMX_OPTIONS_TIMEUNITMANAGER_H
-#include "../utility/gmxassert.h"
+#include "gromacs/utility/gmxassert.h"
namespace gmx
{
//! Returns the scaling factor to convert times from ps.
double inverseTimeScaleFactor() const;
+ /*! \brief
+ * Sets the time unit in this manager from an environment variable.
+ */
+ void setTimeUnitFromEnvironment();
/*! \brief
* Adds a common option for selecting the time unit.
*
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+file(GLOB PBCUTIL_SOURCES *.cpp *.c)
+set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${PBCUTIL_SOURCES} PARENT_SCOPE)
+
+gmx_install_headers(
+ ishift.h
+ pbc.h
+ rmpbc.h
+ )
+
+if (BUILD_TESTING)
+# add_subdirectory(tests)
+endif()
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-
-/* not really neccesary, right now: */
-#ifdef __cplusplus
-extern "C" {
-#endif
-
+#ifndef GMX_PBCUTIL_ISHIFT_H
+#define GMX_PBCUTIL_ISHIFT_H
#define D_BOX_Z 1
#define D_BOX_Y 1
#define IS2Y(iv) ((((iv) / N_BOX_X) % N_BOX_Y) - D_BOX_Y)
#define IS2Z(iv) ((iv) / (N_BOX_X*N_BOX_Y) - D_BOX_Z)
-
-#ifdef __cplusplus
-}
#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "mshift.h"
#include <string.h>
+
+#include <algorithm>
+
+#include "gromacs/legacyheaders/types/ifunc.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-#include "vec.h"
-#include "gromacs/fileio/futil.h"
-#include "mshift.h"
-#include "main.h"
-#include "pbc.h"
/************************************************************
*
}
}
-GMX_ATTRIBUTE_NORETURN static void g_error(int line, const char *file)
+gmx_noreturn static void g_error(int line, const char *file)
{
gmx_fatal(FARGS, "Tring to print non existant graph (file %s, line %d)",
file, line);
g->nedge[i]);
for (j = 0; (j < g->nedge[i]); j++)
{
- fprintf(log, " %5u", g->edge[i][j]+1);
+ fprintf(log, " %5d", g->edge[i][j]+1);
}
fprintf(log, "\n");
}
nbond[iaa] += 2;
nbond[ia[2]] += 1;
nbond[ia[3]] += 1;
- g->at_start = min(g->at_start, iaa);
- g->at_end = max(g->at_end, iaa+2+1);
+ g->at_start = std::min(g->at_start, iaa);
+ g->at_end = std::max(g->at_end, iaa+2+1);
}
}
else
iaa = ia[k];
if (iaa >= at_start && iaa < at_end)
{
- g->at_start = min(g->at_start, iaa);
- g->at_end = max(g->at_end, iaa+1);
+ g->at_start = std::min(g->at_start, iaa);
+ g->at_end = std::max(g->at_end, iaa+1);
/* When making the graph we (might) link all atoms in an interaction
* sequentially. Therefore the end atoms add 1 to the count,
* the middle atoms 2.
for (i = g->at_start; (i < g->at_end); i++)
{
nbtot += nbond[i];
- nnb = max(nnb, nbond[i]);
+ nnb = std::max(nnb, nbond[i]);
}
if (fplog)
{
static void compact_graph(FILE *fplog, t_graph *g)
{
int i, j, n, max_nedge;
- atom_id *e;
max_nedge = 0;
n = 0;
{
g->edge[0][n++] = g->edge[i][j];
}
- max_nedge = max(max_nedge, g->nedge[i]);
+ max_nedge = std::max(max_nedge, g->nedge[i]);
}
srenew(g->edge[0], n);
/* set pointers after srenew because edge[0] might move */
void done_graph(t_graph *g)
{
- int i;
-
GCHECK(g);
if (g->nnodes > 0)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_PBCUTIL_MSHIFT_H
+#define GMX_PBCUTIL_MSHIFT_H
-#ifndef _mshift_h
-#define _mshift_h
+#include <stdio.h>
-#include "typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_idef;
+struct t_ilist;
+
+typedef enum {
+ egcolWhite, egcolGrey, egcolBlack, egcolNR
+} egCol;
+
+typedef struct t_graph {
+ int at0; /* The first atom the graph was constructed for */
+ int at1; /* The last atom the graph was constructed for */
+ int nnodes; /* The number of nodes, nnodes=at_end-at_start */
+ int nbound; /* The number of nodes with edges */
+ int at_start; /* The first connected atom in this graph */
+ int at_end; /* The last+1 connected atom in this graph */
+ int *nedge; /* For each node the number of edges */
+ atom_id **edge; /* For each node, the actual edges (bidirect.) */
+ gmx_bool bScrewPBC; /* Screw boundary conditions */
+ ivec *ishift; /* Shift for each particle */
+ int negc;
+ egCol *egc; /* color of each node */
+} t_graph;
+
+#define SHIFT_IVEC(g, i) ((g)->ishift[i])
+
t_graph *mk_graph(FILE *fplog,
- t_idef *idef, int at_start, int at_end,
+ struct t_idef *idef, int at_start, int at_end,
gmx_bool bShakeOnly, gmx_bool bSettle);
/* Build a graph from an idef description. The graph can be used
* to generate mol-shift indices.
*/
void mk_graph_ilist(FILE *fplog,
- t_ilist *ilist, int at_start, int at_end,
+ struct t_ilist *ilist, int at_start, int at_end,
gmx_bool bShakeOnly, gmx_bool bSettle,
t_graph *g);
/* As mk_graph, but takes t_ilist iso t_idef and does not allocate g */
}
#endif
-#endif /* _mshift_h */
+#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "pbc.h"
-#include <math.h>
#include <assert.h>
+#include <math.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "vec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
#include "gromacs/math/utilities.h"
-#include "main.h"
-#include "pbc.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "txtdump.h"
-#include "gmx_fatal.h"
-#include "names.h"
-#include "macros.h"
-#include "gmx_omp_nthreads.h"
/* Skip 0 so we have more chance of detecting if we forgot to call set_pbc. */
enum {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_PBCUTIL_PBC_H
+#define GMX_PBCUTIL_PBC_H
-#ifndef _types_pbc_h
-#define _types_pbc_h
+#include <stdio.h>
-#include "sysstuff.h"
-#include "typedefs.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#endif
+/* Maximum number of combinations of single triclinic box vectors
+ * required to shift atoms that are within a brick of the size of
+ * the diagonal of the box to within the maximum cut-off distance.
+ */
+#define MAX_NTRICVEC 12
+
+typedef struct t_pbc {
+ int ePBC;
+ int ndim_ePBC;
+ int ePBCDX;
+ int dim;
+ matrix box;
+ rvec fbox_diag;
+ rvec hbox_diag;
+ rvec mhbox_diag;
+ real max_cutoff2;
+ gmx_bool bLimitDistance;
+ real limit_distance2;
+ int ntric_vec;
+ ivec tric_shift[MAX_NTRICVEC];
+ rvec tric_vec[MAX_NTRICVEC];
+} t_pbc;
+
#define TRICLINIC(box) (box[YY][XX] != 0 || box[ZZ][XX] != 0 || box[ZZ][YY] != 0)
#define NTRICIMG 14
ecenterDEF = ecenterTRIC
};
+struct t_graph;
+
int ePBC2npbcdim(int ePBC);
/* Returns the number of dimensions that use pbc, starting at X */
int guess_ePBC(matrix box);
/* Guesses the type of periodic boundary conditions using the box */
-gmx_bool correct_box(FILE *fplog, int step, tensor box, t_graph *graph);
+gmx_bool correct_box(FILE *fplog, int step, tensor box, struct t_graph *graph);
/* Checks for un-allowed box angles and corrects the box
* and the integer shift vectors in the graph (if graph!=NULL) if necessary.
* Returns TRUE when the box was corrected.
}
#endif
-#endif /* _pbc_h */
+#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "mshift.h"
-#include "pbc.h"
+#include "gmxpre.h"
+
#include "rmpbc.h"
-#include "vec.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
typedef struct {
t_graph *gr;
} rmpbc_graph_t;
-typedef struct gmx_rmpbc {
+struct gmx_rmpbc {
t_idef *idef;
int natoms_init;
int ePBC;
int ngraph;
rmpbc_graph_t *graph;
-} koeiepoep;
+};
static t_graph *gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc, int ePBC, int natoms)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_PBCUTIL_RMPBC_H
+#define GMX_PBCUTIL_RMPBC_H
-#ifndef _rmpbc_h
-#define _rmpbc_h
-
-#include "typedefs.h"
+#include "gromacs/math/vectypes.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_atoms;
+struct t_idef;
+struct t_trxframe;
+
typedef struct gmx_rmpbc *gmx_rmpbc_t;
-gmx_rmpbc_t gmx_rmpbc_init(t_idef *idef, int ePBC, int natoms);
+gmx_rmpbc_t gmx_rmpbc_init(struct t_idef *idef, int ePBC, int natoms);
void gmx_rmpbc_done(gmx_rmpbc_t gpbc);
rvec x_s[]);
/* As gmx_rmpbc, but outputs in x_s and does not modify x. */
-void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc, t_trxframe *fr);
+void gmx_rmpbc_trxfr(gmx_rmpbc_t gpbc, struct t_trxframe *fr);
/* As gmx_rmpbc but operates on a t_trxframe data structure. */
-/*void rm_pbc(t_idef *idef,int ePBC,int natoms,
- matrix box,rvec x[],rvec x_s[]);*/
-/* Convenience function that still holds a static variable. */
-
-void rm_gropbc(t_atoms *atoms, rvec x[], matrix box);
+void rm_gropbc(struct t_atoms *atoms, rvec x[], matrix box);
/* Simple routine for use in analysis tools that just have a pdb or
* similar file.
*/
}
#endif
-#endif /* _rmpbc_h */
+#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "pull.h"
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
-#include "gromacs/fileio/futil.h"
-#include "index.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "vec.h"
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "network.h"
-#include "gromacs/fileio/filenm.h"
#include <string.h>
+
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "pull.h"
-#include "xvgr.h"
-#include "names.h"
-#include "pbc.h"
-#include "mtop_util.h"
-#include "mdrun.h"
-#include "gmx_ga2la.h"
-#include "copyrite.h"
-#include "macros.h"
-#include "vec.h"
static void pull_print_group_x(FILE *out, ivec dim, const t_pull_group *pgrp)
{
if (pull->dim[m])
{
sprintf(buf, "%d %s%c", c+1, "c", 'X'+m);
- setname[nsets] = strdup(buf);
+ setname[nsets] = gmx_strdup(buf);
nsets++;
}
}
if (pull->dim[m])
{
sprintf(buf, "%d %s%c", c+1, "d", 'X'+m);
- setname[nsets] = strdup(buf);
+ setname[nsets] = gmx_strdup(buf);
nsets++;
}
}
else
{
sprintf(buf, "%d", c+1);
- setname[nsets] = strdup(buf);
+ setname[nsets] = gmx_strdup(buf);
nsets++;
}
}
#ifndef GMX_PULLING_PULL_H
#define GMX_PULLING_PULL_H
-#include "typedefs.h"
-#include "../fileio/filenm.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_pbc;
/*! \brief Get the distance to the reference and deviation for pull coord coord_ind.
*
*/
void get_pull_coord_distance(const t_pull *pull,
int coord_ind,
- const t_pbc *pbc, double t,
+ const struct t_pbc *pbc, double t,
dvec dr, double *dev);
*
* \returns The pull potential energy.
*/
-real pull_potential(int ePull, t_pull *pull, t_mdatoms *md, t_pbc *pbc,
+real pull_potential(int ePull, t_pull *pull, t_mdatoms *md, struct t_pbc *pbc,
t_commrec *cr, double t, real lambda,
rvec *x, rvec *f, tensor vir, real *dvdlambda);
* \param[in,out] v Velocities, which may get a pull correction.
* \param[in,out] vir The virial, which, if != NULL, gets a pull correction.
*/
-void pull_constraint(t_pull *pull, t_mdatoms *md, t_pbc *pbc,
+void pull_constraint(t_pull *pull, t_mdatoms *md, struct t_pbc *pbc,
t_commrec *cr, double dt, double t,
rvec *x, rvec *xp, rvec *v, tensor vir);
* \param[in,out] xp Updated x, can be NULL.
*
*/
-void pull_calc_coms(t_commrec *cr,
- t_pull *pull,
- t_mdatoms *md,
- t_pbc *pbc,
- double t,
- rvec x[],
- rvec *xp);
+void pull_calc_coms(t_commrec *cr,
+ t_pull *pull,
+ t_mdatoms *md,
+ struct t_pbc *pbc,
+ double t,
+ rvec x[],
+ rvec *xp);
#ifdef __cplusplus
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "pull_rotation.h"
+
+#include "config.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include "domdec.h"
-#include "gromacs/utility/smalloc.h"
-#include "network.h"
-#include "pbc.h"
-#include "mdrun.h"
-#include "txtdump.h"
-#include "names.h"
-#include "mtop_util.h"
-#include "names.h"
-#include "vec.h"
-#include "gmx_ga2la.h"
-#include "xvgr.h"
-#include "copyrite.h"
-#include "macros.h"
-
-#include "gromacs/fileio/futil.h"
+#include "gromacs/domdec/domdec.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/txtdump.h"
#include "gromacs/linearalgebra/nrjac.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/groupcoord.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/cyclecounter.h"
#include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/qsort_threadsafe.h"
-#include "gromacs/pulling/pull_rotation.h"
-#include "gromacs/mdlib/groupcoord.h"
-#include "gromacs/math/utilities.h"
+#include "gromacs/utility/smalloc.h"
static char *RotStr = {"Enforced rotation:"};
add_to_string_aligned(&LegendStr, buf);
sprintf(buf2, "%s (degrees)", buf);
- setname[nsets] = strdup(buf2);
+ setname[nsets] = gmx_strdup(buf2);
nsets++;
}
for (g = 0; g < rot->ngrp; g++)
}
add_to_string_aligned(&LegendStr, buf);
sprintf(buf2, "%s (degrees)", buf);
- setname[nsets] = strdup(buf2);
+ setname[nsets] = gmx_strdup(buf2);
nsets++;
sprintf(buf, "tau%d", g);
add_to_string_aligned(&LegendStr, buf);
sprintf(buf2, "%s (kJ/mol)", buf);
- setname[nsets] = strdup(buf2);
+ setname[nsets] = gmx_strdup(buf2);
nsets++;
sprintf(buf, "energy%d", g);
add_to_string_aligned(&LegendStr, buf);
sprintf(buf2, "%s (kJ/mol)", buf);
- setname[nsets] = strdup(buf2);
+ setname[nsets] = gmx_strdup(buf2);
nsets++;
}
fprintf(fp, "#\n");
#ifndef GMX_PULLING_PULL_ROTATION_H
#define GMX_PULLING_PULL_ROTATION_H
-#include "typedefs.h"
-#include "../fileio/filenm.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/timing/wallcycle.h"
#ifdef __cplusplus
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <stdlib.h>
-#include "sysstuff.h"
-#include "princ.h"
-#include "gromacs/fileio/futil.h"
-#include "vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-#include "symtab.h"
-#include "index.h"
#include "gromacs/fileio/confio.h"
-#include "network.h"
-#include "pbc.h"
-#include "pull.h"
-#include "gmx_ga2la.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void pull_set_pbcatom(t_commrec *cr, t_pull_group *pgrp,
rvec *x,
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include "random.h"
+#include "config.h"
+
+#include <math.h>
#include <stdio.h>
#include <stdlib.h>
-#ifdef HAVE_UNISTD_H
-#include <unistd.h>
-#endif
#include <time.h>
-#include <math.h>
-#ifdef GMX_NATIVE_WINDOWS
-#include <process.h>
-#endif
#include "external/Random123-1.08/include/Random123/threefry.h"
#include "gromacs/math/utilities.h"
-#include "random_gausstable.h"
+#include "gromacs/random/random_gausstable.h"
+#include "gromacs/utility/sysinfo.h"
#define RNG_N 624
#define RNG_M 397
else
{
/* No random device available, use time-of-day and process id */
-#ifdef GMX_NATIVE_WINDOWS
- my_pid = (long)_getpid();
-#else
- my_pid = (long)getpid();
-#endif
- data = (unsigned int)(((long)time(NULL)+my_pid) % (long)1000000);
+ my_pid = gmx_getpid();
+ data = (unsigned int)(((long)time(NULL)+my_pid) % (long)1000000);
}
return data;
}
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _GMX_RANDOM_H_
-#define _GMX_RANDOM_H_
+#ifndef GMX_RANDOM_RANDOM_H
+#define GMX_RANDOM_RANDOM_H
-#include <stdio.h>
-#include "types/simple.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#endif
/*! Fixed random number seeds for different types of RNG */
-#define RND_SEED_UPDATE 1 /*!< For coordinate update (sd, bd, ..) */
-#define RND_SEED_REPLEX 2 /*!< For replica exchange */
-#define RND_SEED_VRESCALE 3 /*!< For V-rescale thermostat */
-#define RND_SEED_ANDERSEN 4 /*!< For Andersen thermostat */
-#define RND_SEED_TPI 5 /*!< For test particle insertion */
-#define RND_SEED_EXPANDED 6 /*!< For expanded emseble methods */
+#define RND_SEED_UPDATE 1 /**< For coordinate update (sd, bd, ..) */
+#define RND_SEED_REPLEX 2 /**< For replica exchange */
+#define RND_SEED_VRESCALE 3 /**< For V-rescale thermostat */
+#define RND_SEED_ANDERSEN 4 /**< For Andersen thermostat */
+#define RND_SEED_TPI 5 /**< For test particle insertion */
+#define RND_SEED_EXPANDED 6 /**< For expanded emseble methods */
/*! \brief Abstract datatype for a random number generator
*
}
#endif
-#endif /* _GMX_RANDOM_H_ */
+#endif
* \author Roland Schulz <roland@utk.edu>
* \ingroup module_random
*/
+#include "gmxpre.h"
+
#include <vector>
#include <gtest/gtest.h>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_SELECTION_H
#define GMX_SELECTION_H
-#include "selection/selection.h"
-#include "selection/selectioncollection.h"
-#include "selection/selectionoption.h"
-#include "selection/selectionoptionmanager.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectioncollection.h"
+#include "gromacs/selection/selectionoption.h"
+#include "gromacs/selection/selectionoptionmanager.h"
#endif
file(GLOB SELECTION_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${SELECTION_SOURCES} PARENT_SCOPE)
-set(SELECTION_PUBLIC_HEADERS
+gmx_install_headers(
nbsearch.h
indexutil.h
position.h
selectioncollection.h
selectionenums.h
selectionoption.h
- selectionoptionmanager.h)
-gmx_install_headers(selection ${SELECTION_PUBLIC_HEADERS})
+ selectionoptionmanager.h
+ )
if (BUILD_TESTING)
add_subdirectory(tests)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#include "gromacs/selection/centerofmass.h"
+#include "gmxpre.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/vec.h"
+#include "centerofmass.h"
+
+#include <errno.h>
+
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/topology.h"
int
gmx_calc_cog(t_topology * /* top */, rvec x[], int nrefat, atom_id index[], rvec xout)
#ifndef GMX_SELECTION_CENTEROFMASS_H
#define GMX_SELECTION_CENTEROFMASS_H
-#include "../legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vectypes.h"
+
+struct t_block;
+struct t_blocka;
+struct t_pbc;
+struct t_topology;
/*! \brief
* Calculate a single center of geometry.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* calculated.
* Currently, no other processing is done.
*/
-#include "compiler.h"
+#include "gmxpre.h"
-#include <algorithm>
+#include "compiler.h"
#include <math.h>
#include <stdarg.h>
-#include "gromacs/legacyheaders/vec.h"
+#include <algorithm>
+#include "gromacs/math/vec.h"
#include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
#include "gromacs/selection/selection.h"
-#include "gromacs/selection/selmethod.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "evaluate.h"
#include "keywords.h"
#include "mempool.h"
+#include "poscalc.h"
#include "selectioncollection-impl.h"
#include "selelem.h"
+#include "selmethod.h"
using std::min;
+using gmx::SelectionLocation;
using gmx::SelectionTreeElement;
using gmx::SelectionTreeElementPointer;
/* The latter check excludes variable references. */
if (child->type == SEL_SUBEXPRREF && child->child->type != SEL_SUBEXPR)
{
+ SelectionLocation location = child->child->location();
/* Create the root element for the subexpression */
if (!root)
{
- root.reset(new SelectionTreeElement(SEL_ROOT));
+ root.reset(new SelectionTreeElement(SEL_ROOT, location));
subexpr = root;
}
else
{
- subexpr->next.reset(new SelectionTreeElement(SEL_ROOT));
+ subexpr->next.reset(new SelectionTreeElement(SEL_ROOT, location));
subexpr = subexpr->next;
}
/* Create the subexpression element and
* move the actual subexpression under the created element. */
- subexpr->child.reset(new SelectionTreeElement(SEL_SUBEXPR));
+ subexpr->child.reset(new SelectionTreeElement(SEL_SUBEXPR, location));
_gmx_selelem_set_vtype(subexpr->child, child->v.type);
subexpr->child->child = child->child;
child->child = subexpr->child;
{
// Add a dummy head element that precedes the first child.
SelectionTreeElementPointer dummy(
- new SelectionTreeElement(SEL_BOOLEAN));
+ new SelectionTreeElement(SEL_BOOLEAN, SelectionLocation::createEmpty()));
dummy->next = sel->child;
SelectionTreeElementPointer prev = dummy;
SelectionTreeElementPointer child = dummy;
* \param[in,out] sc Selection collection data.
*
* The evaluation group of each \ref SEL_ROOT element corresponding to a
- * selection in \p sc is set to NULL. The evaluation grop for \ref SEL_ROOT
+ * selection in \p sc is set to NULL. The evaluation group for \ref SEL_ROOT
* elements corresponding to subexpressions that need full evaluation is set
* to \c sc->gall.
*/
if ((sel->flags & SEL_DYNAMIC)
&& sel->v.type != GROUP_VALUE && sel->v.type != POS_VALUE)
{
- sel->v.nr = isize;
+ sel->v.nr = ((sel->flags & SEL_SINGLEVAL) ? 1 : isize);
}
/* If the method is char-valued, pre-allocate the strings. */
if (sel->u.expr.method->flags & SMETH_CHARVAL)
child->next.reset();
sel->cdata->evaluate(data, sel, g);
/* Replace the subexpressions with the result */
- child.reset(new SelectionTreeElement(SEL_CONST));
+ child.reset(new SelectionTreeElement(SEL_CONST, SelectionLocation::createEmpty()));
child->flags = SEL_FLAGSSET | SEL_SINGLEVAL | SEL_ALLOCVAL | SEL_ALLOCDATA;
_gmx_selelem_set_vtype(child, GROUP_VALUE);
child->evaluate = NULL;
{
child->cdata->evaluate = &_gmx_sel_evaluate_static;
/* The cgrp has only been allocated if it originated from an
- * external index group. In that case, we need special handling
- * to preserve the name of the group and to not leak memory.
+ * external index group.
* If cgrp has been set in make_static(), it is not allocated,
* and hence we can overwrite it safely. */
if (child->u.cgrp.nalloc_index > 0)
}
+/********************************************************************
+ * REQUIRED ATOMS ANALYSIS
+ ********************************************************************/
+
+/*! \brief
+ * Finds the highest atom index required to evaluate a selection subtree.
+ *
+ * \param[in] sel Root of the selection subtree to process.
+ * \param[in,out] maxAtomIndex The highest atom index required to evaluate the
+ * subtree. The existing value is never decreased, so multiple calls with
+ * the same parameter will compute the maximum over several subtrees.
+ *
+ * For evaluation that starts from a \ref SEL_ROOT element with a fixed group,
+ * children will never extend the evaluation group except for method parameter
+ * evaluation (which have their own root element), so it is sufficient to check
+ * the root. However, children of \ref SEL_EXPRESSION elements (i.e., the
+ * method parameters) may have been independently evaluated to a static group
+ * that no longer has a separate root, so those need to be checked as well.
+ *
+ * Position calculations are not considered here, but are analyzed through the
+ * position calculation collection in the main compilation method.
+ */
+static void
+init_required_atoms(const SelectionTreeElementPointer &sel, int *maxAtomIndex)
+{
+ // Process children.
+ if (sel->type != SEL_SUBEXPRREF)
+ {
+ SelectionTreeElementPointer child = sel->child;
+ while (child)
+ {
+ init_required_atoms(child, maxAtomIndex);
+ child = child->next;
+ }
+ }
+
+ if (sel->type == SEL_ROOT
+ || (sel->type == SEL_CONST && sel->v.type == GROUP_VALUE))
+ {
+ if (sel->u.cgrp.isize > 0)
+ {
+ *maxAtomIndex =
+ std::max(*maxAtomIndex, gmx_ana_index_get_max_index(&sel->u.cgrp));
+ }
+ }
+}
+
+
/********************************************************************
* FINAL SUBEXPRESSION OPTIMIZATION
********************************************************************/
coll->printTree(stderr, false);
}
- /* Initialize evaluation groups, position calculations for methods, perform
- * some final optimization, and free the memory allocated for the
- * compilation. */
+ // Initialize evaluation groups, maximum atom index needed for evaluation,
+ // position calculations for methods, perform some final optimization, and
+ // free the memory allocated for the compilation.
+ coll->impl_->maxAtomIndex_ = 0;
/* By default, use whole residues/molecules. */
flags = POS_COMPLWHOLE;
PositionCalculationCollection::typeFromEnum(coll->impl_->rpost_.c_str(),
{
init_root_item(item, &sc->gall);
postprocess_item_subexpressions(item);
+ init_required_atoms(item, &coll->impl_->maxAtomIndex_);
init_item_comg(item, &sc->pcc, post, flags);
free_item_compilerdata(item);
item = item->next;
}
+ coll->impl_->maxAtomIndex_ =
+ std::max(coll->impl_->maxAtomIndex_,
+ sc->pcc.getHighestRequiredAtomIndex());
/* Allocate memory for the evaluation memory pool. */
_gmx_sel_mempool_reserve(sc->mempool, 0);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
+#include "evaluate.h"
+
#include <string.h>
-#include "gromacs/legacyheaders/vec.h"
+#include <algorithm>
#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
#include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
#include "gromacs/selection/selection.h"
-#include "gromacs/selection/selmethod.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
-#include "evaluate.h"
#include "mempool.h"
+#include "poscalc.h"
#include "selectioncollection-impl.h"
#include "selelem.h"
+#include "selmethod.h"
using gmx::SelectionTreeElement;
using gmx::SelectionTreeElementPointer;
"Can only assign one element with one instance");
GMX_RELEASE_ASSERT(sel->v.type == vsource.v.type,
"Mismatching selection value types");
- old_ptr_ = sel->v.u.ptr;
- old_nalloc_ = sel->v.nalloc;
+ _gmx_selvalue_getstore_and_release(&sel->v, &old_ptr_, &old_nalloc_);
_gmx_selvalue_setstore(&sel->v, vsource.v.u.ptr);
sel_ = sel;
}
int old_nalloc_;
};
+/*! \brief
+ * Expands a value array from one-per-position to one-per-atom.
+ *
+ * \param[in,out] value Array to expand.
+ * \param[in,out] nr Number of values in \p value.
+ * \param[in] pos Position data.
+ * \tparam T Value type of the array to expand.
+ *
+ * On input, \p value contains one value for each position in \p pos (and `*nr`
+ * must match). On output, \p value will contain a value for each atom used to
+ * evaluate `pos`: each input value is replicated to all atoms that make up the
+ * corresponding position.
+ * The operation is done in-place.
+ *
+ * Does not throw.
+ */
+template <typename T>
+void expandValueForPositions(T value[], int *nr, gmx_ana_pos_t *pos)
+{
+ GMX_RELEASE_ASSERT(*nr == pos->count(),
+ "Position update method did not return the correct number of values");
+ *nr = pos->m.mapb.nra;
+ // Loop over the positions in reverse order so that the expansion can be
+ // done in-place (assumes that each position has at least one atom, which
+ // should always be the case).
+ int outputIndex = pos->m.mapb.nra;
+ for (int i = pos->count() - 1; i >= 0; --i)
+ {
+ const int atomCount = pos->m.mapb.index[i + 1] - pos->m.mapb.index[i];
+ outputIndex -= atomCount;
+ GMX_ASSERT(outputIndex >= i,
+ "In-place algorithm would overwrite data not yet used");
+ std::fill(&value[outputIndex], &value[outputIndex + atomCount], value[i]);
+ }
+}
+
} // namespace
/*!
sel->u.expr.method->pupdate(data->top, data->fr, data->pbc,
sel->u.expr.pos, &sel->v,
sel->u.expr.mdata);
+ if ((sel->flags & SEL_ATOMVAL) && sel->v.nr < g->isize)
+ {
+ switch (sel->v.type)
+ {
+ case REAL_VALUE:
+ expandValueForPositions(sel->v.u.r, &sel->v.nr,
+ sel->u.expr.pos);
+ break;
+ default:
+ GMX_RELEASE_ASSERT(false, "Unimplemented value type for position update method");
+ }
+ }
}
else
{
sel->u.expr.method->init_frame(data->top, data->fr, data->pbc,
sel->u.expr.mdata);
}
- GMX_RELEASE_ASSERT(sel->child != NULL,
- "Modifier element with a value must have a child");
- if (sel->child->v.type != POS_VALUE)
+ if (sel->child && sel->child->v.type != POS_VALUE)
{
GMX_THROW(gmx::NotImplementedError("Non-position valued modifiers not implemented"));
}
sel->u.expr.method->pupdate(data->top, data->fr, data->pbc,
- sel->child->v.u.p,
- &sel->v, sel->u.expr.mdata);
+ NULL, &sel->v, sel->u.expr.mdata);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_SELECTION_EVALUATE_H
#define GMX_SELECTION_EVALUATE_H
-#include "gromacs/legacyheaders/typedefs.h"
-
-#include "gromacs/selection/indexutil.h"
-
#include "selelem.h"
+struct gmx_ana_index_t;
struct gmx_sel_mempool_t;
+struct t_pbc;
+struct t_topology;
+struct t_trxframe;
/*! \internal \brief
* Data structure for passing information required during evaluation.
*/
-typedef struct gmx_sel_evaluate_t
+struct gmx_sel_evaluate_t
{
/** Memory pool for intermediate values. */
- struct gmx_sel_mempool_t *mp;
+ gmx_sel_mempool_t *mp;
/** Index group that contains all the atoms. */
gmx_ana_index_t *gall;
/** Topology information. */
t_trxframe *fr;
/** PBC data. */
t_pbc *pbc;
-} gmx_sel_evaluate_t;
+};
/*! \name Utility functions
*/
/** Initializes an evaluation data structure. */
void
_gmx_sel_evaluate_init(gmx_sel_evaluate_t *data,
- struct gmx_sel_mempool_t *mp, gmx_ana_index_t *gall,
+ gmx_sel_mempool_t *mp, gmx_ana_index_t *gall,
t_topology *top, t_trxframe *fr, t_pbc *pbc);
/** Evaluates the children of a general selection element. */
void
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#include "gromacs/selection/indexutil.h"
+#include "gmxpre.h"
+#include "indexutil.h"
+
+#include <cstdlib>
#include <cstring>
+#include <algorithm>
#include <string>
#include <vector>
-#include "gromacs/legacyheaders/index.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/legacyheaders/typedefs.h"
-
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
/********************************************************************
int n = find_group(const_cast<char *>(name), src->nr,
const_cast<char **>(names));
sfree(names);
- if (n == NOTSET)
+ if (n < 0)
{
dest->isize = 0;
return false;
fprintf(fp, "\n");
}
+int
+gmx_ana_index_get_max_index(gmx_ana_index_t *g)
+{
+ if (g->isize == 0)
+ {
+ return 0;
+ }
+ else
+ {
+ return *std::max_element(g->index, g->index + g->isize);
+ }
+}
+
/*!
* \param[in] g Index group to check.
* \returns true if the index group is sorted and has no duplicates,
return true;
}
+bool
+gmx_ana_index_check_range(gmx_ana_index_t *g, int natoms)
+{
+ for (int i = 0; i < g->isize; ++i)
+ {
+ if (g->index[i] < 0 || g->index[i] >= natoms)
+ {
+ return false;
+ }
+ }
+ return true;
+}
+
/********************************************************************
* Set operations
********************************************************************/
void
gmx_ana_index_sort(gmx_ana_index_t *g)
{
- qsort(g->index, g->isize, sizeof(*g->index), cmp_atomid);
+ std::qsort(g->index, g->isize, sizeof(*g->index), cmp_atomid);
}
/*!
* gmx_ana_indexmap_t and related things
********************************************************************/
+/*! \brief
+ * Helper for splitting a sequence of atom indices into groups.
+ *
+ * \param[in] atomIndex Index of the next atom in the sequence.
+ * \param[in] top Topology structure.
+ * \param[in] type Type of group to split into.
+ * \param[in,out] id Variable to receive the next group id.
+ * \returns `true` if \p atomIndex starts a new group in the sequence, i.e.,
+ * if \p *id was changed.
+ *
+ * \p *id should be initialized to `-1` before first call of this function, and
+ * then each atom index in the sequence passed to the function in turn.
+ *
+ * \ingroup module_selection
+ */
+static bool
+next_group_index(int atomIndex, t_topology *top, e_index_t type, int *id)
+{
+ int prev = *id;
+ switch (type)
+ {
+ case INDEX_ATOM:
+ *id = atomIndex;
+ break;
+ case INDEX_RES:
+ *id = top->atoms.atom[atomIndex].resind;
+ break;
+ case INDEX_MOL:
+ if (*id >= 0 && top->mols.index[*id] > atomIndex)
+ {
+ *id = 0;
+ }
+ while (*id < top->mols.nr && atomIndex >= top->mols.index[*id+1])
+ {
+ ++*id;
+ }
+ GMX_ASSERT(*id < top->mols.nr, "Molecules do not span all the atoms");
+ break;
+ case INDEX_UNKNOWN:
+ case INDEX_ALL:
+ *id = 0;
+ break;
+ }
+ return prev != *id;
+}
+
/*!
* \param[in,out] t Output block.
* \param[in] top Topology structure
* (depending on \p type) that is partially contained in the group.
* If \p type is not INDEX_RES or INDEX_MOL, this has no effect.
*
- * \p m should have been initialized somehow (calloc() is enough) unless
- * \p type is INDEX_UNKNOWN.
+ * \p m should have been initialized somehow (calloc() is enough).
* \p g should be sorted.
*/
void
gmx_ana_index_make_block(t_blocka *t, t_topology *top, gmx_ana_index_t *g,
e_index_t type, bool bComplete)
{
- int i, j, ai;
- int id, cur;
-
if (type == INDEX_UNKNOWN)
{
+ sfree(t->a);
+ srenew(t->index, 2);
t->nr = 1;
- snew(t->index, 2);
t->nalloc_index = 2;
t->index[0] = 0;
t->index[1] = 0;
return;
}
+ // TODO: Check callers and either check these there as well, or turn these
+ // into exceptions.
+ GMX_RELEASE_ASSERT(top != NULL || (type != INDEX_RES && type != INDEX_MOL),
+ "Topology must be provided for residue or molecule blocks");
+ GMX_RELEASE_ASSERT(!(type == INDEX_MOL && top->mols.nr == 0),
+ "Molecule information must be present for molecule blocks");
+
/* bComplete only does something for INDEX_RES or INDEX_MOL, so turn it
* off otherwise. */
if (type != INDEX_RES && type != INDEX_MOL)
t->nalloc_index = g->isize + 1;
}
/* Clear counters */
- t->nr = 0;
- j = 0; /* j is used by residue completion for the first atom not stored */
- id = cur = -1;
- for (i = 0; i < g->isize; ++i)
+ t->nr = 0;
+ int j = 0; /* j is used by residue completion for the first atom not stored */
+ int id = -1;
+ for (int i = 0; i < g->isize; ++i)
{
- ai = g->index[i];
/* Find the ID number of the atom/residue/molecule corresponding to
- * atom ai. */
- switch (type)
- {
- case INDEX_ATOM:
- id = ai;
- break;
- case INDEX_RES:
- id = top->atoms.atom[ai].resind;
- break;
- case INDEX_MOL:
- while (ai >= top->mols.index[id+1])
- {
- id++;
- }
- break;
- case INDEX_UNKNOWN: /* Should not occur */
- case INDEX_ALL:
- id = 0;
- break;
- }
- /* If this is the first atom in a new block, initialize the block. */
- if (id != cur)
+ * the atom. */
+ if (next_group_index(g->index[i], top, type, &id))
{
+ /* If this is the first atom in a new block, initialize the block. */
if (bComplete)
{
/* For completion, we first set the start of the block. */
break;
default: /* Should not be reached */
- gmx_bug("internal error");
+ GMX_RELEASE_ASSERT(false, "Unreachable code was reached");
break;
}
}
/* If not using completion, simply store the start of the block. */
t->index[t->nr++] = i;
}
- cur = id;
}
}
/* Set the end of the last block */
gmx_ana_indexmap_init(gmx_ana_indexmap_t *m, gmx_ana_index_t *g,
t_topology *top, e_index_t type)
{
- int i, ii, mi;
-
m->type = type;
gmx_ana_index_make_block(&m->b, top, g, type, false);
gmx_ana_indexmap_reserve(m, m->b.nr, m->b.nra);
- for (i = mi = 0; i < m->b.nr; ++i)
- {
- ii = (type == INDEX_UNKNOWN ? 0 : m->b.a[m->b.index[i]]);
- switch (type)
- {
- case INDEX_ATOM:
- m->orgid[i] = ii;
- break;
- case INDEX_RES:
- m->orgid[i] = top->atoms.atom[ii].resind;
- break;
- case INDEX_MOL:
- while (top->mols.index[mi+1] <= ii)
- {
- ++mi;
- }
- m->orgid[i] = mi;
- break;
- case INDEX_ALL:
- case INDEX_UNKNOWN:
- m->orgid[i] = 0;
- break;
- }
- }
- for (i = 0; i < m->b.nr; ++i)
+ int id = -1;
+ for (int i = 0; i < m->b.nr; ++i)
{
+ const int ii = (type == INDEX_UNKNOWN ? 0 : m->b.a[m->b.index[i]]);
+ next_group_index(ii, top, type, &id);
m->refid[i] = i;
- m->mapid[i] = m->orgid[i];
+ m->mapid[i] = id;
+ m->orgid[i] = id;
}
m->mapb.nr = m->b.nr;
m->mapb.nra = m->b.nra;
m->bStatic = true;
}
+int
+gmx_ana_indexmap_init_orgid_group(gmx_ana_indexmap_t *m, t_topology *top,
+ e_index_t type)
+{
+ GMX_RELEASE_ASSERT(m->bStatic,
+ "Changing original IDs is not supported after starting "
+ "to use the mapping");
+ GMX_RELEASE_ASSERT(top != NULL || (type != INDEX_RES && type != INDEX_MOL),
+ "Topology must be provided for residue or molecule blocks");
+ GMX_RELEASE_ASSERT(!(type == INDEX_MOL && top->mols.nr == 0),
+ "Molecule information must be present for molecule blocks");
+ // Check that all atoms in each block belong to the same group.
+ // This is a separate loop for better error handling (no state is modified
+ // if there is an error.
+ if (type == INDEX_RES || type == INDEX_MOL)
+ {
+ int id = -1;
+ for (int i = 0; i < m->b.nr; ++i)
+ {
+ const int ii = m->b.a[m->b.index[i]];
+ if (next_group_index(ii, top, type, &id))
+ {
+ for (int j = m->b.index[i] + 1; j < m->b.index[i+1]; ++j)
+ {
+ if (next_group_index(m->b.a[j], top, type, &id))
+ {
+ std::string message("Grouping into residues/molecules is ambiguous");
+ GMX_THROW(gmx::InconsistentInputError(message));
+ }
+ }
+ }
+ }
+ }
+ // Do a second loop, where things are actually set.
+ int id = -1;
+ int group = -1;
+ for (int i = 0; i < m->b.nr; ++i)
+ {
+ const int ii = (type == INDEX_UNKNOWN ? 0 : m->b.a[m->b.index[i]]);
+ if (next_group_index(ii, top, type, &id))
+ {
+ ++group;
+ }
+ m->mapid[i] = group;
+ m->orgid[i] = group;
+ }
+ // Count also the last group.
+ ++group;
+ return group;
+}
+
/*!
* \param[in,out] m Mapping structure to initialize.
* \param[in] b Block information to use for data.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_SELECTION_INDEXUTIL_H
#define GMX_SELECTION_INDEXUTIL_H
+#include <cstdio>
+
#include <string>
-#include "../legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/topology/block.h"
+
+struct t_topology;
/** Stores a set of index groups. */
-typedef struct gmx_ana_indexgrps_t gmx_ana_indexgrps_t;
+struct gmx_ana_indexgrps_t;
/*! \brief
* Specifies the type of index partition or index mapping in several contexts.
/*! \brief
* Stores a single index group.
*/
-typedef struct gmx_ana_index_t
+struct gmx_ana_index_t
{
/** Number of atoms. */
int isize;
atom_id *index;
/** Number of items allocated for \p index. */
int nalloc_index;
-} gmx_ana_index_t;
+};
/*! \brief
* Data structure for calculating index group mappings.
*/
-typedef struct gmx_ana_indexmap_t
+struct gmx_ana_indexmap_t
{
/** Type of the mapping. */
e_index_t type;
/*! \brief
* Current mapped IDs.
*
- * This array provides an arbitrary mapping from the current index group
- * to the original index group. Instead of a zero-based mapping, the
- * values from the \p orgid array are used. That is,
- * \c mapid[i]=orgid[refid[i]].
+ * This array provides IDs for the current index group. Instead of a
+ * zero-based mapping that \p refid provides, the values from the \p orgid
+ * array are used, thus allowing the mapping to be customized.
+ * In other words, `mapid[i] = orgid[refid[i]]`.
* If \p bMaskOnly is provided to gmx_ana_indexmap_update(), this array
* equals \p orgid.
*/
t_blocka mapb;
/*! \brief
- * Arbitrary ID numbers for the blocks.
+ * Customizable ID numbers for the original blocks.
*
- * This array has \p b.nr elements, each defining an ID number for a
- * block in \p b.
+ * This array has \p b.nr elements, each defining an original ID number for
+ * a block in \p b (i.e., in the original group passed to
+ * gmx_ana_indexmap_init()).
* These are initialized in gmx_ana_indexmap_init() based on the type:
* - \ref INDEX_ATOM : the atom indices
- * - \ref INDEX_RES : the residue numbers
- * - \ref INDEX_MOL : the molecule numbers
+ * - \ref INDEX_RES : the residue indices
+ * - \ref INDEX_MOL : the molecule indices
*
* All the above numbers are zero-based.
- * After gmx_ana_indexmap_init(), the user is free to change these values
+ * After gmx_ana_indexmap_init(), the caller is free to change these values
* if the above are not appropriate.
* The mapped values can be read through \p mapid.
*/
* actually static.
*/
bool bStatic;
-} gmx_ana_indexmap_t;
+};
/*! \name Functions for handling gmx_ana_indexgrps_t
void
gmx_ana_index_dump(FILE *fp, gmx_ana_index_t *g, int maxn);
+/*! \brief
+ * Returns maximum atom index that appears in an index group.
+ *
+ * \param[in] g Index group to query.
+ * \returns Largest atom index that appears in \p g, or zero if \p g is empty.
+ */
+int
+gmx_ana_index_get_max_index(gmx_ana_index_t *g);
/** Checks whether an index group is sorted. */
bool
gmx_ana_index_check_sorted(gmx_ana_index_t *g);
+/*! \brief
+ * Checks whether an index group has atoms from a defined range.
+ *
+ * \param[in] g Index group to check.
+ * \param[in] natoms Largest atom number allowed.
+ * \returns true if all atoms in the index group are in the
+ * range 0 to \p natoms (i.e., no atoms over \p natoms are referenced).
+ */
+bool
+gmx_ana_index_check_range(gmx_ana_index_t *g, int natoms);
/*@}*/
/*! \name Functions for set operations on gmx_ana_index_t
void
gmx_ana_indexmap_init(gmx_ana_indexmap_t *m, gmx_ana_index_t *g,
t_topology *top, e_index_t type);
+/*! \brief
+ * Initializes `orgid` entries based on topology grouping.
+ *
+ * \param[in,out] m Mapping structure to use/initialize.
+ * \param[in] top Topology structure
+ * (can be NULL if not required for \p type).
+ * \param[in] type Type of groups to use.
+ * \returns The number of groups of type \p type that were present in \p m.
+ * \throws InconsistentInputError if the blocks in \p m do not have a unique
+ * group (e.g., contain atoms from multiple residues with `type == INDEX_RES`).
+ *
+ * By default, the gmx_ana_indexmap_t::orgid fields are initialized to
+ * atom/residue/molecule indices from the topology (see documentation for the
+ * struct for more details).
+ * This function can be used to set the field to a zero-based group index
+ * instead. The first block will always get `orgid[0] = 0`, and all following
+ * blocks that belong to the same residue/molecule (\p type) will get the same
+ * index. Each time a block does not belong to the same group, it will get the
+ * next available number.
+ * If `type == INDEX_ATOM`, the `orgid` field is initialized as 0, 1, ...,
+ * independent of whether the blocks are single atoms or not.
+ *
+ * Strong exception safety guarantee.
+ */
+int
+gmx_ana_indexmap_init_orgid_group(gmx_ana_indexmap_t *m, t_topology *top,
+ e_index_t type);
/** Sets an index group mapping to be static. */
void
gmx_ana_indexmap_set_static(gmx_ana_indexmap_t *m, t_blocka *b);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2012, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx::SelectionStringMatchType matchType);
/** Does custom processing for parameters of the \c same selection method. */
-int
+void
_gmx_selelem_custom_init_same(struct gmx_ana_selmethod_t **method,
const gmx::SelectionParserParameterListPointer ¶ms,
void *scanner);
-/** Initializes a selection element for evaluating a keyword in a given group. */
+/*! \brief
+ * Initializes a selection element for evaluating a keyword in a given group.
+ *
+ * \param[in] method Keyword selection method to evaluate.
+ * \param[in] child The group/positions to evaluate \p method in.
+ * \param[in] scanner Scanner data structure.
+ * \returns Pointer to the created selection element.
+ *
+ * Creates a \ref SEL_EXPRESSION selection element that evaluates the keyword
+ * method given by \p method in the group/positions given by \p child.
+ *
+ * \p child should be a selection tree that evaluates to \ref GROUP_VALUE or
+ * \ref POS_VALUE.
+ */
gmx::SelectionTreeElementPointer
_gmx_sel_init_keyword_evaluator(struct gmx_ana_selmethod_t *method,
- const gmx::SelectionParserParameterList ¶ms,
+ const gmx::SelectionTreeElementPointer &child,
void *scanner);
#endif
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
+#include "mempool.h"
+
#include <stdlib.h>
#include <new>
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
-#include "mempool.h"
-
//! Alignment in bytes for all returned blocks.
#define ALIGN_STEP 8
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_SELECTION_MEMPOOL_H
#define GMX_SELECTION_MEMPOOL_H
+#include <cstddef>
+
struct gmx_ana_index_t;
/** Opaque struct for memory pooling. */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* \todo
* The grid implementation could still be optimized in several different ways:
- * - Triclinic grid cells are not the most efficient shape, but make PBC
- * handling easier.
- * - Precalculating the required PBC shift for a pair of cells outside the
- * inner loop. After this is done, it should be quite straightforward to
- * move to rectangular cells.
* - Pruning grid cells from the search list if they are completely outside
* the sphere that is being considered.
* - A better heuristic could be added for falling back to simple loops for a
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#include "gromacs/selection/nbsearch.h"
+#include "gmxpre.h"
-#include <math.h>
+#include "nbsearch.h"
+
+#include <cmath>
+#include <cstring>
#include <algorithm>
#include <vector>
#include "thread_mpi/mutex.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/vec.h"
-
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/position.h"
+#include "gromacs/topology/block.h"
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
namespace gmx
{
+namespace
+{
+
+/*! \brief
+ * Computes the bounding box for a set of positions.
+ *
+ * \param[in] posCount Number of positions in \p x.
+ * \param[in] x Positions to compute the bounding box for.
+ * \param[out] origin Origin of the bounding box.
+ * \param[out] size Size of the bounding box.
+ */
+void computeBoundingBox(int posCount, const rvec x[], rvec origin, rvec size)
+{
+ rvec maxBound;
+ copy_rvec(x[0], origin);
+ copy_rvec(x[0], maxBound);
+ for (int i = 1; i < posCount; ++i)
+ {
+ for (int d = 0; d < DIM; ++d)
+ {
+ if (origin[d] > x[i][d])
+ {
+ origin[d] = x[i][d];
+ }
+ if (maxBound[d] < x[i][d])
+ {
+ maxBound[d] = x[i][d];
+ }
+ }
+ }
+ rvec_sub(maxBound, origin, size);
+}
+
+} // namespace
+
namespace internal
{
/*! \brief
* Initializes the search with a given box and reference positions.
*
- * \param[in] mode Search mode to use.
- * \param[in] pbc PBC information.
- * \param[in] positions Set of reference positions.
+ * \param[in] mode Search mode to use.
+ * \param[in] bXY Whether to use 2D searching.
+ * \param[in] excls Exclusions.
+ * \param[in] pbc PBC information.
+ * \param[in] positions Set of reference positions.
*/
void init(AnalysisNeighborhood::SearchMode mode,
+ bool bXY,
+ const t_blocka *excls,
const t_pbc *pbc,
const AnalysisNeighborhoodPositions &positions);
PairSearchImplPointer getPairSearch();
bool usesGridSearch() const { return bGrid_; }
private:
- //! Calculates offsets to neighboring grid cells that should be considered.
- void initGridCellNeighborList();
+ /*! \brief
+ * Checks the efficiency and possibility of doing grid-based searching.
+ *
+ * \param[in] bForce If `true`, grid search will be forced if possible.
+ * \returns `false` if grid search is not suitable.
+ */
+ bool checkGridSearchEfficiency(bool bForce);
/*! \brief
* Determines a suitable grid size and sets up the cells.
*
- * \param[in] pbc Information about the box.
- * \returns false if grid search is not suitable.
+ * \param[in] box Box vectors (should not have zero vectors).
+ * \param[in] bSingleCell If `true`, the corresponding dimension will
+ * be forced to use a single cell.
+ * \param[in] posCount Number of positions that will be put on the
+ * grid.
+ * \returns `false` if grid search is not suitable.
*/
- bool initGridCells(const t_pbc *pbc);
+ bool initGridCells(const matrix box, bool bSingleCell[DIM],
+ int posCount);
/*! \brief
* Sets ua a search grid for a given box.
*
- * \param[in] pbc Information about the box.
- * \returns false if grid search is not suitable.
+ * \param[in] pbc Information about the box.
+ * \param[in] posCount Number of positions in \p x.
+ * \param[in] x Reference positions that will be put on the grid.
+ * \param[in] bForce If `true`, grid searching will be used if at all
+ * possible, even if a simple search might give better performance.
+ * \returns `false` if grid search is not suitable.
*/
- bool initGrid(const t_pbc *pbc);
+ bool initGrid(const t_pbc &pbc, int posCount, const rvec x[], bool bForce);
/*! \brief
* Maps a point into a grid cell.
*
* \param[in] x Point to map.
- * \param[out] cell Indices of the grid cell in which \p x lies.
- * \param[out] xout Coordinates to use
- * (will be within the triclinic unit cell).
+ * \param[out] cell Fractional cell coordinates of \p x on the grid.
+ * \param[out] xout Coordinates to use.
+ *
+ * \p xout will be within the rectangular unit cell in dimensions where
+ * the grid is periodic. For other dimensions, both \p xout and
+ * \p cell can be outside the grid/unit cell.
*/
- void mapPointToGridCell(const rvec x, ivec cell, rvec xout) const;
+ void mapPointToGridCell(const rvec x, rvec cell, rvec xout) const;
/*! \brief
* Calculates linear index of a grid cell.
*
- * \param[in] cell Cell indices.
+ * \param[in] cell Cell indices (must be within the grid).
* \returns Linear index of \p cell.
*/
int getGridCellIndex(const ivec cell) const;
/*! \brief
* Adds an index into a grid cell.
*
- * \param[in] cell Cell into which \p i should be added.
- * \param[in] i Index to add.
+ * \param[in] cell Fractional cell coordinates into which \p i should
+ * be added.
+ * \param[in] i Index to add.
+ *
+ * \p cell should satisfy the conditions that \p mapPointToGridCell()
+ * produces.
+ */
+ void addToGridCell(const rvec cell, int i);
+ /*! \brief
+ * Initializes a cell pair loop for a dimension.
+ *
+ * \param[in] centerCell Fractional cell coordiates of the particle
+ * for which pairs are being searched.
+ * \param[in,out] cell Current/initial cell to loop over.
+ * \param[in,out] upperBound Last cell to loop over.
+ * \param[in] dim Dimension to initialize in this call.
+ *
+ * Initializes `cell[dim]` and `upperBound[dim]` for looping over
+ * neighbors of a particle at position given by \p centerCell.
+ * If 'dim != ZZ`, `cell[d]` (`d > dim`) set the plane/row of cells
+ * for which the loop is initialized. The loop should then go from
+ * `cell[dim]` until `upperBound[dim]`, inclusive.
+ * `cell[d]` with `d < dim` or `upperBound[d]` with `d != dim` are not
+ * modified by this function.
+ *
+ * `cell` and `upperBound` may be outside the grid for periodic
+ * dimensions and need to be shifted separately: to simplify the
+ * looping, the range is always (roughly) symmetric around the value in
+ * `centerCell`.
*/
- void addToGridCell(const ivec cell, int i);
+ void initCellRange(const rvec centerCell, ivec cell,
+ ivec upperBound, int dim) const;
+ /*! \brief
+ * Advances cell pair loop to the next cell.
+ *
+ * \param[in] centerCell Fractional cell coordiates of the particle
+ * for which pairs are being searched.
+ * \param[in,out] cell Current (in)/next (out) cell in the loop.
+ * \param[in,out] upperBound Last cell in the loop for each dimension.
+ */
+ bool nextCell(const rvec centerCell, ivec cell, ivec upperBound) const;
+ /*! \brief
+ * Calculates the index and shift of a grid cell during looping.
+ *
+ * \param[in] cell Unshifted cell index.
+ * \param[out] shift Shift to apply to get the periodic distance
+ * for distances between the cells.
+ * \returns Grid cell index corresponding to `cell`.
+ */
+ int shiftCell(const ivec cell, rvec shift) const;
//! Whether to try grid searching.
bool bTryGrid_;
real cutoff_;
//! The cutoff squared.
real cutoff2_;
+ //! Whether to do searching in XY plane only.
+ bool bXY_;
//! Number of reference points for the current frame.
int nref_;
//! Reference point positions.
const rvec *xref_;
- //! Reference position ids (NULL if not available).
- const int *refid_;
+ //! Reference position exclusion IDs.
+ const int *refExclusionIds_;
+ //! Reference position indices (NULL if no indices).
+ const int *refIndices_;
+ //! Exclusions.
+ const t_blocka *excls_;
//! PBC data.
- t_pbc *pbc_;
-
- //! Number of excluded reference positions for current test particle.
- int nexcl_;
- //! Exclusions for current test particle.
- int *excl_;
+ t_pbc pbc_;
//! Whether grid searching is actually used for the current positions.
bool bGrid_;
- //! Array allocated for storing in-unit-cell reference positions.
- rvec *xref_alloc_;
- //! Allocation count for xref_alloc.
- int xref_nalloc_;
//! false if the box is rectangular.
bool bTric_;
- //! Box vectors of a single grid cell.
- matrix cellbox_;
- //! The reciprocal cell vectors as columns; the inverse of \p cellbox.
- matrix recipcell_;
+ //! Whether the grid is periodic in a dimension.
+ bool bGridPBC_[DIM];
+ //! Array for storing in-unit-cell reference positions.
+ std::vector<RVec> xrefAlloc_;
+ //! Origin of the grid (zero for periodic dimensions).
+ rvec gridOrigin_;
+ //! Size of a single grid cell.
+ rvec cellSize_;
+ //! Inverse of \p cellSize_. Zero for dimensions where grid is not used.
+ rvec invCellSize_;
+ /*! \brief
+ * Shift in cell coordinates (for triclinic boxes) in X when crossing
+ * the Z periodic boundary.
+ */
+ real cellShiftZX_;
+ /*! \brief
+ * Shift in cell coordinates (for triclinic boxes) in Y when crossing
+ * the Z periodic boundary.
+ */
+ real cellShiftZY_;
+ /*! \brief
+ * Shift in cell coordinates (for triclinic boxes) in X when crossing
+ * the Y periodic boundary.
+ */
+ real cellShiftYX_;
//! Number of cells along each dimension.
ivec ncelldim_;
//! Data structure to hold the grid cell contents.
CellList cells_;
- //! Number of neighboring cells to consider.
- int ngridnb_;
- //! Offsets of the neighboring cells to consider.
- ivec *gnboffs_;
- //! Allocation count for \p gnboffs.
- int gnboffs_nalloc_;
tMPI::mutex createPairSearchMutex_;
PairSearchList pairSearchList_;
explicit AnalysisNeighborhoodPairSearchImpl(const AnalysisNeighborhoodSearchImpl &search)
: search_(search)
{
+ testPosCount_ = 0;
+ testPositions_ = NULL;
+ testExclusionIds_ = NULL;
+ testIndices_ = NULL;
+ nexcl_ = 0;
+ excl_ = NULL;
clear_rvec(xtest_);
- clear_ivec(testcell_);
+ clear_rvec(testcell_);
+ clear_ivec(currCell_);
+ clear_ivec(cellBound_);
reset(-1);
}
//! Parent search object.
const AnalysisNeighborhoodSearchImpl &search_;
+ //! Number of test positions.
+ int testPosCount_;
//! Reference to the test positions.
- ConstArrayRef<rvec> testPositions_;
+ const rvec *testPositions_;
+ //! Reference to the test exclusion indices.
+ const int *testExclusionIds_;
+ //! Reference to the test position indices.
+ const int *testIndices_;
+ //! Number of excluded reference positions for current test particle.
+ int nexcl_;
+ //! Exclusions for current test particle.
+ const int *excl_;
//! Index of the currently active test position in \p testPositions_.
int testIndex_;
//! Stores test position during a pair loop.
rvec xtest_;
//! Stores the previous returned position during a pair loop.
int previ_;
+ //! Stores the pair distance corresponding to previ_;
+ real prevr2_;
+ //! Stores the shortest distance vector corresponding to previ_;
+ rvec prevdx_;
//! Stores the current exclusion index during loops.
int exclind_;
- //! Stores the test particle cell index during loops.
- ivec testcell_;
- //! Stores the current cell neighbor index during pair loops.
- int prevnbi_;
+ //! Stores the fractional test particle cell location during loops.
+ rvec testcell_;
+ //! Stores the current cell during pair loops.
+ ivec currCell_;
+ //! Stores the current loop upper bounds for each dimension during pair loops.
+ ivec cellBound_;
//! Stores the index within the current cell during pair loops.
int prevcai_;
cutoff_ = cutoff;
if (cutoff_ <= 0)
{
- cutoff_ = GMX_REAL_MAX;
+ cutoff_ = cutoff2_ = GMX_REAL_MAX;
bTryGrid_ = false;
}
- cutoff2_ = sqr(cutoff_);
-
- nref_ = 0;
- xref_ = NULL;
- refid_ = NULL;
- pbc_ = NULL;
-
- nexcl_ = 0;
- excl_ = NULL;
+ else
+ {
+ cutoff2_ = sqr(cutoff_);
+ }
+ bXY_ = false;
+ nref_ = 0;
+ xref_ = NULL;
+ refExclusionIds_ = NULL;
+ refIndices_ = NULL;
+ std::memset(&pbc_, 0, sizeof(pbc_));
bGrid_ = false;
-
- xref_alloc_ = NULL;
- xref_nalloc_ = 0;
bTric_ = false;
- clear_mat(cellbox_);
- clear_mat(recipcell_);
- clear_ivec(ncelldim_);
+ bGridPBC_[XX] = true;
+ bGridPBC_[YY] = true;
+ bGridPBC_[ZZ] = true;
- ngridnb_ = 0;
- gnboffs_ = NULL;
- gnboffs_nalloc_ = 0;
+ clear_rvec(gridOrigin_);
+ clear_rvec(cellSize_);
+ clear_rvec(invCellSize_);
+ clear_ivec(ncelldim_);
}
AnalysisNeighborhoodSearchImpl::~AnalysisNeighborhoodSearchImpl()
GMX_RELEASE_ASSERT(i->unique(),
"Dangling AnalysisNeighborhoodPairSearch reference");
}
- sfree(xref_alloc_);
- sfree(gnboffs_);
}
AnalysisNeighborhoodSearchImpl::PairSearchImplPointer
return pairSearch;
}
-void AnalysisNeighborhoodSearchImpl::initGridCellNeighborList()
+bool AnalysisNeighborhoodSearchImpl::checkGridSearchEfficiency(bool bForce)
{
- int maxx, maxy, maxz;
- real rvnorm;
-
- /* Find the extent of the sphere in triclinic coordinates */
- maxz = static_cast<int>(cutoff_ * recipcell_[ZZ][ZZ]) + 1;
- rvnorm = sqrt(sqr(recipcell_[YY][YY]) + sqr(recipcell_[ZZ][YY]));
- maxy = static_cast<int>(cutoff_ * rvnorm) + 1;
- rvnorm = sqrt(sqr(recipcell_[XX][XX]) + sqr(recipcell_[YY][XX])
- + sqr(recipcell_[ZZ][XX]));
- maxx = static_cast<int>(cutoff_ * rvnorm) + 1;
-
- /* Calculate the number of cells and reallocate if necessary */
- ngridnb_ = (2 * maxx + 1) * (2 * maxy + 1) * (2 * maxz + 1);
- if (gnboffs_nalloc_ < ngridnb_)
+ // Find the extent of the sphere in cells.
+ ivec range;
+ for (int dd = 0; dd < DIM; ++dd)
{
- gnboffs_nalloc_ = ngridnb_;
- srenew(gnboffs_, gnboffs_nalloc_);
+ range[dd] = static_cast<int>(ceil(cutoff_ * invCellSize_[dd]));
}
- /* Store the whole cube */
- /* TODO: Prune off corners that are not needed */
- int i = 0;
- for (int x = -maxx; x <= maxx; ++x)
+ // Calculate the fraction of cell pairs that need to be searched,
+ // and check that the cutoff is not too large for periodic dimensions.
+ real coveredCells = 1.0;
+ for (int dd = 0; dd < DIM; ++dd)
{
- for (int y = -maxy; y <= maxy; ++y)
+ const int cellCount = ncelldim_[dd];
+ const int coveredCount = 2 * range[dd] + 1;
+ if (bGridPBC_[dd])
{
- for (int z = -maxz; z <= maxz; ++z)
+ if (coveredCount > cellCount)
{
- gnboffs_[i][XX] = x;
- gnboffs_[i][YY] = y;
- gnboffs_[i][ZZ] = z;
- ++i;
+ // Cutoff is too close to half the box size for grid searching
+ // (it is not possible to find a single shift for every pair of
+ // grid cells).
+ return false;
}
+ coveredCells *= coveredCount;
}
+ else
+ {
+ if (range[dd] >= cellCount - 1)
+ {
+ range[dd] = cellCount - 1;
+ coveredCells *= cellCount;
+ }
+ else if (coveredCount > cellCount)
+ {
+ // The sum of range+1, range+2, ..., range+N/2, ... range+1.
+ coveredCells *= range[dd] +
+ static_cast<real>((cellCount + 1)/2 * (cellCount/2 + 1)) / cellCount;
+ }
+ else
+ {
+ // The sum of range+1, ..., 2*range+1, ..., 2*range+1, ... range+1.
+ coveredCells *= coveredCount -
+ static_cast<real>(range[dd] * (range[dd] + 1)) / cellCount;
+ }
+ }
+ }
+ // Magic constant that would need tuning for optimal performance:
+ // Don't do grid searching if nearly all cell pairs would anyways need to
+ // be looped through.
+ const int totalCellCount = ncelldim_[XX] * ncelldim_[YY] * ncelldim_[ZZ];
+ if (!bForce && coveredCells >= 0.5 * totalCellCount)
+ {
+ return false;
}
+ return true;
}
-bool AnalysisNeighborhoodSearchImpl::initGridCells(const t_pbc *pbc)
+bool AnalysisNeighborhoodSearchImpl::initGridCells(
+ const matrix box, bool bSingleCell[DIM], int posCount)
{
- const real targetsize =
- pow(pbc->box[XX][XX] * pbc->box[YY][YY] * pbc->box[ZZ][ZZ]
- * 10 / nref_, static_cast<real>(1./3.));
+ // Determine the size of cubes where there are on average 10 positions.
+ // The loop takes care of cases where some of the box edges are shorter
+ // than the the desired cube size; in such cases, a single grid cell is
+ // used in these dimensions, and the cube size is determined only from the
+ // larger box vectors. Such boxes should be rare, but the bounding box
+ // approach can result in very flat boxes with certain types of selections
+ // (e.g., for interfacial systems or for small number of atoms).
+ real targetsize = 0.0;
+ int prevDimCount = 4;
+ while (true)
+ {
+ real volume = 1.0;
+ int dimCount = 3;
+ for (int dd = 0; dd < DIM; ++dd)
+ {
+ const real boxSize = box[dd][dd];
+ if (boxSize < targetsize)
+ {
+ bSingleCell[dd] = true;
+ if (bGridPBC_[dd])
+ {
+ return false;
+ }
+ }
+ if (bSingleCell[dd])
+ {
+ --dimCount;
+ }
+ else
+ {
+ volume *= boxSize;
+ }
+ }
+ if (dimCount == 0 || dimCount == prevDimCount)
+ {
+ break;
+ }
+ targetsize = pow(volume * 10 / posCount, static_cast<real>(1./dimCount));
+ prevDimCount = dimCount;
+ }
- int cellCount = 1;
+ int totalCellCount = 1;
for (int dd = 0; dd < DIM; ++dd)
{
- ncelldim_[dd] = static_cast<int>(pbc->box[dd][dd] / targetsize);
- cellCount *= ncelldim_[dd];
- if (ncelldim_[dd] < 3)
+ int cellCount;
+ if (bSingleCell[dd])
{
- return false;
+ cellCount = 1;
+ }
+ else
+ {
+ cellCount = std::max(1, static_cast<int>(box[dd][dd] / targetsize));
+ if (bGridPBC_[dd] && cellCount < 3)
+ {
+ return false;
+ }
}
+ totalCellCount *= cellCount;
+ ncelldim_[dd] = cellCount;
+ }
+ if (totalCellCount <= 3)
+ {
+ return false;
}
// Never decrease the size of the cell vector to avoid reallocating
// memory for the nested vectors. The actual size of the vector is not
// used outside this function.
- if (cells_.size() < static_cast<size_t>(cellCount))
+ if (cells_.size() < static_cast<size_t>(totalCellCount))
{
- cells_.resize(cellCount);
+ cells_.resize(totalCellCount);
}
- for (int ci = 0; ci < cellCount; ++ci)
+ for (int ci = 0; ci < totalCellCount; ++ci)
{
cells_[ci].clear();
}
return true;
}
-bool AnalysisNeighborhoodSearchImpl::initGrid(const t_pbc *pbc)
+bool AnalysisNeighborhoodSearchImpl::initGrid(
+ const t_pbc &pbc, int posCount, const rvec x[], bool bForce)
{
- /* TODO: This check could be improved. */
- if (0.5*pbc->max_cutoff2 < cutoff2_)
+ if (posCount == 0)
{
return false;
}
- if (!initGridCells(pbc))
+ switch (pbc.ePBC)
{
- return false;
+ case epbcNONE:
+ bGridPBC_[XX] = false;
+ bGridPBC_[YY] = false;
+ bGridPBC_[ZZ] = false;
+ break;
+ case epbcXY:
+ bGridPBC_[XX] = true;
+ bGridPBC_[YY] = true;
+ bGridPBC_[ZZ] = false;
+ break;
+ case epbcXYZ:
+ bGridPBC_[XX] = true;
+ bGridPBC_[YY] = true;
+ bGridPBC_[ZZ] = true;
+ break;
+ default:
+ // Grid searching not supported for now with screw.
+ return false;
}
- bTric_ = TRICLINIC(pbc->box);
- if (bTric_)
+ bool bSingleCell[DIM] = {false, false, bXY_};
+ matrix box;
+ copy_mat(pbc.box, box);
+ // TODO: In principle, we could use the bounding box for periodic
+ // dimensions as well if the bounding box is sufficiently far from the box
+ // edges.
+ rvec origin, boundingBoxSize;
+ computeBoundingBox(posCount, x, origin, boundingBoxSize);
+ clear_rvec(gridOrigin_);
+ for (int dd = 0; dd < DIM; ++dd)
{
- for (int dd = 0; dd < DIM; ++dd)
+ if (!bGridPBC_[dd] && !bSingleCell[dd])
{
- svmul(1.0 / ncelldim_[dd], pbc->box[dd], cellbox_[dd]);
+ gridOrigin_[dd] = origin[dd];
+ clear_rvec(box[dd]);
+ box[dd][dd] = boundingBoxSize[dd];
+ }
+ // TODO: In case the zero vector comes from the bounding box, this does
+ // not lead to a very efficient grid search, but that should be rare.
+ if (box[dd][dd] <= 0.0)
+ {
+ GMX_ASSERT(!bGridPBC_[dd], "Periodic box vector is zero");
+ bSingleCell[dd] = true;
+ clear_rvec(box[dd]);
+ box[dd][dd] = 1.0;
}
- m_inv_ur0(cellbox_, recipcell_);
}
- else
+
+ if (!initGridCells(box, bSingleCell, posCount))
{
- for (int dd = 0; dd < DIM; ++dd)
+ return false;
+ }
+
+ bTric_ = TRICLINIC(pbc.box);
+ for (int dd = 0; dd < DIM; ++dd)
+ {
+ cellSize_[dd] = box[dd][dd] / ncelldim_[dd];
+ if (bSingleCell[dd])
+ {
+ invCellSize_[dd] = 0.0;
+ }
+ else
{
- cellbox_[dd][dd] = pbc->box[dd][dd] / ncelldim_[dd];
- recipcell_[dd][dd] = 1.0 / cellbox_[dd][dd];
+ invCellSize_[dd] = 1.0 / cellSize_[dd];
}
}
- initGridCellNeighborList();
- return true;
+ if (bTric_)
+ {
+ cellShiftZY_ = box[ZZ][YY] * invCellSize_[YY];
+ cellShiftZX_ = box[ZZ][XX] * invCellSize_[XX];
+ cellShiftYX_ = box[YY][XX] * invCellSize_[XX];
+ }
+ return checkGridSearchEfficiency(bForce);
}
void AnalysisNeighborhoodSearchImpl::mapPointToGridCell(const rvec x,
- ivec cell,
+ rvec cell,
rvec xout) const
{
rvec xtmp;
- copy_rvec(x, xtmp);
- if (bTric_)
- {
- rvec tx;
- tmvmul_ur0(recipcell_, xtmp, tx);
- for (int dd = 0; dd < DIM; ++dd)
- {
- const int cellCount = ncelldim_[dd];
- int cellIndex = static_cast<int>(floor(tx[dd]));
- while (cellIndex < 0)
- {
- cellIndex += cellCount;
- rvec_add(xtmp, pbc_->box[dd], xtmp);
- }
- while (cellIndex >= cellCount)
- {
- cellIndex -= cellCount;
- rvec_sub(xtmp, pbc_->box[dd], xtmp);
- }
- cell[dd] = cellIndex;
- }
- }
- else
+ rvec_sub(x, gridOrigin_, xtmp);
+ // The reverse order is necessary for triclinic cells: shifting in Z may
+ // modify also X and Y, and shifting in Y may modify X, so the mapping to
+ // a rectangular grid needs to be done in this order.
+ for (int dd = DIM - 1; dd >= 0; --dd)
{
- for (int dd = 0; dd < DIM; ++dd)
+ real cellIndex = xtmp[dd] * invCellSize_[dd];
+ if (bGridPBC_[dd])
{
- const int cellCount = ncelldim_[dd];
- int cellIndex = static_cast<int>(floor(xtmp[dd] * recipcell_[dd][dd]));
+ const real cellCount = ncelldim_[dd];
while (cellIndex < 0)
{
cellIndex += cellCount;
- xtmp[dd] += pbc_->box[dd][dd];
+ rvec_inc(xtmp, pbc_.box[dd]);
}
while (cellIndex >= cellCount)
{
cellIndex -= cellCount;
- xtmp[dd] -= pbc_->box[dd][dd];
+ rvec_dec(xtmp, pbc_.box[dd]);
}
- cell[dd] = cellIndex;
}
+ cell[dd] = cellIndex;
}
copy_rvec(xtmp, xout);
}
+ cell[ZZ] * ncelldim_[XX] * ncelldim_[YY];
}
-void AnalysisNeighborhoodSearchImpl::addToGridCell(const ivec cell, int i)
+void AnalysisNeighborhoodSearchImpl::addToGridCell(const rvec cell, int i)
{
- const int ci = getGridCellIndex(cell);
+ ivec icell;
+ for (int dd = 0; dd < DIM; ++dd)
+ {
+ int cellIndex = static_cast<int>(floor(cell[dd]));
+ if (!bGridPBC_[dd])
+ {
+ const int cellCount = ncelldim_[dd];
+ if (cellIndex < 0)
+ {
+ cellIndex = 0;
+ }
+ else if (cellIndex >= cellCount)
+ {
+ cellIndex = cellCount - 1;
+ }
+ }
+ icell[dd] = cellIndex;
+ }
+ const int ci = getGridCellIndex(icell);
cells_[ci].push_back(i);
}
+void AnalysisNeighborhoodSearchImpl::initCellRange(
+ const rvec centerCell, ivec currCell, ivec upperBound, int dim) const
+{
+ // TODO: Prune off cells that are completely outside the cutoff.
+ const real range = cutoff_ * invCellSize_[dim];
+ real startOffset = centerCell[dim] - range;
+ real endOffset = centerCell[dim] + range;
+ if (bTric_)
+ {
+ switch (dim)
+ {
+ case ZZ:
+ break;
+ case YY:
+ if (currCell[ZZ] < 0)
+ {
+ startOffset += cellShiftZY_;
+ endOffset += cellShiftZY_;
+ }
+ else if (currCell[ZZ] >= ncelldim_[ZZ])
+ {
+ startOffset -= cellShiftZY_;
+ endOffset -= cellShiftZY_;
+ }
+ break;
+ case XX:
+ if (currCell[ZZ] < 0)
+ {
+ startOffset += cellShiftZX_;
+ endOffset += cellShiftZX_;
+ }
+ else if (currCell[ZZ] >= ncelldim_[ZZ])
+ {
+ startOffset -= cellShiftZX_;
+ endOffset -= cellShiftZX_;
+ }
+ if (currCell[YY] < 0)
+ {
+ startOffset += cellShiftYX_;
+ endOffset += cellShiftYX_;
+ }
+ else if (currCell[YY] >= ncelldim_[YY])
+ {
+ startOffset -= cellShiftYX_;
+ endOffset -= cellShiftYX_;
+ }
+ break;
+ }
+ }
+ // For non-periodic dimensions, clamp to the actual grid edges.
+ if (!bGridPBC_[dim])
+ {
+ // If endOffset < 0 or startOffset > N, these may cause the whole
+ // test position/grid plane/grid row to be skipped.
+ if (startOffset < 0)
+ {
+ startOffset = 0;
+ }
+ const int cellCount = ncelldim_[dim];
+ if (endOffset > cellCount - 1)
+ {
+ endOffset = cellCount - 1;
+ }
+ }
+ currCell[dim] = static_cast<int>(floor(startOffset));
+ upperBound[dim] = static_cast<int>(floor(endOffset));
+}
+
+bool AnalysisNeighborhoodSearchImpl::nextCell(
+ const rvec centerCell, ivec cell, ivec upperBound) const
+{
+ int dim = 0;
+ while (dim < DIM)
+ {
+next:
+ ++cell[dim];
+ if (cell[dim] > upperBound[dim])
+ {
+ ++dim;
+ continue;
+ }
+ for (int d = dim - 1; d >= 0; --d)
+ {
+ initCellRange(centerCell, cell, upperBound, d);
+ if (cell[d] > upperBound[d])
+ {
+ dim = d + 1;
+ goto next;
+ }
+ }
+ return true;
+ }
+ return false;
+}
+
+int AnalysisNeighborhoodSearchImpl::shiftCell(const ivec cell, rvec shift) const
+{
+ ivec shiftedCell;
+ copy_ivec(cell, shiftedCell);
+
+ clear_rvec(shift);
+ for (int d = 0; d < DIM; ++d)
+ {
+ const int cellCount = ncelldim_[d];
+ if (bGridPBC_[d])
+ {
+ // A single shift may not be sufficient if the cell must be shifted
+ // in more than one dimension, although for each individual
+ // dimension it would be.
+ while (shiftedCell[d] < 0)
+ {
+ shiftedCell[d] += cellCount;
+ rvec_inc(shift, pbc_.box[d]);
+ }
+ while (shiftedCell[d] >= cellCount)
+ {
+ shiftedCell[d] -= cellCount;
+ rvec_dec(shift, pbc_.box[d]);
+ }
+ }
+ }
+
+ return getGridCellIndex(shiftedCell);
+}
+
void AnalysisNeighborhoodSearchImpl::init(
AnalysisNeighborhood::SearchMode mode,
+ bool bXY,
+ const t_blocka *excls,
const t_pbc *pbc,
const AnalysisNeighborhoodPositions &positions)
{
GMX_RELEASE_ASSERT(positions.index_ == -1,
"Individual indexed positions not supported as reference");
- pbc_ = const_cast<t_pbc *>(pbc);
+ bXY_ = bXY;
+ if (bXY_ && pbc != NULL && pbc->ePBC != epbcNONE)
+ {
+ if (pbc->ePBC != epbcXY && pbc->ePBC != epbcXYZ)
+ {
+ std::string message =
+ formatString("Computations in the XY plane are not supported with PBC type '%s'",
+ EPBC(pbc->ePBC));
+ GMX_THROW(NotImplementedError(message));
+ }
+ if (pbc->ePBC == epbcXYZ &&
+ (std::fabs(pbc->box[ZZ][XX]) > GMX_REAL_EPS*pbc->box[ZZ][ZZ] ||
+ std::fabs(pbc->box[ZZ][YY]) > GMX_REAL_EPS*pbc->box[ZZ][ZZ]))
+ {
+ GMX_THROW(NotImplementedError("Computations in the XY plane are not supported when the last box vector is not parallel to the Z axis"));
+ }
+ // Use a single grid cell in Z direction.
+ matrix box;
+ copy_mat(pbc->box, box);
+ clear_rvec(box[ZZ]);
+ set_pbc(&pbc_, epbcXY, box);
+ }
+ else if (pbc != NULL)
+ {
+ pbc_ = *pbc;
+ }
+ else
+ {
+ pbc_.ePBC = epbcNONE;
+ clear_mat(pbc_.box);
+ }
nref_ = positions.count_;
- // TODO: Consider whether it would be possible to support grid searching in
- // more cases.
- if (mode == AnalysisNeighborhood::eSearchMode_Simple
- || pbc_ == NULL || pbc_->ePBC != epbcXYZ)
+ if (mode == AnalysisNeighborhood::eSearchMode_Simple)
{
bGrid_ = false;
}
else if (bTryGrid_)
{
- // TODO: Actually implement forcing eSearchMode_Grid
- bGrid_ = initGrid(pbc_);
+ bGrid_ = initGrid(pbc_, positions.count_, positions.x_,
+ mode == AnalysisNeighborhood::eSearchMode_Grid);
}
+ refIndices_ = positions.indices_;
if (bGrid_)
{
- if (xref_nalloc_ < nref_)
- {
- srenew(xref_alloc_, nref_);
- xref_nalloc_ = nref_;
- }
- xref_ = xref_alloc_;
+ xrefAlloc_.resize(nref_);
+ xref_ = as_rvec_array(&xrefAlloc_[0]);
for (int i = 0; i < nref_; ++i)
{
- ivec refcell;
- mapPointToGridCell(positions.x_[i], refcell, xref_alloc_[i]);
+ const int ii = (refIndices_ != NULL) ? refIndices_[i] : i;
+ rvec refcell;
+ mapPointToGridCell(positions.x_[ii], refcell, xrefAlloc_[i]);
addToGridCell(refcell, i);
}
}
+ else if (refIndices_ != NULL)
+ {
+ xrefAlloc_.resize(nref_);
+ xref_ = as_rvec_array(&xrefAlloc_[0]);
+ for (int i = 0; i < nref_; ++i)
+ {
+ copy_rvec(positions.x_[refIndices_[i]], xrefAlloc_[i]);
+ }
+ }
else
{
xref_ = positions.x_;
}
- // TODO: Once exclusions are supported, this may need to be initialized.
- refid_ = NULL;
-}
-
-#if 0
-/*! \brief
- * Sets the exclusions for the next neighborhood search.
- *
- * \param[in,out] d Neighborhood search data structure.
- * \param[in] nexcl Number of reference positions to exclude from next
- * search.
- * \param[in] excl Indices of reference positions to exclude.
- *
- * The set exclusions remain in effect until the next call of this function.
- */
-void
-gmx_ana_nbsearch_set_excl(gmx_ana_nbsearch_t *d, int nexcl, int excl[])
-{
-
- d->nexcl = nexcl;
- d->excl = excl;
+ excls_ = excls;
+ refExclusionIds_ = NULL;
+ if (excls != NULL)
+ {
+ // TODO: Check that the IDs are ascending, or remove the limitation.
+ refExclusionIds_ = positions.exclusionIds_;
+ GMX_RELEASE_ASSERT(refExclusionIds_ != NULL,
+ "Exclusion IDs must be set for reference positions "
+ "when exclusions are enabled");
+ }
}
-#endif
/********************************************************************
* AnalysisNeighborhoodPairSearchImpl
void AnalysisNeighborhoodPairSearchImpl::reset(int testIndex)
{
testIndex_ = testIndex;
- if (testIndex_ >= 0 && testIndex_ < static_cast<int>(testPositions_.size()))
+ if (testIndex_ >= 0 && testIndex_ < testPosCount_)
{
+ const int index =
+ (testIndices_ != NULL ? testIndices_[testIndex] : testIndex);
if (search_.bGrid_)
{
- search_.mapPointToGridCell(testPositions_[testIndex], testcell_, xtest_);
+ search_.mapPointToGridCell(testPositions_[index], testcell_, xtest_);
+ search_.initCellRange(testcell_, currCell_, cellBound_, ZZ);
+ search_.initCellRange(testcell_, currCell_, cellBound_, YY);
+ search_.initCellRange(testcell_, currCell_, cellBound_, XX);
}
else
{
- copy_rvec(testPositions_[testIndex_], xtest_);
+ copy_rvec(testPositions_[index], xtest_);
+ }
+ if (search_.excls_ != NULL)
+ {
+ const int exclIndex = testExclusionIds_[index];
+ if (exclIndex < search_.excls_->nr)
+ {
+ const int startIndex = search_.excls_->index[exclIndex];
+ nexcl_ = search_.excls_->index[exclIndex + 1] - startIndex;
+ excl_ = &search_.excls_->a[startIndex];
+ }
+ else
+ {
+ nexcl_ = 0;
+ excl_ = NULL;
+ }
}
}
previ_ = -1;
+ prevr2_ = 0.0;
+ clear_rvec(prevdx_);
exclind_ = 0;
- prevnbi_ = 0;
prevcai_ = -1;
}
void AnalysisNeighborhoodPairSearchImpl::nextTestPosition()
{
- if (testIndex_ < static_cast<int>(testPositions_.size()))
+ if (testIndex_ < testPosCount_)
{
++testIndex_;
reset(testIndex_);
bool AnalysisNeighborhoodPairSearchImpl::isExcluded(int j)
{
- if (exclind_ < search_.nexcl_)
+ if (exclind_ < nexcl_)
{
- if (search_.refid_)
+ const int index =
+ (search_.refIndices_ != NULL ? search_.refIndices_[j] : j);
+ const int refId = search_.refExclusionIds_[index];
+ while (exclind_ < nexcl_ && excl_[exclind_] < refId)
{
- while (exclind_ < search_.nexcl_
- && search_.excl_[exclind_] < search_.refid_[j])
- {
- ++exclind_;
- }
- if (exclind_ < search_.nexcl_
- && search_.refid_[j] == search_.excl_[exclind_])
- {
- ++exclind_;
- return true;
- }
+ ++exclind_;
}
- else
+ if (exclind_ < nexcl_ && refId == excl_[exclind_])
{
- while (search_.bGrid_ && exclind_ < search_.nexcl_
- && search_.excl_[exclind_] < j)
- {
- ++exclind_;
- }
- if (search_.excl_[exclind_] == j)
- {
- ++exclind_;
- return true;
- }
+ ++exclind_;
+ return true;
}
}
return false;
void AnalysisNeighborhoodPairSearchImpl::startSearch(
const AnalysisNeighborhoodPositions &positions)
{
+ testPosCount_ = positions.count_;
+ testPositions_ = positions.x_;
+ testExclusionIds_ = positions.exclusionIds_;
+ testIndices_ = positions.indices_;
+ GMX_RELEASE_ASSERT(search_.excls_ == NULL || testExclusionIds_ != NULL,
+ "Exclusion IDs must be set when exclusions are enabled");
if (positions.index_ < 0)
{
- testPositions_ = constArrayRefFromArray<rvec>(positions.x_, positions.count_);
reset(0);
}
else
{
// Somewhat of a hack: setup the array such that only the last position
// will be used.
- testPositions_ = constArrayRefFromArray<rvec>(positions.x_, positions.index_ + 1);
+ testPosCount_ = positions.index_ + 1;
reset(positions.index_);
}
}
template <class Action>
bool AnalysisNeighborhoodPairSearchImpl::searchNext(Action action)
{
- while (testIndex_ < static_cast<int>(testPositions_.size()))
+ while (testIndex_ < testPosCount_)
{
if (search_.bGrid_)
{
- int nbi = prevnbi_;
int cai = prevcai_ + 1;
- for (; nbi < search_.ngridnb_; ++nbi)
+ do
{
- ivec cell;
-
- ivec_add(testcell_, search_.gnboffs_[nbi], cell);
- cell[XX] = (cell[XX] + search_.ncelldim_[XX]) % search_.ncelldim_[XX];
- cell[YY] = (cell[YY] + search_.ncelldim_[YY]) % search_.ncelldim_[YY];
- cell[ZZ] = (cell[ZZ] + search_.ncelldim_[ZZ]) % search_.ncelldim_[ZZ];
-
- const int ci = search_.getGridCellIndex(cell);
+ rvec shift;
+ const int ci = search_.shiftCell(currCell_, shift);
const int cellSize = static_cast<int>(search_.cells_[ci].size());
- /* TODO: Calculate the required PBC shift outside the inner loop */
for (; cai < cellSize; ++cai)
{
const int i = search_.cells_[ci][cai];
continue;
}
rvec dx;
- pbc_dx_aiuc(search_.pbc_, xtest_, search_.xref_[i], dx);
- const real r2 = norm2(dx);
+ rvec_sub(search_.xref_[i], xtest_, dx);
+ rvec_sub(dx, shift, dx);
+ const real r2
+ = search_.bXY_
+ ? dx[XX]*dx[XX] + dx[YY]*dx[YY]
+ : norm2(dx);
if (r2 <= search_.cutoff2_)
{
- if (action(i, r2))
+ if (action(i, r2, dx))
{
- prevnbi_ = nbi;
prevcai_ = cai;
previ_ = i;
+ prevr2_ = r2;
+ copy_rvec(dx, prevdx_);
return true;
}
}
exclind_ = 0;
cai = 0;
}
+ while (search_.nextCell(testcell_, currCell_, cellBound_));
}
else
{
continue;
}
rvec dx;
- if (search_.pbc_)
+ if (search_.pbc_.ePBC != epbcNONE)
{
- pbc_dx(search_.pbc_, xtest_, search_.xref_[i], dx);
+ pbc_dx(&search_.pbc_, search_.xref_[i], xtest_, dx);
}
else
{
- rvec_sub(xtest_, search_.xref_[i], dx);
+ rvec_sub(search_.xref_[i], xtest_, dx);
}
- const real r2 = norm2(dx);
+ const real r2
+ = search_.bXY_
+ ? dx[XX]*dx[XX] + dx[YY]*dx[YY]
+ : norm2(dx);
if (r2 <= search_.cutoff2_)
{
- if (action(i, r2))
+ if (action(i, r2, dx))
{
- previ_ = i;
+ previ_ = i;
+ prevr2_ = r2;
+ copy_rvec(dx, prevdx_);
return true;
}
}
}
else
{
- *pair = AnalysisNeighborhoodPair(previ_, testIndex_);
+ *pair = AnalysisNeighborhoodPair(previ_, testIndex_, prevr2_, prevdx_);
}
}
*
* Simply breaks the loop on the first found neighbor.
*/
-bool withinAction(int /*i*/, real /*r2*/)
+bool withinAction(int /*i*/, real /*r2*/, const rvec /* dx */)
{
return true;
}
*
* \param[out] closestPoint Index of the closest reference location.
* \param[out] minDist2 Minimum distance squared.
+ * \param[out] dx Shortest distance vector.
*
* The constructor call does not modify the pointed values, but only
* stores the pointers for later use.
* See the class description for additional semantics.
*/
- MindistAction(int *closestPoint, real *minDist2)
- : closestPoint_(*closestPoint), minDist2_(*minDist2)
+ MindistAction(int *closestPoint, real *minDist2, rvec *dx)
+ : closestPoint_(*closestPoint), minDist2_(*minDist2), dx_(*dx)
{
}
//! Processes a neighbor to find the nearest point.
- bool operator()(int i, real r2)
+ bool operator()(int i, real r2, const rvec dx)
{
if (r2 < minDist2_)
{
closestPoint_ = i;
minDist2_ = r2;
+ copy_rvec(dx, dx_);
}
return false;
}
private:
int &closestPoint_;
real &minDist2_;
+ rvec &dx_;
GMX_DISALLOW_ASSIGN(MindistAction);
};
typedef AnalysisNeighborhoodSearch::ImplPointer SearchImplPointer;
typedef std::vector<SearchImplPointer> SearchList;
- Impl() : cutoff_(0), mode_(eSearchMode_Automatic)
+ Impl()
+ : cutoff_(0), excls_(NULL), mode_(eSearchMode_Automatic), bXY_(false)
{
}
~Impl()
tMPI::mutex createSearchMutex_;
SearchList searchList_;
real cutoff_;
+ const t_blocka *excls_;
SearchMode mode_;
+ bool bXY_;
};
AnalysisNeighborhood::Impl::SearchImplPointer
impl_->cutoff_ = cutoff;
}
+void AnalysisNeighborhood::setXYMode(bool bXY)
+{
+ impl_->bXY_ = bXY;
+}
+
+void AnalysisNeighborhood::setTopologyExclusions(const t_blocka *excls)
+{
+ GMX_RELEASE_ASSERT(impl_->searchList_.empty(),
+ "Changing the exclusions after initSearch() not currently supported");
+ impl_->excls_ = excls;
+}
+
void AnalysisNeighborhood::setMode(SearchMode mode)
{
impl_->mode_ = mode;
const AnalysisNeighborhoodPositions &positions)
{
Impl::SearchImplPointer search(impl_->getSearch());
- search->init(mode(), pbc, positions);
+ search->init(mode(), impl_->bXY_, impl_->excls_,
+ pbc, positions);
return AnalysisNeighborhoodSearch(search);
}
pairSearch.startSearch(positions);
real minDist2 = impl_->cutoffSquared();
int closestPoint = -1;
- MindistAction action(&closestPoint, &minDist2);
+ rvec dx = {0.0, 0.0, 0.0};
+ MindistAction action(&closestPoint, &minDist2, &dx);
(void)pairSearch.searchNext(action);
return sqrt(minDist2);
}
pairSearch.startSearch(positions);
real minDist2 = impl_->cutoffSquared();
int closestPoint = -1;
- MindistAction action(&closestPoint, &minDist2);
+ rvec dx = {0.0, 0.0, 0.0};
+ MindistAction action(&closestPoint, &minDist2, &dx);
(void)pairSearch.searchNext(action);
- return AnalysisNeighborhoodPair(closestPoint, 0);
+ return AnalysisNeighborhoodPair(closestPoint, 0, minDist2, dx);
}
AnalysisNeighborhoodPairSearch
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_SELECTION_NBSEARCH_H
#define GMX_SELECTION_NBSEARCH_H
-#include <boost/shared_ptr.hpp>
+#include <vector>
-#include "../legacyheaders/typedefs.h"
-#include "../utility/common.h"
-#include "../utility/gmxassert.h"
+#include <boost/shared_ptr.hpp>
-#include "indexutil.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
-struct gmx_ana_pos_t;
+struct t_blocka;
+struct t_pbc;
namespace gmx
{
* to methods that accept positions.
*/
AnalysisNeighborhoodPositions(const rvec &x)
- : count_(1), index_(-1), x_(&x)
+ : count_(1), index_(-1), x_(&x), exclusionIds_(NULL), indices_(NULL)
{
}
/*! \brief
* Initializes positions from an array of position vectors.
*/
AnalysisNeighborhoodPositions(const rvec x[], int count)
- : count_(count), index_(-1), x_(x)
+ : count_(count), index_(-1), x_(x), exclusionIds_(NULL), indices_(NULL)
+ {
+ }
+ /*! \brief
+ * Initializes positions from a vector of position vectors.
+ */
+ AnalysisNeighborhoodPositions(const std::vector<RVec> &x)
+ : count_(x.size()), index_(-1), x_(as_rvec_array(&x[0])),
+ exclusionIds_(NULL), indices_(NULL)
{
}
+ /*! \brief
+ * Sets indices to use for mapping exclusions to these positions.
+ *
+ * The exclusion IDs can always be set, but they are ignored unless
+ * actual exclusions have been set with
+ * AnalysisNeighborhood::setTopologyExclusions().
+ */
+ AnalysisNeighborhoodPositions &
+ exclusionIds(ConstArrayRef<int> ids)
+ {
+ GMX_ASSERT(static_cast<int>(ids.size()) == count_,
+ "Exclusion id array should match the number of positions");
+ exclusionIds_ = ids.data();
+ return *this;
+ }
+ /*! \brief
+ * Sets indices that select a subset of all positions from the array.
+ *
+ * If called, selected positions from the array of positions passed to
+ * the constructor is used instead of the whole array.
+ * All returned indices from AnalysisNeighborhoodPair objects are
+ * indices to the \p indices array passed here.
+ */
+ AnalysisNeighborhoodPositions &
+ indexed(ConstArrayRef<int> indices)
+ {
+ count_ = indices.size();
+ indices_ = indices.data();
+ return *this;
+ }
+
/*! \brief
* Selects a single position to use from an array.
*
* In contrast to the AnalysisNeighborhoodPositions(const rvec &)
* constructor, AnalysisNeighborhoodPair objects return \p index
* instead of zero.
+ *
+ * If used together with indexed(), \p index references the index array
+ * passed to indexed() instead of the position array.
*/
AnalysisNeighborhoodPositions &selectSingleFromArray(int index)
{
int count_;
int index_;
const rvec *x_;
+ const int *exclusionIds_;
+ const int *indices_;
//! To access the positions for initialization.
friend class internal::AnalysisNeighborhoodSearchImpl;
* a single thread.
*
* \todo
- * Support for exclusions.
- * The 4.5/4.6 C API had very low-level support for exclusions, which was not
- * very convenient to use, and hadn't been tested much. The internal code that
- * it used to do the exclusion during the search itself is still there, but it
- * needs more thought on what would be a convenient way to initialize it.
- * Can be implemented once there is need for it in some calling code.
+ * Generalize the exclusion machinery to make it easier to use for other cases
+ * than atom-atom exclusions from the topology.
*
* \inpublicapi
* \ingroup module_selection
~AnalysisNeighborhood();
/*! \brief
- * Set cutoff distance for the neighborhood searching.
+ * Sets cutoff distance for the neighborhood searching.
*
* \param[in] cutoff Cutoff distance for the search
* (<=0 stands for no cutoff).
* Does not throw.
*/
void setCutoff(real cutoff);
+ /*! \brief
+ * Sets the search to only happen in the XY plane.
+ *
+ * Z component of the coordinates is not used in the searching,
+ * and returned distances are computed in the XY plane.
+ * Only boxes with the third box vector parallel to the Z axis are
+ * currently implemented.
+ *
+ * Does not throw.
+ */
+ void setXYMode(bool bXY);
+ /*! \brief
+ * Sets atom exclusions from a topology.
+ *
+ * The \p excls structure specifies the exclusions from test positions
+ * to reference positions, i.e., a block starting at `excls->index[i]`
+ * specifies the exclusions for test position `i`, and the indices in
+ * `excls->a` are indices of the reference positions. If `excls->nr`
+ * is smaller than a test position id, then such test positions do not
+ * have any exclusions.
+ * It is assumed that the indices within a block of indices in
+ * `excls->a` is ascending.
+ *
+ * Does not throw.
+ *
+ * \see AnalysisNeighborhoodPositions::exclusionIds()
+ */
+ void setTopologyExclusions(const t_blocka *excls);
/*! \brief
* Sets the algorithm to use for searching.
*
{
public:
//! Initializes an invalid pair.
- AnalysisNeighborhoodPair() : refIndex_(-1), testIndex_(0) {}
+ AnalysisNeighborhoodPair() : refIndex_(-1), testIndex_(0), distance2_(0.0)
+ {
+ clear_rvec(dx_);
+ }
//! Initializes a pair object with the given data.
- AnalysisNeighborhoodPair(int refIndex, int testIndex)
- : refIndex_(refIndex), testIndex_(testIndex)
+ AnalysisNeighborhoodPair(int refIndex, int testIndex, real distance2,
+ const rvec dx)
+ : refIndex_(refIndex), testIndex_(testIndex), distance2_(distance2)
{
+ copy_rvec(dx, dx_);
}
/*! \brief
GMX_ASSERT(isValid(), "Accessing invalid object");
return testIndex_;
}
+ /*! \brief
+ * Returns the squared distance between the pair of positions.
+ */
+ real distance2() const
+ {
+ GMX_ASSERT(isValid(), "Accessing invalid object");
+ return distance2_;
+ }
+ /*! \brief
+ * Returns the shortest vector between the pair of positions.
+ *
+ * The vector is from the test position to the reference position.
+ */
+ const rvec &dx() const
+ {
+ GMX_ASSERT(isValid(), "Accessing invalid object");
+ return dx_;
+ }
private:
int refIndex_;
int testIndex_;
+ real distance2_;
+ rvec dx_;
};
/*! \brief
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
#include <algorithm>
#include <string>
-#include "gromacs/legacyheaders/vec.h"
-
+#include "gromacs/math/vec.h"
#include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
-#include "gromacs/selection/selparam.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/messagestringcollector.h"
+#include "gromacs/utility/scoped_cptr.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "parsetree.h"
-#include "position.h"
#include "scanner.h"
#include "selelem.h"
+#include "selmethod.h"
+#include "selparam.h"
-using gmx::SelectionParserValue;
-using gmx::SelectionParserValueList;
-using gmx::SelectionParserParameter;
-using gmx::SelectionParserParameterList;
-using gmx::SelectionTreeElement;
-using gmx::SelectionTreeElementPointer;
+using namespace gmx;
/*!
* \param[in] name Name of the parameter to search.
*
* \param[in,out] value Value to convert.
* \param[in] type Type to convert to.
+ * \param[in] errors Errors will be reported into this as nested exceptions.
* \param[in] scanner Scanner data structure.
- * \returns 0 on success, a non-zero value on error.
*/
-static int
-convert_value(SelectionParserValue *value, e_selvalue_t type, void *scanner)
+static void
+convert_value(SelectionParserValue *value, e_selvalue_t type,
+ ExceptionInitializer *errors, void *scanner)
{
if (value->type == type || type == NO_VALUE)
{
- return 0;
+ return;
}
if (value->hasExpressionValue())
{
* reference positions. */
if (value->type == GROUP_VALUE && type == POS_VALUE)
{
- SelectionTreeElementPointer expr =
- _gmx_sel_init_position(value->expr, NULL, scanner);
- // FIXME: Use exceptions
- if (!expr)
+ try
+ {
+ SelectionTreeElementPointer expr =
+ _gmx_sel_init_position(value->expr, NULL, scanner);
+ *value = SelectionParserValue::createExpr(expr);
+ }
+ catch (UserInputError &ex)
{
- return -1;
+ std::string text(_gmx_sel_lexer_get_text(scanner, value->location()));
+ std::string context(formatString("In '%s'", text.c_str()));
+ ex.prependContext(context);
+ errors->addCurrentExceptionAsNested();
}
- *value = SelectionParserValue::createExpr(expr);
- return 0;
+ return;
}
- return -1;
}
else
{
if (value->type == INT_VALUE && type == REAL_VALUE)
{
*value = SelectionParserValue::createRealRange(value->u.i.i1,
- value->u.i.i2);
- return 0;
+ value->u.i.i2,
+ value->location());
+ return;
}
/* Reals that are integer-valued can also be converted */
if (value->type == REAL_VALUE && type == INT_VALUE)
if (gmx_within_tol(value->u.r.r1, i1, GMX_REAL_EPS)
&& gmx_within_tol(value->u.r.r2, i2, GMX_REAL_EPS))
{
- *value = SelectionParserValue::createIntegerRange(i1, i2);
- return 0;
+ *value = SelectionParserValue::createIntegerRange(i1, i2, value->location());
+ return;
}
}
}
- return -1;
+ std::string text(_gmx_sel_lexer_get_text(scanner, value->location()));
+ std::string message(
+ formatString("Expression '%s' evaluates to a type is not valid in this context",
+ text.c_str()));
+ InvalidInputError ex(message);
+ errors->addNested(ex);
}
/*! \brief
* \param[in,out] values Values to convert.
* \param[in] type Type to convert to.
* \param[in] scanner Scanner data structure.
- * \returns 0 on success, a non-zero value on error.
*/
-static int
+static void
convert_values(SelectionParserValueList *values, e_selvalue_t type, void *scanner)
{
- int rc = 0;
+ ExceptionInitializer errors("");
SelectionParserValueList::iterator value;
for (value = values->begin(); value != values->end(); ++value)
{
- int rc1 = convert_value(&*value, type, scanner);
- if (rc1 != 0 && rc == 0)
- {
- rc = rc1;
- }
+ convert_value(&*value, type, &errors, scanner);
+ }
+ if (errors.hasNestedExceptions())
+ {
+ GMX_THROW(InvalidInputError(errors));
}
- /* FIXME: More informative error messages */
- return rc;
}
/*! \brief
* \param[in] values List of values.
* \param param Parameter to parse.
* \param[in] scanner Scanner data structure.
- * \returns true if the values were parsed successfully, false otherwise.
*/
-static bool
+static void
parse_values_range(const SelectionParserValueList &values,
gmx_ana_selparam_t *param, void *scanner)
{
- int *idata;
- real *rdata;
int i, j, n;
param->flags &= ~SPAR_DYNAMIC;
GMX_RELEASE_ASSERT(param->val.type == INT_VALUE || param->val.type == REAL_VALUE,
"Invalid range parameter type");
- idata = NULL;
- rdata = NULL;
+ int *idata = NULL;
+ real *rdata = NULL;
+ scoped_guard_sfree dataGuard;
if (param->val.type == INT_VALUE)
{
snew(idata, values.size()*2);
+ dataGuard.reset(idata);
}
else
{
snew(rdata, values.size()*2);
+ dataGuard.reset(rdata);
}
i = 0;
SelectionParserValueList::const_iterator value;
for (value = values.begin(); value != values.end(); ++value)
{
+ GMX_RELEASE_ASSERT(value->type == param->val.type,
+ "Invalid range value type (should have been caught earlier)");
if (value->hasExpressionValue())
{
- _gmx_selparser_error(scanner, "expressions not supported within range parameters");
- return false;
+ std::string text(_gmx_sel_lexer_get_text(scanner, value->location()));
+ std::string message("Only simple values or 'A to B' ranges are "
+ "supported in this context");
+ InvalidInputError ex(message);
+ ex.prependContext(formatString("Invalid expression '%s'", text.c_str()));
+ GMX_THROW(ex);
}
- GMX_RELEASE_ASSERT(value->type == param->val.type,
- "Invalid range value type (should have been caught earlier)");
if (param->val.type == INT_VALUE)
{
int i1 = std::min(value->u.i.i1, value->u.i.i2);
/* Store the values */
if (param->flags & SPAR_VARNUM)
{
+ dataGuard.release();
param->val.nr = n;
if (param->val.type == INT_VALUE)
{
{
if (n != param->val.nr)
{
- _gmx_selparser_error(scanner, "the value should consist of exactly one range");
- sfree(idata);
- sfree(rdata);
- return false;
+ GMX_ASSERT(n == 1,
+ "Range parameters with a fixed count > 1 do not make sense");
+ GMX_THROW(InvalidInputError("Only one value or 'A to B' range is "
+ "supported in this context"));
}
if (param->val.type == INT_VALUE)
{
memcpy(param->val.u.i, idata, 2*n*sizeof(int));
- sfree(idata);
}
else
{
memcpy(param->val.u.r, rdata, 2*n*sizeof(real));
- sfree(rdata);
}
}
if (param->nvalptr)
*param->nvalptr = param->val.nr;
}
param->nvalptr = NULL;
-
- return true;
}
/*! \brief
* \param param Parameter to parse.
* \param root Selection element to which child expressions are added.
* \param[in] scanner Scanner data structure.
- * \returns true if the values were parsed successfully, false otherwise.
*
* For integer ranges, the sequence of numbers from the first to second value
* is stored, each as a separate value.
*/
-static bool
+static void
parse_values_varnum(const SelectionParserValueList &values,
gmx_ana_selparam_t *param,
const SelectionTreeElementPointer &root,
param->flags &= ~SPAR_DYNAMIC;
/* Compute number of values, considering also integer ranges. */
- size_t valueCount = values.size();
+ int valueCount = static_cast<int>(values.size());
if (param->val.type == INT_VALUE)
{
SelectionParserValueList::const_iterator value;
if (param->val.type != INT_VALUE && param->val.type != REAL_VALUE
&& param->val.type != STR_VALUE && param->val.type != POS_VALUE)
{
- GMX_THROW(gmx::InternalError("Variable-count value type not implemented"));
+ GMX_THROW(InternalError("Variable-count value type not implemented"));
}
/* Reserve appropriate amount of memory */
{
_gmx_selvalue_reserve(¶m->val, valueCount);
}
+ /* Create a dummy child element to store the string values.
+ * This element is responsible for freeing the values, but carries no
+ * other function. */
+ if (param->val.type == STR_VALUE)
+ {
+ SelectionTreeElementPointer child(
+ new SelectionTreeElement(SEL_CONST, SelectionLocation::createEmpty()));
+ _gmx_selelem_set_vtype(child, STR_VALUE);
+ child->setName(param->name);
+ child->flags &= ~SEL_ALLOCVAL;
+ child->flags |= SEL_FLAGSSET | SEL_VARNUMVAL | SEL_ALLOCDATA;
+ child->v.nr = valueCount;
+ _gmx_selvalue_setstore(&child->v, param->val.u.s);
+ /* Because the child is not group-valued, the u union is not used
+ * for anything, so we can abuse it by storing the parameter value
+ * as place_child() expects, but this is really ugly... */
+ child->u.param = param;
+ place_child(root, child, param);
+ }
+ param->val.nr = valueCount;
i = 0;
SelectionParserValueList::const_iterator value;
for (value = values.begin(); value != values.end(); ++value)
{
+ GMX_RELEASE_ASSERT(value->type == param->val.type,
+ "Invalid value type (should have been caught earlier)");
if (value->hasExpressionValue())
{
- _gmx_selparser_error(scanner, "expressions not supported within value lists");
- return false;
+ std::string text(_gmx_sel_lexer_get_text(scanner, value->location()));
+ std::string message("Selection expressions are not supported in this "
+ "context when multiple values are provided");
+ InvalidInputError ex(message);
+ ex.prependContext(formatString("Invalid expression '%s'", text.c_str()));
+ GMX_THROW(ex);
}
- GMX_RELEASE_ASSERT(value->type == param->val.type,
- "Invalid value type (should have been caught earlier)");
switch (param->val.type)
{
case INT_VALUE:
case REAL_VALUE:
if (value->u.r.r1 != value->u.r.r2)
{
- _gmx_selparser_error(scanner, "real ranges not supported");
- return false;
+ std::string text(_gmx_sel_lexer_get_text(scanner, value->location()));
+ std::string message
+ = formatString("Real range ('%s') is not supported in this context",
+ text.c_str());
+ InvalidInputError ex(message);
+ GMX_THROW(ex);
}
param->val.u.r[i++] = value->u.r.r1;
break;
case STR_VALUE:
- param->val.u.s[i++] = strdup(value->stringValue().c_str());
+ param->val.u.s[i++] = gmx_strdup(value->stringValue().c_str());
break;
case POS_VALUE: copy_rvec(value->u.x, param->val.u.p->x[i++]); break;
default: /* Should not be reached */
- GMX_THROW(gmx::InternalError("Variable-count value type not implemented"));
+ GMX_RELEASE_ASSERT(false, "Variable-count value type not implemented");
}
}
- param->val.nr = i;
+ GMX_RELEASE_ASSERT(i == valueCount,
+ "Inconsistent value count wrt. the actual value population");
if (param->nvalptr)
{
*param->nvalptr = param->val.nr;
}
param->nvalptr = NULL;
- /* Create a dummy child element to store the string values.
- * This element is responsible for freeing the values, but carries no
- * other function. */
- if (param->val.type == STR_VALUE)
- {
- SelectionTreeElementPointer child(new SelectionTreeElement(SEL_CONST));
- _gmx_selelem_set_vtype(child, STR_VALUE);
- child->setName(param->name);
- child->flags &= ~SEL_ALLOCVAL;
- child->flags |= SEL_FLAGSSET | SEL_VARNUMVAL | SEL_ALLOCDATA;
- child->v.nr = param->val.nr;
- _gmx_selvalue_setstore(&child->v, param->val.u.s);
- /* Because the child is not group-valued, the u union is not used
- * for anything, so we can abuse it by storing the parameter value
- * as place_child() expects, but this is really ugly... */
- child->u.param = param;
- place_child(root, child, param);
- }
-
- return true;
}
/*! \brief
}
else
{
- child.reset(new SelectionTreeElement(SEL_SUBEXPRREF));
+ // TODO: Initialize such that it includes the parameter.
+ child.reset(new SelectionTreeElement(SEL_SUBEXPRREF, expr->location()));
_gmx_selelem_set_vtype(child, expr->v.type);
child->child = expr;
}
child->u.param = param;
if (child->v.type != param->val.type)
{
- _gmx_selparser_error(scanner, "invalid expression value");
- // FIXME: Use exceptions.
- return SelectionTreeElementPointer();
+ // TODO: It would be nice to say what is the expected type.
+ std::string text(_gmx_sel_lexer_get_text(scanner, expr->location()));
+ std::string message
+ = formatString("Expression '%s' is not valid in this context "
+ "(produces the wrong type of values)",
+ text.c_str());
+ GMX_THROW(InvalidInputError(message));
}
_gmx_selelem_update_flags(child);
if ((child->flags & SEL_DYNAMIC) && !(param->flags & SPAR_DYNAMIC))
{
- _gmx_selparser_error(scanner, "dynamic values not supported");
- // FIXME: Use exceptions.
- return SelectionTreeElementPointer();
+ std::string text(_gmx_sel_lexer_get_text(scanner, expr->location()));
+ std::string message
+ = formatString("Expression '%s' is dynamic, which is not "
+ "valid in this context",
+ text.c_str());
+ GMX_THROW(InvalidInputError(message));
}
if (!(child->flags & SEL_DYNAMIC))
{
* \param param Parameter to parse.
* \param root Selection element to which child expressions are added.
* \param[in] scanner Scanner data structure.
- * \returns true if the values were parsed successfully, false otherwise.
*/
-static bool
+static void
parse_values_varnum_expr(const SelectionParserValueList &values,
gmx_ana_selparam_t *param,
const SelectionTreeElementPointer &root,
SelectionTreeElementPointer child
= add_child(root, param, values.front().expr, scanner);
- if (!child)
- {
- return false;
- }
/* Process single-valued expressions */
/* TODO: We should also handle SEL_SINGLEVAL expressions here */
*param->nvalptr = param->val.nr;
}
param->nvalptr = NULL;
- return true;
+ return;
}
if (!(child->flags & SEL_VARNUMVAL))
{
- _gmx_selparser_error(scanner, "invalid expression value");
- return false;
+ std::string text(_gmx_sel_lexer_get_text(scanner, values.front().location()));
+ std::string message
+ = formatString("Expression '%s' is invalid in this context",
+ text.c_str());
+ GMX_THROW(InvalidInputError(message));
}
child->flags |= SEL_ALLOCVAL;
*param->nvalptr = param->val.nr;
/* Rest of the initialization is done during compilation in
* init_method(). */
-
- return true;
}
/*! \brief
* as the value \p i of \p param.
* This function is used internally by parse_values_std().
*/
-static bool
+static void
set_expr_value_store(const SelectionTreeElementPointer &sel,
gmx_ana_selparam_t *param, int i, void *scanner)
{
if (sel->v.type != GROUP_VALUE && !(sel->flags & SEL_SINGLEVAL))
{
- _gmx_selparser_error(scanner, "invalid expression value");
- return false;
+ std::string text(_gmx_sel_lexer_get_text(scanner, sel->location()));
+ std::string message
+ = formatString("Expression '%s' is invalid in this context",
+ text.c_str());
+ GMX_THROW(InvalidInputError(message));
}
switch (sel->v.type)
{
case POS_VALUE: sel->v.u.p = ¶m->val.u.p[i]; break;
case GROUP_VALUE: sel->v.u.g = ¶m->val.u.g[i]; break;
default: /* Error */
- GMX_THROW(gmx::InternalError("Invalid value type"));
+ GMX_THROW(InternalError("Invalid value type"));
}
sel->v.nr = 1;
sel->v.nalloc = -1;
- return true;
}
/*! \brief
* \param param Parameter to parse.
* \param root Selection element to which child expressions are added.
* \param[in] scanner Scanner data structure.
- * \returns true if the values were parsed successfully, false otherwise.
*
* For integer ranges, the sequence of numbers from the first to second value
* is stored, each as a separate value.
*/
-static bool
+static void
parse_values_std(const SelectionParserValueList &values,
gmx_ana_selparam_t *param,
const SelectionTreeElementPointer &root, void *scanner)
{
if (values.size() > 1)
{
- _gmx_selparser_error(scanner, "more than one value not supported");
- return false;
+ GMX_THROW(InvalidInputError(
+ "Only a single value or a single expression is "
+ "supported in this context"));
}
if (values.front().hasExpressionValue())
{
SelectionTreeElementPointer child
- = add_child(root, param, values.front().expr, scanner);
- if (!child)
- {
- return false;
- }
+ = add_child(root, param, values.front().expr, scanner);
child->flags |= SEL_ALLOCVAL;
if (child->v.type != GROUP_VALUE && (child->flags & SEL_ATOMVAL))
{
{
*param->nvalptr = -1;
}
- return true;
+ return;
}
param->flags &= ~SPAR_ATOMVAL;
param->val.nr = 1;
{
_gmx_selvalue_reserve(¶m->val, 1);
}
- return set_expr_value_store(child, param, 0, scanner);
+ set_expr_value_store(child, param, 0, scanner);
+ return;
}
/* If we reach here, proceed with normal parameter handling */
param->val.nr = 1;
SelectionParserValueList::const_iterator value;
for (value = values.begin(); value != values.end() && i < param->val.nr; ++value)
{
- if (value->type != param->val.type)
- {
- _gmx_selparser_error(scanner, "incorrect value skipped");
- continue;
- }
+ GMX_RELEASE_ASSERT(value->type == param->val.type,
+ "Invalid value type (should have been caught earlier)");
if (value->hasExpressionValue())
{
SelectionTreeElementPointer child
= add_child(root, param, value->expr, scanner);
- /* Check that the expression is valid */
- if (!child)
- {
- return false;
- }
- if (!set_expr_value_store(child, param, i, scanner))
- {
- return false;
- }
+ set_expr_value_store(child, param, i, scanner);
if (child->flags & SEL_DYNAMIC)
{
bDynamic = true;
switch (value->type)
{
case INT_VALUE:
+ {
+ bool bTooManyValues;
if (value->u.i.i1 <= value->u.i.i2)
{
for (j = value->u.i.i1; j <= value->u.i.i2 && i < param->val.nr; ++j)
{
param->val.u.i[i++] = j;
}
- if (j != value->u.i.i2 + 1)
- {
- _gmx_selparser_error(scanner, "extra values skipped");
- }
+ bTooManyValues = (j != value->u.i.i2 + 1);
}
else
{
{
param->val.u.i[i++] = j;
}
- if (j != value->u.i.i2 - 1)
- {
- _gmx_selparser_error(scanner, "extra values skipped");
- }
+ bTooManyValues = (j != value->u.i.i2 - 1);
+ }
+ if (bTooManyValues)
+ {
+ std::string text(_gmx_sel_lexer_get_text(scanner, value->location()));
+ std::string message
+ = formatString("Range ('%s') produces more values than is "
+ "accepted in this context",
+ text.c_str());
+ GMX_THROW(InvalidInputError(message));
}
--i;
break;
+ }
case REAL_VALUE:
if (value->u.r.r1 != value->u.r.r2)
{
- _gmx_selparser_error(scanner, "real ranges not supported");
- return false;
+ std::string text(_gmx_sel_lexer_get_text(scanner, value->location()));
+ std::string message
+ = formatString("Real range ('%s') is not supported in this context",
+ text.c_str());
+ GMX_THROW(InvalidInputError(message));
}
param->val.u.r[i] = value->u.r.r1;
break;
case STR_VALUE:
- param->val.u.s[i] = strdup(value->stringValue().c_str());
+ param->val.u.s[i] = gmx_strdup(value->stringValue().c_str());
break;
case POS_VALUE:
gmx_ana_pos_init_const(¶m->val.u.p[i], value->u.x);
break;
case NO_VALUE:
case GROUP_VALUE:
- GMX_THROW(gmx::InternalError("Invalid non-expression value type"));
+ GMX_THROW(InternalError("Invalid non-expression value type"));
}
}
++i;
}
if (value != values.end())
{
- _gmx_selparser_error(scanner, "extra values");
- return false;
+ std::string message
+ = formatString("Too many values provided, expected %d",
+ param->val.nr);
+ GMX_THROW(InvalidInputError(message));
}
if (i < param->val.nr)
{
- _gmx_selparser_error(scanner, "not enough values");
- return false;
+ std::string message
+ = formatString("Too few values provided, expected %d",
+ param->val.nr);
+ GMX_THROW(InvalidInputError(message));
}
if (!bDynamic)
{
*param->nvalptr = param->val.nr;
}
param->nvalptr = NULL;
-
- return true;
}
/*! \brief
* \param[in] values List of values.
* \param param Parameter to parse.
* \param[in] scanner Scanner data structure.
- * \returns true if the values were parsed successfully, false otherwise.
*/
-static bool
+static void
parse_values_bool(const std::string &name,
const SelectionParserValueList &values,
gmx_ana_selparam_t *param, void *scanner)
{
+ GMX_UNUSED_VALUE(scanner);
GMX_ASSERT(param->val.type == NO_VALUE,
"Boolean parser called for non-boolean parameter");
if (values.size() > 1 || (!values.empty() && values.front().type != INT_VALUE))
{
- _gmx_selparser_error(scanner, "parameter takes only a yes/no/on/off/0/1 value");
- return false;
+ std::string message
+ = formatString("'%s' only accepts yes/no/on/off/0/1 (and empty) as a value",
+ param->name);
+ GMX_THROW(InvalidInputError(message));
}
bool bSetNo = false;
}
if (bSetNo && !values.empty())
{
- _gmx_selparser_error(scanner, "parameter 'no%s' should not have a value",
- param->name);
- return false;
+ std::string message
+ = formatString("'no%s' cannot be followed by any value",
+ param->name);
+ GMX_THROW(InvalidInputError(message));
}
if (!values.empty() && values.front().u.i.i1 == 0)
{
}
*param->val.u.b = bSetNo ? false : true;
- return true;
}
/*! \brief
* \param[in] scanner Scanner data structure.
* \returns true if the values were parsed successfully, false otherwise.
*/
-static bool
+static void
parse_values_enum(const SelectionParserValueList &values,
gmx_ana_selparam_t *param,
void *scanner)
"Enum parser called for non-string parameter");
if (values.size() != 1)
{
- _gmx_selparser_error(scanner, "a single value is required");
- return false;
+ GMX_THROW(InvalidInputError(
+ "Only a single string value is supported in this context"));
}
const SelectionParserValue &value = values.front();
GMX_RELEASE_ASSERT(value.type == param->val.type,
"Invalid value type (should have been caught earlier)");
if (value.hasExpressionValue())
{
- _gmx_selparser_error(scanner, "expression value for enumerated parameter not supported");
- return false;
+ std::string text(_gmx_sel_lexer_get_text(scanner, value.location()));
+ std::string message
+ = formatString("Expression ('%s') is not supported in this context",
+ text.c_str());
+ GMX_THROW(InvalidInputError(message));
}
const std::string &svalue = value.stringValue();
int match = 0;
while (param->val.u.s[i] != NULL)
{
- if (gmx::startsWith(param->val.u.s[i], svalue))
+ if (startsWith(param->val.u.s[i], svalue))
{
/* Check if there is a duplicate match */
if (match > 0)
{
- _gmx_selparser_error(scanner, "ambiguous value");
- return false;
+ std::string message
+ = formatString("Value '%s' is ambiguous", svalue.c_str());
+ GMX_THROW(InvalidInputError(message));
}
match = i;
}
}
if (match == 0)
{
- _gmx_selparser_error(scanner, "invalid value");
- return false;
+ std::string message
+ = formatString("Value '%s' is not recognized", svalue.c_str());
+ GMX_THROW(InvalidInputError(message));
}
param->val.u.s[0] = param->val.u.s[match];
- return true;
}
/*! \brief
if (value->hasExpressionValue() && value->expr->v.type != GROUP_VALUE &&
value->expr->type == SEL_CONST)
{
- SelectionTreeElementPointer expr = value->expr;
+ SelectionTreeElementPointer expr = value->expr;
+ const SelectionLocation &location = value->location();
switch (expr->v.type)
{
case INT_VALUE:
- *value = SelectionParserValue::createInteger(expr->v.u.i[0]);
+ *value = SelectionParserValue::createInteger(expr->v.u.i[0], location);
break;
case REAL_VALUE:
- *value = SelectionParserValue::createReal(expr->v.u.r[0]);
+ *value = SelectionParserValue::createReal(expr->v.u.r[0], location);
break;
case STR_VALUE:
- *value = SelectionParserValue::createString(expr->v.u.s[0]);
+ *value = SelectionParserValue::createString(expr->v.u.s[0], location);
break;
case POS_VALUE:
- *value = SelectionParserValue::createPosition(expr->v.u.p->x[0]);
+ *value = SelectionParserValue::createPosition(expr->v.u.p->x[0], location);
break;
default:
- GMX_THROW(gmx::InternalError(
- "Unsupported constant expression value type"));
+ GMX_RELEASE_ASSERT(false,
+ "Unsupported constant expression value type");
}
}
}
* \param params Array of parameters to parse.
* \param root Selection element to which child expressions are added.
* \param[in] scanner Scanner data structure.
- * \returns true if the parameters were parsed successfully, false otherwise.
*
* Initializes the \p params array based on the parameters in \p pparams.
* See the documentation of \c gmx_ana_selparam_t for different options
* The list \p pparams and any associated values are freed after the parameters
* have been processed, no matter is there was an error or not.
*/
-bool
+void
_gmx_sel_parse_params(const gmx::SelectionParserParameterList &pparams,
int nparam, gmx_ana_selparam_t *params,
const gmx::SelectionTreeElementPointer &root,
void *scanner)
{
- gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
- gmx_ana_selparam_t *oparam;
- bool bOk, rc;
- int i;
-
+ ExceptionInitializer errors("");
/* Check that the value pointers of SPAR_VARNUM parameters are NULL and
* that they are not NULL for other parameters */
- bOk = true;
- for (i = 0; i < nparam; ++i)
+ for (int i = 0; i < nparam; ++i)
{
- std::string contextStr = gmx::formatString("In parameter '%s'", params[i].name);
- gmx::MessageStringContext context(errors, contextStr);
- if (params[i].val.type != POS_VALUE && (params[i].flags & (SPAR_VARNUM | SPAR_ATOMVAL)))
+ if (params[i].val.type != POS_VALUE
+ && (params[i].flags & (SPAR_VARNUM | SPAR_ATOMVAL)))
{
- if (params[i].val.u.ptr != NULL)
- {
- _gmx_selparser_error(scanner, "value pointer is not NULL "
- "although it should be for SPAR_VARNUM "
- "and SPAR_ATOMVAL parameters");
- }
- if ((params[i].flags & SPAR_VARNUM)
- && (params[i].flags & SPAR_DYNAMIC) && !params[i].nvalptr)
- {
- _gmx_selparser_error(scanner, "nvalptr is NULL but both "
- "SPAR_VARNUM and SPAR_DYNAMIC are specified");
- bOk = false;
- }
+ GMX_RELEASE_ASSERT(params[i].val.u.ptr == NULL,
+ "value pointer is not NULL "
+ "although it should be for SPAR_VARNUM "
+ "and SPAR_ATOMVAL parameters");
+ GMX_RELEASE_ASSERT(!((params[i].flags & SPAR_VARNUM)
+ && (params[i].flags & SPAR_DYNAMIC))
+ || params[i].nvalptr != NULL,
+ "nvalptr is NULL but both "
+ "SPAR_VARNUM and SPAR_DYNAMIC are specified");
}
else
{
- if (params[i].val.u.ptr == NULL)
- {
- _gmx_selparser_error(scanner, "value pointer is NULL");
- bOk = false;
- }
+ GMX_RELEASE_ASSERT(params[i].val.u.ptr != NULL,
+ "value pointer is NULL");
}
}
- if (!bOk)
- {
- return false;
- }
/* Parse the parameters */
- i = 0;
+ int nullParamIndex = 0;
SelectionParserParameterList::const_iterator pparam;
for (pparam = pparams.begin(); pparam != pparams.end(); ++pparam)
{
- std::string contextStr;
- /* Find the parameter and make some checks */
- if (!pparam->name().empty())
- {
- contextStr = gmx::formatString("In parameter '%s'", pparam->name().c_str());
- i = -1;
- oparam = gmx_ana_selparam_find(pparam->name().c_str(), nparam, params);
- }
- else if (i >= 0)
+ try
{
- contextStr = gmx::formatString("In value %d", i + 1);
- oparam = ¶ms[i];
- if (oparam->name != NULL)
+ // Always assigned afterwards, but cppcheck does not see that.
+ gmx_ana_selparam_t *oparam = NULL;
+ /* Find the parameter and make some checks */
+ if (!pparam->name().empty())
{
- oparam = NULL;
- _gmx_selparser_error(scanner, "too many NULL parameters provided");
- bOk = false;
- continue;
+ nullParamIndex = -1;
+ oparam
+ = gmx_ana_selparam_find(pparam->name().c_str(), nparam, params);
+ GMX_RELEASE_ASSERT(oparam != NULL, "Inconsistent selection parameter");
}
- ++i;
- }
- else
- {
- _gmx_selparser_error(scanner, "all NULL parameters should appear in the beginning of the list");
- bOk = false;
- continue;
- }
- gmx::MessageStringContext context(errors, contextStr);
- if (!oparam)
- {
- _gmx_selparser_error(scanner, "unknown parameter skipped");
- bOk = false;
- continue;
- }
- if (oparam->val.type != NO_VALUE && pparam->values().empty())
- {
- _gmx_selparser_error(scanner, "no value provided");
- bOk = false;
- continue;
- }
- if (oparam->flags & SPAR_SET)
- {
- _gmx_selparser_error(scanner, "parameter set multiple times, extra values skipped");
- bOk = false;
- continue;
- }
- oparam->flags |= SPAR_SET;
- /* Process the values for the parameter */
- convert_const_values(pparam->values_.get());
- if (convert_values(pparam->values_.get(), oparam->val.type, scanner) != 0)
- {
- _gmx_selparser_error(scanner, "invalid value");
- bOk = false;
- continue;
- }
- if (oparam->val.type == NO_VALUE)
- {
- rc = parse_values_bool(pparam->name(), pparam->values(), oparam, scanner);
- }
- else if (oparam->flags & SPAR_RANGES)
- {
- rc = parse_values_range(pparam->values(), oparam, scanner);
- }
- else if (oparam->flags & SPAR_VARNUM)
- {
- if (pparam->values().size() == 1
- && pparam->values().front().hasExpressionValue())
+ else if (nullParamIndex >= 0)
+ {
+ oparam = ¶ms[nullParamIndex];
+ if (oparam->name != NULL)
+ {
+ std::string text(_gmx_sel_lexer_get_text(scanner, pparam->location()));
+ std::string message
+ = formatString("Unexpected '%s'", text.c_str());
+ GMX_THROW(InvalidInputError(message));
+ }
+ ++nullParamIndex;
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(false, "All NULL parameters should appear in "
+ "the beginning of the list");
+ }
+ if (oparam->flags & SPAR_SET)
+ {
+ std::string message
+ = formatString("'%s' appears multiple times",
+ pparam->name().c_str());
+ GMX_THROW(InvalidInputError(message));
+ }
+ oparam->flags |= SPAR_SET;
+ if (oparam->val.type != NO_VALUE && pparam->values().empty())
+ {
+ std::string text;
+ if (pparam->name().empty())
+ {
+ text = root->name();
+ }
+ else
+ {
+ text = _gmx_sel_lexer_get_text(scanner, pparam->location());
+ }
+ std::string message
+ = formatString("'%s' should be followed by a value/expression",
+ text.c_str());
+ GMX_THROW(InvalidInputError(message));
+ }
+ /* Process the values for the parameter */
+ convert_const_values(pparam->values_.get());
+ convert_values(pparam->values_.get(), oparam->val.type, scanner);
+ if (oparam->val.type == NO_VALUE)
+ {
+ parse_values_bool(pparam->name(), pparam->values(), oparam, scanner);
+ }
+ else if (oparam->flags & SPAR_RANGES)
+ {
+ parse_values_range(pparam->values(), oparam, scanner);
+ }
+ else if (oparam->flags & SPAR_VARNUM)
+ {
+ if (pparam->values().size() == 1
+ && pparam->values().front().hasExpressionValue())
+ {
+ parse_values_varnum_expr(pparam->values(), oparam, root, scanner);
+ }
+ else
+ {
+ parse_values_varnum(pparam->values(), oparam, root, scanner);
+ }
+ }
+ else if (oparam->flags & SPAR_ENUMVAL)
{
- rc = parse_values_varnum_expr(pparam->values(), oparam, root, scanner);
+ parse_values_enum(pparam->values(), oparam, scanner);
}
else
{
- rc = parse_values_varnum(pparam->values(), oparam, root, scanner);
+ parse_values_std(pparam->values(), oparam, root, scanner);
}
}
- else if (oparam->flags & SPAR_ENUMVAL)
- {
- rc = parse_values_enum(pparam->values(), oparam, scanner);
- }
- else
- {
- rc = parse_values_std(pparam->values(), oparam, root, scanner);
- }
- if (!rc)
+ catch (UserInputError &ex)
{
- bOk = false;
+ if (!pparam->name().empty())
+ {
+ std::string text(_gmx_sel_lexer_get_text(scanner, pparam->location()));
+ ex.prependContext(formatString("In '%s'", text.c_str()));
+ }
+ errors.addCurrentExceptionAsNested();
}
}
/* Check that all required parameters are present */
- for (i = 0; i < nparam; ++i)
+ for (int i = 0; i < nparam; ++i)
{
if (!(params[i].flags & SPAR_OPTIONAL) && !(params[i].flags & SPAR_SET))
{
- _gmx_selparser_error(scanner, "required parameter '%s' not specified", params[i].name);
- bOk = false;
+ std::string message;
+ if (params[i].name == NULL)
+ {
+ message = formatString("'%s' should be followed by a value/expression",
+ root->name().c_str());
+ }
+ else
+ {
+ message = formatString("'%s' is missing", params[i].name);
+ }
+ InvalidInputError ex(message);
+ errors.addNested(ex);
}
}
-
- return bOk;
+ if (errors.hasNestedExceptions())
+ {
+ GMX_THROW(InvalidInputError(errors));
+ }
}
-/* A Bison parser, made by GNU Bison 2.6.2. */
+/* A Bison parser, made by GNU Bison 2.7.12-4996. */
/* Bison implementation for Yacc-like parsers in C
- Copyright (C) 1984, 1989-1990, 2000-2012 Free Software Foundation, Inc.
+ Copyright (C) 1984, 1989-1990, 2000-2013 Free Software Foundation, Inc.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
#define YYBISON 1
/* Bison version. */
-#define YYBISON_VERSION "2.6.2"
+#define YYBISON_VERSION "2.7.12-4996"
/* Skeleton name. */
#define YYSKELETON_NAME "yacc.c"
/* Pull parsers. */
#define YYPULL 0
+/* "%code top" blocks. */
+/* Line 349 of yacc.c */
+#line 43 "parser.y"
+
+/*! \internal \file parser.cpp
+ * \brief Generated (from parser.y by Bison) parser for the selection language.
+ *
+ * \ingroup module_selection
+ */
+/*! \internal \file parser.h
+ * \brief Generated (from parser.y by Bison) parser include file.
+ *
+ * \ingroup module_selection
+ */
+#include "gmxpre.h"
+
+
+/* Line 349 of yacc.c */
+#line 80 "parser.cpp"
/* Substitute the variable and function names. */
#define yypush_parse _gmx_sel_yypush_parse
#define yychar _gmx_sel_yychar
#define yydebug _gmx_sel_yydebug
#define yynerrs _gmx_sel_yynerrs
+#define yylloc _gmx_sel_yylloc
/* Copy the first part of user declarations. */
-/* Line 336 of yacc.c */
-#line 43 "parser.y"
+/* Line 371 of yacc.c */
+#line 56 "parser.y"
-/*! \internal \file parser.cpp
- * \brief Generated (from parser.y by Bison) parser for the selection language.
- *
- * \ingroup module_selection
- */
-/*! \internal \file parser.h
- * \brief Generated (from parser.y by Bison) parser include file.
- *
- * \ingroup module_selection
- */
-#include "gromacs/utility/scoped_ptr_sfree.h"
+#include "gromacs/utility/scoped_cptr.h"
#include "parser_internal.h"
-using gmx::scoped_ptr_sfree;
+using gmx::scoped_guard_sfree;
using gmx::SelectionParserValue;
using gmx::SelectionParserValueList;
using gmx::SelectionParserValueListPointer;
#pragma warning(disable: 4065)
#endif
-/* Line 336 of yacc.c */
-#line 108 "parser.cpp"
+/* Line 371 of yacc.c */
+#line 118 "parser.cpp"
# ifndef YY_NULL
# if defined __cplusplus && 201103L <= __cplusplus
/* In a future release of Bison, this section will be replaced
by #include "parser.h". */
-#ifndef _GMX_SEL_YY_PARSER_H
-# define _GMX_SEL_YY_PARSER_H
+#ifndef YY__GMX_SEL_YY_PARSER_H_INCLUDED
+# define YY__GMX_SEL_YY_PARSER_H_INCLUDED
/* Enabling traces. */
#ifndef YYDEBUG
# define YYDEBUG 1
extern int _gmx_sel_yydebug;
#endif
/* "%code requires" blocks. */
-/* Line 350 of yacc.c */
+/* Line 387 of yacc.c */
#line 1 "parser.y"
/*
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/* Line 350 of yacc.c */
-#line 73 "parser.y"
+/* Line 387 of yacc.c */
+#line 76 "parser.y"
#include "parsetree.h"
#include "selelem.h"
+#define YYLTYPE ::gmx::SelectionLocation
-/* Line 350 of yacc.c */
-#line 184 "parser.cpp"
+
+/* Line 387 of yacc.c */
+#line 196 "parser.cpp"
/* Tokens. */
#ifndef YYTOKENTYPE
#if ! defined YYSTYPE && ! defined YYSTYPE_IS_DECLARED
typedef union YYSTYPE
{
-/* Line 350 of yacc.c */
-#line 78 "parser.y"
+/* Line 387 of yacc.c */
+#line 83 "parser.y"
int i;
real r;
gmx::SelectionParserParameterListPointer *plist;
-/* Line 350 of yacc.c */
-#line 248 "parser.cpp"
+/* Line 387 of yacc.c */
+#line 260 "parser.cpp"
} YYSTYPE;
# define YYSTYPE_IS_TRIVIAL 1
# define yystype YYSTYPE /* obsolescent; will be withdrawn */
# define YYSTYPE_IS_DECLARED 1
#endif
+#if ! defined YYLTYPE && ! defined YYLTYPE_IS_DECLARED
+typedef struct YYLTYPE
+{
+ int first_line;
+ int first_column;
+ int last_line;
+ int last_column;
+} YYLTYPE;
+# define yyltype YYLTYPE /* obsolescent; will be withdrawn */
+# define YYLTYPE_IS_DECLARED 1
+# define YYLTYPE_IS_TRIVIAL 1
+#endif
+
#ifndef YYPUSH_MORE_DEFINED
# define YYPUSH_MORE_DEFINED
typedef struct _gmx_sel_yypstate _gmx_sel_yypstate;
#if defined __STDC__ || defined __cplusplus
-int _gmx_sel_yypush_parse (_gmx_sel_yypstate *ps, int pushed_char, YYSTYPE const *pushed_val, void *scanner);
+int _gmx_sel_yypush_parse (_gmx_sel_yypstate *ps, int pushed_char, YYSTYPE const *pushed_val, YYLTYPE *pushed_loc, void *scanner);
#else
int _gmx_sel_yypush_parse ();
#endif
void _gmx_sel_yypstate_delete ();
#endif
-#endif /* !_GMX_SEL_YY_PARSER_H */
+#endif /* !YY__GMX_SEL_YY_PARSER_H_INCLUDED */
/* Copy the second part of user declarations. */
-/* Line 353 of yacc.c */
-#line 285 "parser.cpp"
+/* Line 390 of yacc.c */
+#line 310 "parser.cpp"
#ifdef short
# undef short
# if defined YYENABLE_NLS && YYENABLE_NLS
# if ENABLE_NLS
# include <libintl.h> /* INFRINGES ON USER NAME SPACE */
-# define YY_(msgid) dgettext ("bison-runtime", msgid)
+# define YY_(Msgid) dgettext ("bison-runtime", Msgid)
# endif
# endif
# ifndef YY_
-# define YY_(msgid) msgid
+# define YY_(Msgid) Msgid
+# endif
+#endif
+
+#ifndef __attribute__
+/* This feature is available in gcc versions 2.5 and later. */
+# if (! defined __GNUC__ || __GNUC__ < 2 \
+ || (__GNUC__ == 2 && __GNUC_MINOR__ < 5))
+# define __attribute__(Spec) /* empty */
# endif
#endif
/* Suppress unused-variable warnings by "using" E. */
#if ! defined lint || defined __GNUC__
-# define YYUSE(e) ((void) (e))
+# define YYUSE(E) ((void) (E))
#else
-# define YYUSE(e) /* empty */
+# define YYUSE(E) /* empty */
#endif
+
/* Identity function, used to suppress warnings about constant conditions. */
#ifndef lint
-# define YYID(n) (n)
+# define YYID(N) (N)
#else
#if (defined __STDC__ || defined __C99__FUNC__ \
|| defined __cplusplus || defined _MSC_VER)
#if (! defined yyoverflow \
- && (! defined __cplusplus \
- || (defined YYSTYPE_IS_TRIVIAL && YYSTYPE_IS_TRIVIAL)))
+ && (! defined __cplusplus || defined GMX_YYFORCE_C_STACK_EXTENSION \
+ || (defined YYLTYPE_IS_TRIVIAL && YYLTYPE_IS_TRIVIAL \
+ && defined YYSTYPE_IS_TRIVIAL && YYSTYPE_IS_TRIVIAL)))
/* A type that is properly aligned for any stack member. */
union yyalloc
{
yytype_int16 yyss_alloc;
YYSTYPE yyvs_alloc;
+ YYLTYPE yyls_alloc;
};
/* The size of the maximum gap between one aligned stack and the next. */
/* The size of an array large to enough to hold all stacks, each with
N elements. */
# define YYSTACK_BYTES(N) \
- ((N) * (sizeof (yytype_int16) + sizeof (YYSTYPE)) \
- + YYSTACK_GAP_MAXIMUM)
+ ((N) * (sizeof (yytype_int16) + sizeof (YYSTYPE) + sizeof (YYLTYPE)) \
+ + 2 * YYSTACK_GAP_MAXIMUM)
# define YYCOPY_NEEDED 1
/* YYFINAL -- State number of the termination state. */
#define YYFINAL 2
/* YYLAST -- Last index in YYTABLE. */
-#define YYLAST 378
+#define YYLAST 367
/* YYNTOKENS -- Number of terminals. */
#define YYNTOKENS 49
/* YYNNTS -- Number of nonterminals. */
#define YYNNTS 25
/* YYNRULES -- Number of rules. */
-#define YYNRULES 89
+#define YYNRULES 90
/* YYNRULES -- Number of states. */
-#define YYNSTATES 149
+#define YYNSTATES 154
/* YYTRANSLATE(YYLEX) -- Bison symbol number corresponding to YYLEX. */
#define YYUNDEFTOK 2
#if YYDEBUG
/* YYPRHS[YYN] -- Index of the first RHS symbol of rule number YYN in
YYRHS. */
-static const yytype_uint8 yyprhs[] =
+static const yytype_uint16 yyprhs[] =
{
0, 0, 3, 4, 7, 10, 13, 14, 16, 18,
20, 23, 27, 31, 35, 37, 39, 43, 47, 49,
52, 54, 57, 59, 61, 63, 65, 68, 72, 76,
80, 84, 87, 90, 92, 94, 96, 98, 100, 103,
- 107, 112, 116, 120, 122, 124, 127, 131, 135, 139,
- 143, 147, 150, 154, 158, 160, 163, 171, 175, 178,
- 182, 184, 186, 188, 190, 193, 194, 197, 200, 202,
- 206, 207, 210, 214, 216, 220, 222, 225, 229, 231,
- 233, 235, 237, 239, 241, 243, 245, 247, 251, 255
+ 107, 112, 116, 120, 122, 124, 127, 132, 136, 140,
+ 144, 148, 152, 155, 159, 163, 165, 168, 176, 180,
+ 183, 187, 189, 191, 193, 195, 198, 199, 202, 205,
+ 207, 211, 212, 215, 219, 221, 225, 227, 230, 234,
+ 236, 238, 240, 242, 244, 246, 248, 250, 252, 256,
+ 260
};
/* YYRHS -- A `-1'-separated list of the rules' RHS. */
{
50, 0, -1, -1, 50, 51, -1, 52, 8, -1,
1, 8, -1, -1, 4, -1, 57, -1, 53, -1,
- 57, 53, -1, 7, 39, 58, -1, 7, 39, 61,
+ 6, 53, -1, 7, 39, 58, -1, 7, 39, 61,
-1, 7, 39, 63, -1, 63, -1, 58, -1, 40,
53, 41, -1, 53, 21, 64, -1, 4, -1, 33,
4, -1, 5, -1, 33, 5, -1, 54, -1, 55,
22, -1, 16, -1, 42, -1, 43, -1, 39, -1,
59, 17, -1, 59, 15, 69, -1, 59, 15, 60,
69, -1, 59, 14, 69, -1, 59, 19, 64, -1,
- 4, -1, 5, -1, 59, 14, -1, 59, 18, 64,
- -1, 61, 32, 61, -1, 61, 33, 61, -1, 61,
- 34, 61, -1, 61, 35, 61, -1, 33, 61, -1,
- 61, 37, 61, -1, 40, 61, 41, -1, 57, -1,
- 59, 15, -1, 44, 56, 45, 56, 45, 56, 46,
- -1, 40, 63, 41, -1, 20, 64, -1, 16, 25,
- 58, -1, 12, -1, 11, -1, 13, -1, 65, -1,
- 65, 24, -1, -1, 65, 66, -1, 23, 67, -1,
- 68, -1, 47, 68, 48, -1, -1, 68, 71, -1,
- 68, 45, 71, -1, 70, -1, 47, 70, 48, -1,
- 72, -1, 70, 72, -1, 70, 45, 72, -1, 58,
- -1, 63, -1, 61, -1, 62, -1, 73, -1, 54,
- -1, 55, -1, 57, -1, 73, -1, 54, 10, 54,
- -1, 54, 10, 55, -1, 55, 10, 56, -1
+ 4, -1, 5, -1, 59, 14, -1, 59, 14, 25,
+ 63, -1, 59, 18, 64, -1, 61, 32, 61, -1,
+ 61, 33, 61, -1, 61, 34, 61, -1, 61, 35,
+ 61, -1, 33, 61, -1, 61, 37, 61, -1, 40,
+ 61, 41, -1, 57, -1, 59, 15, -1, 44, 56,
+ 45, 56, 45, 56, 46, -1, 40, 63, 41, -1,
+ 20, 64, -1, 16, 25, 58, -1, 12, -1, 11,
+ -1, 13, -1, 65, -1, 65, 24, -1, -1, 65,
+ 66, -1, 23, 67, -1, 68, -1, 47, 68, 48,
+ -1, -1, 68, 71, -1, 68, 45, 71, -1, 70,
+ -1, 47, 70, 48, -1, 72, -1, 70, 72, -1,
+ 70, 45, 72, -1, 58, -1, 63, -1, 61, -1,
+ 62, -1, 73, -1, 54, -1, 55, -1, 57, -1,
+ 73, -1, 54, 10, 54, -1, 54, 10, 55, -1,
+ 55, 10, 56, -1
};
/* YYRLINE[YYN] -- source line where rule number YYN was defined. */
static const yytype_uint16 yyrline[] =
{
- 0, 193, 193, 198, 209, 210, 232, 237, 248, 260,
- 266, 273, 280, 287, 297, 298, 305, 306, 320, 321,
- 325, 326, 329, 330, 333, 334, 342, 353, 364, 375,
- 379, 390, 397, 406, 407, 412, 413, 414, 418, 426,
- 434, 442, 453, 468, 479, 493, 501, 512, 518, 524,
- 530, 536, 542, 548, 555, 566, 581, 590, 594, 604,
- 618, 626, 634, 647, 649, 655, 660, 671, 680, 681,
- 686, 691, 699, 710, 711, 715, 721, 729, 739, 745,
- 751, 757, 763, 767, 773, 779, 786, 790, 796, 802
+ 0, 199, 199, 204, 215, 216, 236, 241, 252, 264,
+ 270, 277, 284, 291, 301, 302, 309, 310, 324, 325,
+ 329, 330, 333, 334, 337, 338, 346, 357, 368, 379,
+ 383, 394, 401, 410, 411, 416, 417, 418, 422, 430,
+ 438, 446, 457, 472, 483, 497, 505, 513, 524, 530,
+ 536, 542, 548, 554, 560, 567, 578, 593, 602, 606,
+ 616, 630, 638, 646, 659, 661, 667, 672, 683, 692,
+ 693, 698, 703, 711, 722, 723, 727, 733, 741, 751,
+ 757, 763, 769, 775, 779, 785, 791, 798, 802, 808,
+ 814
};
#endif
55, 55, 56, 56, 57, 57, 58, 58, 58, 58,
58, 58, 58, 59, 59, 60, 60, 60, 58, 58,
58, 58, 58, 61, 61, 61, 61, 61, 61, 61,
- 61, 61, 61, 61, 62, 62, 63, 63, 63, 63,
- 58, 61, 63, 64, 64, 65, 65, 66, 67, 67,
- 68, 68, 68, 69, 69, 70, 70, 70, 71, 71,
- 71, 71, 71, 72, 72, 72, 72, 73, 73, 73
+ 61, 61, 61, 61, 61, 62, 62, 63, 63, 63,
+ 63, 58, 61, 63, 64, 64, 65, 65, 66, 67,
+ 67, 68, 68, 68, 69, 69, 70, 70, 70, 71,
+ 71, 71, 71, 71, 72, 72, 72, 72, 73, 73,
+ 73
};
/* YYR2[YYN] -- Number of symbols composing right hand side of rule YYN. */
2, 3, 3, 3, 1, 1, 3, 3, 1, 2,
1, 2, 1, 1, 1, 1, 2, 3, 3, 3,
3, 2, 2, 1, 1, 1, 1, 1, 2, 3,
- 4, 3, 3, 1, 1, 2, 3, 3, 3, 3,
- 3, 2, 3, 3, 1, 2, 7, 3, 2, 3,
- 1, 1, 1, 1, 2, 0, 2, 2, 1, 3,
- 0, 2, 3, 1, 3, 1, 2, 3, 1, 1,
- 1, 1, 1, 1, 1, 1, 1, 3, 3, 3
+ 4, 3, 3, 1, 1, 2, 4, 3, 3, 3,
+ 3, 3, 2, 3, 3, 1, 2, 7, 3, 2,
+ 3, 1, 1, 1, 1, 2, 0, 2, 2, 1,
+ 3, 0, 2, 3, 1, 3, 1, 2, 3, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 3, 3,
+ 3
};
/* YYDEFACT[STATE-NAME] -- Default reduction number in state STATE-NUM.
means the default is an error. */
static const yytype_uint8 yydefact[] =
{
- 2, 0, 1, 0, 43, 44, 24, 25, 0, 61,
- 60, 62, 34, 65, 33, 0, 0, 0, 0, 3,
- 0, 9, 8, 15, 0, 0, 14, 5, 0, 32,
- 25, 31, 0, 58, 63, 43, 34, 0, 26, 0,
- 0, 51, 0, 15, 0, 14, 18, 20, 0, 22,
- 23, 0, 4, 65, 10, 0, 0, 45, 0, 38,
- 65, 65, 0, 0, 0, 0, 0, 0, 0, 11,
- 12, 13, 59, 70, 64, 66, 0, 0, 45, 16,
- 29, 53, 57, 19, 21, 0, 17, 28, 27, 0,
- 83, 84, 85, 41, 73, 75, 86, 37, 35, 36,
- 0, 39, 46, 42, 30, 47, 48, 49, 50, 52,
- 0, 70, 67, 68, 0, 0, 0, 0, 0, 76,
- 40, 0, 43, 44, 0, 0, 0, 0, 54, 78,
- 0, 80, 81, 79, 71, 82, 0, 74, 87, 88,
- 89, 77, 69, 43, 44, 72, 55, 0, 56
+ 2, 0, 1, 0, 43, 44, 24, 25, 0, 62,
+ 61, 63, 34, 66, 33, 0, 0, 0, 0, 3,
+ 0, 9, 8, 15, 0, 0, 14, 5, 43, 10,
+ 0, 32, 24, 25, 31, 0, 59, 64, 34, 0,
+ 26, 0, 0, 52, 0, 15, 0, 14, 18, 20,
+ 0, 22, 23, 0, 4, 66, 0, 0, 45, 0,
+ 38, 66, 66, 0, 0, 0, 0, 0, 0, 0,
+ 11, 12, 13, 60, 71, 65, 67, 0, 0, 45,
+ 16, 29, 54, 58, 19, 21, 0, 17, 28, 27,
+ 0, 0, 84, 85, 86, 41, 74, 76, 87, 37,
+ 35, 36, 0, 39, 47, 42, 30, 48, 49, 50,
+ 51, 53, 0, 71, 68, 69, 0, 0, 0, 46,
+ 0, 0, 0, 0, 77, 40, 0, 43, 44, 0,
+ 0, 0, 0, 55, 79, 0, 81, 82, 80, 72,
+ 83, 0, 75, 88, 89, 90, 78, 70, 43, 44,
+ 73, 56, 0, 57
};
/* YYDEFGOTO[NTERM-NUM]. */
static const yytype_int16 yydefgoto[] =
{
- -1, 1, 19, 20, 21, 90, 91, 51, 92, 129,
- 24, 100, 25, 132, 133, 33, 34, 75, 112, 113,
- 101, 94, 134, 95, 96
+ -1, 1, 19, 20, 21, 92, 93, 53, 94, 134,
+ 24, 102, 25, 137, 138, 36, 37, 76, 114, 115,
+ 103, 96, 139, 97, 98
};
/* YYPACT[STATE-NUM] -- Index in YYTABLE of the portion describing
STATE-NUM. */
-#define YYPACT_NINF -84
+#define YYPACT_NINF -85
static const yytype_int16 yypact[] =
{
- -84, 148, -84, 4, 6, -84, -84, -20, 189, -84,
- -84, -84, 1, -84, -84, 322, 216, 285, 0, -84,
- 27, 16, 285, 22, 122, 173, -84, -84, 308, -84,
- -84, -84, 322, -84, 71, -84, -84, 322, -84, 216,
- 49, 24, -11, -13, 232, 23, -84, -84, 140, -84,
- -84, 21, -84, -84, 16, 322, 322, 40, 197, -84,
- -84, -84, 216, 216, 216, 216, 216, 216, 308, 22,
- 173, -84, 22, 30, -84, -84, -13, 47, -84, -84,
- -84, -84, -84, -84, -84, 0, -84, 56, -84, 85,
- 93, 99, -84, -84, 210, -84, -84, -84, -84, -84,
- 36, -84, -84, -84, 139, 94, 94, 24, 24, 24,
- 23, -84, -84, 241, 78, 17, 0, 0, 85, -84,
- -84, 178, 116, 125, 338, 271, 93, 99, -84, 22,
- 349, 139, -84, -84, -84, -84, 0, -84, -84, -84,
- -84, -84, -84, 133, 136, -84, 197, 104, -84
+ -85, 10, -85, -2, 17, -85, 273, -12, 55, -85,
+ -85, -85, 9, -85, -85, 310, 204, 273, 69, -85,
+ 31, 44, -85, 110, 179, 312, -85, -85, -85, 44,
+ 296, -85, -85, -85, -85, 310, -85, 96, -85, 310,
+ -85, 204, -6, 33, 15, 124, 220, 58, -85, -85,
+ 139, -85, -85, 56, -85, -85, 310, 310, 41, 185,
+ -85, -85, -85, 204, 204, 204, 204, 204, 204, 296,
+ 110, 312, -85, 110, 61, -85, -85, 124, 319, 78,
+ -85, -85, -85, -85, -85, -85, 69, -85, 80, -85,
+ 24, 206, 102, 106, -85, -85, 90, -85, -85, -85,
+ -85, -85, 85, -85, -85, -85, 330, 213, 213, 33,
+ 33, 33, 58, -85, -85, 229, 83, 9, 24, -85,
+ 174, 69, 69, 206, -85, -85, 155, 137, 140, 326,
+ 259, 102, 106, -85, 110, 187, 330, -85, -85, -85,
+ -85, 69, -85, -85, -85, -85, -85, -85, 142, 146,
+ -85, 185, 111, -85
};
/* YYPGOTO[NTERM-NUM]. */
static const yytype_int8 yypgoto[] =
{
- -84, -84, -84, -84, -4, -17, -15, -83, -1, 110,
- 9, -84, -8, -84, 10, 54, -84, -84, -84, 51,
- -51, 62, 33, -79, -28
+ -85, -85, -85, -85, 7, -17, -15, -84, -1, 116,
+ 19, -85, 12, -85, 3, 75, -85, -85, -85, 45,
+ -53, 72, 39, -65, -63
};
/* YYTABLE[YYPACT[STATE-NUM]]. What to do in state STATE-NUM. If
#define YYTABLE_NINF -22
static const yytype_int16 yytable[] =
{
- 22, 49, 114, 50, 46, 47, 93, 31, 41, 44,
- 53, 26, 27, 42, -7, 119, 55, 56, 54, 28,
- 70, 46, 47, 6, 30, 40, 32, 45, 80, 44,
- 79, 77, 26, 48, 140, 52, 119, 53, 71, 141,
- 46, 47, 6, 30, 46, 47, 6, 30, 40, 120,
- 48, 55, 56, 147, 104, 105, 106, 107, 108, 109,
- 44, 67, 118, 78, 82, 137, 85, 60, 49, 48,
- 50, 40, 40, 40, 40, 40, 40, 111, 110, 63,
- 64, 65, 66, 89, 67, 135, 56, 89, 81, 46,
- 47, 6, 30, 135, 73, 74, 126, 135, 127, 138,
- 49, 139, 50, 116, 126, 131, 127, 86, 126, 117,
- 127, 23, 128, 131, 102, 103, 41, 131, 48, 49,
- 128, 50, 130, 136, 128, 38, -18, 43, 65, 66,
- 130, 67, 23, 40, 130, -20, 57, 58, 69, 59,
- 60, 61, 72, -19, 83, 84, -21, 76, 2, 3,
- 148, 115, 4, 5, 6, 7, -6, 8, 145, 9,
- 10, 11, 121, 0, 12, 87, 88, 0, 13, 0,
- 14, 63, 64, 65, 66, 0, 67, 0, 76, 15,
- 0, 16, 122, 123, 6, 30, 0, 8, 17, 9,
- 10, 11, 18, 29, 12, 6, 30, 0, 13, 62,
- 14, 46, 47, 6, 30, 63, 64, 65, 66, 15,
- 67, 124, 0, 0, 46, 47, 6, 30, 68, 0,
- 35, 5, 18, 125, 0, 0, 142, 9, 0, 0,
- 48, 0, 36, 0, 0, 0, 97, 0, 14, 98,
- 99, 0, 0, 48, 89, 122, 123, 6, 30, 16,
- 8, 0, 9, 10, 11, 118, 39, 12, 62, 0,
- 0, 13, 0, 14, 63, 64, 65, 66, 0, 67,
- 0, 0, 15, 81, 124, 122, 123, 6, 30, 0,
- 8, 68, 9, 10, 11, 18, 125, 12, 0, 35,
- 5, 13, 0, 14, 8, 0, 9, 10, 11, 0,
- 0, 12, 15, 0, 124, 13, 0, 14, 0, 0,
- 0, 68, 35, 5, 0, 18, 15, 8, 16, 9,
- 10, 11, 0, 0, 12, 17, 35, 5, 13, 18,
- 14, 8, 0, 9, 10, 0, 0, 0, 36, 15,
- 0, 16, 143, 144, 14, 0, 0, 0, 68, 9,
- 0, 0, 18, 15, 36, 16, 0, 0, 0, 0,
- 14, 0, 37, 57, 146, 0, 59, 60, 61, 0,
- 0, 16, 0, 0, 0, 0, 0, 0, 39
+ 22, 51, 116, 52, 26, 95, 27, 34, 79, 26,
+ 2, 3, 61, 29, 4, 5, 6, 7, -6, 8,
+ 47, 9, 10, 11, 44, -7, 12, 30, 43, 46,
+ 13, 124, 14, 72, 35, 42, 55, 11, 145, 54,
+ 117, 15, 71, 16, 13, 48, 49, 32, 33, 125,
+ 17, 46, 140, 78, 18, 124, 80, 152, 146, 31,
+ 42, 32, 33, 140, 118, 55, 90, 140, 18, 51,
+ 68, 52, 112, 48, 49, 106, 107, 108, 109, 110,
+ 111, 46, 42, 42, 42, 42, 42, 42, 91, 48,
+ 49, 32, 33, 119, 48, 49, 32, 33, 131, 83,
+ 132, 86, 50, 90, 143, 51, 144, 52, 113, 131,
+ 57, 132, 121, 131, 133, 132, 122, 23, 50, 74,
+ 75, 112, 23, 50, 51, 133, 52, 136, 141, 133,
+ 87, 40, 91, 45, 135, 123, 104, 105, 136, 56,
+ 57, 43, 136, 84, 85, 135, 70, -18, 42, 135,
+ -20, 73, -19, 56, 57, 77, -21, 153, 126, 127,
+ 128, 32, 33, 120, 8, 81, 9, 10, 11, 150,
+ 0, 12, 88, 89, 0, 13, 0, 14, 48, 49,
+ 32, 33, 0, 0, 0, 77, 15, 0, 129, 48,
+ 49, 32, 33, 58, 59, 69, 60, 61, 62, 18,
+ 130, 58, 151, 147, 60, 61, 62, 50, 28, 5,
+ 48, 49, 32, 33, 0, 9, 0, 0, 50, 123,
+ 38, 0, 142, 0, 99, 0, 14, 100, 101, 0,
+ 0, 0, 91, 127, 128, 32, 33, 16, 8, 50,
+ 9, 10, 11, 0, 41, 12, 63, 66, 67, 13,
+ 68, 14, 64, 65, 66, 67, 0, 68, 0, 0,
+ 15, 82, 129, 127, 128, 32, 33, 0, 8, 69,
+ 9, 10, 11, 18, 130, 12, 0, 28, 5, 13,
+ 0, 14, 8, 0, 9, 10, 11, 0, 0, 12,
+ 15, 0, 129, 13, 0, 14, 0, 0, 0, 69,
+ 28, 5, 0, 18, 15, 8, 16, 9, 10, 11,
+ 0, 0, 12, 17, 28, 5, 13, 18, 14, 8,
+ 0, 9, 10, 0, 0, 0, 38, 15, 0, 16,
+ 148, 149, 14, 0, 0, 0, 69, 9, 63, 0,
+ 18, 15, 38, 16, 64, 65, 66, 67, 14, 68,
+ 39, 64, 65, 66, 67, 0, 68, 0, 0, 16,
+ 82, 0, 64, 65, 66, 67, 41, 68
};
-#define yypact_value_is_default(yystate) \
- ((yystate) == (-84))
+#define yypact_value_is_default(Yystate) \
+ (!!((Yystate) == (-85)))
-#define yytable_value_is_error(yytable_value) \
+#define yytable_value_is_error(Yytable_value) \
YYID (0)
static const yytype_int16 yycheck[] =
{
- 1, 18, 85, 18, 4, 5, 57, 8, 16, 17,
- 21, 1, 8, 17, 8, 94, 29, 30, 22, 39,
- 28, 4, 5, 6, 7, 16, 25, 17, 41, 37,
- 41, 39, 22, 33, 117, 8, 115, 21, 28, 118,
- 4, 5, 6, 7, 4, 5, 6, 7, 39, 100,
- 33, 29, 30, 136, 62, 63, 64, 65, 66, 67,
- 68, 37, 45, 14, 41, 48, 45, 18, 85, 33,
- 85, 62, 63, 64, 65, 66, 67, 47, 68, 32,
- 33, 34, 35, 47, 37, 113, 30, 47, 41, 4,
- 5, 6, 7, 121, 23, 24, 113, 125, 113, 116,
- 117, 116, 117, 10, 121, 113, 121, 53, 125, 10,
- 125, 1, 113, 121, 60, 61, 124, 125, 33, 136,
- 121, 136, 113, 45, 125, 15, 10, 17, 34, 35,
- 121, 37, 22, 124, 125, 10, 14, 15, 28, 17,
- 18, 19, 32, 10, 4, 5, 10, 37, 0, 1,
- 46, 89, 4, 5, 6, 7, 8, 9, 125, 11,
- 12, 13, 111, -1, 16, 55, 56, -1, 20, -1,
- 22, 32, 33, 34, 35, -1, 37, -1, 68, 31,
- -1, 33, 4, 5, 6, 7, -1, 9, 40, 11,
- 12, 13, 44, 4, 16, 6, 7, -1, 20, 26,
- 22, 4, 5, 6, 7, 32, 33, 34, 35, 31,
- 37, 33, -1, -1, 4, 5, 6, 7, 40, -1,
- 4, 5, 44, 45, -1, -1, 48, 11, -1, -1,
- 33, -1, 16, -1, -1, -1, 39, -1, 22, 42,
- 43, -1, -1, 33, 47, 4, 5, 6, 7, 33,
- 9, -1, 11, 12, 13, 45, 40, 16, 26, -1,
- -1, 20, -1, 22, 32, 33, 34, 35, -1, 37,
- -1, -1, 31, 41, 33, 4, 5, 6, 7, -1,
- 9, 40, 11, 12, 13, 44, 45, 16, -1, 4,
- 5, 20, -1, 22, 9, -1, 11, 12, 13, -1,
- -1, 16, 31, -1, 33, 20, -1, 22, -1, -1,
- -1, 40, 4, 5, -1, 44, 31, 9, 33, 11,
- 12, 13, -1, -1, 16, 40, 4, 5, 20, 44,
- 22, 9, -1, 11, 12, -1, -1, -1, 16, 31,
- -1, 33, 4, 5, 22, -1, -1, -1, 40, 11,
- -1, -1, 44, 31, 16, 33, -1, -1, -1, -1,
- 22, -1, 40, 14, 15, -1, 17, 18, 19, -1,
- -1, 33, -1, -1, -1, -1, -1, -1, 40
+ 1, 18, 86, 18, 1, 58, 8, 8, 14, 6,
+ 0, 1, 18, 6, 4, 5, 6, 7, 8, 9,
+ 17, 11, 12, 13, 17, 8, 16, 39, 16, 17,
+ 20, 96, 22, 30, 25, 16, 21, 13, 122, 8,
+ 16, 31, 30, 33, 20, 4, 5, 6, 7, 102,
+ 40, 39, 115, 41, 44, 120, 41, 141, 123, 4,
+ 41, 6, 7, 126, 40, 21, 25, 130, 44, 86,
+ 37, 86, 69, 4, 5, 63, 64, 65, 66, 67,
+ 68, 69, 63, 64, 65, 66, 67, 68, 47, 4,
+ 5, 6, 7, 90, 4, 5, 6, 7, 115, 41,
+ 115, 45, 33, 25, 121, 122, 121, 122, 47, 126,
+ 30, 126, 10, 130, 115, 130, 10, 1, 33, 23,
+ 24, 118, 6, 33, 141, 126, 141, 115, 45, 130,
+ 55, 15, 47, 17, 115, 45, 61, 62, 126, 29,
+ 30, 129, 130, 4, 5, 126, 30, 10, 129, 130,
+ 10, 35, 10, 29, 30, 39, 10, 46, 113, 4,
+ 5, 6, 7, 91, 9, 41, 11, 12, 13, 130,
+ -1, 16, 56, 57, -1, 20, -1, 22, 4, 5,
+ 6, 7, -1, -1, -1, 69, 31, -1, 33, 4,
+ 5, 6, 7, 14, 15, 40, 17, 18, 19, 44,
+ 45, 14, 15, 48, 17, 18, 19, 33, 4, 5,
+ 4, 5, 6, 7, -1, 11, -1, -1, 33, 45,
+ 16, -1, 48, -1, 39, -1, 22, 42, 43, -1,
+ -1, -1, 47, 4, 5, 6, 7, 33, 9, 33,
+ 11, 12, 13, -1, 40, 16, 26, 34, 35, 20,
+ 37, 22, 32, 33, 34, 35, -1, 37, -1, -1,
+ 31, 41, 33, 4, 5, 6, 7, -1, 9, 40,
+ 11, 12, 13, 44, 45, 16, -1, 4, 5, 20,
+ -1, 22, 9, -1, 11, 12, 13, -1, -1, 16,
+ 31, -1, 33, 20, -1, 22, -1, -1, -1, 40,
+ 4, 5, -1, 44, 31, 9, 33, 11, 12, 13,
+ -1, -1, 16, 40, 4, 5, 20, 44, 22, 9,
+ -1, 11, 12, -1, -1, -1, 16, 31, -1, 33,
+ 4, 5, 22, -1, -1, -1, 40, 11, 26, -1,
+ 44, 31, 16, 33, 32, 33, 34, 35, 22, 37,
+ 40, 32, 33, 34, 35, -1, 37, -1, -1, 33,
+ 41, -1, 32, 33, 34, 35, 40, 37
};
/* YYSTOS[STATE-NUM] -- The (internal number of the) accessing
{
0, 50, 0, 1, 4, 5, 6, 7, 9, 11,
12, 13, 16, 20, 22, 31, 33, 40, 44, 51,
- 52, 53, 57, 58, 59, 61, 63, 8, 39, 4,
- 7, 57, 25, 64, 65, 4, 16, 40, 58, 40,
- 59, 61, 53, 58, 61, 63, 4, 5, 33, 54,
- 55, 56, 8, 21, 53, 29, 30, 14, 15, 17,
- 18, 19, 26, 32, 33, 34, 35, 37, 40, 58,
- 61, 63, 58, 23, 24, 66, 58, 61, 14, 41,
- 41, 41, 41, 4, 5, 45, 64, 58, 58, 47,
- 54, 55, 57, 69, 70, 72, 73, 39, 42, 43,
- 60, 69, 64, 64, 61, 61, 61, 61, 61, 61,
- 63, 47, 67, 68, 56, 70, 10, 10, 45, 72,
- 69, 68, 4, 5, 33, 45, 54, 55, 57, 58,
- 59, 61, 62, 63, 71, 73, 45, 48, 54, 55,
- 56, 72, 48, 4, 5, 71, 15, 56, 46
+ 52, 53, 57, 58, 59, 61, 63, 8, 4, 53,
+ 39, 4, 6, 7, 57, 25, 64, 65, 16, 40,
+ 58, 40, 59, 61, 53, 58, 61, 63, 4, 5,
+ 33, 54, 55, 56, 8, 21, 29, 30, 14, 15,
+ 17, 18, 19, 26, 32, 33, 34, 35, 37, 40,
+ 58, 61, 63, 58, 23, 24, 66, 58, 61, 14,
+ 41, 41, 41, 41, 4, 5, 45, 64, 58, 58,
+ 25, 47, 54, 55, 57, 69, 70, 72, 73, 39,
+ 42, 43, 60, 69, 64, 64, 61, 61, 61, 61,
+ 61, 61, 63, 47, 67, 68, 56, 16, 40, 63,
+ 70, 10, 10, 45, 72, 69, 68, 4, 5, 33,
+ 45, 54, 55, 57, 58, 59, 61, 62, 63, 71,
+ 73, 45, 48, 54, 55, 56, 72, 48, 4, 5,
+ 71, 15, 56, 46
};
#define yyerrok (yyerrstatus = 0)
} \
else \
{ \
- yyerror (scanner, YY_("syntax error: cannot back up")); \
+ yyerror (&yylloc, scanner, YY_("syntax error: cannot back up")); \
YYERROR; \
} \
while (YYID (0))
-
+/* Error token number */
#define YYTERROR 1
#define YYERRCODE 256
+
/* YYLLOC_DEFAULT -- Set CURRENT to span from RHS[1] to RHS[N].
If N is 0, then set CURRENT to the empty location which ends
the previous symbol: RHS[0] (always defined). */
#define YYRHSLOC(Rhs, K) ((Rhs)[K])
-
-/* This macro is provided for backward compatibility. */
+/* YY_LOCATION_PRINT -- Print the location on the stream.
+ This macro was not mandated originally: define only if we know
+ we won't break user code: when these are the locations we know. */
#ifndef YY_LOCATION_PRINT
-# define YY_LOCATION_PRINT(File, Loc) ((void) 0)
+# if defined YYLTYPE_IS_TRIVIAL && YYLTYPE_IS_TRIVIAL
+
+/* Print *YYLOCP on YYO. Private, do not rely on its existence. */
+
+__attribute__((__unused__))
+#if (defined __STDC__ || defined __C99__FUNC__ \
+ || defined __cplusplus || defined _MSC_VER)
+static unsigned
+yy_location_print_ (FILE *yyo, YYLTYPE const * const yylocp)
+#else
+static unsigned
+yy_location_print_ (yyo, yylocp)
+ FILE *yyo;
+ YYLTYPE const * const yylocp;
+#endif
+{
+ unsigned res = 0;
+ int end_col = 0 != yylocp->last_column ? yylocp->last_column - 1 : 0;
+ if (0 <= yylocp->first_line)
+ {
+ res += fprintf (yyo, "%d", yylocp->first_line);
+ if (0 <= yylocp->first_column)
+ res += fprintf (yyo, ".%d", yylocp->first_column);
+ }
+ if (0 <= yylocp->last_line)
+ {
+ if (yylocp->first_line < yylocp->last_line)
+ {
+ res += fprintf (yyo, "-%d", yylocp->last_line);
+ if (0 <= end_col)
+ res += fprintf (yyo, ".%d", end_col);
+ }
+ else if (0 <= end_col && yylocp->first_column < end_col)
+ res += fprintf (yyo, "-%d", end_col);
+ }
+ return res;
+ }
+
+# define YY_LOCATION_PRINT(File, Loc) \
+ yy_location_print_ (File, &(Loc))
+
+# else
+# define YY_LOCATION_PRINT(File, Loc) ((void) 0)
+# endif
#endif
/* YYLEX -- calling `yylex' with the right arguments. */
-
#ifdef YYLEX_PARAM
-# define YYLEX yylex (&yylval, YYLEX_PARAM)
+# define YYLEX yylex (&yylval, &yylloc, YYLEX_PARAM)
#else
-# define YYLEX yylex (&yylval)
+# define YYLEX yylex (&yylval, &yylloc)
#endif
/* Enable debugging if requested. */
{ \
YYFPRINTF (stderr, "%s ", Title); \
yy_symbol_print (stderr, \
- Type, Value, scanner); \
+ Type, Value, Location, scanner); \
YYFPRINTF (stderr, "\n"); \
} \
} while (YYID (0))
#if (defined __STDC__ || defined __C99__FUNC__ \
|| defined __cplusplus || defined _MSC_VER)
static void
-yy_symbol_value_print (FILE *yyoutput, int yytype, YYSTYPE const * const yyvaluep, void *scanner)
+yy_symbol_value_print (FILE *yyoutput, int yytype, YYSTYPE const * const yyvaluep, YYLTYPE const * const yylocationp, void *scanner)
#else
static void
-yy_symbol_value_print (yyoutput, yytype, yyvaluep, scanner)
+yy_symbol_value_print (yyoutput, yytype, yyvaluep, yylocationp, scanner)
FILE *yyoutput;
int yytype;
YYSTYPE const * const yyvaluep;
+ YYLTYPE const * const yylocationp;
void *scanner;
#endif
{
YYUSE (yyo);
if (!yyvaluep)
return;
+ YYUSE (yylocationp);
YYUSE (scanner);
# ifdef YYPRINT
if (yytype < YYNTOKENS)
# else
YYUSE (yyoutput);
# endif
- switch (yytype)
- {
- default:
- break;
- }
+ YYUSE (yytype);
}
#if (defined __STDC__ || defined __C99__FUNC__ \
|| defined __cplusplus || defined _MSC_VER)
static void
-yy_symbol_print (FILE *yyoutput, int yytype, YYSTYPE const * const yyvaluep, void *scanner)
+yy_symbol_print (FILE *yyoutput, int yytype, YYSTYPE const * const yyvaluep, YYLTYPE const * const yylocationp, void *scanner)
#else
static void
-yy_symbol_print (yyoutput, yytype, yyvaluep, scanner)
+yy_symbol_print (yyoutput, yytype, yyvaluep, yylocationp, scanner)
FILE *yyoutput;
int yytype;
YYSTYPE const * const yyvaluep;
+ YYLTYPE const * const yylocationp;
void *scanner;
#endif
{
else
YYFPRINTF (yyoutput, "nterm %s (", yytname[yytype]);
- yy_symbol_value_print (yyoutput, yytype, yyvaluep, scanner);
+ YY_LOCATION_PRINT (yyoutput, *yylocationp);
+ YYFPRINTF (yyoutput, ": ");
+ yy_symbol_value_print (yyoutput, yytype, yyvaluep, yylocationp, scanner);
YYFPRINTF (yyoutput, ")");
}
#if (defined __STDC__ || defined __C99__FUNC__ \
|| defined __cplusplus || defined _MSC_VER)
static void
-yy_reduce_print (YYSTYPE *yyvsp, int yyrule, void *scanner)
+yy_reduce_print (YYSTYPE *yyvsp, YYLTYPE *yylsp, int yyrule, void *scanner)
#else
static void
-yy_reduce_print (yyvsp, yyrule, scanner)
+yy_reduce_print (yyvsp, yylsp, yyrule, scanner)
YYSTYPE *yyvsp;
+ YYLTYPE *yylsp;
int yyrule;
void *scanner;
#endif
YYFPRINTF (stderr, " $%d = ", yyi + 1);
yy_symbol_print (stderr, yyrhs[yyprhs[yyrule] + yyi],
&(yyvsp[(yyi + 1) - (yynrhs)])
- , scanner);
+ , &(yylsp[(yyi + 1) - (yynrhs)]) , scanner);
YYFPRINTF (stderr, "\n");
}
}
# define YY_REDUCE_PRINT(Rule) \
do { \
if (yydebug) \
- yy_reduce_print (yyvsp, Rule, scanner); \
+ yy_reduce_print (yyvsp, yylsp, Rule, scanner); \
} while (YYID (0))
/* Nonzero means print parse trace. It is left uninitialized so that
{
YYSIZE_T yysize0 = yytnamerr (YY_NULL, yytname[yytoken]);
YYSIZE_T yysize = yysize0;
- YYSIZE_T yysize1;
enum { YYERROR_VERBOSE_ARGS_MAXIMUM = 5 };
/* Internationalized format string. */
const char *yyformat = YY_NULL;
break;
}
yyarg[yycount++] = yytname[yyx];
- yysize1 = yysize + yytnamerr (YY_NULL, yytname[yyx]);
- if (! (yysize <= yysize1
- && yysize1 <= YYSTACK_ALLOC_MAXIMUM))
- return 2;
- yysize = yysize1;
+ {
+ YYSIZE_T yysize1 = yysize + yytnamerr (YY_NULL, yytname[yyx]);
+ if (! (yysize <= yysize1
+ && yysize1 <= YYSTACK_ALLOC_MAXIMUM))
+ return 2;
+ yysize = yysize1;
+ }
}
}
}
# undef YYCASE_
}
- yysize1 = yysize + yystrlen (yyformat);
- if (! (yysize <= yysize1 && yysize1 <= YYSTACK_ALLOC_MAXIMUM))
- return 2;
- yysize = yysize1;
+ {
+ YYSIZE_T yysize1 = yysize + yystrlen (yyformat);
+ if (! (yysize <= yysize1 && yysize1 <= YYSTACK_ALLOC_MAXIMUM))
+ return 2;
+ yysize = yysize1;
+ }
if (*yymsg_alloc < yysize)
{
#if (defined __STDC__ || defined __C99__FUNC__ \
|| defined __cplusplus || defined _MSC_VER)
static void
-yydestruct (const char *yymsg, int yytype, YYSTYPE *yyvaluep, void *scanner)
+yydestruct (const char *yymsg, int yytype, YYSTYPE *yyvaluep, YYLTYPE *yylocationp, void *scanner)
#else
static void
-yydestruct (yymsg, yytype, yyvaluep, scanner)
+yydestruct (yymsg, yytype, yyvaluep, yylocationp, scanner)
const char *yymsg;
int yytype;
YYSTYPE *yyvaluep;
+ YYLTYPE *yylocationp;
void *scanner;
#endif
{
YYUSE (yyvaluep);
+ YYUSE (yylocationp);
YYUSE (scanner);
if (!yymsg)
switch (yytype)
{
case 6: /* STR */
-/* Line 1381 of yacc.c */
-#line 173 "parser.y"
- { free(((*yyvaluep).str)); };
-/* Line 1381 of yacc.c */
-#line 1380 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 178 "parser.y"
+ { free(((*yyvaluep).str)); };
+/* Line 1393 of yacc.c */
+#line 1473 "parser.cpp"
+ break;
case 7: /* IDENTIFIER */
-/* Line 1381 of yacc.c */
-#line 173 "parser.y"
- { free(((*yyvaluep).str)); };
-/* Line 1381 of yacc.c */
-#line 1387 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 178 "parser.y"
+ { free(((*yyvaluep).str)); };
+/* Line 1393 of yacc.c */
+#line 1480 "parser.cpp"
+ break;
case 16: /* KEYWORD_POS */
-/* Line 1381 of yacc.c */
-#line 173 "parser.y"
- { free(((*yyvaluep).str)); };
-/* Line 1381 of yacc.c */
-#line 1394 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 178 "parser.y"
+ { free(((*yyvaluep).str)); };
+/* Line 1393 of yacc.c */
+#line 1487 "parser.cpp"
+ break;
case 23: /* PARAM */
-/* Line 1381 of yacc.c */
-#line 174 "parser.y"
- { if(((*yyvaluep).str)) free(((*yyvaluep).str)); };
-/* Line 1381 of yacc.c */
-#line 1401 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 179 "parser.y"
+ { if(((*yyvaluep).str)) free(((*yyvaluep).str)); };
+/* Line 1393 of yacc.c */
+#line 1494 "parser.cpp"
+ break;
case 26: /* CMP_OP */
-/* Line 1381 of yacc.c */
-#line 173 "parser.y"
- { free(((*yyvaluep).str)); };
-/* Line 1381 of yacc.c */
-#line 1408 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 178 "parser.y"
+ { free(((*yyvaluep).str)); };
+/* Line 1393 of yacc.c */
+#line 1501 "parser.cpp"
+ break;
case 50: /* commands */
-/* Line 1381 of yacc.c */
-#line 175 "parser.y"
- { delete ((*yyvaluep).sel); };
-/* Line 1381 of yacc.c */
-#line 1415 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 180 "parser.y"
+ { delete ((*yyvaluep).sel); };
+/* Line 1393 of yacc.c */
+#line 1508 "parser.cpp"
+ break;
case 51: /* command */
-/* Line 1381 of yacc.c */
-#line 175 "parser.y"
- { delete ((*yyvaluep).sel); };
-/* Line 1381 of yacc.c */
-#line 1422 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 180 "parser.y"
+ { delete ((*yyvaluep).sel); };
+/* Line 1393 of yacc.c */
+#line 1515 "parser.cpp"
+ break;
case 52: /* cmd_plain */
-/* Line 1381 of yacc.c */
-#line 175 "parser.y"
- { delete ((*yyvaluep).sel); };
-/* Line 1381 of yacc.c */
-#line 1429 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 180 "parser.y"
+ { delete ((*yyvaluep).sel); };
+/* Line 1393 of yacc.c */
+#line 1522 "parser.cpp"
+ break;
case 53: /* selection */
-/* Line 1381 of yacc.c */
-#line 175 "parser.y"
- { delete ((*yyvaluep).sel); };
-/* Line 1381 of yacc.c */
-#line 1436 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 180 "parser.y"
+ { delete ((*yyvaluep).sel); };
+/* Line 1393 of yacc.c */
+#line 1529 "parser.cpp"
+ break;
case 57: /* string */
-/* Line 1381 of yacc.c */
-#line 173 "parser.y"
- { free(((*yyvaluep).str)); };
-/* Line 1381 of yacc.c */
-#line 1443 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 178 "parser.y"
+ { free(((*yyvaluep).str)); };
+/* Line 1393 of yacc.c */
+#line 1536 "parser.cpp"
+ break;
case 58: /* sel_expr */
-/* Line 1381 of yacc.c */
-#line 176 "parser.y"
- { delete ((*yyvaluep).sel); };
-/* Line 1381 of yacc.c */
-#line 1450 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 181 "parser.y"
+ { delete ((*yyvaluep).sel); };
+/* Line 1393 of yacc.c */
+#line 1543 "parser.cpp"
+ break;
case 59: /* pos_mod */
-/* Line 1381 of yacc.c */
-#line 174 "parser.y"
- { if(((*yyvaluep).str)) free(((*yyvaluep).str)); };
-/* Line 1381 of yacc.c */
-#line 1457 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 179 "parser.y"
+ { if(((*yyvaluep).str)) free(((*yyvaluep).str)); };
+/* Line 1393 of yacc.c */
+#line 1550 "parser.cpp"
+ break;
case 61: /* num_expr */
-/* Line 1381 of yacc.c */
-#line 176 "parser.y"
- { delete ((*yyvaluep).sel); };
-/* Line 1381 of yacc.c */
-#line 1464 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 181 "parser.y"
+ { delete ((*yyvaluep).sel); };
+/* Line 1393 of yacc.c */
+#line 1557 "parser.cpp"
+ break;
case 62: /* str_expr */
-/* Line 1381 of yacc.c */
-#line 176 "parser.y"
- { delete ((*yyvaluep).sel); };
-/* Line 1381 of yacc.c */
-#line 1471 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 181 "parser.y"
+ { delete ((*yyvaluep).sel); };
+/* Line 1393 of yacc.c */
+#line 1564 "parser.cpp"
+ break;
case 63: /* pos_expr */
-/* Line 1381 of yacc.c */
-#line 176 "parser.y"
- { delete ((*yyvaluep).sel); };
-/* Line 1381 of yacc.c */
-#line 1478 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 181 "parser.y"
+ { delete ((*yyvaluep).sel); };
+/* Line 1393 of yacc.c */
+#line 1571 "parser.cpp"
+ break;
case 64: /* method_params */
-/* Line 1381 of yacc.c */
-#line 177 "parser.y"
- { delete ((*yyvaluep).plist); };
-/* Line 1381 of yacc.c */
-#line 1485 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 182 "parser.y"
+ { delete ((*yyvaluep).plist); };
+/* Line 1393 of yacc.c */
+#line 1578 "parser.cpp"
+ break;
case 65: /* method_param_list */
-/* Line 1381 of yacc.c */
-#line 177 "parser.y"
- { delete ((*yyvaluep).plist); };
-/* Line 1381 of yacc.c */
-#line 1492 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 182 "parser.y"
+ { delete ((*yyvaluep).plist); };
+/* Line 1393 of yacc.c */
+#line 1585 "parser.cpp"
+ break;
case 66: /* method_param */
-/* Line 1381 of yacc.c */
-#line 177 "parser.y"
- { delete ((*yyvaluep).param); };
-/* Line 1381 of yacc.c */
-#line 1499 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 182 "parser.y"
+ { delete ((*yyvaluep).param); };
+/* Line 1393 of yacc.c */
+#line 1592 "parser.cpp"
+ break;
case 67: /* value_list */
-/* Line 1381 of yacc.c */
-#line 178 "parser.y"
- { delete ((*yyvaluep).vlist); };
-/* Line 1381 of yacc.c */
-#line 1506 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 183 "parser.y"
+ { delete ((*yyvaluep).vlist); };
+/* Line 1393 of yacc.c */
+#line 1599 "parser.cpp"
+ break;
case 68: /* value_list_contents */
-/* Line 1381 of yacc.c */
-#line 178 "parser.y"
- { delete ((*yyvaluep).vlist); };
-/* Line 1381 of yacc.c */
-#line 1513 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 183 "parser.y"
+ { delete ((*yyvaluep).vlist); };
+/* Line 1393 of yacc.c */
+#line 1606 "parser.cpp"
+ break;
case 69: /* basic_value_list */
-/* Line 1381 of yacc.c */
-#line 178 "parser.y"
- { delete ((*yyvaluep).vlist); };
-/* Line 1381 of yacc.c */
-#line 1520 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 183 "parser.y"
+ { delete ((*yyvaluep).vlist); };
+/* Line 1393 of yacc.c */
+#line 1613 "parser.cpp"
+ break;
case 70: /* basic_value_list_contents */
-/* Line 1381 of yacc.c */
-#line 178 "parser.y"
- { delete ((*yyvaluep).vlist); };
-/* Line 1381 of yacc.c */
-#line 1527 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 183 "parser.y"
+ { delete ((*yyvaluep).vlist); };
+/* Line 1393 of yacc.c */
+#line 1620 "parser.cpp"
+ break;
case 71: /* value_item */
-/* Line 1381 of yacc.c */
-#line 179 "parser.y"
- { delete ((*yyvaluep).val); };
-/* Line 1381 of yacc.c */
-#line 1534 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 184 "parser.y"
+ { delete ((*yyvaluep).val); };
+/* Line 1393 of yacc.c */
+#line 1627 "parser.cpp"
+ break;
case 72: /* basic_value_item */
-/* Line 1381 of yacc.c */
-#line 179 "parser.y"
- { delete ((*yyvaluep).val); };
-/* Line 1381 of yacc.c */
-#line 1541 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 184 "parser.y"
+ { delete ((*yyvaluep).val); };
+/* Line 1393 of yacc.c */
+#line 1634 "parser.cpp"
+ break;
case 73: /* value_item_range */
-/* Line 1381 of yacc.c */
-#line 179 "parser.y"
- { delete ((*yyvaluep).val); };
-/* Line 1381 of yacc.c */
-#line 1548 "parser.cpp"
- break;
+/* Line 1393 of yacc.c */
+#line 184 "parser.y"
+ { delete ((*yyvaluep).val); };
+/* Line 1393 of yacc.c */
+#line 1641 "parser.cpp"
+ break;
default:
- break;
+ break;
}
}
/* The stacks and their tools:
`yyss': related to states.
`yyvs': related to semantic values.
+ `yyls': related to locations.
Refer to the stacks through separate pointers, to allow yyoverflow
to reallocate them elsewhere. */
YYSTYPE *yyvs;
YYSTYPE *yyvsp;
+ /* The location stack. */
+ YYLTYPE yylsa[YYINITDEPTH];
+ YYLTYPE *yyls;
+ YYLTYPE *yylsp;
+
+ /* The locations where the error started and ended. */
+ YYLTYPE yyerror_range[3];
+
YYSIZE_T yystacksize;
/* Used to determine if this is the first time this instance has
been used. */
#define yyvsa yyps->yyvsa
#define yyvs yyps->yyvs
#define yyvsp yyps->yyvsp
+#define yylsa yyps->yylsa
+#define yyls yyps->yyls
+#define yylsp yyps->yylsp
+#define yyerror_range yyps->yyerror_range
#define yystacksize yyps->yystacksize
#if (defined __STDC__ || defined __C99__FUNC__ \
|| defined __cplusplus || defined _MSC_VER)
int
-yypush_parse (yypstate *yyps, int yypushed_char, YYSTYPE const *yypushed_val, void *scanner)
+yypush_parse (yypstate *yyps, int yypushed_char, YYSTYPE const *yypushed_val, YYLTYPE *yypushed_loc, void *scanner)
#else
int
-yypush_parse (yyps, yypushed_char, yypushed_val, scanner)
+yypush_parse (yyps, yypushed_char, yypushed_val, yypushed_loc, scanner)
yypstate *yyps;
int yypushed_char;
YYSTYPE const *yypushed_val;
+ YYLTYPE *yypushed_loc;
void *scanner;
#endif
{
/* The lookahead symbol. */
int yychar;
+
+#if defined __GNUC__ && 407 <= __GNUC__ * 100 + __GNUC_MINOR__
+/* Suppress an incorrect diagnostic about yylval being uninitialized. */
+# define YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN \
+ _Pragma ("GCC diagnostic push") \
+ _Pragma ("GCC diagnostic ignored \"-Wuninitialized\"")\
+ _Pragma ("GCC diagnostic ignored \"-Wmaybe-uninitialized\"")
+# define YY_IGNORE_MAYBE_UNINITIALIZED_END \
+ _Pragma ("GCC diagnostic pop")
+#else
+/* Default value used for initialization, for pacifying older GCCs
+ or non-GCC compilers. */
+static YYSTYPE yyval_default;
+# define YY_INITIAL_VALUE(Value) = Value
+#endif
+static YYLTYPE yyloc_default
+# if defined YYLTYPE_IS_TRIVIAL && YYLTYPE_IS_TRIVIAL
+ = { 1, 1, 1, 1 }
+# endif
+;
+#ifndef YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN
+# define YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN
+# define YY_IGNORE_MAYBE_UNINITIALIZED_END
+#endif
+#ifndef YY_INITIAL_VALUE
+# define YY_INITIAL_VALUE(Value) /* Nothing. */
+#endif
+
/* The semantic value of the lookahead symbol. */
-YYSTYPE yylval;
+YYSTYPE yylval YY_INITIAL_VALUE(yyval_default);
+
+/* Location data for the lookahead symbol. */
+YYLTYPE yylloc = yyloc_default;
+
int yyn;
int yyresult;
/* Lookahead token as an internal (translated) token number. */
- int yytoken;
+ int yytoken = 0;
/* The variables used to return semantic value and location from the
action routines. */
YYSTYPE yyval;
+ YYLTYPE yyloc;
#if YYERROR_VERBOSE
/* Buffer for error messages, and its allocated size. */
YYSIZE_T yymsg_alloc = sizeof yymsgbuf;
#endif
-#define YYPOPSTACK(N) (yyvsp -= (N), yyssp -= (N))
+#define YYPOPSTACK(N) (yyvsp -= (N), yyssp -= (N), yylsp -= (N))
/* The number of symbols on the RHS of the reduced rule.
Keep to zero when no symbol should be popped. */
goto yyread_pushed_token;
}
- yytoken = 0;
- yyss = yyssa;
- yyvs = yyvsa;
+ yyssp = yyss = yyssa;
+ yyvsp = yyvs = yyvsa;
+ yylsp = yyls = yylsa;
yystacksize = YYINITDEPTH;
YYDPRINTF ((stderr, "Starting parse\n"));
yyerrstatus = 0;
yynerrs = 0;
yychar = YYEMPTY; /* Cause a token to be read. */
-
- /* Initialize stack pointers.
- Waste one element of value and location stack
- so that they stay on the same level as the state stack.
- The wasted elements are never initialized. */
- yyssp = yyss;
- yyvsp = yyvs;
+ yylsp[0] = *yypushed_loc;
goto yysetstate;
/*------------------------------------------------------------.
memory. */
YYSTYPE *yyvs1 = yyvs;
yytype_int16 *yyss1 = yyss;
+ YYLTYPE *yyls1 = yyls;
/* Each stack pointer address is followed by the size of the
data in use in that stack, in bytes. This used to be a
yyoverflow (YY_("memory exhausted"),
&yyss1, yysize * sizeof (*yyssp),
&yyvs1, yysize * sizeof (*yyvsp),
+ &yyls1, yysize * sizeof (*yylsp),
&yystacksize);
+ yyls = yyls1;
yyss = yyss1;
yyvs = yyvs1;
}
goto yyexhaustedlab;
YYSTACK_RELOCATE (yyss_alloc, yyss);
YYSTACK_RELOCATE (yyvs_alloc, yyvs);
+ YYSTACK_RELOCATE (yyls_alloc, yyls);
# undef YYSTACK_RELOCATE
if (yyss1 != yyssa)
YYSTACK_FREE (yyss1);
yyssp = yyss + yysize - 1;
yyvsp = yyvs + yysize - 1;
+ yylsp = yyls + yysize - 1;
YYDPRINTF ((stderr, "Stack size increased to %lu\n",
(unsigned long int) yystacksize));
yychar = yypushed_char;
if (yypushed_val)
yylval = *yypushed_val;
+ if (yypushed_loc)
+ yylloc = *yypushed_loc;
}
if (yychar <= YYEOF)
yychar = YYEMPTY;
yystate = yyn;
+ YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN
*++yyvsp = yylval;
-
+ YY_IGNORE_MAYBE_UNINITIALIZED_END
+ *++yylsp = yylloc;
goto yynewstate;
GCC warning that YYVAL may be used uninitialized. */
yyval = yyvsp[1-yylen];
-
+ /* Default location. */
+ YYLLOC_DEFAULT (yyloc, (yylsp - yylen), yylen);
YY_REDUCE_PRINT (yyn);
switch (yyn)
{
case 2:
/* Line 1787 of yacc.c */
-#line 193 "parser.y"
+#line 199 "parser.y"
{
BEGIN_ACTION;
set_empty((yyval.sel));
- END_ACTION;
+ END_ACTION_TOPLEVEL;
}
break;
case 3:
/* Line 1787 of yacc.c */
-#line 199 "parser.y"
+#line 205 "parser.y"
{
BEGIN_ACTION;
set((yyval.sel), _gmx_sel_append_selection(get((yyvsp[(2) - (2)].sel)), get((yyvsp[(1) - (2)].sel)), scanner));
if (_gmx_sel_parser_should_finish(scanner))
YYACCEPT;
- END_ACTION;
+ END_ACTION_TOPLEVEL;
}
break;
case 4:
/* Line 1787 of yacc.c */
-#line 209 "parser.y"
+#line 215 "parser.y"
{ (yyval.sel) = (yyvsp[(1) - (2)].sel); }
break;
case 5:
/* Line 1787 of yacc.c */
-#line 211 "parser.y"
+#line 217 "parser.y"
{
BEGIN_ACTION;
- _gmx_selparser_error(scanner, "invalid selection '%s'",
- _gmx_sel_lexer_pselstr(scanner));
_gmx_sel_lexer_clear_method_stack(scanner);
- if (_gmx_sel_is_lexer_interactive(scanner))
+ if (_gmx_selparser_handle_error(scanner))
{
- _gmx_sel_lexer_clear_pselstr(scanner);
yyerrok;
}
else
{
YYABORT;
}
+ _gmx_sel_lexer_clear_pselstr(scanner);
set_empty((yyval.sel));
- END_ACTION;
+ END_ACTION_TOPLEVEL;
}
break;
case 6:
/* Line 1787 of yacc.c */
-#line 232 "parser.y"
+#line 236 "parser.y"
{
BEGIN_ACTION;
set_empty((yyval.sel));
case 7:
/* Line 1787 of yacc.c */
-#line 238 "parser.y"
+#line 242 "parser.y"
{
BEGIN_ACTION;
SelectionTreeElementPointer s
case 8:
/* Line 1787 of yacc.c */
-#line 249 "parser.y"
+#line 253 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree nameGuard((yyvsp[(1) - (1)].str));
+ scoped_guard_sfree nameGuard((yyvsp[(1) - (1)].str));
SelectionTreeElementPointer s
= _gmx_sel_init_group_by_name((yyvsp[(1) - (1)].str), scanner);
SelectionTreeElementPointer p
case 9:
/* Line 1787 of yacc.c */
-#line 261 "parser.y"
+#line 265 "parser.y"
{
BEGIN_ACTION;
set((yyval.sel), _gmx_sel_init_selection(NULL, get((yyvsp[(1) - (1)].sel)), scanner));
case 10:
/* Line 1787 of yacc.c */
-#line 267 "parser.y"
+#line 271 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree nameGuard((yyvsp[(1) - (2)].str));
+ scoped_guard_sfree nameGuard((yyvsp[(1) - (2)].str));
set((yyval.sel), _gmx_sel_init_selection((yyvsp[(1) - (2)].str), get((yyvsp[(2) - (2)].sel)), scanner));
END_ACTION;
}
case 11:
/* Line 1787 of yacc.c */
-#line 274 "parser.y"
+#line 278 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree nameGuard((yyvsp[(1) - (3)].str));
+ scoped_guard_sfree nameGuard((yyvsp[(1) - (3)].str));
set((yyval.sel), _gmx_sel_assign_variable((yyvsp[(1) - (3)].str), get((yyvsp[(3) - (3)].sel)), scanner));
END_ACTION;
}
case 12:
/* Line 1787 of yacc.c */
-#line 281 "parser.y"
+#line 285 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree nameGuard((yyvsp[(1) - (3)].str));
+ scoped_guard_sfree nameGuard((yyvsp[(1) - (3)].str));
set((yyval.sel), _gmx_sel_assign_variable((yyvsp[(1) - (3)].str), get((yyvsp[(3) - (3)].sel)), scanner));
END_ACTION;
}
case 13:
/* Line 1787 of yacc.c */
-#line 288 "parser.y"
+#line 292 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree nameGuard((yyvsp[(1) - (3)].str));
+ scoped_guard_sfree nameGuard((yyvsp[(1) - (3)].str));
set((yyval.sel), _gmx_sel_assign_variable((yyvsp[(1) - (3)].str), get((yyvsp[(3) - (3)].sel)), scanner));
END_ACTION;
}
case 14:
/* Line 1787 of yacc.c */
-#line 297 "parser.y"
+#line 301 "parser.y"
{ (yyval.sel) = (yyvsp[(1) - (1)].sel); }
break;
case 15:
/* Line 1787 of yacc.c */
-#line 299 "parser.y"
+#line 303 "parser.y"
{
BEGIN_ACTION;
set((yyval.sel), _gmx_sel_init_position(get((yyvsp[(1) - (1)].sel)), NULL, scanner));
case 16:
/* Line 1787 of yacc.c */
-#line 305 "parser.y"
+#line 309 "parser.y"
{ (yyval.sel) = (yyvsp[(2) - (3)].sel); }
break;
case 17:
/* Line 1787 of yacc.c */
-#line 307 "parser.y"
+#line 311 "parser.y"
{
BEGIN_ACTION;
set((yyval.sel), _gmx_sel_init_modifier((yyvsp[(2) - (3)].meth), get((yyvsp[(3) - (3)].plist)), get((yyvsp[(1) - (3)].sel)), scanner));
case 18:
/* Line 1787 of yacc.c */
-#line 320 "parser.y"
+#line 324 "parser.y"
{ (yyval.i) = (yyvsp[(1) - (1)].i); }
break;
case 19:
/* Line 1787 of yacc.c */
-#line 321 "parser.y"
+#line 325 "parser.y"
{ (yyval.i) = -(yyvsp[(2) - (2)].i); }
break;
case 20:
/* Line 1787 of yacc.c */
-#line 325 "parser.y"
+#line 329 "parser.y"
{ (yyval.r) = (yyvsp[(1) - (1)].r); }
break;
case 21:
/* Line 1787 of yacc.c */
-#line 326 "parser.y"
+#line 330 "parser.y"
{ (yyval.r) = -(yyvsp[(2) - (2)].r); }
break;
case 22:
/* Line 1787 of yacc.c */
-#line 329 "parser.y"
+#line 333 "parser.y"
{ (yyval.r) = (yyvsp[(1) - (1)].i); }
break;
case 23:
/* Line 1787 of yacc.c */
-#line 330 "parser.y"
+#line 334 "parser.y"
{ (yyval.r) = (yyvsp[(1) - (1)].r); }
break;
case 24:
/* Line 1787 of yacc.c */
-#line 333 "parser.y"
+#line 337 "parser.y"
{ (yyval.str) = (yyvsp[(1) - (1)].str); }
break;
case 25:
/* Line 1787 of yacc.c */
-#line 334 "parser.y"
+#line 338 "parser.y"
{ (yyval.str) = (yyvsp[(1) - (1)].str); }
break;
case 26:
/* Line 1787 of yacc.c */
-#line 343 "parser.y"
+#line 347 "parser.y"
{
BEGIN_ACTION;
SelectionTreeElementPointer arg(get((yyvsp[(2) - (2)].sel)));
SelectionTreeElementPointer sel(
- new SelectionTreeElement(SEL_BOOLEAN));
+ new SelectionTreeElement(SEL_BOOLEAN, (yyloc)));
sel->u.boolt = BOOL_NOT;
sel->child = arg;
set((yyval.sel), sel);
case 27:
/* Line 1787 of yacc.c */
-#line 354 "parser.y"
+#line 358 "parser.y"
{
BEGIN_ACTION;
SelectionTreeElementPointer arg1(get((yyvsp[(1) - (3)].sel))), arg2(get((yyvsp[(3) - (3)].sel)));
SelectionTreeElementPointer sel(
- new SelectionTreeElement(SEL_BOOLEAN));
+ new SelectionTreeElement(SEL_BOOLEAN, (yyloc)));
sel->u.boolt = BOOL_AND;
sel->child = arg1; sel->child->next = arg2;
set((yyval.sel), sel);
case 28:
/* Line 1787 of yacc.c */
-#line 365 "parser.y"
+#line 369 "parser.y"
{
BEGIN_ACTION;
SelectionTreeElementPointer arg1(get((yyvsp[(1) - (3)].sel))), arg2(get((yyvsp[(3) - (3)].sel)));
SelectionTreeElementPointer sel(
- new SelectionTreeElement(SEL_BOOLEAN));
+ new SelectionTreeElement(SEL_BOOLEAN, (yyloc)));
sel->u.boolt = BOOL_OR;
sel->child = arg1; sel->child->next = arg2;
set((yyval.sel), sel);
case 29:
/* Line 1787 of yacc.c */
-#line 375 "parser.y"
+#line 379 "parser.y"
{ (yyval.sel) = (yyvsp[(2) - (3)].sel); }
break;
case 30:
/* Line 1787 of yacc.c */
-#line 380 "parser.y"
+#line 384 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree opGuard((yyvsp[(2) - (3)].str));
+ scoped_guard_sfree opGuard((yyvsp[(2) - (3)].str));
set((yyval.sel), _gmx_sel_init_comparison(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), (yyvsp[(2) - (3)].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
case 31:
/* Line 1787 of yacc.c */
-#line 391 "parser.y"
+#line 395 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree nameGuard((yyvsp[(2) - (2)].str));
+ scoped_guard_sfree nameGuard((yyvsp[(2) - (2)].str));
set((yyval.sel), _gmx_sel_init_group_by_name((yyvsp[(2) - (2)].str), scanner));
END_ACTION;
}
case 32:
/* Line 1787 of yacc.c */
-#line 398 "parser.y"
+#line 402 "parser.y"
{
BEGIN_ACTION;
set((yyval.sel), _gmx_sel_init_group_by_id((yyvsp[(2) - (2)].i), scanner));
case 33:
/* Line 1787 of yacc.c */
-#line 406 "parser.y"
+#line 410 "parser.y"
{ (yyval.str) = NULL; }
break;
case 34:
/* Line 1787 of yacc.c */
-#line 407 "parser.y"
+#line 411 "parser.y"
{ (yyval.str) = (yyvsp[(1) - (1)].str); }
break;
case 35:
/* Line 1787 of yacc.c */
-#line 412 "parser.y"
+#line 416 "parser.y"
{ (yyval.smt) = gmx::eStringMatchType_RegularExpression; }
break;
case 36:
/* Line 1787 of yacc.c */
-#line 413 "parser.y"
+#line 417 "parser.y"
{ (yyval.smt) = gmx::eStringMatchType_Wildcard; }
break;
case 37:
/* Line 1787 of yacc.c */
-#line 414 "parser.y"
+#line 418 "parser.y"
{ (yyval.smt) = gmx::eStringMatchType_Exact; }
break;
case 38:
/* Line 1787 of yacc.c */
-#line 419 "parser.y"
+#line 423 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree posmodGuard((yyvsp[(1) - (2)].str));
+ scoped_guard_sfree posmodGuard((yyvsp[(1) - (2)].str));
set((yyval.sel), _gmx_sel_init_keyword((yyvsp[(2) - (2)].meth), SelectionParserValueListPointer(), (yyvsp[(1) - (2)].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
case 39:
/* Line 1787 of yacc.c */
-#line 427 "parser.y"
+#line 431 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree posmodGuard((yyvsp[(1) - (3)].str));
+ scoped_guard_sfree posmodGuard((yyvsp[(1) - (3)].str));
set((yyval.sel), _gmx_sel_init_keyword_strmatch((yyvsp[(2) - (3)].meth), gmx::eStringMatchType_Auto, get((yyvsp[(3) - (3)].vlist)), (yyvsp[(1) - (3)].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
case 40:
/* Line 1787 of yacc.c */
-#line 435 "parser.y"
+#line 439 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree posmodGuard((yyvsp[(1) - (4)].str));
+ scoped_guard_sfree posmodGuard((yyvsp[(1) - (4)].str));
set((yyval.sel), _gmx_sel_init_keyword_strmatch((yyvsp[(2) - (4)].meth), (yyvsp[(3) - (4)].smt), get((yyvsp[(4) - (4)].vlist)), (yyvsp[(1) - (4)].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
case 41:
/* Line 1787 of yacc.c */
-#line 443 "parser.y"
+#line 447 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree posmodGuard((yyvsp[(1) - (3)].str));
+ scoped_guard_sfree posmodGuard((yyvsp[(1) - (3)].str));
set((yyval.sel), _gmx_sel_init_keyword((yyvsp[(2) - (3)].meth), get((yyvsp[(3) - (3)].vlist)), (yyvsp[(1) - (3)].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
case 42:
/* Line 1787 of yacc.c */
-#line 454 "parser.y"
+#line 458 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree posmodGuard((yyvsp[(1) - (3)].str));
+ scoped_guard_sfree posmodGuard((yyvsp[(1) - (3)].str));
set((yyval.sel), _gmx_sel_init_method((yyvsp[(2) - (3)].meth), get((yyvsp[(3) - (3)].plist)), (yyvsp[(1) - (3)].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
case 43:
/* Line 1787 of yacc.c */
-#line 469 "parser.y"
+#line 473 "parser.y"
{
BEGIN_ACTION;
SelectionTreeElementPointer sel(
- new SelectionTreeElement(SEL_CONST));
+ new SelectionTreeElement(SEL_CONST, (yyloc)));
_gmx_selelem_set_vtype(sel, INT_VALUE);
_gmx_selvalue_reserve(&sel->v, 1);
sel->v.u.i[0] = (yyvsp[(1) - (1)].i);
case 44:
/* Line 1787 of yacc.c */
-#line 480 "parser.y"
+#line 484 "parser.y"
{
BEGIN_ACTION;
SelectionTreeElementPointer sel(
- new SelectionTreeElement(SEL_CONST));
+ new SelectionTreeElement(SEL_CONST, (yyloc)));
_gmx_selelem_set_vtype(sel, REAL_VALUE);
_gmx_selvalue_reserve(&sel->v, 1);
sel->v.u.r[0] = (yyvsp[(1) - (1)].r);
case 45:
/* Line 1787 of yacc.c */
-#line 494 "parser.y"
+#line 498 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree posmodGuard((yyvsp[(1) - (2)].str));
+ scoped_guard_sfree posmodGuard((yyvsp[(1) - (2)].str));
set((yyval.sel), _gmx_sel_init_keyword((yyvsp[(2) - (2)].meth), SelectionParserValueListPointer(), (yyvsp[(1) - (2)].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
case 46:
/* Line 1787 of yacc.c */
-#line 502 "parser.y"
+#line 506 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree posmodGuard((yyvsp[(1) - (3)].str));
- set((yyval.sel), _gmx_sel_init_method((yyvsp[(2) - (3)].meth), get((yyvsp[(3) - (3)].plist)), (yyvsp[(1) - (3)].str), scanner));
+ scoped_guard_sfree posmodGuard((yyvsp[(1) - (4)].str));
+ set((yyval.sel), _gmx_sel_init_keyword_of((yyvsp[(2) - (4)].meth), get((yyvsp[(4) - (4)].sel)), (yyvsp[(1) - (4)].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
case 47:
/* Line 1787 of yacc.c */
-#line 513 "parser.y"
+#line 514 "parser.y"
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '+', scanner));
+ scoped_guard_sfree posmodGuard((yyvsp[(1) - (3)].str));
+ set((yyval.sel), _gmx_sel_init_method((yyvsp[(2) - (3)].meth), get((yyvsp[(3) - (3)].plist)), (yyvsp[(1) - (3)].str), scanner));
+ CHECK_SEL((yyval.sel));
END_ACTION;
}
break;
case 48:
/* Line 1787 of yacc.c */
-#line 519 "parser.y"
+#line 525 "parser.y"
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '-', scanner));
+ set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '+', scanner));
END_ACTION;
}
break;
case 49:
/* Line 1787 of yacc.c */
-#line 525 "parser.y"
+#line 531 "parser.y"
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '*', scanner));
+ set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '-', scanner));
END_ACTION;
}
break;
case 50:
/* Line 1787 of yacc.c */
-#line 531 "parser.y"
+#line 537 "parser.y"
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '/', scanner));
+ set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '*', scanner));
END_ACTION;
}
break;
case 51:
/* Line 1787 of yacc.c */
-#line 537 "parser.y"
+#line 543 "parser.y"
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(2) - (2)].sel)), SelectionTreeElementPointer(), '-', scanner));
+ set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '/', scanner));
END_ACTION;
}
break;
case 52:
/* Line 1787 of yacc.c */
-#line 543 "parser.y"
+#line 549 "parser.y"
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '^', scanner));
+ set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(2) - (2)].sel)), SelectionTreeElementPointer(), '-', scanner));
END_ACTION;
}
break;
case 53:
/* Line 1787 of yacc.c */
-#line 548 "parser.y"
- { (yyval.sel) = (yyvsp[(2) - (3)].sel); }
+#line 555 "parser.y"
+ {
+ BEGIN_ACTION;
+ set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '^', scanner));
+ END_ACTION;
+ }
break;
case 54:
/* Line 1787 of yacc.c */
-#line 556 "parser.y"
+#line 560 "parser.y"
+ { (yyval.sel) = (yyvsp[(2) - (3)].sel); }
+ break;
+
+ case 55:
+/* Line 1787 of yacc.c */
+#line 568 "parser.y"
{
BEGIN_ACTION;
SelectionTreeElementPointer sel(
- new SelectionTreeElement(SEL_CONST));
+ new SelectionTreeElement(SEL_CONST, (yyloc)));
_gmx_selelem_set_vtype(sel, STR_VALUE);
_gmx_selvalue_reserve(&sel->v, 1);
sel->v.u.s[0] = (yyvsp[(1) - (1)].str);
}
break;
- case 55:
+ case 56:
/* Line 1787 of yacc.c */
-#line 567 "parser.y"
+#line 579 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree posmodGuard((yyvsp[(1) - (2)].str));
+ scoped_guard_sfree posmodGuard((yyvsp[(1) - (2)].str));
set((yyval.sel), _gmx_sel_init_keyword((yyvsp[(2) - (2)].meth), SelectionParserValueListPointer(), (yyvsp[(1) - (2)].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
break;
- case 56:
+ case 57:
/* Line 1787 of yacc.c */
-#line 582 "parser.y"
+#line 594 "parser.y"
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_const_position((yyvsp[(2) - (7)].r), (yyvsp[(4) - (7)].r), (yyvsp[(6) - (7)].r)));
+ set((yyval.sel), _gmx_sel_init_const_position((yyvsp[(2) - (7)].r), (yyvsp[(4) - (7)].r), (yyvsp[(6) - (7)].r), scanner));
END_ACTION;
}
break;
- case 57:
+ case 58:
/* Line 1787 of yacc.c */
-#line 590 "parser.y"
+#line 602 "parser.y"
{ (yyval.sel) = (yyvsp[(2) - (3)].sel); }
break;
- case 58:
+ case 59:
/* Line 1787 of yacc.c */
-#line 595 "parser.y"
+#line 607 "parser.y"
{
BEGIN_ACTION;
set((yyval.sel), _gmx_sel_init_method((yyvsp[(1) - (2)].meth), get((yyvsp[(2) - (2)].plist)), NULL, scanner));
}
break;
- case 59:
+ case 60:
/* Line 1787 of yacc.c */
-#line 605 "parser.y"
+#line 617 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree keywordGuard((yyvsp[(1) - (3)].str));
+ scoped_guard_sfree keywordGuard((yyvsp[(1) - (3)].str));
set((yyval.sel), _gmx_sel_init_position(get((yyvsp[(3) - (3)].sel)), (yyvsp[(1) - (3)].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
break;
- case 60:
+ case 61:
/* Line 1787 of yacc.c */
-#line 619 "parser.y"
+#line 631 "parser.y"
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_variable_ref(get((yyvsp[(1) - (1)].sel))));
+ set((yyval.sel), _gmx_sel_init_variable_ref(get((yyvsp[(1) - (1)].sel)), scanner));
END_ACTION;
}
break;
- case 61:
+ case 62:
/* Line 1787 of yacc.c */
-#line 627 "parser.y"
+#line 639 "parser.y"
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_variable_ref(get((yyvsp[(1) - (1)].sel))));
+ set((yyval.sel), _gmx_sel_init_variable_ref(get((yyvsp[(1) - (1)].sel)), scanner));
END_ACTION;
}
break;
- case 62:
+ case 63:
/* Line 1787 of yacc.c */
-#line 635 "parser.y"
+#line 647 "parser.y"
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_variable_ref(get((yyvsp[(1) - (1)].sel))));
+ set((yyval.sel), _gmx_sel_init_variable_ref(get((yyvsp[(1) - (1)].sel)), scanner));
END_ACTION;
}
break;
- case 63:
+ case 64:
/* Line 1787 of yacc.c */
-#line 648 "parser.y"
+#line 660 "parser.y"
{ (yyval.plist) = (yyvsp[(1) - (1)].plist); }
break;
- case 64:
+ case 65:
/* Line 1787 of yacc.c */
-#line 650 "parser.y"
+#line 662 "parser.y"
{ (yyval.plist) = (yyvsp[(1) - (2)].plist); }
break;
- case 65:
+ case 66:
/* Line 1787 of yacc.c */
-#line 655 "parser.y"
+#line 667 "parser.y"
{
BEGIN_ACTION;
set((yyval.plist), SelectionParserParameter::createList());
}
break;
- case 66:
+ case 67:
/* Line 1787 of yacc.c */
-#line 661 "parser.y"
+#line 673 "parser.y"
{
BEGIN_ACTION;
SelectionParserParameterListPointer list(get((yyvsp[(1) - (2)].plist)));
}
break;
- case 67:
+ case 68:
/* Line 1787 of yacc.c */
-#line 672 "parser.y"
+#line 684 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree nameGuard((yyvsp[(1) - (2)].str));
- set((yyval.param), SelectionParserParameter::create((yyvsp[(1) - (2)].str), get((yyvsp[(2) - (2)].vlist))));
+ scoped_guard_sfree nameGuard((yyvsp[(1) - (2)].str));
+ set((yyval.param), SelectionParserParameter::create((yyvsp[(1) - (2)].str), get((yyvsp[(2) - (2)].vlist)), (yyloc)));
END_ACTION;
}
break;
- case 68:
+ case 69:
/* Line 1787 of yacc.c */
-#line 680 "parser.y"
+#line 692 "parser.y"
{ (yyval.vlist) = (yyvsp[(1) - (1)].vlist); }
break;
- case 69:
+ case 70:
/* Line 1787 of yacc.c */
-#line 681 "parser.y"
+#line 693 "parser.y"
{ (yyval.vlist) = (yyvsp[(2) - (3)].vlist); }
break;
- case 70:
+ case 71:
/* Line 1787 of yacc.c */
-#line 686 "parser.y"
+#line 698 "parser.y"
{
BEGIN_ACTION;
set((yyval.vlist), SelectionParserValue::createList());
}
break;
- case 71:
+ case 72:
/* Line 1787 of yacc.c */
-#line 692 "parser.y"
+#line 704 "parser.y"
{
BEGIN_ACTION;
SelectionParserValueListPointer list(get((yyvsp[(1) - (2)].vlist)));
}
break;
- case 72:
+ case 73:
/* Line 1787 of yacc.c */
-#line 700 "parser.y"
+#line 712 "parser.y"
{
BEGIN_ACTION;
SelectionParserValueListPointer list(get((yyvsp[(1) - (3)].vlist)));
}
break;
- case 73:
+ case 74:
/* Line 1787 of yacc.c */
-#line 710 "parser.y"
+#line 722 "parser.y"
{ (yyval.vlist) = (yyvsp[(1) - (1)].vlist); }
break;
- case 74:
+ case 75:
/* Line 1787 of yacc.c */
-#line 711 "parser.y"
+#line 723 "parser.y"
{ (yyval.vlist) = (yyvsp[(2) - (3)].vlist); }
break;
- case 75:
+ case 76:
/* Line 1787 of yacc.c */
-#line 716 "parser.y"
+#line 728 "parser.y"
{
BEGIN_ACTION;
set((yyval.vlist), SelectionParserValue::createList(get((yyvsp[(1) - (1)].val))));
}
break;
- case 76:
+ case 77:
/* Line 1787 of yacc.c */
-#line 722 "parser.y"
+#line 734 "parser.y"
{
BEGIN_ACTION;
SelectionParserValueListPointer list(get((yyvsp[(1) - (2)].vlist)));
}
break;
- case 77:
+ case 78:
/* Line 1787 of yacc.c */
-#line 730 "parser.y"
+#line 742 "parser.y"
{
BEGIN_ACTION;
SelectionParserValueListPointer list(get((yyvsp[(1) - (3)].vlist)));
}
break;
- case 78:
+ case 79:
/* Line 1787 of yacc.c */
-#line 740 "parser.y"
+#line 752 "parser.y"
{
BEGIN_ACTION;
set((yyval.val), SelectionParserValue::createExpr(get((yyvsp[(1) - (1)].sel))));
}
break;
- case 79:
+ case 80:
/* Line 1787 of yacc.c */
-#line 746 "parser.y"
+#line 758 "parser.y"
{
BEGIN_ACTION;
set((yyval.val), SelectionParserValue::createExpr(get((yyvsp[(1) - (1)].sel))));
}
break;
- case 80:
+ case 81:
/* Line 1787 of yacc.c */
-#line 752 "parser.y"
+#line 764 "parser.y"
{
BEGIN_ACTION;
set((yyval.val), SelectionParserValue::createExpr(get((yyvsp[(1) - (1)].sel))));
}
break;
- case 81:
+ case 82:
/* Line 1787 of yacc.c */
-#line 758 "parser.y"
+#line 770 "parser.y"
{
BEGIN_ACTION;
set((yyval.val), SelectionParserValue::createExpr(get((yyvsp[(1) - (1)].sel))));
}
break;
- case 82:
+ case 83:
/* Line 1787 of yacc.c */
-#line 763 "parser.y"
+#line 775 "parser.y"
{ (yyval.val) = (yyvsp[(1) - (1)].val); }
break;
- case 83:
+ case 84:
/* Line 1787 of yacc.c */
-#line 768 "parser.y"
+#line 780 "parser.y"
{
BEGIN_ACTION;
- set((yyval.val), SelectionParserValue::createInteger((yyvsp[(1) - (1)].i)));
+ set((yyval.val), SelectionParserValue::createInteger((yyvsp[(1) - (1)].i), (yyloc)));
END_ACTION;
}
break;
- case 84:
+ case 85:
/* Line 1787 of yacc.c */
-#line 774 "parser.y"
+#line 786 "parser.y"
{
BEGIN_ACTION;
- set((yyval.val), SelectionParserValue::createReal((yyvsp[(1) - (1)].r)));
+ set((yyval.val), SelectionParserValue::createReal((yyvsp[(1) - (1)].r), (yyloc)));
END_ACTION;
}
break;
- case 85:
+ case 86:
/* Line 1787 of yacc.c */
-#line 780 "parser.y"
+#line 792 "parser.y"
{
BEGIN_ACTION;
- scoped_ptr_sfree stringGuard((yyvsp[(1) - (1)].str));
- set((yyval.val), SelectionParserValue::createString((yyvsp[(1) - (1)].str)));
+ scoped_guard_sfree stringGuard((yyvsp[(1) - (1)].str));
+ set((yyval.val), SelectionParserValue::createString((yyvsp[(1) - (1)].str), (yyloc)));
END_ACTION;
}
break;
- case 86:
+ case 87:
/* Line 1787 of yacc.c */
-#line 786 "parser.y"
+#line 798 "parser.y"
{ (yyval.val) = (yyvsp[(1) - (1)].val); }
break;
- case 87:
+ case 88:
/* Line 1787 of yacc.c */
-#line 791 "parser.y"
+#line 803 "parser.y"
{
BEGIN_ACTION;
- set((yyval.val), SelectionParserValue::createIntegerRange((yyvsp[(1) - (3)].i), (yyvsp[(3) - (3)].i)));
+ set((yyval.val), SelectionParserValue::createIntegerRange((yyvsp[(1) - (3)].i), (yyvsp[(3) - (3)].i), (yyloc)));
END_ACTION;
}
break;
- case 88:
+ case 89:
/* Line 1787 of yacc.c */
-#line 797 "parser.y"
+#line 809 "parser.y"
{
BEGIN_ACTION;
- set((yyval.val), SelectionParserValue::createRealRange((yyvsp[(1) - (3)].i), (yyvsp[(3) - (3)].r)));
+ set((yyval.val), SelectionParserValue::createRealRange((yyvsp[(1) - (3)].i), (yyvsp[(3) - (3)].r), (yyloc)));
END_ACTION;
}
break;
- case 89:
+ case 90:
/* Line 1787 of yacc.c */
-#line 803 "parser.y"
+#line 815 "parser.y"
{
BEGIN_ACTION;
- set((yyval.val), SelectionParserValue::createRealRange((yyvsp[(1) - (3)].r), (yyvsp[(3) - (3)].r)));
+ set((yyval.val), SelectionParserValue::createRealRange((yyvsp[(1) - (3)].r), (yyvsp[(3) - (3)].r), (yyloc)));
END_ACTION;
}
break;
/* Line 1787 of yacc.c */
-#line 2763 "parser.cpp"
+#line 2917 "parser.cpp"
default: break;
}
/* User semantic actions sometimes alter yychar, and that requires
YY_STACK_PRINT (yyss, yyssp);
*++yyvsp = yyval;
+ *++yylsp = yyloc;
/* Now `shift' the result of the reduction. Determine what state
that goes to, based on the state we popped back to and the rule
{
++yynerrs;
#if ! YYERROR_VERBOSE
- yyerror (scanner, YY_("syntax error"));
+ yyerror (&yylloc, scanner, YY_("syntax error"));
#else
# define YYSYNTAX_ERROR yysyntax_error (&yymsg_alloc, &yymsg, \
yyssp, yytoken)
yymsgp = yymsg;
}
}
- yyerror (scanner, yymsgp);
+ yyerror (&yylloc, scanner, yymsgp);
if (yysyntax_error_status == 2)
goto yyexhaustedlab;
}
#endif
}
-
+ yyerror_range[1] = yylloc;
if (yyerrstatus == 3)
{
else
{
yydestruct ("Error: discarding",
- yytoken, &yylval, scanner);
+ yytoken, &yylval, &yylloc, scanner);
yychar = YYEMPTY;
}
}
if (/*CONSTCOND*/ 0)
goto yyerrorlab;
+ yyerror_range[1] = yylsp[1-yylen];
/* Do not reclaim the symbols of the rule which action triggered
this YYERROR. */
YYPOPSTACK (yylen);
if (yyssp == yyss)
YYABORT;
-
+ yyerror_range[1] = *yylsp;
yydestruct ("Error: popping",
- yystos[yystate], yyvsp, scanner);
+ yystos[yystate], yyvsp, yylsp, scanner);
YYPOPSTACK (1);
yystate = *yyssp;
YY_STACK_PRINT (yyss, yyssp);
}
+ YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN
*++yyvsp = yylval;
+ YY_IGNORE_MAYBE_UNINITIALIZED_END
+ yyerror_range[2] = yylloc;
+ /* Using YYLLOC is tempting, but would change the location of
+ the lookahead. YYLOC is available though. */
+ YYLLOC_DEFAULT (yyloc, yyerror_range, 2);
+ *++yylsp = yyloc;
/* Shift the error token. */
YY_SYMBOL_PRINT ("Shifting", yystos[yyn], yyvsp, yylsp);
| yyexhaustedlab -- memory exhaustion comes here. |
`-------------------------------------------------*/
yyexhaustedlab:
- yyerror (scanner, YY_("memory exhausted"));
+ yyerror (&yylloc, scanner, YY_("memory exhausted"));
yyresult = 2;
/* Fall through. */
#endif
user semantic actions for why this is necessary. */
yytoken = YYTRANSLATE (yychar);
yydestruct ("Cleanup: discarding lookahead",
- yytoken, &yylval, scanner);
+ yytoken, &yylval, &yylloc, scanner);
}
/* Do not reclaim the symbols of the rule which action triggered
this YYABORT or YYACCEPT. */
while (yyssp != yyss)
{
yydestruct ("Cleanup: popping",
- yystos[*yyssp], yyvsp, scanner);
+ yystos[*yyssp], yyvsp, yylsp, scanner);
YYPOPSTACK (1);
}
#ifndef yyoverflow
-/* A Bison parser, made by GNU Bison 2.6.2. */
+/* A Bison parser, made by GNU Bison 2.7.12-4996. */
/* Bison interface for Yacc-like parsers in C
- Copyright (C) 1984, 1989-1990, 2000-2012 Free Software Foundation, Inc.
+ Copyright (C) 1984, 1989-1990, 2000-2013 Free Software Foundation, Inc.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
This special exception was added by the Free Software Foundation in
version 2.2 of Bison. */
-#ifndef _GMX_SEL_YY_PARSER_H
-# define _GMX_SEL_YY_PARSER_H
+#ifndef YY__GMX_SEL_YY_PARSER_H_INCLUDED
+# define YY__GMX_SEL_YY_PARSER_H_INCLUDED
/* Enabling traces. */
#ifndef YYDEBUG
# define YYDEBUG 1
extern int _gmx_sel_yydebug;
#endif
/* "%code requires" blocks. */
-/* Line 2049 of yacc.c */
+/* Line 2053 of yacc.c */
#line 1 "parser.y"
/*
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/* Line 2049 of yacc.c */
-#line 73 "parser.y"
+/* Line 2053 of yacc.c */
+#line 76 "parser.y"
#include "parsetree.h"
#include "selelem.h"
+#define YYLTYPE ::gmx::SelectionLocation
-/* Line 2049 of yacc.c */
-#line 90 "parser.h"
+
+/* Line 2053 of yacc.c */
+#line 92 "parser.h"
/* Tokens. */
#ifndef YYTOKENTYPE
#if ! defined YYSTYPE && ! defined YYSTYPE_IS_DECLARED
typedef union YYSTYPE
{
-/* Line 2049 of yacc.c */
-#line 78 "parser.y"
+/* Line 2053 of yacc.c */
+#line 83 "parser.y"
int i;
real r;
gmx::SelectionParserParameterListPointer *plist;
-/* Line 2049 of yacc.c */
-#line 154 "parser.h"
+/* Line 2053 of yacc.c */
+#line 156 "parser.h"
} YYSTYPE;
# define YYSTYPE_IS_TRIVIAL 1
# define yystype YYSTYPE /* obsolescent; will be withdrawn */
# define YYSTYPE_IS_DECLARED 1
#endif
+#if ! defined YYLTYPE && ! defined YYLTYPE_IS_DECLARED
+typedef struct YYLTYPE
+{
+ int first_line;
+ int first_column;
+ int last_line;
+ int last_column;
+} YYLTYPE;
+# define yyltype YYLTYPE /* obsolescent; will be withdrawn */
+# define YYLTYPE_IS_DECLARED 1
+# define YYLTYPE_IS_TRIVIAL 1
+#endif
+
#ifndef YYPUSH_MORE_DEFINED
# define YYPUSH_MORE_DEFINED
typedef struct _gmx_sel_yypstate _gmx_sel_yypstate;
#if defined __STDC__ || defined __cplusplus
-int _gmx_sel_yypush_parse (_gmx_sel_yypstate *ps, int pushed_char, YYSTYPE const *pushed_val, void *scanner);
+int _gmx_sel_yypush_parse (_gmx_sel_yypstate *ps, int pushed_char, YYSTYPE const *pushed_val, YYLTYPE *pushed_loc, void *scanner);
#else
int _gmx_sel_yypush_parse ();
#endif
void _gmx_sel_yypstate_delete ();
#endif
-#endif /* !_GMX_SEL_YY_PARSER_H */
+#endif /* !YY__GMX_SEL_YY_PARSER_H_INCLUDED */
---- parser.cpp 2014-08-11 22:24:31.000000000 +0200
-+++ parser.cpp 2014-08-11 22:24:40.000000000 +0200
-@@ -963,7 +963,7 @@
+--- parser.cpp 2014-11-03 06:56:28.000000000 +0200
++++ parser.cpp 2014-11-03 06:57:35.000000000 +0200
+@@ -470,7 +470,7 @@
+
+
+ #if (! defined yyoverflow \
+- && (! defined __cplusplus \
++ && (! defined __cplusplus || defined GMX_YYFORCE_C_STACK_EXTENSION \
+ || (defined YYLTYPE_IS_TRIVIAL && YYLTYPE_IS_TRIVIAL \
+ && defined YYSTYPE_IS_TRIVIAL && YYSTYPE_IS_TRIVIAL)))
+
+@@ -1076,7 +1076,7 @@
void *scanner;
#endif
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-%{
+%code top {
/*! \internal \file parser.cpp
* \brief Generated (from parser.y by Bison) parser for the selection language.
*
*
* \ingroup module_selection
*/
-#include "gromacs/utility/scoped_ptr_sfree.h"
+#include "gmxpre.h"
+}
+%{
+#include "gromacs/utility/scoped_cptr.h"
#include "parser_internal.h"
-using gmx::scoped_ptr_sfree;
+using gmx::scoped_guard_sfree;
using gmx::SelectionParserValue;
using gmx::SelectionParserValueList;
using gmx::SelectionParserValueListPointer;
%code requires{
#include "parsetree.h"
#include "selelem.h"
+
+#define YYLTYPE ::gmx::SelectionLocation
}
%union{
%debug
%pure-parser
%define api.push-pull push
+%locations
%name-prefix="_gmx_sel_yy"
%parse-param { void *scanner }
{
BEGIN_ACTION;
set_empty($$);
- END_ACTION;
+ END_ACTION_TOPLEVEL;
}
| commands command
{
set($$, _gmx_sel_append_selection(get($2), get($1), scanner));
if (_gmx_sel_parser_should_finish(scanner))
YYACCEPT;
- END_ACTION;
+ END_ACTION_TOPLEVEL;
}
;
| error CMD_SEP
{
BEGIN_ACTION;
- _gmx_selparser_error(scanner, "invalid selection '%s'",
- _gmx_sel_lexer_pselstr(scanner));
_gmx_sel_lexer_clear_method_stack(scanner);
- if (_gmx_sel_is_lexer_interactive(scanner))
+ if (_gmx_selparser_handle_error(scanner))
{
- _gmx_sel_lexer_clear_pselstr(scanner);
yyerrok;
}
else
{
YYABORT;
}
+ _gmx_sel_lexer_clear_pselstr(scanner);
set_empty($$);
- END_ACTION;
+ END_ACTION_TOPLEVEL;
}
;
| string
{
BEGIN_ACTION;
- scoped_ptr_sfree nameGuard($1);
+ scoped_guard_sfree nameGuard($1);
SelectionTreeElementPointer s
= _gmx_sel_init_group_by_name($1, scanner);
SelectionTreeElementPointer p
set($$, _gmx_sel_init_selection(NULL, get($1), scanner));
END_ACTION;
}
- | string selection
+ | STR selection
{
BEGIN_ACTION;
- scoped_ptr_sfree nameGuard($1);
+ scoped_guard_sfree nameGuard($1);
set($$, _gmx_sel_init_selection($1, get($2), scanner));
END_ACTION;
}
| IDENTIFIER '=' sel_expr
{
BEGIN_ACTION;
- scoped_ptr_sfree nameGuard($1);
+ scoped_guard_sfree nameGuard($1);
set($$, _gmx_sel_assign_variable($1, get($3), scanner));
END_ACTION;
}
| IDENTIFIER '=' num_expr
{
BEGIN_ACTION;
- scoped_ptr_sfree nameGuard($1);
+ scoped_guard_sfree nameGuard($1);
set($$, _gmx_sel_assign_variable($1, get($3), scanner));
END_ACTION;
}
| IDENTIFIER '=' pos_expr
{
BEGIN_ACTION;
- scoped_ptr_sfree nameGuard($1);
+ scoped_guard_sfree nameGuard($1);
set($$, _gmx_sel_assign_variable($1, get($3), scanner));
END_ACTION;
}
BEGIN_ACTION;
SelectionTreeElementPointer arg(get($2));
SelectionTreeElementPointer sel(
- new SelectionTreeElement(SEL_BOOLEAN));
+ new SelectionTreeElement(SEL_BOOLEAN, @$));
sel->u.boolt = BOOL_NOT;
sel->child = arg;
set($$, sel);
BEGIN_ACTION;
SelectionTreeElementPointer arg1(get($1)), arg2(get($3));
SelectionTreeElementPointer sel(
- new SelectionTreeElement(SEL_BOOLEAN));
+ new SelectionTreeElement(SEL_BOOLEAN, @$));
sel->u.boolt = BOOL_AND;
sel->child = arg1; sel->child->next = arg2;
set($$, sel);
BEGIN_ACTION;
SelectionTreeElementPointer arg1(get($1)), arg2(get($3));
SelectionTreeElementPointer sel(
- new SelectionTreeElement(SEL_BOOLEAN));
+ new SelectionTreeElement(SEL_BOOLEAN, @$));
sel->u.boolt = BOOL_OR;
sel->child = arg1; sel->child->next = arg2;
set($$, sel);
sel_expr: num_expr CMP_OP num_expr
{
BEGIN_ACTION;
- scoped_ptr_sfree opGuard($2);
+ scoped_guard_sfree opGuard($2);
set($$, _gmx_sel_init_comparison(get($1), get($3), $2, scanner));
CHECK_SEL($$);
END_ACTION;
sel_expr: GROUP string
{
BEGIN_ACTION;
- scoped_ptr_sfree nameGuard($2);
+ scoped_guard_sfree nameGuard($2);
set($$, _gmx_sel_init_group_by_name($2, scanner));
END_ACTION;
}
sel_expr: pos_mod KEYWORD_GROUP
{
BEGIN_ACTION;
- scoped_ptr_sfree posmodGuard($1);
+ scoped_guard_sfree posmodGuard($1);
set($$, _gmx_sel_init_keyword($2, SelectionParserValueListPointer(), $1, scanner));
CHECK_SEL($$);
END_ACTION;
| pos_mod KEYWORD_STR basic_value_list
{
BEGIN_ACTION;
- scoped_ptr_sfree posmodGuard($1);
+ scoped_guard_sfree posmodGuard($1);
set($$, _gmx_sel_init_keyword_strmatch($2, gmx::eStringMatchType_Auto, get($3), $1, scanner));
CHECK_SEL($$);
END_ACTION;
| pos_mod KEYWORD_STR str_match_type basic_value_list
{
BEGIN_ACTION;
- scoped_ptr_sfree posmodGuard($1);
+ scoped_guard_sfree posmodGuard($1);
set($$, _gmx_sel_init_keyword_strmatch($2, $3, get($4), $1, scanner));
CHECK_SEL($$);
END_ACTION;
| pos_mod KEYWORD_NUMERIC basic_value_list
{
BEGIN_ACTION;
- scoped_ptr_sfree posmodGuard($1);
+ scoped_guard_sfree posmodGuard($1);
set($$, _gmx_sel_init_keyword($2, get($3), $1, scanner));
CHECK_SEL($$);
END_ACTION;
sel_expr: pos_mod METHOD_GROUP method_params
{
BEGIN_ACTION;
- scoped_ptr_sfree posmodGuard($1);
+ scoped_guard_sfree posmodGuard($1);
set($$, _gmx_sel_init_method($2, get($3), $1, scanner));
CHECK_SEL($$);
END_ACTION;
{
BEGIN_ACTION;
SelectionTreeElementPointer sel(
- new SelectionTreeElement(SEL_CONST));
+ new SelectionTreeElement(SEL_CONST, @$));
_gmx_selelem_set_vtype(sel, INT_VALUE);
_gmx_selvalue_reserve(&sel->v, 1);
sel->v.u.i[0] = $1;
{
BEGIN_ACTION;
SelectionTreeElementPointer sel(
- new SelectionTreeElement(SEL_CONST));
+ new SelectionTreeElement(SEL_CONST, @$));
_gmx_selelem_set_vtype(sel, REAL_VALUE);
_gmx_selvalue_reserve(&sel->v, 1);
sel->v.u.r[0] = $1;
num_expr: pos_mod KEYWORD_NUMERIC %prec NUM_REDUCT
{
BEGIN_ACTION;
- scoped_ptr_sfree posmodGuard($1);
+ scoped_guard_sfree posmodGuard($1);
set($$, _gmx_sel_init_keyword($2, SelectionParserValueListPointer(), $1, scanner));
CHECK_SEL($$);
END_ACTION;
}
+ | pos_mod KEYWORD_NUMERIC OF pos_expr
+ {
+ BEGIN_ACTION;
+ scoped_guard_sfree posmodGuard($1);
+ set($$, _gmx_sel_init_keyword_of($2, get($4), $1, scanner));
+ CHECK_SEL($$);
+ END_ACTION;
+ }
| pos_mod METHOD_NUMERIC method_params
{
BEGIN_ACTION;
- scoped_ptr_sfree posmodGuard($1);
+ scoped_guard_sfree posmodGuard($1);
set($$, _gmx_sel_init_method($2, get($3), $1, scanner));
CHECK_SEL($$);
END_ACTION;
{
BEGIN_ACTION;
SelectionTreeElementPointer sel(
- new SelectionTreeElement(SEL_CONST));
+ new SelectionTreeElement(SEL_CONST, @$));
_gmx_selelem_set_vtype(sel, STR_VALUE);
_gmx_selvalue_reserve(&sel->v, 1);
sel->v.u.s[0] = $1;
| pos_mod KEYWORD_STR
{
BEGIN_ACTION;
- scoped_ptr_sfree posmodGuard($1);
+ scoped_guard_sfree posmodGuard($1);
set($$, _gmx_sel_init_keyword($2, SelectionParserValueListPointer(), $1, scanner));
CHECK_SEL($$);
END_ACTION;
pos_expr: '[' number ',' number ',' number ']'
{
BEGIN_ACTION;
- set($$, _gmx_sel_init_const_position($2, $4, $6));
+ set($$, _gmx_sel_init_const_position($2, $4, $6, scanner));
END_ACTION;
}
;
pos_expr: KEYWORD_POS OF sel_expr %prec PARAM_REDUCT
{
BEGIN_ACTION;
- scoped_ptr_sfree keywordGuard($1);
+ scoped_guard_sfree keywordGuard($1);
set($$, _gmx_sel_init_position(get($3), $1, scanner));
CHECK_SEL($$);
END_ACTION;
sel_expr: VARIABLE_GROUP
{
BEGIN_ACTION;
- set($$, _gmx_sel_init_variable_ref(get($1)));
+ set($$, _gmx_sel_init_variable_ref(get($1), scanner));
END_ACTION;
}
;
num_expr: VARIABLE_NUMERIC
{
BEGIN_ACTION;
- set($$, _gmx_sel_init_variable_ref(get($1)));
+ set($$, _gmx_sel_init_variable_ref(get($1), scanner));
END_ACTION;
}
;
pos_expr: VARIABLE_POS
{
BEGIN_ACTION;
- set($$, _gmx_sel_init_variable_ref(get($1)));
+ set($$, _gmx_sel_init_variable_ref(get($1), scanner));
END_ACTION;
}
;
PARAM value_list
{
BEGIN_ACTION;
- scoped_ptr_sfree nameGuard($1);
- set($$, SelectionParserParameter::create($1, get($2)));
+ scoped_guard_sfree nameGuard($1);
+ set($$, SelectionParserParameter::create($1, get($2), @$));
END_ACTION;
}
;
integer_number %prec PARAM_REDUCT
{
BEGIN_ACTION;
- set($$, SelectionParserValue::createInteger($1));
+ set($$, SelectionParserValue::createInteger($1, @$));
END_ACTION;
}
| real_number %prec PARAM_REDUCT
{
BEGIN_ACTION;
- set($$, SelectionParserValue::createReal($1));
+ set($$, SelectionParserValue::createReal($1, @$));
END_ACTION;
}
| string %prec PARAM_REDUCT
{
BEGIN_ACTION;
- scoped_ptr_sfree stringGuard($1);
- set($$, SelectionParserValue::createString($1));
+ scoped_guard_sfree stringGuard($1);
+ set($$, SelectionParserValue::createString($1, @$));
END_ACTION;
}
| value_item_range { $$ = $1; }
integer_number TO integer_number
{
BEGIN_ACTION;
- set($$, SelectionParserValue::createIntegerRange($1, $3));
+ set($$, SelectionParserValue::createIntegerRange($1, $3, @$));
END_ACTION;
}
| integer_number TO real_number
{
BEGIN_ACTION;
- set($$, SelectionParserValue::createRealRange($1, $3));
+ set($$, SelectionParserValue::createRealRange($1, $3, @$));
END_ACTION;
}
| real_number TO number
{
BEGIN_ACTION;
- set($$, SelectionParserValue::createRealRange($1, $3));
+ set($$, SelectionParserValue::createRealRange($1, $3, @$));
END_ACTION;
}
;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_SELECTION_PARSER_INTERNAL_H
#define GMX_SELECTION_PARSER_INTERNAL_H
+#include "config.h"
+
#include <exception>
+#include <boost/exception_ptr.hpp>
#include <boost/scoped_ptr.hpp>
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/stringutil.h"
#include "parsetree.h"
-#include "selelem.h"
-
#include "scanner.h"
+#include "selelem.h"
//! Error handler needed by Bison.
static void
-yyerror(yyscan_t scanner, char const *s)
+yyerror(YYLTYPE *location, yyscan_t scanner, char const *s)
{
- _gmx_selparser_error(scanner, "%s", s);
+ try
+ {
+ std::string context(_gmx_sel_lexer_get_text(scanner, *location));
+ gmx::InvalidInputError ex(s);
+ // TODO: Examine how to show better context information.
+ if (!context.empty())
+ {
+ context = gmx::formatString("Near '%s'", context.c_str());
+ ex.prependContext(context);
+ }
+ _gmx_sel_lexer_set_exception(scanner, boost::copy_exception(ex));
+ }
+ catch (const std::exception &)
+ {
+ _gmx_sel_lexer_set_exception(scanner, boost::current_exception());
+ }
}
+//! Logic for computing the location of the output of Bison reduction.
+#define YYLLOC_DEFAULT(Current, Rhs, N) \
+ do { \
+ if (N != 0) \
+ { \
+ (Current).startIndex = YYRHSLOC(Rhs, 1).startIndex; \
+ (Current).endIndex = YYRHSLOC(Rhs, N).endIndex; \
+ } \
+ else \
+ { \
+ (Current).startIndex = (Current).endIndex = \
+ YYRHSLOC(Rhs, 0).endIndex; \
+ } \
+ _gmx_sel_lexer_set_current_location(scanner, (Current)); \
+ } while (0)
+
+/*! \brief
+ * Custom macro to influence Bison behavior.
+ *
+ * This macro added to parser.cpp through our patch to force Bison to
+ * use C-style logic for stack reallocation even though we have provided
+ * YYLTYPE and are compiling the code in C++ (our YYLTYPE can safely be copied
+ * this way).
+ * An alternative would be to provide the whole reallocation logic through an
+ * undocumented yyoverflow() macro, but that is probably also more trouble than
+ * it is worth.
+ */
+#define GMX_YYFORCE_C_STACK_EXTENSION 1
+
/*! \name Exception handling macros for actions
*
* These macros should be used at the beginning and end of each semantic action
#define BEGIN_ACTION \
try {
//! Finishes an action that may throw exceptions.
-#define END_ACTION \
- } \
- catch (const std::exception &ex) \
- { \
- if (_gmx_selparser_handle_exception(scanner, ex)) { \
- YYERROR; } \
- else{ \
- YYABORT; } \
+#define END_ACTION \
+ } \
+ catch (std::exception &ex) \
+ { \
+ if (_gmx_selparser_handle_exception(scanner, &ex)) \
+ { \
+ YYERROR; \
+ } \
+ else \
+ { \
+ YYABORT; \
+ } \
+ }
+//! Finishes an action that may throw exceptions and does not support resuming.
+#define END_ACTION_TOPLEVEL \
+ } \
+ catch (const std::exception &) \
+ { \
+ _gmx_sel_lexer_set_exception(scanner, boost::current_exception()); \
+ YYABORT; \
}
//!\}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* Each element has exactly two children (one for unary negation elements),
* which are in the order given in the input.
*/
-#include <stdio.h>
+#include "gmxpre.h"
+
+#include "parsetree.h"
+
#include <stdarg.h>
+#include <stdio.h>
#include <boost/exception_ptr.hpp>
#include <boost/shared_ptr.hpp>
-#include "gromacs/fileio/futil.h"
-#include "gromacs/selection/poscalc.h"
#include "gromacs/selection/selection.h"
-#include "gromacs/selection/selmethod.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/file.h"
-#include "gromacs/utility/messagestringcollector.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "keywords.h"
-#include "parsetree.h"
+#include "poscalc.h"
+#include "scanner.h"
#include "selectioncollection-impl.h"
#include "selelem.h"
+#include "selmethod.h"
#include "symrec.h"
-#include "scanner.h"
-
+using gmx::SelectionLocation;
using gmx::SelectionParserValue;
using gmx::SelectionParserValueList;
using gmx::SelectionParserValueListPointer;
using gmx::SelectionTreeElement;
using gmx::SelectionTreeElementPointer;
-void
-_gmx_selparser_error(yyscan_t scanner, const char *fmt, ...)
+namespace
+{
+
+/*! \brief
+ * Formats context string for errors.
+ *
+ * The returned string is used as the context for errors reported during
+ * parsing.
+ */
+std::string
+formatCurrentErrorContext(yyscan_t scanner)
+{
+ return gmx::formatString(
+ "While parsing '%s'",
+ _gmx_sel_lexer_get_current_text(scanner).c_str());
+}
+
+} // namespace
+
+bool
+_gmx_selparser_handle_exception(yyscan_t scanner, std::exception *ex)
{
- gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
- // FIXME: Use an arbitrary length buffer.
- char buf[1024];
- va_list ap;
- va_start(ap, fmt);
- vsnprintf(buf, 1024, fmt, ap);
- va_end(ap);
- errors->append(buf);
+ try
+ {
+ bool canContinue = false;
+ gmx::GromacsException *gromacsException
+ = dynamic_cast<gmx::GromacsException *>(ex);
+ if (gromacsException != NULL)
+ {
+ gromacsException->prependContext(formatCurrentErrorContext(scanner));
+ canContinue = (dynamic_cast<gmx::UserInputError *>(ex) != NULL);
+ }
+ _gmx_sel_lexer_set_exception(scanner, boost::current_exception());
+ return canContinue;
+ }
+ catch (const std::exception &)
+ {
+ _gmx_sel_lexer_set_exception(scanner, boost::current_exception());
+ return false;
+ }
}
bool
-_gmx_selparser_handle_exception(yyscan_t scanner, const std::exception &ex)
+_gmx_selparser_handle_error(yyscan_t scanner)
{
- if (dynamic_cast<const gmx::UserInputError *>(&ex) != NULL)
+ std::string context(gmx::formatString("Invalid selection '%s'",
+ _gmx_sel_lexer_pselstr(scanner)));
+ // The only way to prepend context to the exception is to rethrow it.
+ try
+ {
+ _gmx_sel_lexer_rethrow_exception_if_occurred(scanner);
+ }
+ catch (gmx::UserInputError &ex)
{
- // TODO: Consider whether also the non-interactive parser should
- // postpone the exception such that the whole selection can be added as
- // context.
+ ex.prependContext(context);
if (_gmx_sel_is_lexer_interactive(scanner))
{
- // TODO: Handle exceptions that printing the message may produce.
gmx::formatExceptionMessageToFile(stderr, ex);
return true;
}
+ throw;
}
- _gmx_sel_lexer_set_exception(scanner, boost::current_exception());
- return false;
+ catch (gmx::GromacsException &ex)
+ {
+ ex.prependContext(context);
+ throw;
+ }
+ GMX_RELEASE_ASSERT(false, "All parsing errors should result in a captured exception");
+ return false; // Some compilers will not believe that the above never returns.
}
namespace gmx
* SelectionParserValue
*/
-SelectionParserValue::SelectionParserValue(e_selvalue_t type)
- : type(type)
+SelectionParserValue::SelectionParserValue(
+ e_selvalue_t type, const SelectionLocation &location)
+ : type(type), location_(location)
{
memset(&u, 0, sizeof(u));
}
SelectionParserValue::SelectionParserValue(
const SelectionTreeElementPointer &expr)
- : type(expr->v.type), expr(expr)
+ : type(expr->v.type), expr(expr), location_(expr->location())
{
memset(&u, 0, sizeof(u));
}
*/
SelectionParserParameter::SelectionParserParameter(
- const char *name,
- SelectionParserValueListPointer values)
- : name_(name != NULL ? name : ""),
+ const char *name,
+ SelectionParserValueListPointer values,
+ const SelectionLocation &location)
+ : name_(name != NULL ? name : ""), location_(location),
values_(values ? move(values)
: SelectionParserValueListPointer(new SelectionParserValueList))
{
* \param[in,out] pcc Position calculation collection to use.
* \param[in,out] sel Selection element to initialize.
* \param[in] rpost Reference position type to use (NULL = default).
- * \param[in] scanner Scanner data structure.
- * \returns 0 on success, a non-zero error code on error.
*/
static void
set_refpos_type(gmx::PositionCalculationCollection *pcc,
- const SelectionTreeElementPointer &sel,
- const char *rpost, yyscan_t scanner)
+ const SelectionTreeElementPointer &sel,
+ const char *rpost)
{
if (!rpost)
{
}
else
{
- // TODO: Should this be treated as a real error?
- _gmx_selparser_error(scanner, "modifier '%s' is not applicable for '%s'",
- rpost, sel->u.expr.method->name);
+ std::string message
+ = gmx::formatString("Position modifiers ('%s') is not applicable for '%s'",
+ rpost, sel->u.expr.method->name);
+ GMX_THROW(gmx::InvalidInputError(message));
}
}
gmx::SelectionTreeElementPointer
_gmx_sel_init_arithmetic(const gmx::SelectionTreeElementPointer &left,
const gmx::SelectionTreeElementPointer &right,
- char op, yyscan_t /* scanner */)
+ char op, yyscan_t scanner)
{
- SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_ARITHMETIC));
+ SelectionTreeElementPointer sel(
+ new SelectionTreeElement(
+ SEL_ARITHMETIC, _gmx_sel_lexer_get_current_location(scanner)));
sel->v.type = REAL_VALUE;
switch (op)
{
buf[0] = op;
buf[1] = 0;
sel->setName(buf);
- sel->u.arith.opstr = strdup(buf);
+ sel->u.arith.opstr = gmx_strdup(buf);
sel->child = left;
sel->child->next = right;
return sel;
const gmx::SelectionTreeElementPointer &right,
const char *cmpop, yyscan_t scanner)
{
- gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
- gmx::MessageStringContext context(errors, "In comparison initialization");
-
- SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_EXPRESSION));
+ SelectionTreeElementPointer sel(
+ new SelectionTreeElement(
+ SEL_EXPRESSION, _gmx_sel_lexer_get_current_location(scanner)));
_gmx_selelem_set_method(sel, &sm_compare, scanner);
SelectionParserParameterList params;
name = right->v.type == INT_VALUE ? "int2" : "real2";
params.push_back(SelectionParserParameter::createFromExpression(name, right));
// Create the parameter for the operator.
+ // TODO: Consider whether a proper location is needed.
+ SelectionLocation location(SelectionLocation::createEmpty());
params.push_back(
SelectionParserParameter::create(
- "op", SelectionParserValue::createString(cmpop)));
- if (!_gmx_sel_parse_params(params, sel->u.expr.method->nparams,
- sel->u.expr.method->param, sel, scanner))
- {
- return SelectionTreeElementPointer();
- }
+ "op", SelectionParserValue::createString(cmpop, location),
+ location));
+ _gmx_sel_parse_params(params, sel->u.expr.method->nparams,
+ sel->u.expr.method->param, sel, scanner);
return sel;
}
{
gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
- gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
- char buf[128];
- sprintf(buf, "In keyword '%s'", method->name);
- gmx::MessageStringContext context(errors, buf);
-
if (method->nparams > 0)
{
// TODO: Would assert be better?
"Keyword initialization called with non-keyword method"));
}
- SelectionTreeElementPointer root(new SelectionTreeElement(SEL_EXPRESSION));
+ const SelectionLocation &location = _gmx_sel_lexer_get_current_location(scanner);
+ // TODO: If there are arguments, the location would be better as just the
+ // location of the keyword itself.
+ SelectionTreeElementPointer root(new SelectionTreeElement(SEL_EXPRESSION, location));
SelectionTreeElementPointer child = root;
_gmx_selelem_set_method(child, method, scanner);
"Unknown type for keyword selection"));
}
/* Initialize the selection element */
- root.reset(new SelectionTreeElement(SEL_EXPRESSION));
+ root.reset(new SelectionTreeElement(SEL_EXPRESSION, location));
_gmx_selelem_set_method(root, kwmethod, scanner);
if (method->type == STR_VALUE)
{
SelectionParserParameterList params;
params.push_back(
SelectionParserParameter::createFromExpression(NULL, child));
- params.push_back(SelectionParserParameter::create(NULL, move(args)));
- if (!_gmx_sel_parse_params(params, root->u.expr.method->nparams,
- root->u.expr.method->param, root, scanner))
- {
- return SelectionTreeElementPointer();
- }
+ params.push_back(
+ SelectionParserParameter::create(NULL, move(args), location));
+ _gmx_sel_parse_params(params, root->u.expr.method->nparams,
+ root->u.expr.method->param, root, scanner);
}
- set_refpos_type(&sc->pcc, child, rpost, scanner);
+ set_refpos_type(&sc->pcc, child, rpost);
return root;
}
return init_keyword_internal(method, matchType, move(args), rpost, scanner);
}
+/*!
+ * \param[in] method Method to use for initialization.
+ * \param[in] group Selection in which the keyword should be evaluated.
+ * \param[in] rpost Reference position type to use (NULL = default).
+ * \param[in] scanner Scanner data structure.
+ * \returns The created selection element.
+ *
+ * This function handles the creation of a gmx::SelectionTreeElement object for
+ * expressions like "z of ...".
+ */
+SelectionTreeElementPointer
+_gmx_sel_init_keyword_of(gmx_ana_selmethod_t *method,
+ const gmx::SelectionTreeElementPointer &group,
+ const char *rpost, yyscan_t scanner)
+{
+ // TODO Provide an error if rpost is provided.
+ GMX_UNUSED_VALUE(rpost);
+ return _gmx_sel_init_keyword_evaluator(method, group, scanner);
+}
+
/*!
* \param[in] method Method to use for initialization.
* \param[in] params Pointer to the first parameter.
const char *rpost, yyscan_t scanner)
{
gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
- int rc;
-
- gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
- char buf[128];
- sprintf(buf, "In keyword '%s'", method->name);
- gmx::MessageStringContext context(errors, buf);
_gmx_sel_finish_method(scanner);
/* The "same" keyword needs some custom massaging of the parameters. */
- rc = _gmx_selelem_custom_init_same(&method, params, scanner);
- if (rc != 0)
- {
- return SelectionTreeElementPointer();
- }
- SelectionTreeElementPointer root(new SelectionTreeElement(SEL_EXPRESSION));
+ _gmx_selelem_custom_init_same(&method, params, scanner);
+ SelectionTreeElementPointer root(
+ new SelectionTreeElement(
+ SEL_EXPRESSION, _gmx_sel_lexer_get_current_location(scanner)));
_gmx_selelem_set_method(root, method, scanner);
/* Process the parameters */
- if (!_gmx_sel_parse_params(*params, root->u.expr.method->nparams,
- root->u.expr.method->param, root, scanner))
- {
- return SelectionTreeElementPointer();
- }
- set_refpos_type(&sc->pcc, root, rpost, scanner);
+ _gmx_sel_parse_params(*params, root->u.expr.method->nparams,
+ root->u.expr.method->param, root, scanner);
+ set_refpos_type(&sc->pcc, root, rpost);
return root;
}
const gmx::SelectionTreeElementPointer &sel,
yyscan_t scanner)
{
- gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
- char buf[128];
- sprintf(buf, "In keyword '%s'", method->name);
- gmx::MessageStringContext context(errors, buf);
-
_gmx_sel_finish_method(scanner);
- SelectionTreeElementPointer modifier(new SelectionTreeElement(SEL_MODIFIER));
+ SelectionTreeElementPointer modifier(
+ new SelectionTreeElement(
+ SEL_MODIFIER, _gmx_sel_lexer_get_current_location(scanner)));
_gmx_selelem_set_method(modifier, method, scanner);
SelectionTreeElementPointer root;
if (method->type == NO_VALUE)
root = modifier;
}
/* Process the parameters */
- if (!_gmx_sel_parse_params(*params, modifier->u.expr.method->nparams,
- modifier->u.expr.method->param, modifier, scanner))
- {
- return SelectionTreeElementPointer();
- }
+ _gmx_sel_parse_params(*params, modifier->u.expr.method->nparams,
+ modifier->u.expr.method->param, modifier, scanner);
return root;
}
_gmx_sel_init_position(const gmx::SelectionTreeElementPointer &expr,
const char *type, yyscan_t scanner)
{
- gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
- char buf[128];
- sprintf(buf, "In position evaluation");
- gmx::MessageStringContext context(errors, buf);
-
- SelectionTreeElementPointer root(new SelectionTreeElement(SEL_EXPRESSION));
+ SelectionTreeElementPointer root(
+ new SelectionTreeElement(
+ SEL_EXPRESSION, _gmx_sel_lexer_get_current_location(scanner)));
_gmx_selelem_set_method(root, &sm_keyword_pos, scanner);
_gmx_selelem_set_kwpos_type(root.get(), type);
/* Create the parameters for the parameter parser. */
SelectionParserParameterList params;
params.push_back(SelectionParserParameter::createFromExpression(NULL, expr));
/* Parse the parameters. */
- if (!_gmx_sel_parse_params(params, root->u.expr.method->nparams,
- root->u.expr.method->param, root, scanner))
- {
- return SelectionTreeElementPointer();
- }
+ _gmx_sel_parse_params(params, root->u.expr.method->nparams,
+ root->u.expr.method->param, root, scanner);
return root;
}
/*!
- * \param[in] x,y,z Coordinates for the position.
+ * \param[in] x,y,z Coordinates for the position.
+ * \param[in] scanner Scanner data structure.
* \returns The creates selection element.
*/
SelectionTreeElementPointer
-_gmx_sel_init_const_position(real x, real y, real z)
+_gmx_sel_init_const_position(real x, real y, real z, yyscan_t scanner)
{
rvec pos;
- SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_CONST));
+ SelectionTreeElementPointer sel(
+ new SelectionTreeElement(
+ SEL_CONST, _gmx_sel_lexer_get_current_location(scanner)));
_gmx_selelem_set_vtype(sel, POS_VALUE);
_gmx_selvalue_reserve(&sel->v, 1);
pos[XX] = x;
_gmx_sel_init_group_by_name(const char *name, yyscan_t scanner)
{
- SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_GROUPREF));
+ SelectionTreeElementPointer sel(
+ new SelectionTreeElement(
+ SEL_GROUPREF, _gmx_sel_lexer_get_current_location(scanner)));
_gmx_selelem_set_vtype(sel, GROUP_VALUE);
sel->setName(gmx::formatString("group \"%s\"", name));
- sel->u.gref.name = strdup(name);
+ sel->u.gref.name = gmx_strdup(name);
sel->u.gref.id = -1;
if (_gmx_sel_lexer_has_groups_set(scanner))
{
- gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
- sel->resolveIndexGroupReference(grps);
+ gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
+ gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
+ sel->resolveIndexGroupReference(grps, sc->gall.isize);
}
return sel;
SelectionTreeElementPointer
_gmx_sel_init_group_by_id(int id, yyscan_t scanner)
{
- SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_GROUPREF));
+ SelectionTreeElementPointer sel(
+ new SelectionTreeElement(
+ SEL_GROUPREF, _gmx_sel_lexer_get_current_location(scanner)));
_gmx_selelem_set_vtype(sel, GROUP_VALUE);
sel->setName(gmx::formatString("group %d", id));
sel->u.gref.name = NULL;
if (_gmx_sel_lexer_has_groups_set(scanner))
{
- gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
- sel->resolveIndexGroupReference(grps);
+ gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
+ gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
+ sel->resolveIndexGroupReference(grps, sc->gall.isize);
}
return sel;
}
/*!
- * \param[in,out] sel Value of the variable.
+ * \param[in,out] sel Value of the variable.
+ * \param scanner Scanner data structure.
* \returns The created selection element that references \p sel.
*
* The reference count of \p sel is updated, but no other modifications are
* made.
*/
SelectionTreeElementPointer
-_gmx_sel_init_variable_ref(const gmx::SelectionTreeElementPointer &sel)
+_gmx_sel_init_variable_ref(const gmx::SelectionTreeElementPointer &sel,
+ yyscan_t scanner)
{
SelectionTreeElementPointer ref;
}
else
{
- ref.reset(new SelectionTreeElement(SEL_SUBEXPRREF));
+ ref.reset(new SelectionTreeElement(
+ SEL_SUBEXPRREF, _gmx_sel_lexer_get_current_location(scanner)));
_gmx_selelem_set_vtype(ref, sel->v.type);
ref->setName(sel->name());
ref->child = sel;
"Each selection must evaluate to a position"));
}
- SelectionTreeElementPointer root(new SelectionTreeElement(SEL_ROOT));
+ SelectionTreeElementPointer root(
+ new SelectionTreeElement(
+ SEL_ROOT, _gmx_sel_lexer_get_current_location(scanner)));
root->child = sel;
if (name)
{
}
else
{
+ SelectionLocation location(_gmx_sel_lexer_get_current_location(scanner));
/* Create the root element */
- root.reset(new SelectionTreeElement(SEL_ROOT));
+ root.reset(new SelectionTreeElement(SEL_ROOT, location));
root->setName(name);
/* Create the subexpression element */
- root->child.reset(new SelectionTreeElement(SEL_SUBEXPR));
+ root->child.reset(new SelectionTreeElement(SEL_SUBEXPR, location));
root->child->setName(name);
_gmx_selelem_set_vtype(root->child, expr->v.type);
root->child->child = expr;
sc->symtab->addVariable(name, root->child);
}
srenew(sc->varstrs, sc->nvars + 1);
- sc->varstrs[sc->nvars] = strdup(pselstr);
+ sc->varstrs[sc->nvars] = gmx_strdup(pselstr);
++sc->nvars;
if (_gmx_sel_is_lexer_interactive(scanner))
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <list>
#include <string>
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/vec.h"
-
+#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
#include "gromacs/utility/uniqueptr.h"
#include "selelem.h"
/*! \brief
* Allocates and initializes a constant integer value.
*
- * \param[in] value Integer value to assign to the value.
+ * \param[in] value Integer value to assign to the value.
+ * \param[in] location Location of the value.
* \returns The newly created value.
*/
- static SelectionParserValue createInteger(int value)
+ static SelectionParserValue
+ createInteger(int value, const SelectionLocation &location)
{
- SelectionParserValue result(INT_VALUE);
+ SelectionParserValue result(INT_VALUE, location);
result.u.i.i1 = result.u.i.i2 = value;
return result;
}
/*! \brief
* Allocates and initializes a constant integer range value.
*
- * \param[in] from Beginning of the range to assign to the value.
- * \param[in] to End of the range to assign to the value.
+ * \param[in] from Beginning of the range to assign to the value.
+ * \param[in] to End of the range to assign to the value.
+ * \param[in] location Location of the value.
* \returns The newly created value.
*/
- static SelectionParserValue createIntegerRange(int from, int to)
+ static SelectionParserValue
+ createIntegerRange(int from, int to, const SelectionLocation &location)
{
- SelectionParserValue result(INT_VALUE);
+ SelectionParserValue result(INT_VALUE, location);
result.u.i.i1 = from;
result.u.i.i2 = to;
return result;
/*! \brief
* Allocates and initializes a constant floating-point value.
*
- * \param[in] value Floating-point value to assign to the value.
+ * \param[in] value Floating-point value to assign to the value.
+ * \param[in] location Location of the value.
* \returns The newly created value.
*/
- static SelectionParserValue createReal(real value)
+ static SelectionParserValue
+ createReal(real value, const SelectionLocation &location)
{
- SelectionParserValue result(REAL_VALUE);
+ SelectionParserValue result(REAL_VALUE, location);
result.u.r.r1 = result.u.r.r2 = value;
return result;
}
/*! \brief
* Allocates and initializes a constant floating-point range value.
*
- * \param[in] from Beginning of the range to assign to the value.
- * \param[in] to End of the range to assign to the value.
+ * \param[in] from Beginning of the range to assign to the value.
+ * \param[in] to End of the range to assign to the value.
+ * \param[in] location Location of the value.
* \returns The newly created value.
*/
- static SelectionParserValue createRealRange(real from, real to)
+ static SelectionParserValue
+ createRealRange(real from, real to, const SelectionLocation &location)
{
- SelectionParserValue result(REAL_VALUE);
+ SelectionParserValue result(REAL_VALUE, location);
result.u.r.r1 = from;
result.u.r.r2 = to;
return result;
/*! \brief
* Allocates and initializes a constant string value.
*
- * \param[in] value String to assign to the value.
+ * \param[in] value String to assign to the value.
+ * \param[in] location Location of the value.
* \returns The newly created value.
*/
- static SelectionParserValue createString(const char *value)
+ static SelectionParserValue
+ createString(const char *value, const SelectionLocation &location)
{
- SelectionParserValue result(STR_VALUE);
+ SelectionParserValue result(STR_VALUE, location);
result.str = value;
return result;
}
/*! \brief
* Allocates and initializes a constant position value.
*
- * \param[in] value Position vector to assign to the value.
+ * \param[in] value Position vector to assign to the value.
+ * \param[in] location Location of the value.
* \returns The newly created value.
*/
- static SelectionParserValue createPosition(rvec value)
+ static SelectionParserValue
+ createPosition(rvec value, const SelectionLocation &location)
{
- SelectionParserValue result(POS_VALUE);
+ SelectionParserValue result(POS_VALUE, location);
copy_rvec(value, result.u.x);
return result;
}
+ //! Returns the location of this value in the parsed selection text.
+ const SelectionLocation &location() const { return location_; }
//! Returns true if the value comes from expression evaluation.
bool hasExpressionValue() const { return static_cast<bool>(expr); }
/*! \brief
* Initializes a new value.
*
- * \param[in] type Type for the new value.
+ * \param[in] type Type for the new value.
+ * \param[in] location Location for the value.
*/
- explicit SelectionParserValue(e_selvalue_t type);
+ SelectionParserValue(e_selvalue_t type, const SelectionLocation &location);
/*! \brief
* Initializes a new expression value.
*
* \param[in] expr Expression for the value.
*/
explicit SelectionParserValue(const gmx::SelectionTreeElementPointer &expr);
+
+ //! Location of the value in the parsed text.
+ SelectionLocation location_;
};
class SelectionParserParameter;
/*! \brief
* Allocates and initializes a parsed method parameter.
*
- * \param[in] name Name for the new parameter (can be NULL).
- * \param[in] values List of values for the parameter.
+ * \param[in] name Name for the new parameter (can be NULL).
+ * \param[in] values List of values for the parameter.
+ * \param[in] location Location of the parameter.
* \returns Pointer to the newly allocated parameter.
* \throws std::bad_alloc if out of memory.
*/
static SelectionParserParameter
- create(const char *name, SelectionParserValueListPointer values)
+ create(const char *name, SelectionParserValueListPointer values,
+ const SelectionLocation &location)
{
- return SelectionParserParameter(name, move(values));
+ return SelectionParserParameter(name, move(values), location);
}
- //! \copydoc create(const char *, SelectionParserValueListPointer)
+ //! \copydoc create(const char *, SelectionParserValueListPointer, const SelectionLocation &)
static SelectionParserParameter
- create(const std::string &name, SelectionParserValueListPointer values)
+ create(const std::string &name, SelectionParserValueListPointer values,
+ const SelectionLocation &location)
{
- return SelectionParserParameter(name.c_str(), move(values));
+ return SelectionParserParameter(name.c_str(), move(values), location);
}
/*! \brief
* Allocates and initializes a parsed method parameter.
*
- * \param[in] name Name for the new parameter (can be NULL).
- * \param[in] value Value for the parameter.
+ * \param[in] name Name for the new parameter (can be NULL).
+ * \param[in] value Value for the parameter.
+ * \param[in] location Location of the parameter.
* \returns Pointer to the newly allocated parameter.
* \throws std::bad_alloc if out of memory.
*
* is necessary.
*/
static SelectionParserParameter
- create(const char *name, const SelectionParserValue &value)
+ create(const char *name, const SelectionParserValue &value,
+ const SelectionLocation &location)
{
- return create(name, SelectionParserValue::createList(value));
+ return create(name, SelectionParserValue::createList(value), location);
}
/*! \brief
* Allocates and initializes a parsed method parameter.
createFromExpression(const char *name,
const SelectionTreeElementPointer &expr)
{
- return create(name, SelectionParserValue::createExpr(expr));
+ return create(name, SelectionParserValue::createExpr(expr),
+ expr->location());
}
//! \copydoc createFromExpression(const char *, const SelectionTreeElementPointer &)
static SelectionParserParameter
createFromExpression(const std::string &name,
const SelectionTreeElementPointer &expr)
{
- return create(name.c_str(), SelectionParserValue::createExpr(expr));
+ return create(name.c_str(), SelectionParserValue::createExpr(expr),
+ expr->location());
}
+ //! Returns the name of the parameter (may be empty).
+ const std::string &name() const { return name_; }
+ //! Returns the location of this parameter in the parsed selection text.
+ const SelectionLocation &location() const { return location_; }
+ //! Returns the values for the parameter.
+ const SelectionParserValueList &values() const { return *values_; }
+
+ private:
/*! \brief
* Initializes a parsed method parameter.
*
- * \param[in] name Name for the new parameter (can be NULL).
- * \param[in] values List of values for the parameter.
+ * \param[in] name Name for the new parameter (can be NULL).
+ * \param[in] values List of values for the parameter.
+ * \param[in] location Location of the parameter.
* \throws std::bad_alloc if out of memory.
*/
- SelectionParserParameter(const char *name,
- SelectionParserValueListPointer values);
-
- //! Returns the name of the parameter (may be empty).
- const std::string &name() const { return name_; }
- //! Returns the values for the parameter.
- const SelectionParserValueList &values() const { return *values_; }
+ SelectionParserParameter(const char *name,
+ SelectionParserValueListPointer values,
+ const SelectionLocation &location);
//! Name of the parameter.
std::string name_;
+ //! Location of the parameter in the parsed text.
+ SelectionLocation location_;
+
+ // TODO: Make private, there is only one direct user.
+ public:
//! Values for this parameter.
SelectionParserValueListPointer values_;
};
} // namespace gmx
-/** Error reporting function for the selection parser. */
-void
-_gmx_selparser_error(void *scanner, const char *fmt, ...);
-/** Handle exceptions caught within the Bison code. */
+/*! \brief
+ * Handles exceptions caught within the Bison code.
+ *
+ * \retval `true` if the parser should attempt error recovery.
+ * \retval `false` if the parser should immediately abort.
+ *
+ * This function is called whenever an exception is caught within Bison
+ * actions. Since exceptions cannot propagate through Bison code, the
+ * exception is saved (potentially with some extra context information) so that
+ * the caller of the parser can rethrow the exception.
+ *
+ * If it is possible to recover from the exception, then the function returns
+ * `true`, and Bison enters error recovery state. At the end of the recovery,
+ * _gmx_selparser_handle_error() is called.
+ * If this function returns false, then Bison immediately aborts the parsing
+ * so that the caller can rethrow the exception.
+ */
bool
-_gmx_selparser_handle_exception(void *scanner, const std::exception &ex);
+_gmx_selparser_handle_exception(void *scanner, std::exception *ex);
+/*! \brief
+ * Handles errors in the selection parser.
+ *
+ * \returns `true` if parsing can continue with the next selection.
+ * \throws std::bad_alloc if out of memory during the error processing.
+ * \throws unspecified Can throw the stored exception if recovery from that
+ * exception is not possible.
+ *
+ * This function is called during error recovery, after Bison has discarded all
+ * the symbols for the erroneous selection.
+ * At this point, the full selection that caused the error is known, and can be
+ * added to the error context.
+ *
+ * For an interactive parser, this function returns `true` to let the parsing
+ * continue with the next selection, or to let the user enter the next
+ * selection, if it was possible to recover from the exception.
+ * For other cases, this will either rethrow the original exception with added
+ * context, or return `false` after adding the context to the error reporter.
+ * Any exceptions thrown from this method are again caught by Bison and result
+ * in termination of the parsing; the caller can then rethrow them.
+ */
+bool
+_gmx_selparser_handle_error(void *scanner);
/** Propagates the flags for selection elements. */
void
gmx::SelectionStringMatchType matchType,
gmx::SelectionParserValueListPointer args,
const char *rpost, void *scanner);
+/** Creates a gmx::SelectionTreeElement for "keyword of" expression. */
+gmx::SelectionTreeElementPointer
+_gmx_sel_init_keyword_of(struct gmx_ana_selmethod_t *method,
+ const gmx::SelectionTreeElementPointer &group,
+ const char *rpost, void *scanner);
/** Creates a gmx::SelectionTreeElement for a method expression from the parsed data. */
gmx::SelectionTreeElementPointer
_gmx_sel_init_method(struct gmx_ana_selmethod_t *method,
/** Creates a gmx::SelectionTreeElement for a constant position. */
gmx::SelectionTreeElementPointer
-_gmx_sel_init_const_position(real x, real y, real z);
+_gmx_sel_init_const_position(real x, real y, real z, void *scanner);
/** Creates a gmx::SelectionTreeElement for a index group expression using group name. */
gmx::SelectionTreeElementPointer
_gmx_sel_init_group_by_name(const char *name, void *scanner);
_gmx_sel_init_group_by_id(int id, void *scanner);
/** Creates a gmx::SelectionTreeElement for a variable reference */
gmx::SelectionTreeElementPointer
-_gmx_sel_init_variable_ref(const gmx::SelectionTreeElementPointer &sel);
+_gmx_sel_init_variable_ref(const gmx::SelectionTreeElementPointer &sel,
+ void *scanner);
/** Creates a root gmx::SelectionTreeElement for a selection. */
gmx::SelectionTreeElementPointer
/* In params.c */
/** Initializes an array of parameters based on input from the selection parser. */
-bool
+void
_gmx_sel_parse_params(const gmx::SelectionParserParameterList ¶ms,
int nparam, struct gmx_ana_selparam_t *param,
const gmx::SelectionTreeElementPointer &root,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
+#include "poscalc.h"
+
#include <string.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/vec.h"
+#include <algorithm>
-#include "gromacs/selection/centerofmass.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/math/vec.h"
#include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
#include "gromacs/selection/position.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
+#include "centerofmass.h"
+
namespace gmx
{
* already been calculated in \p sbase.
* The structure pointed by \p sbase is always a static calculation.
*/
- struct gmx_ana_poscalc_t *sbase;
+ gmx_ana_poscalc_t *sbase;
/** Next structure in the linked list of calculations. */
- struct gmx_ana_poscalc_t *next;
+ gmx_ana_poscalc_t *next;
/** Previous structure in the linked list of calculations. */
- struct gmx_ana_poscalc_t *prev;
+ gmx_ana_poscalc_t *prev;
/** Number of references to this structure. */
int refcount;
/** Collection this calculation belongs to. */
return impl_->createCalculation(type, cflags);
}
+int PositionCalculationCollection::getHighestRequiredAtomIndex() const
+{
+ int result = 0;
+ gmx_ana_poscalc_t *pc = impl_->first_;
+ while (pc)
+ {
+ // Calculations with a base just copy positions from the base, so
+ // those do not need to be considered in the check.
+ if (!pc->sbase)
+ {
+ gmx_ana_index_t g;
+ gmx_ana_index_set(&g, pc->b.nra, pc->b.a, 0);
+ result = std::max(result, gmx_ana_index_get_max_index(&g));
+ }
+ pc = pc->next;
+ }
+ return result;
+}
+
void PositionCalculationCollection::initEvaluation()
{
if (impl_->bInit_)
{
gmx_ana_indexmap_set_static(&p->m, &pc->b);
}
- gmx_ana_pos_reserve(p, p->m.mapb.nr, 0);
+ gmx_ana_pos_reserve(p, p->m.mapb.nr, -1);
if (pc->flags & POS_VELOCITIES)
{
gmx_ana_pos_reserve_velocities(p);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_SELECTION_POSCALC_H
#define GMX_SELECTION_POSCALC_H
-#include "../legacyheaders/typedefs.h"
+#include <cstdio>
-#include "../utility/common.h"
+#include "gromacs/utility/classhelpers.h"
/*! \name Flags for position calculation.
* \anchor poscalc_flags
} e_poscalc_t;
/** Data structure for position calculation. */
-typedef struct gmx_ana_poscalc_t gmx_ana_poscalc_t;
+struct gmx_ana_poscalc_t;
struct gmx_ana_index_t;
struct gmx_ana_pos_t;
+struct t_pbc;
+struct t_topology;
+struct t_trxframe;
namespace gmx
{
*/
gmx_ana_poscalc_t *createCalculationFromEnum(const char *post, int flags);
+ /*! \brief
+ * Computes the highest atom index required to evaluate this collection.
+ *
+ * Does not throw.
+ */
+ int getHighestRequiredAtomIndex() const;
+
/*! \brief
* Initializes evaluation for a position calculation collection.
*
gmx_ana_poscalc_set_flags(gmx_ana_poscalc_t *pc, int flags);
/** Sets the maximum possible input index group for position calculation. */
void
-gmx_ana_poscalc_set_maxindex(gmx_ana_poscalc_t *pc, struct gmx_ana_index_t *g);
+gmx_ana_poscalc_set_maxindex(gmx_ana_poscalc_t *pc, gmx_ana_index_t *g);
/** Initializes positions for position calculation output. */
void
-gmx_ana_poscalc_init_pos(gmx_ana_poscalc_t *pc, struct gmx_ana_pos_t *p);
+gmx_ana_poscalc_init_pos(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p);
/** Frees the memory allocated for position calculation. */
void
gmx_ana_poscalc_free(gmx_ana_poscalc_t *pc);
/** Updates a single COM/COG structure for a frame. */
void
gmx_ana_poscalc_update(gmx_ana_poscalc_t *pc,
- struct gmx_ana_pos_t *p, struct gmx_ana_index_t *g,
+ gmx_ana_pos_t *p, gmx_ana_index_t *g,
t_trxframe *fr, t_pbc *pbc);
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#include "gromacs/selection/position.h"
+#include "gmxpre.h"
-#include <string.h>
+#include "position.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vec.h"
+#include <string.h>
+#include "gromacs/math/vec.h"
#include "gromacs/selection/indexutil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
srenew(pos->f, n);
}
}
- if (isize > 0)
+ if (isize >= 0)
{
gmx_ana_indexmap_reserve(&pos->m, n, isize);
}
{
if (bFirst)
{
- gmx_ana_pos_reserve(dest, src->count(), 0);
+ gmx_ana_pos_reserve(dest, src->count(), -1);
if (src->v)
{
gmx_ana_pos_reserve_velocities(dest);
pos->m.mapb.nra = 0;
pos->m.b.nr = 0;
pos->m.b.nra = 0;
- /* This should not really be necessary, but do it for safety... */
+ /* Initializing these should not really be necessary, but do it for
+ * safety... */
pos->m.mapb.index[0] = 0;
pos->m.b.index[0] = 0;
/* This function should only be used to construct all the possible
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_SELECTION_POSITION_H
#define GMX_SELECTION_POSITION_H
-#include "../legacyheaders/types/simple.h"
-
-#include "indexutil.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/selection/indexutil.h"
/*! \brief
* Stores a set of positions together with their origins.
# We apply some trivial patches to the output to avoid warnings for PGI
# (and maybe other) compilers
-[[ $FORCE || parser.y -nt parser.cpp ]] && $BISON -t -o parser.cpp --defines=parser.h parser.y && patch -p0 < parser.patch && rm -f parser.cpp.orig
-[[ $FORCE || scanner.l -nt scanner.cpp ]] && $FLEX -o scanner.cpp scanner.l && patch -p0 < scanner.patch && rm -f scanner.cpp.orig
+[[ $FORCE || parser.y -nt parser.cpp ]] && \
+ echo Generating parser.cpp and parser.h... && \
+ $BISON -t -o parser.cpp --defines=parser.h parser.y && \
+ patch -p0 < parser.patch && \
+ rm -f parser.cpp.orig
+[[ $FORCE || scanner.l -nt scanner.cpp ]] && \
+ echo Generating scanner.cpp and scanner_flex.h... && \
+ $FLEX -o scanner.cpp scanner.l && \
+ patch -p0 < scanner.patch && \
+ rm -f scanner.cpp.orig
#line 2 "scanner.cpp"
#line 50 "scanner.l"
+#if !_gmx_sel_yyIN_HEADER
+#include "gmxpre.h"
+#endif
+
// Required before flex definitions, since it includes <stdint.h>.
// Otherwise, compilers not strictly C99 get macro redefinition errors,
// since flex defines INT32_MAX etc. in such cases.
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/utility/basedefinitions.h"
-#line 11 "scanner.cpp"
+#line 15 "scanner.cpp"
#define YY_INT_ALIGNED short int
* \ingroup module_selection
*/
-#line 56 "scanner.l"
+#line 60 "scanner.l"
#include "gromacs/utility/cstringutil.h"
#include "parser.h"
// This macro makes the actions a bit shorter, since nearly every action needs
// this call.
-#define ADD_TOKEN _gmx_sel_lexer_add_token(yytext, yyleng, state)
+#define ADD_TOKEN _gmx_sel_lexer_add_token(yylloc, yytext, yyleng, state)
// Set YY_BREAK to an empty value to avoid warnings (for the PGI compiler)
// when we have return statements followed by break. Instead, we add breaks
-#line 560 "scanner.cpp"
+#line 564 "scanner.cpp"
#define INITIAL 0
#define matchof 1
register int yy_act;
struct yyguts_t * yyg = (struct yyguts_t*)yyscanner;
-#line 94 "scanner.l"
+#line 98 "scanner.l"
gmx_sel_lexer_t *state = _gmx_sel_yyget_extra(yyscanner);
int retval;
/* Return a token if one is pending */
- retval = _gmx_sel_lexer_process_pending(yylval, state);
+ retval = _gmx_sel_lexer_process_pending(yylval, yylloc, state);
if (retval != 0)
{
return retval;
}
-#line 822 "scanner.cpp"
+#line 826 "scanner.cpp"
if ( !yyg->yy_init )
{
case 1:
YY_RULE_SETUP
-#line 127 "scanner.l"
+#line 131 "scanner.l"
break;
YY_BREAK
case 2:
YY_RULE_SETUP
-#line 128 "scanner.l"
+#line 132 "scanner.l"
{ yylval->i = strtol(yytext, NULL, 10); ADD_TOKEN; return TOK_INT; }
YY_BREAK
case 3:
YY_RULE_SETUP
-#line 129 "scanner.l"
+#line 133 "scanner.l"
{ yylval->r = strtod(yytext, NULL); ADD_TOKEN; return TOK_REAL; }
YY_BREAK
case 4:
YY_RULE_SETUP
-#line 130 "scanner.l"
+#line 134 "scanner.l"
{ yylval->str = gmx_strndup(yytext+1, yyleng-2); ADD_TOKEN; return STR; }
YY_BREAK
case 5:
/* rule 5 can match eol */
YY_RULE_SETUP
-#line 132 "scanner.l"
-{ _gmx_sel_lexer_add_token(" ", 1, state); break; }
+#line 136 "scanner.l"
+{ _gmx_sel_lexer_add_token(yylloc, " ", 1, state); break; }
YY_BREAK
case 6:
/* rule 6 can match eol */
YY_RULE_SETUP
-#line 133 "scanner.l"
+#line 137 "scanner.l"
{
if (yytext[0] == ';' || state->bInteractive)
{
}
else
{
- _gmx_sel_lexer_add_token(" ", 1, state);
+ _gmx_sel_lexer_add_token(yylloc, " ", 1, state);
}
break;
}
YY_BREAK
case YY_STATE_EOF(cmdstart):
-#line 147 "scanner.l"
+#line 151 "scanner.l"
{ state->bCmdStart = true; yyterminate(); }
YY_BREAK
case YY_STATE_EOF(INITIAL):
case YY_STATE_EOF(matchof):
case YY_STATE_EOF(matchbool):
-#line 148 "scanner.l"
+#line 152 "scanner.l"
{ state->bCmdStart = true; return CMD_SEP; }
YY_BREAK
case 7:
YY_RULE_SETUP
-#line 151 "scanner.l"
+#line 155 "scanner.l"
{ ADD_TOKEN; yylval->i = 1; return TOK_INT; }
YY_BREAK
case 8:
YY_RULE_SETUP
-#line 152 "scanner.l"
+#line 156 "scanner.l"
{ ADD_TOKEN; yylval->i = 0; return TOK_INT; }
YY_BREAK
case 9:
YY_RULE_SETUP
-#line 154 "scanner.l"
+#line 158 "scanner.l"
{ ADD_TOKEN; return GROUP; }
YY_BREAK
case 10:
YY_RULE_SETUP
-#line 155 "scanner.l"
+#line 159 "scanner.l"
{ ADD_TOKEN; return TO; }
YY_BREAK
case 11:
YY_RULE_SETUP
-#line 156 "scanner.l"
+#line 160 "scanner.l"
{ ADD_TOKEN; BEGIN(0); return OF; }
YY_BREAK
case 12:
YY_RULE_SETUP
-#line 157 "scanner.l"
+#line 161 "scanner.l"
{ ADD_TOKEN; return AND; }
YY_BREAK
case 13:
YY_RULE_SETUP
-#line 158 "scanner.l"
+#line 162 "scanner.l"
{ ADD_TOKEN; return OR; }
YY_BREAK
case 14:
YY_RULE_SETUP
-#line 159 "scanner.l"
+#line 163 "scanner.l"
{ ADD_TOKEN; return XOR; }
YY_BREAK
case 15:
YY_RULE_SETUP
-#line 160 "scanner.l"
+#line 164 "scanner.l"
{ ADD_TOKEN; return NOT; }
YY_BREAK
case 16:
YY_RULE_SETUP
-#line 161 "scanner.l"
+#line 165 "scanner.l"
{ yylval->str = gmx_strndup(yytext, yyleng); ADD_TOKEN; return CMP_OP; }
YY_BREAK
case 17:
YY_RULE_SETUP
-#line 163 "scanner.l"
-{ return _gmx_sel_lexer_process_identifier(yylval, yytext, yyleng, state); }
+#line 167 "scanner.l"
+{ return _gmx_sel_lexer_process_identifier(yylval, yylloc, yytext, yyleng, state); }
YY_BREAK
case 18:
/* rule 18 can match eol */
YY_RULE_SETUP
-#line 165 "scanner.l"
-{ _gmx_sel_lexer_add_token(" ", 1, state); break; }
+#line 169 "scanner.l"
+{ _gmx_sel_lexer_add_token(yylloc, " ", 1, state); break; }
YY_BREAK
case 19:
YY_RULE_SETUP
-#line 166 "scanner.l"
+#line 170 "scanner.l"
{ yylval->str = gmx_strndup(yytext, yyleng); ADD_TOKEN; return STR; }
YY_BREAK
case 20:
YY_RULE_SETUP
-#line 167 "scanner.l"
+#line 171 "scanner.l"
{ ADD_TOKEN; return yytext[0]; }
YY_BREAK
case 21:
YY_RULE_SETUP
-#line 168 "scanner.l"
+#line 172 "scanner.l"
YY_FATAL_ERROR( "flex scanner jammed" );
YY_BREAK
-#line 1033 "scanner.cpp"
+#line 1037 "scanner.cpp"
case YY_END_OF_BUFFER:
{
#define YYTABLES_NAME "yytables"
-#line 168 "scanner.l"
+#line 172 "scanner.l"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef SELECTION_SCANNER_H
#define SELECTION_SCANNER_H
+#include <string>
+
#include <boost/exception_ptr.hpp>
#include "parser.h"
-namespace gmx
-{
-class MessageStringCollector;
-}
-
struct gmx_ana_indexgrps_t;
struct gmx_ana_selcollection_t;
/** Frees memory allocated for the selection scanner. */
void
_gmx_sel_free_lexer(yyscan_t scanner);
-/** Sets the error reporter object for the selection scanner. */
-void
-_gmx_sel_set_lexer_error_reporter(yyscan_t scanner,
- gmx::MessageStringCollector *errors);
/** Stores an exception that is caught during parsing. */
void
_gmx_sel_lexer_set_exception(yyscan_t scanner,
/** Returns the selection collection for the scanner. */
struct gmx_ana_selcollection_t *
_gmx_sel_lexer_selcollection(yyscan_t scanner);
-/** Returns the error reporter for the scanner. */
-gmx::MessageStringCollector *
-_gmx_sel_lexer_error_reporter(yyscan_t scanner);
/** Returns true if the external index groups for the scanner are set. */
bool
_gmx_sel_lexer_has_groups_set(yyscan_t scanner);
/** Returns a pretty string of the current selection. */
const char *
_gmx_sel_lexer_pselstr(yyscan_t scanner);
+/*! \brief
+ * Sets the current parser context location.
+ *
+ * This location is set while Bison reductions are being processed, and
+ * identifies the location of the current rule/reduction.
+ */
+void
+_gmx_sel_lexer_set_current_location(yyscan_t scanner,
+ const gmx::SelectionLocation &location);
+/*! \brief
+ * Returns the current parser context location.
+ *
+ * This returns the location last set with
+ * _gmx_sel_lexer_set_current_location().
+ */
+const gmx::SelectionLocation &
+_gmx_sel_lexer_get_current_location(yyscan_t scanner);
+/*! \brief
+ * Returns the selection text for the current parser context.
+ *
+ * This returns the selection text that corresponds to the position set last
+ * with _gmx_sel_lexer_set_current_location().
+ */
+std::string
+_gmx_sel_lexer_get_current_text(yyscan_t scanner);
+/*! \brief
+ * Returns the selection text at the given location.
+ */
+std::string
+_gmx_sel_lexer_get_text(yyscan_t scanner,
+ const gmx::SelectionLocation &location);
/** Clears the current selection string. */
void
_gmx_sel_lexer_clear_pselstr(yyscan_t scanner);
_gmx_sel_set_lex_input_str(yyscan_t scanner, const char *str);
/** The scanning function generated by Flex. */
-#define YY_DECL int _gmx_sel_yylex(YYSTYPE *yylval, yyscan_t yyscanner)
+#define YY_DECL int _gmx_sel_yylex(YYSTYPE *yylval, YYLTYPE *yylloc, yyscan_t yyscanner)
YY_DECL;
#endif
* \ingroup module_selection
*/
%top{
+#if !_gmx_sel_yyIN_HEADER
+#include "gmxpre.h"
+#endif
+
// Required before flex definitions, since it includes <stdint.h>.
// Otherwise, compilers not strictly C99 get macro redefinition errors,
// since flex defines INT32_MAX etc. in such cases.
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/utility/basedefinitions.h"
}
%{
#include "gromacs/utility/cstringutil.h"
// This macro makes the actions a bit shorter, since nearly every action needs
// this call.
-#define ADD_TOKEN _gmx_sel_lexer_add_token(yytext, yyleng, state)
+#define ADD_TOKEN _gmx_sel_lexer_add_token(yylloc, yytext, yyleng, state)
// Set YY_BREAK to an empty value to avoid warnings (for the PGI compiler)
// when we have return statements followed by break. Instead, we add breaks
gmx_sel_lexer_t *state = yyget_extra(yyscanner);
int retval;
/* Return a token if one is pending */
- retval = _gmx_sel_lexer_process_pending(yylval, state);
+ retval = _gmx_sel_lexer_process_pending(yylval, yylloc, state);
if (retval != 0)
{
return retval;
{REAL} { yylval->r = strtod(yytext, NULL); ADD_TOKEN; return TOK_REAL; }
{STRING} { yylval->str = gmx_strndup(yytext+1, yyleng-2); ADD_TOKEN; return STR; }
-\\\n { _gmx_sel_lexer_add_token(" ", 1, state); break; }
+\\\n { _gmx_sel_lexer_add_token(yylloc, " ", 1, state); break; }
";"|\n {
if (yytext[0] == ';' || state->bInteractive)
{
}
else
{
- _gmx_sel_lexer_add_token(" ", 1, state);
+ _gmx_sel_lexer_add_token(yylloc, " ", 1, state);
}
break;
}
not|"!" { ADD_TOKEN; return NOT; }
{CMPOP} { yylval->str = gmx_strndup(yytext, yyleng); ADD_TOKEN; return CMP_OP; }
-{IDENTIFIER} { return _gmx_sel_lexer_process_identifier(yylval, yytext, yyleng, state); }
+{IDENTIFIER} { return _gmx_sel_lexer_process_identifier(yylval, yylloc, yytext, yyleng, state); }
-[[:space:]]+ { _gmx_sel_lexer_add_token(" ", 1, state); break; }
+[[:space:]]+ { _gmx_sel_lexer_add_token(yylloc, " ", 1, state); break; }
[_[:alnum:]]+ { yylval->str = gmx_strndup(yytext, yyleng); ADD_TOKEN; return STR; }
. { ADD_TOKEN; return yytext[0]; }
#line 6 "scanner_flex.h"
#line 50 "scanner.l"
+#if !_gmx_sel_yyIN_HEADER
+#include "gmxpre.h"
+#endif
+
// Required before flex definitions, since it includes <stdint.h>.
// Otherwise, compilers not strictly C99 get macro redefinition errors,
// since flex defines INT32_MAX etc. in such cases.
-#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/utility/basedefinitions.h"
-#line 15 "scanner_flex.h"
+#line 19 "scanner_flex.h"
#define YY_INT_ALIGNED short int
#undef YY_DECL
#endif
-#line 168 "scanner.l"
+#line 172 "scanner.l"
-#line 346 "scanner_flex.h"
+#line 350 "scanner_flex.h"
#undef _gmx_sel_yyIN_HEADER
#endif /* _gmx_sel_yyHEADER_H */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \ingroup module_selection
* \endcond
*/
+#include "gmxpre.h"
+
+#include "scanner_internal.h"
+
#include <stdlib.h>
#include <string.h>
#include <string>
-#include "gromacs/legacyheaders/typedefs.h"
-
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/messagestringcollector.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
+#include "parser.h"
#include "parsetree.h"
+#include "scanner.h"
#include "selectioncollection-impl.h"
#include "selelem.h"
#include "selmethod.h"
#include "symrec.h"
-#include "parser.h"
-#include "scanner.h"
-#include "scanner_internal.h"
-
/*! \brief
* Step in which the allocated memory for pretty-printed input is incremented.
*/
}
else
{
- yylval->str = param->name ? strdup(param->name) : NULL;
+ yylval->str = param->name ? gmx_strdup(param->name) : NULL;
}
return PARAM;
}
* Processes a selection method token.
*/
static int
-init_method_token(YYSTYPE *yylval, gmx_ana_selmethod_t *method, bool bPosMod,
- gmx_sel_lexer_t *state)
+init_method_token(YYSTYPE *yylval, YYLTYPE *yylloc,
+ const gmx::SelectionParserSymbol *symbol,
+ bool bPosMod, gmx_sel_lexer_t *state)
{
+ gmx_ana_selmethod_t *method = symbol->methodValue();
/* If the previous token was not KEYWORD_POS, return EMPTY_POSMOD
* before the actual method to work around a limitation in Bison. */
if (!bPosMod && method->type != POS_VALUE)
{
- state->nextmethod = method;
+ state->nextMethodSymbol = symbol;
+ _gmx_sel_lexer_add_token(yylloc, NULL, 0, state);
return EMPTY_POSMOD;
}
+ _gmx_sel_lexer_add_token(yylloc, symbol->name().c_str(), -1, state);
yylval->meth = method;
if (!(method->flags & SMETH_MODIFIER) && method->nparams == 0)
{
/* Keyword */
switch (method->type)
{
- case INT_VALUE: return KEYWORD_NUMERIC;
- case REAL_VALUE: return KEYWORD_NUMERIC;
+ case INT_VALUE:
+ case REAL_VALUE:
+ state->bMatchOf = true;
+ return KEYWORD_NUMERIC;
case STR_VALUE: return KEYWORD_STR;
case GROUP_VALUE: return KEYWORD_GROUP;
default:
}
int
-_gmx_sel_lexer_process_pending(YYSTYPE *yylval, gmx_sel_lexer_t *state)
+_gmx_sel_lexer_process_pending(YYSTYPE *yylval, YYLTYPE *yylloc,
+ gmx_sel_lexer_t *state)
{
if (state->nextparam)
{
if (state->neom > 0)
{
--state->neom;
+ _gmx_sel_lexer_add_token(yylloc, NULL, 0, state);
return END_OF_METHOD;
}
state->nextparam = NULL;
state->bBoolNo = false;
- _gmx_sel_lexer_add_token(param->name, -1, state);
+ _gmx_sel_lexer_add_token(yylloc, param->name, -1, state);
return init_param_token(yylval, param, bBoolNo);
}
if (state->prev_pos_kw > 0)
{
--state->prev_pos_kw;
}
- if (state->nextmethod)
+ if (state->nextMethodSymbol)
{
- gmx_ana_selmethod_t *method = state->nextmethod;
-
- state->nextmethod = NULL;
- return init_method_token(yylval, method, true, state);
+ const gmx::SelectionParserSymbol *symbol = state->nextMethodSymbol;
+ state->nextMethodSymbol = NULL;
+ return init_method_token(yylval, yylloc, symbol, true, state);
}
return 0;
}
int
-_gmx_sel_lexer_process_identifier(YYSTYPE *yylval, char *yytext, size_t yyleng,
+_gmx_sel_lexer_process_identifier(YYSTYPE *yylval, YYLTYPE *yylloc,
+ char *yytext, size_t yyleng,
gmx_sel_lexer_t *state)
{
/* Check if the identifier matches with a parameter name */
state->bBoolNo = bBoolNo;
return END_OF_METHOD;
}
- _gmx_sel_lexer_add_token(param->name, -1, state);
+ _gmx_sel_lexer_add_token(yylloc, param->name, -1, state);
return init_param_token(yylval, param, bBoolNo);
}
}
if (!symbol)
{
yylval->str = gmx_strndup(yytext, yyleng);
- _gmx_sel_lexer_add_token(yytext, yyleng, state);
+ _gmx_sel_lexer_add_token(yylloc, yytext, yyleng, state);
return IDENTIFIER;
}
- _gmx_sel_lexer_add_token(symbol->name().c_str(), -1, state);
gmx::SelectionParserSymbol::SymbolType symtype = symbol->type();
+ /* For method symbols, we need some extra processing. */
+ if (symtype == gmx::SelectionParserSymbol::MethodSymbol)
+ {
+ return init_method_token(yylval, yylloc, symbol, state->prev_pos_kw > 0, state);
+ }
+ _gmx_sel_lexer_add_token(yylloc, symbol->name().c_str(), -1, state);
/* Reserved symbols should have been caught earlier */
if (symtype == gmx::SelectionParserSymbol::ReservedSymbol)
{
}
/* This position should not be reached. */
}
- /* For method symbols, return the correct type */
- if (symtype == gmx::SelectionParserSymbol::MethodSymbol)
- {
- gmx_ana_selmethod_t *method = symbol->methodValue();
- return init_method_token(yylval, method, state->prev_pos_kw > 0, state);
- }
/* For position symbols, we need to return KEYWORD_POS, but we also need
* some additional handling. */
if (symtype == gmx::SelectionParserSymbol::PositionSymbol)
{
state->bMatchOf = true;
- yylval->str = strdup(symbol->name().c_str());
+ yylval->str = gmx_strdup(symbol->name().c_str());
state->prev_pos_kw = 2;
return KEYWORD_POS;
}
}
void
-_gmx_sel_lexer_add_token(const char *str, int len, gmx_sel_lexer_t *state)
+_gmx_sel_lexer_add_token(YYLTYPE *yylloc, const char *str, int len,
+ gmx_sel_lexer_t *state)
{
+ yylloc->startIndex = yylloc->endIndex = state->pslen;
/* Do nothing if the string is empty, or if it is a space and there is
* no other text yet, or if there already is a space. */
if (!str || len == 0 || strlen(str) == 0
strncpy(state->pselstr + state->pslen, str, len);
state->pslen += len;
state->pselstr[state->pslen] = 0;
+ yylloc->endIndex = state->pslen;
}
void
gmx_sel_lexer_t *state = new gmx_sel_lexer_t;
state->sc = sc;
- state->errors = NULL;
state->bGroups = bGroups;
state->grps = grps;
state->nexpsel = (maxnr > 0 ? static_cast<int>(sc->sel.size()) + maxnr : -1);
state->bInteractive = bInteractive;
snew(state->pselstr, STRSTORE_ALLOCSTEP);
- state->pselstr[0] = 0;
- state->pslen = 0;
- state->nalloc_psel = STRSTORE_ALLOCSTEP;
+ state->pselstr[0] = 0;
+ state->pslen = 0;
+ state->nalloc_psel = STRSTORE_ALLOCSTEP;
+ state->currentLocation.startIndex = 0;
+ state->currentLocation.endIndex = 0;
snew(state->mstack, 20);
- state->mstack_alloc = 20;
- state->msp = -1;
- state->neom = 0;
- state->nextparam = NULL;
- state->nextmethod = NULL;
- state->prev_pos_kw = 0;
- state->bBoolNo = false;
- state->bMatchOf = false;
- state->bMatchBool = false;
- state->bCmdStart = true;
- state->bBuffer = false;
+ state->mstack_alloc = 20;
+ state->msp = -1;
+ state->neom = 0;
+ state->nextparam = NULL;
+ state->nextMethodSymbol = NULL;
+ state->prev_pos_kw = 0;
+ state->bBoolNo = false;
+ state->bMatchOf = false;
+ state->bMatchBool = false;
+ state->bCmdStart = true;
+ state->bBuffer = false;
_gmx_sel_yyset_extra(state, *scannerp);
}
_gmx_sel_yylex_destroy(scanner);
}
-void
-_gmx_sel_set_lexer_error_reporter(yyscan_t scanner,
- gmx::MessageStringCollector *errors)
-{
- gmx_sel_lexer_t *state = _gmx_sel_yyget_extra(scanner);
- state->errors = errors;
-}
-
void
_gmx_sel_lexer_set_exception(yyscan_t scanner,
const boost::exception_ptr &ex)
return state->sc;
}
-gmx::MessageStringCollector *
-_gmx_sel_lexer_error_reporter(yyscan_t scanner)
-{
- gmx_sel_lexer_t *state = _gmx_sel_yyget_extra(scanner);
- GMX_RELEASE_ASSERT(state->errors != NULL, "Error reporter not set");
- return state->errors;
-}
-
bool
_gmx_sel_lexer_has_groups_set(yyscan_t scanner)
{
return state->pselstr;
}
+void
+_gmx_sel_lexer_set_current_location(yyscan_t scanner,
+ const gmx::SelectionLocation &location)
+{
+ gmx_sel_lexer_t *state = _gmx_sel_yyget_extra(scanner);
+ state->currentLocation = location;
+}
+
+const gmx::SelectionLocation &
+_gmx_sel_lexer_get_current_location(yyscan_t scanner)
+{
+ gmx_sel_lexer_t *state = _gmx_sel_yyget_extra(scanner);
+ return state->currentLocation;
+}
+
+std::string
+_gmx_sel_lexer_get_current_text(yyscan_t scanner)
+{
+ gmx_sel_lexer_t *state = _gmx_sel_yyget_extra(scanner);
+ return _gmx_sel_lexer_get_text(scanner, state->currentLocation);
+}
+
+std::string
+_gmx_sel_lexer_get_text(yyscan_t scanner,
+ const gmx::SelectionLocation &location)
+{
+ gmx_sel_lexer_t *state = _gmx_sel_yyget_extra(scanner);
+ const int startIndex = location.startIndex;
+ const int endIndex = location.endIndex;
+ if (startIndex >= endIndex)
+ {
+ return std::string();
+ }
+ return std::string(&state->pselstr[startIndex], endIndex - startIndex);
+}
+
void
_gmx_sel_lexer_clear_pselstr(yyscan_t scanner)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace gmx
{
-class MessageStringCollector;
+class SelectionParserSymbol;
}
/* These need to be defined before including scanner_flex.h, because it
{
//! Selection collection to put parsed selections in.
struct gmx_ana_selcollection_t *sc;
- //! Error reporter object.
- gmx::MessageStringCollector *errors;
//! Stores an exception that occurred during parsing.
boost::exception_ptr exception;
//! Whether external index groups have been set.
int pslen;
//! Number of bytes allocated for \a pselstr.
int nalloc_psel;
+ /*! \brief
+ * Position of the result of the current Bison action.
+ *
+ * This identifies the part of \a pselstr that corresponds to the
+ * subselection that is currently being reduced by Bison.
+ */
+ gmx::SelectionLocation currentLocation;
//! Stack of methods in which parameters should be looked up.
struct gmx_ana_selmethod_t **mstack;
*
* Only used when \p nextparam is NULL.
*/
- struct gmx_ana_selmethod_t *nextmethod;
+ const gmx::SelectionParserSymbol *nextMethodSymbol;
//! Used to track whether the previous token was a position modifier.
- int prev_pos_kw;
+ int prev_pos_kw;
//! Whether the 'of' keyword is acceptable as the next token.
bool bMatchOf;
* we cannot have them here as parameter names... */
/** Internal function for cases where several tokens need to be returned. */
int
-_gmx_sel_lexer_process_pending(YYSTYPE *, gmx_sel_lexer_t *state);
+_gmx_sel_lexer_process_pending(YYSTYPE *, YYLTYPE *, gmx_sel_lexer_t *state);
/** Internal function that processes identifier tokens. */
int
- _gmx_sel_lexer_process_identifier(YYSTYPE *, char *, size_t,
+ _gmx_sel_lexer_process_identifier(YYSTYPE *, YYLTYPE *, char *, size_t,
gmx_sel_lexer_t *state);
/** Internal function to add a token to the pretty-printed selection text. */
void
-_gmx_sel_lexer_add_token(const char *str, int len, gmx_sel_lexer_t *state);
+_gmx_sel_lexer_add_token(YYLTYPE *, const char *str, int len, gmx_sel_lexer_t *state);
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
#include "selection.h"
-#include "nbsearch.h"
-#include "position.h"
+#include <string>
+
+#include "gromacs/selection/nbsearch.h"
+#include "gromacs/selection/position.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/stringutil.h"
+
#include "selelem.h"
#include "selvalue.h"
while (child->type == SEL_MODIFIER)
{
child = child->child;
+ if (!child)
+ {
+ break;
+ }
if (child->type == SEL_SUBEXPRREF)
{
child = child->child;
}
}
}
- /* For variable references, we should skip the
- * SEL_SUBEXPRREF and SEL_SUBEXPR elements. */
- if (child->type == SEL_SUBEXPRREF)
+ if (child)
{
- child = child->child->child;
+ /* For variable references, we should skip the
+ * SEL_SUBEXPRREF and SEL_SUBEXPR elements. */
+ if (child->type == SEL_SUBEXPRREF)
+ {
+ child = child->child->child;
+ }
+ bDynamic_ = (child->child->flags & SEL_DYNAMIC);
}
- bDynamic_ = (child->child->flags & SEL_DYNAMIC);
}
initCoveredFraction(CFRAC_NONE);
}
Selection::operator AnalysisNeighborhoodPositions() const
{
- return AnalysisNeighborhoodPositions(data().rawPositions_.x,
- data().rawPositions_.count());
+ AnalysisNeighborhoodPositions pos(data().rawPositions_.x,
+ data().rawPositions_.count());
+ if (hasOnlyAtoms())
+ {
+ pos.exclusionIds(atomIndices());
+ }
+ return pos;
+}
+
+
+void
+Selection::setOriginalId(int i, int id)
+{
+ data().rawPositions_.m.mapid[i] = id;
+ data().rawPositions_.m.orgid[i] = id;
+}
+
+
+int
+Selection::initOriginalIdsToGroup(t_topology *top, e_index_t type)
+{
+ try
+ {
+ return gmx_ana_indexmap_init_orgid_group(&data().rawPositions_.m, top, type);
+ }
+ catch (const InconsistentInputError &)
+ {
+ GMX_ASSERT(type == INDEX_RES || type == INDEX_MOL,
+ "Expected that only grouping by residue/molecule would fail");
+ std::string message =
+ formatString("Cannot group selection '%s' into %s, because some "
+ "positions have atoms from more than one such group.",
+ name(), type == INDEX_MOL ? "molecules" : "residues");
+ GMX_THROW(InconsistentInputError(message));
+ }
}
SelectionPosition::operator AnalysisNeighborhoodPositions() const
{
- return AnalysisNeighborhoodPositions(sel_->rawPositions_.x,
- sel_->rawPositions_.count())
- .selectSingleFromArray(i_);
+ AnalysisNeighborhoodPositions pos(sel_->rawPositions_.x,
+ sel_->rawPositions_.count());
+ if (sel_->hasOnlyAtoms())
+ {
+ // TODO: Move atomIndices() such that it can be reused here as well.
+ pos.exclusionIds(constArrayRefFromArray<int>(sel_->rawPositions_.m.mapb.a,
+ sel_->rawPositions_.m.mapb.nra));
+ }
+ return pos.selectSingleFromArray(i_);
}
} // namespace gmx
#include <string>
#include <vector>
-#include "../legacyheaders/typedefs.h"
+#include "gromacs/selection/position.h"
+#include "gromacs/selection/selectionenums.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/gmxassert.h"
-#include "../utility/arrayref.h"
-#include "../utility/common.h"
-#include "../utility/gmxassert.h"
-
-#include "position.h"
-#include "indexutil.h"
-#include "selectionenums.h"
+struct t_topology;
namespace gmx
{
bool isDynamic() const { return bDynamic_; }
//! Returns the type of positions in the selection.
e_index_t type() const { return rawPositions_.m.type; }
+ //! Returns true if the selection only contains positions with a single atom each.
+ bool hasOnlyAtoms() const { return type() == INDEX_ATOM; }
//! Number of positions in the selection.
int posCount() const { return rawPositions_.count(); }
bool isDynamic() const { return data().isDynamic(); }
//! Returns the type of positions in the selection.
e_index_t type() const { return data().type(); }
+ //! Returns true if the selection only contains positions with a single atom each.
+ bool hasOnlyAtoms() const { return data().hasOnlyAtoms(); }
//! Total number of atoms in the selection.
int atomCount() const
*
* \see SelectionPosition::mappedId()
*/
- void setOriginalId(int i, int id) { data().rawPositions_.m.orgid[i] = id; }
+ void setOriginalId(int i, int id);
+ /*! \brief
+ * Inits the IDs for use with SelectionPosition::mappedId() for
+ * grouping.
+ *
+ * \param[in] top Topology information
+ * (can be NULL if not required for \p type).
+ * \param[in] type Type of groups to generate.
+ * \returns Number of groups that were present in the selection.
+ * \throws InconsistentInputError if the selection positions cannot
+ * be assigned to groups of the given type.
+ *
+ * If `type == INDEX_ATOM`, the IDs are initialized to 0, 1, 2, ...,
+ * and the return value is the number of positions.
+ * If `type == INDEX_ALL`, all the IDs are initialized to 0, and the
+ * return value is one.
+ * If `type == INDEX_RES` or `type == INDEX_MOL`, the first position
+ * will get ID 0, and all following positions that belong to the same
+ * residue/molecule will get the same ID. The first position that
+ * belongs to a different residue/molecule will get ID 1, and so on.
+ * If some position contains atoms from multiple residues/molecules,
+ * i.e., the mapping is ambiguous, an exception is thrown.
+ * The return value is the number of residues/molecules that are
+ * present in the selection positions.
+ *
+ * This method is useful if the calling code needs to group the
+ * selection, e.g., for computing aggregate properties for each residue
+ * or molecule. It can then use this method to initialize the
+ * appropriate grouping, use the return value to allocate a
+ * sufficiently sized buffer to store the aggregated values, and then
+ * use SelectionPosition::mappedId() to identify the location where to
+ * aggregate to.
+ *
+ * \see setOriginalId()
+ * \see SelectionPosition::mappedId()
+ */
+ int initOriginalIdsToGroup(t_topology *top, e_index_t type);
/*! \brief
* Prints out one-line description of the selection.
* Selection::setOriginalId() has not been called, the default values
* are dependent on type():
* - ::INDEX_ATOM: atom indices
- * - ::INDEX_RES: residue numbers
- * - ::INDEX_MOL: molecule numbers
+ * - ::INDEX_RES: residue indices
+ * - ::INDEX_MOL: molecule indices
* .
- * All the default values are zero-based
+ * All the default values are zero-based.
*/
int mappedId() const
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <boost/scoped_ptr.hpp>
-#include "../legacyheaders/typedefs.h"
+#include "gromacs/onlinehelp/helptopicinterface.h"
+#include "gromacs/selection/indexutil.h"
+#include "gromacs/selection/selection.h" // For gmx::SelectionList
+#include "gromacs/selection/selectioncollection.h"
+#include "gromacs/utility/uniqueptr.h"
-#include "../onlinehelp/helptopicinterface.h"
-#include "../utility/uniqueptr.h"
-#include "indexutil.h"
#include "poscalc.h"
-#include "selection.h" // For gmx::SelectionList
-#include "selectioncollection.h"
#include "selelem.h"
+struct gmx_sel_mempool_t;
+struct t_pbc;
+struct t_topology;
+struct t_trxframe;
+
namespace gmx
{
/** Topology for the collection. */
t_topology *top;
/** Index group that contains all the atoms. */
- struct gmx_ana_index_t gall;
+ gmx_ana_index_t gall;
/** Memory pool used for selection evaluation. */
- struct gmx_sel_mempool_t *mempool;
+ gmx_sel_mempool_t *mempool;
//! Parser symbol table.
boost::scoped_ptr<gmx::SelectionParserSymbolTable> symtab;
//! Root of help topic tree (NULL is no help yet requested).
std::string rpost_;
//! Default output position type for selections.
std::string spost_;
+ //! Largest atom index needed by the selections for evaluation.
+ int maxAtomIndex_;
/*! \brief
* Debugging level for the collection.
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
#include "selectioncollection.h"
#include <cctype>
#include <boost/shared_ptr.hpp>
+#include "gromacs/fileio/trx.h"
#include "gromacs/legacyheaders/oenv.h"
-#include "gromacs/legacyheaders/xvgr.h"
-
#include "gromacs/onlinehelp/helpmanager.h"
#include "gromacs/onlinehelp/helpwritercontext.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selhelp.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/file.h"
#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/messagestringcollector.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "parser.h"
#include "poscalc.h"
#include "scanner.h"
-#include "selection.h"
#include "selectioncollection-impl.h"
#include "selelem.h"
-#include "selhelp.h"
#include "selmethod.h"
#include "symrec.h"
*/
SelectionCollection::Impl::Impl()
- : debugLevel_(0), bExternalGroupsSet_(false), grps_(NULL)
+ : maxAtomIndex_(0), debugLevel_(0), bExternalGroupsSet_(false), grps_(NULL)
{
sc_.nvars = 0;
sc_.varstrs = NULL;
do
{
YYSTYPE value;
- int token = _gmx_sel_yylex(&value, scanner);
+ YYLTYPE location;
+ int token = _gmx_sel_yylex(&value, &location, scanner);
if (bInteractive)
{
if (token == 0)
}
prevToken = token;
}
- status = _gmx_sel_yypush_parse(parserState, token, &value, scanner);
+ status = _gmx_sel_yypush_parse(parserState, token, &value, &location, scanner);
}
while (status == YYPUSH_MORE);
_gmx_sel_lexer_rethrow_exception_if_occurred(scanner);
gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
- MessageStringCollector errors;
- _gmx_sel_set_lexer_error_reporter(scanner, &errors);
-
- size_t oldCount = sc->sel.size();
- bool bOk = false;
+ size_t oldCount = sc->sel.size();
{
boost::shared_ptr<_gmx_sel_yypstate> parserState(
_gmx_sel_yypstate_new(), &_gmx_sel_yypstate_delete);
// error/warning if some input was ignored.
goto early_termination;
}
- if (!errors.isEmpty() && bInteractive)
- {
- fprintf(stderr, "%s", errors.toString().c_str());
- errors.clear();
- }
}
- status = _gmx_sel_yypush_parse(parserState.get(), 0, NULL,
- scanner);
+ {
+ YYLTYPE location;
+ status = _gmx_sel_yypush_parse(parserState.get(), 0, NULL,
+ &location, scanner);
+ }
+ // TODO: Remove added selections from the collection if parsing failed?
_gmx_sel_lexer_rethrow_exception_if_occurred(scanner);
early_termination:
- bOk = (status == 0);
+ GMX_RELEASE_ASSERT(status == 0,
+ "Parser errors should have resulted in an exception");
}
else
{
int status = runParserLoop(scanner, parserState.get(), false);
- bOk = (status == 0);
+ GMX_RELEASE_ASSERT(status == 0,
+ "Parser errors should have resulted in an exception");
}
}
scannerGuard.reset();
int nr = sc->sel.size() - oldCount;
if (maxnr > 0 && nr != maxnr)
{
- bOk = false;
- errors.append("Too few selections provided");
- }
-
- // TODO: Remove added selections from the collection if parsing failed?
- if (!bOk || !errors.isEmpty())
- {
- GMX_ASSERT(!bOk && !errors.isEmpty(), "Inconsistent error reporting");
- GMX_THROW(InvalidInputError(errors.toString()));
+ std::string message
+ = formatString("Too few selections provided; got %d, expected %d",
+ nr, maxnr);
+ GMX_THROW(InvalidInputError(message));
}
SelectionList result;
return result;
}
+/*! \brief
+ * Checks that index groups have valid atom indices.
+ *
+ * \param[in] root Root of selection tree to process.
+ * \param[in] natoms Maximum number of atoms that the selections are set
+ * to evaluate.
+ * \param errors Object for reporting any error messages.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * Recursively checks the selection tree for index groups.
+ * Each found group is checked that it only contains atom indices that match
+ * the topology/maximum number of atoms set for the selection collection.
+ * Any issues are reported to \p errors.
+ */
+void checkExternalGroups(const SelectionTreeElementPointer &root,
+ int natoms,
+ ExceptionInitializer *errors)
+{
+ if (root->type == SEL_CONST && root->v.type == GROUP_VALUE)
+ {
+ try
+ {
+ root->checkIndexGroup(natoms);
+ }
+ catch (const UserInputError &)
+ {
+ errors->addCurrentExceptionAsNested();
+ }
+ }
+
+ SelectionTreeElementPointer child = root->child;
+ while (child)
+ {
+ checkExternalGroups(child, natoms, errors);
+ child = child->next;
+ }
+}
+
} // namespace
{
try
{
- root->resolveIndexGroupReference(grps_);
+ root->resolveIndexGroupReference(grps_, sc_.gall.isize);
}
catch (const UserInputError &)
{
{
natoms = top->atoms.nr;
}
+ if (impl_->bExternalGroupsSet_)
+ {
+ ExceptionInitializer errors("Invalid index group references encountered");
+ SelectionTreeElementPointer root = impl_->sc_.root;
+ while (root)
+ {
+ checkExternalGroups(root, natoms, &errors);
+ root = root->next;
+ }
+ if (errors.hasNestedExceptions())
+ {
+ GMX_THROW(InconsistentInputError(errors));
+ }
+ }
gmx_ana_selcollection_t *sc = &impl_->sc_;
// Do this first, as it allocates memory, while the others don't throw.
gmx_ana_index_init_simple(&sc->gall, natoms);
const internal::SelectionData &sel = **iter;
if (sel.hasFlag(efSelection_OnlyAtoms))
{
- if (sel.type() != INDEX_ATOM)
+ if (!sel.hasOnlyAtoms())
{
std::string message = formatString(
"Selection '%s' does not evaluate to individual atoms. "
void
SelectionCollection::evaluate(t_trxframe *fr, t_pbc *pbc)
{
+ if (fr->natoms <= impl_->maxAtomIndex_)
+ {
+ std::string message = formatString(
+ "Trajectory has less atoms (%d) than what is required for "
+ "evaluating the provided selections (atoms up to index %d "
+ "are required).", fr->natoms, impl_->maxAtomIndex_ + 1);
+ GMX_THROW(InconsistentInputError(message));
+ }
impl_->sc_.pcc.initFrame();
SelectionEvaluator evaluator;
}
}
-// static
-HelpTopicPointer
-SelectionCollection::createDefaultHelpTopic()
-{
- return createSelectionHelpTopic();
-}
-
} // namespace gmx
#ifndef GMX_SELECTION_SELECTIONCOLLECTION_H
#define GMX_SELECTION_SELECTIONCOLLECTION_H
+#include <cstdio>
+
#include <string>
#include <vector>
-#include "../legacyheaders/typedefs.h"
-
-#include "../onlinehelp/helptopicinterface.h"
-#include "../utility/common.h"
-#include "selection.h" // For gmx::SelectionList
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/selection/selection.h" // For gmx::SelectionList
+#include "gromacs/utility/classhelpers.h"
struct gmx_ana_indexgrps_t;
+struct t_pbc;
+struct t_topology;
+struct t_trxframe;
namespace gmx
{
class SelectionCollection
{
public:
- /*! \brief
- * Creates a help tree for selections.
- *
- * \throws std::bad_alloc if out of memory.
- * \returns Root topic of the created selection tree.
- */
- static HelpTopicPointer createDefaultHelpTopic();
-
/*! \brief
* Creates an empty selection collection.
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_SELECTION_SELECTIONENUMS_H
#define GMX_SELECTION_SELECTIONENUMS_H
-#include "../utility/flags.h"
+#include "gromacs/utility/flags.h"
/*! \brief
* Defines the type of covered fraction.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_SELECTION_SELECTIONFILEOPTION_H
#define GMX_SELECTION_SELECTIONFILEOPTION_H
-#include "../options/abstractoption.h"
+#include "gromacs/options/abstractoption.h"
namespace gmx
{
explicit SelectionFileOption(const char *name);
private:
- virtual AbstractOptionStoragePointer createStorage() const;
+ virtual AbstractOptionStorage *createStorage(
+ const OptionManagerContainer &managers) const;
};
/*! \libinternal \brief
* Does not throw.
*/
explicit SelectionFileOptionInfo(SelectionFileOptionStorage *option);
-
- //! \copydoc SelectionOptionInfo::setManager()
- void setManager(SelectionOptionManager *manager);
-
- private:
- SelectionFileOptionStorage &option();
- const SelectionFileOptionStorage &option() const;
};
} // namespace gmx
#ifndef GMX_SELECTION_SELECTIONFILEOPTIONSTORAGE_H
#define GMX_SELECTION_SELECTIONFILEOPTIONSTORAGE_H
-#include "../options/abstractoptionstorage.h"
-#include "selectionfileoption.h"
+#include "gromacs/options/abstractoptionstorage.h"
+#include "gromacs/selection/selectionfileoption.h"
namespace gmx
{
* Initializes the storage from option settings.
*
* \param[in] settings Storage settings.
+ * \param manager Manager for this object.
*/
- SelectionFileOptionStorage(const SelectionFileOption &settings);
+ SelectionFileOptionStorage(const SelectionFileOption &settings,
+ SelectionOptionManager *manager);
virtual OptionInfo &optionInfo() { return info_; }
virtual std::string typeString() const { return "file"; }
virtual int valueCount() const { return 0; }
virtual std::string formatValue(int /*i*/) const { return ""; }
- //! \copydoc SelectionFileOptionInfo::setManager()
- void setManager(SelectionOptionManager *manager)
- {
- manager_ = manager;
- }
-
private:
virtual void clearSet();
virtual void convertValue(const std::string &value);
virtual void processSet();
virtual void processAll() {}
- SelectionFileOptionInfo info_;
- SelectionOptionManager *manager_;
- bool bValueParsed_;
+ SelectionFileOptionInfo info_;
+ SelectionOptionManager &manager_;
+ bool bValueParsed_;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
#include "selectionoption.h"
-#include "selectionfileoption.h"
-#include "selectionoptionstorage.h"
-#include "selectionfileoptionstorage.h"
#include <string>
+#include "gromacs/options/optionmanagercontainer.h"
#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectionfileoption.h"
#include "gromacs/selection/selectionoptionmanager.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/messagestringcollector.h"
+#include "selectionfileoptionstorage.h"
+#include "selectionoptionstorage.h"
+
namespace gmx
{
* SelectionOptionStorage
*/
-SelectionOptionStorage::SelectionOptionStorage(const SelectionOption &settings)
+SelectionOptionStorage::SelectionOptionStorage(const SelectionOption &settings,
+ SelectionOptionManager *manager)
: MyBase(settings, OptionFlags() | efOption_NoDefaultValue
| efOption_DontCheckMinimumCount),
- info_(this), manager_(NULL), defaultText_(settings.defaultText_),
+ info_(this), manager_(*manager), defaultText_(settings.defaultText_),
selectionFlags_(settings.selectionFlags_)
{
+ GMX_RELEASE_ASSERT(manager != NULL,
+ "SelectionOptionManager must be added before SelectionOption");
GMX_RELEASE_ASSERT(!hasFlag(efOption_MultipleTimes),
"allowMultiple() is not supported for selection options");
-}
-
-
-void SelectionOptionStorage::setManager(SelectionOptionManager *manager)
-{
- GMX_RELEASE_ASSERT(manager_ == NULL || manager_ == manager,
- "Manager cannot be changed once set");
- if (manager_ == NULL)
- {
- manager->registerOption(this);
- manager_ = manager;
- }
+ manager_.registerOption(this);
}
void SelectionOptionStorage::convertValue(const std::string &value)
{
- GMX_RELEASE_ASSERT(manager_ != NULL, "Manager is not set");
-
- manager_->convertOptionValue(this, value, false);
+ manager_.convertOptionValue(this, value, false);
}
void SelectionOptionStorage::processSetValues(ValueList *values)
{
- GMX_RELEASE_ASSERT(manager_ != NULL, "Manager is not set");
-
if (values->size() == 0)
{
- manager_->requestOptionDelayedParsing(this);
+ manager_.requestOptionDelayedParsing(this);
}
else if (values->size() < static_cast<size_t>(minValueCount()))
{
void SelectionOptionStorage::processAll()
{
- GMX_RELEASE_ASSERT(manager_ != NULL, "Manager is not set");
if (!isSet() && !defaultText_.empty())
{
- manager_->convertOptionValue(this, defaultText_, true);
+ manager_.convertOptionValue(this, defaultText_, true);
}
if (isRequired() && !isSet())
{
- manager_->requestOptionDelayedParsing(this);
+ manager_.requestOptionDelayedParsing(this);
markAsSet();
}
}
void SelectionOptionStorage::setAllowedValueCount(int count)
{
// TODO: It should be possible to have strong exception safety here.
+ // TODO: Use ExceptionInitializer here.
MessageStringCollector errors;
errors.startContext("In option '" + name() + "'");
if (count >= 0)
return static_cast<const SelectionOptionStorage &>(OptionInfo::option());
}
-void SelectionOptionInfo::setManager(SelectionOptionManager *manager)
-{
- option().setManager(manager);
-}
-
void SelectionOptionInfo::setValueCount(int count)
{
option().setAllowedValueCount(count);
* SelectionOption
*/
-AbstractOptionStoragePointer SelectionOption::createStorage() const
+AbstractOptionStorage *
+SelectionOption::createStorage(const OptionManagerContainer &managers) const
{
- return AbstractOptionStoragePointer(new SelectionOptionStorage(*this));
+ return new SelectionOptionStorage(
+ *this, managers.get<SelectionOptionManager>());
}
* SelectionFileOptionStorage
*/
-SelectionFileOptionStorage::SelectionFileOptionStorage(const SelectionFileOption &settings)
+SelectionFileOptionStorage::SelectionFileOptionStorage(
+ const SelectionFileOption &settings, SelectionOptionManager *manager)
: AbstractOptionStorage(settings, OptionFlags() | efOption_MultipleTimes
| efOption_DontCheckMinimumCount),
- info_(this), manager_(NULL), bValueParsed_(false)
+ info_(this), manager_(*manager), bValueParsed_(false)
{
+ GMX_RELEASE_ASSERT(manager != NULL,
+ "SelectionOptionManager must be added before SelectionFileOption");
}
void SelectionFileOptionStorage::clearSet()
void SelectionFileOptionStorage::convertValue(const std::string &value)
{
- GMX_RELEASE_ASSERT(manager_ != NULL, "Manager is not set");
-
if (bValueParsed_)
{
GMX_THROW(InvalidInputError("More than one file name provided"));
}
bValueParsed_ = true;
// TODO: Should we throw an InvalidInputError if the file does not exist?
- manager_->parseRequestedFromFile(value);
+ manager_.parseRequestedFromFile(value);
}
void SelectionFileOptionStorage::processSet()
{
}
-SelectionFileOptionStorage &SelectionFileOptionInfo::option()
-{
- return static_cast<SelectionFileOptionStorage &>(OptionInfo::option());
-}
-
-const SelectionFileOptionStorage &SelectionFileOptionInfo::option() const
-{
- return static_cast<const SelectionFileOptionStorage &>(OptionInfo::option());
-}
-
-void SelectionFileOptionInfo::setManager(SelectionOptionManager *manager)
-{
- option().setManager(manager);
-}
-
/********************************************************************
* SelectionFileOption
setDescription("Provide selections from files");
}
-AbstractOptionStoragePointer SelectionFileOption::createStorage() const
+AbstractOptionStorage *
+SelectionFileOption::createStorage(const OptionManagerContainer &managers) const
{
- return AbstractOptionStoragePointer(new SelectionFileOptionStorage(*this));
+ return new SelectionFileOptionStorage(
+ *this, managers.get<SelectionOptionManager>());
}
} // namespace gmx
#ifndef GMX_SELECTION_SELECTIONOPTION_H
#define GMX_SELECTION_SELECTIONOPTION_H
-#include "../options/abstractoption.h"
-
-#include "selection.h"
-#include "selectionenums.h"
+#include "gromacs/options/abstractoption.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectionenums.h"
namespace gmx
{
*
* Public methods in this class do not throw.
*
+ * To use options of this type, SelectionOptionManager must first be added to
+ * the Options collection. For trajectory analysis tools, the framework takes
+ * care of this.
+ *
* \todo
* Support for specifying that an option accepts, e.g., two to four selections.
* Currently, only a fixed count or any number of selections is possible.
using MyBase::defaultValue;
using MyBase::defaultValueIfSet;
- virtual AbstractOptionStoragePointer createStorage() const;
+ virtual AbstractOptionStorage *createStorage(
+ const OptionManagerContainer &managers) const;
const char *defaultText_;
SelectionFlags selectionFlags_;
*/
explicit SelectionOptionInfo(SelectionOptionStorage *option);
- /*! \brief
- * Set manager for handling interaction with other options and the
- * selection collection.
- *
- * \param manager Selection manager to set.
- *
- * This must be called before the values are added.
- *
- * Typically it is called through setManagerForSelectionOptions(),
- * which recursively sets the manager for all selection options in
- * an Options object.
- *
- * Does not throw.
- */
- void setManager(SelectionOptionManager *manager);
-
/*! \brief
* Sets the number of selections allowed for the option.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
#include "selectionoptionmanager.h"
#include <cstdio>
-#include "gromacs/options/optionsvisitor.h"
#include "gromacs/selection/selection.h"
#include "gromacs/selection/selectioncollection.h"
-#include "gromacs/selection/selectionoption.h"
#include "gromacs/selection/selectionfileoption.h"
+#include "gromacs/selection/selectionoption.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/stringutil.h"
impl_->placeSelectionsInRequests(selections);
}
-/********************************************************************
- * Global functions
- */
-
-namespace
-{
-
-/*! \internal \brief
- * Visitor that sets the manager for each selection option.
- *
- * \ingroup module_selection
- */
-class SelectionOptionManagerSetter : public OptionsModifyingVisitor
-{
- public:
- //! Construct a visitor that sets given manager.
- explicit SelectionOptionManagerSetter(SelectionOptionManager *manager)
- : manager_(manager)
- {
- }
-
- void visitSubSection(Options *section)
- {
- OptionsModifyingIterator iterator(section);
- iterator.acceptSubSections(this);
- iterator.acceptOptions(this);
- }
-
- void visitOption(OptionInfo *option)
- {
- SelectionOptionInfo *selOption
- = option->toType<SelectionOptionInfo>();
- if (selOption != NULL)
- {
- selOption->setManager(manager_);
- }
- SelectionFileOptionInfo *selFileOption
- = option->toType<SelectionFileOptionInfo>();
- if (selFileOption != NULL)
- {
- selFileOption->setManager(manager_);
- }
- }
-
- private:
- SelectionOptionManager *manager_;
-};
-
-} // namespace
-
-void setManagerForSelectionOptions(Options *options,
- SelectionOptionManager *manager)
-{
- SelectionOptionManagerSetter(manager).visitSubSection(options);
-}
-
} // namespace gmx
#include <string>
-#include "../utility/common.h"
+#include "gromacs/options/options.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
* require actions outside options parsing.
* It also implements the coupling between SelectionOption and
* SelectionFileOption.
+ * It needs to be added using Options::addManager() before SelectionOption or
+ * SelectionFileOption options can be added to an Options collection.
*
* The main features of this class are:
* - convertOptionValue(), which is used to convert string values into
* parseRequestedFromStdin(), parseRequestedFromFile() or
* parseRequstedFromString().
*
- * \see setManagerForSelectionOptions()
- *
* \inpublicapi
* \ingroup module_selection
*/
-class SelectionOptionManager
+class SelectionOptionManager : public OptionManagerInterface
{
public:
/*! \brief
* \throws std::bad_alloc if out of memory.
*/
explicit SelectionOptionManager(SelectionCollection *selections);
- ~SelectionOptionManager();
+ virtual ~SelectionOptionManager();
/*! \brief
* Adds a selection option to be managed.
friend class SelectionOptionStorage;
};
-/*! \brief
- * Set manager for all selection options.
- *
- * Recursively sets the manager to \p manager for all selection options in
- * \p options.
- * Must be called before value assignment starts for \p options.
- *
- * Does not throw.
- *
- * \inpublicapi
- */
-void setManagerForSelectionOptions(Options *options,
- SelectionOptionManager *manager);
-
} // namespace gmx
#endif
#include <string>
-#include "../options/optionstoragetemplate.h"
-#include "selection.h"
-#include "selectionenums.h"
-#include "selectionoption.h"
+#include "gromacs/options/optionstoragetemplate.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectionenums.h"
+#include "gromacs/selection/selectionoption.h"
namespace gmx
{
* Initializes the storage from option settings.
*
* \param[in] settings Storage settings.
+ * \param manager Manager for this object.
*/
- SelectionOptionStorage(const SelectionOption &settings);
+ SelectionOptionStorage(const SelectionOption &settings,
+ SelectionOptionManager *manager);
virtual OptionInfo &optionInfo() { return info_; }
virtual std::string typeString() const { return "selection"; }
virtual std::string formatSingleValue(const Selection &value) const;
- //! \copydoc SelectionOptionInfo::setManager()
- void setManager(SelectionOptionManager *manager);
-
/*! \brief
* Adds selections to the storage.
*
virtual void processAll();
SelectionOptionInfo info_;
- SelectionOptionManager *manager_;
+ SelectionOptionManager &manager_;
std::string defaultText_;
SelectionFlags selectionFlags_;
};
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
+#include "selelem.h"
+
#include <cstring>
#include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
#include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
#include "keywords.h"
#include "mempool.h"
-#include "selelem.h"
+#include "poscalc.h"
#include "selmethod.h"
/*!
namespace gmx
{
-SelectionTreeElement::SelectionTreeElement(e_selelem_t type)
+SelectionTreeElement::SelectionTreeElement(e_selelem_t type,
+ const SelectionLocation &location)
+ : location_(location)
{
this->type = type;
this->flags = (type != SEL_ROOT) ? SEL_ALLOCVAL : 0;
break;
}
}
- if (v.nalloc > 0)
+ _gmx_selvalue_free(&v);
+ if (type == SEL_SUBEXPRREF && u.param != NULL)
{
- if (v.type == POS_VALUE)
- {
- delete [] v.u.p;
- }
- else
- {
- sfree(v.u.ptr);
- }
- }
- _gmx_selvalue_setstore(&v, NULL);
- if (type == SEL_SUBEXPRREF && u.param)
- {
- u.param->val.u.ptr = NULL;
+ // TODO: This is now called from two different locations.
+ // It is likely that one of them is unnecessary, but that requires
+ // extra analysis to clarify.
+ _gmx_selelem_free_param(u.param);
}
}
}
}
-void SelectionTreeElement::resolveIndexGroupReference(gmx_ana_indexgrps_t *grps)
+void SelectionTreeElement::resolveIndexGroupReference(
+ gmx_ana_indexgrps_t *grps, int natoms)
{
GMX_RELEASE_ASSERT(type == SEL_GROUPREF,
"Should only be called for index group reference elements");
gmx_ana_index_set(&u.cgrp, foundGroup.isize, foundGroup.index,
foundGroup.nalloc_index);
setName(foundName);
+
+ if (natoms > 0)
+ {
+ checkIndexGroup(natoms);
+ }
+}
+
+void SelectionTreeElement::checkIndexGroup(int natoms)
+{
+ GMX_RELEASE_ASSERT(type == SEL_CONST && v.type == GROUP_VALUE,
+ "Should only be called for index group elements");
+ if (!gmx_ana_index_check_range(&u.cgrp, natoms))
+ {
+ std::string message = formatString(
+ "Group '%s' cannot be used in selections, because it "
+ "contains negative atom indices and/or references atoms "
+ "not present (largest allowed atom index is %d).",
+ name().c_str(), natoms);
+ GMX_THROW(InconsistentInputError(message));
+ }
}
} // namespace gmx
}
}
-/*!
- * \param[in] method Method to free.
- * \param[in] mdata Method data to free.
- */
+void
+_gmx_selelem_free_param(gmx_ana_selparam_t *param)
+{
+ if (param->val.u.ptr != NULL)
+ {
+ if (param->val.type == GROUP_VALUE)
+ {
+ for (int i = 0; i < param->val.nr; ++i)
+ {
+ gmx_ana_index_deinit(¶m->val.u.g[i]);
+ }
+ }
+ _gmx_selvalue_free(¶m->val);
+ }
+}
+
void
_gmx_selelem_free_method(gmx_ana_selmethod_t *method, void *mdata)
{
* access them. */
if (method)
{
- int i, j;
-
/* Free the memory allocated for the parameters that are not managed
* by the selection method itself. */
- for (i = 0; i < method->nparams; ++i)
+ for (int i = 0; i < method->nparams; ++i)
{
- gmx_ana_selparam_t *param = &method->param[i];
-
- if (param->val.u.ptr)
- {
- if (param->val.type == GROUP_VALUE)
- {
- for (j = 0; j < param->val.nr; ++j)
- {
- gmx_ana_index_deinit(¶m->val.u.g[j]);
- }
- }
- else if (param->val.type == POS_VALUE)
- {
- if (param->val.nalloc > 0)
- {
- delete[] param->val.u.p;
- _gmx_selvalue_setstore(¶m->val, NULL);
- }
- }
-
- if (param->val.nalloc > 0)
- {
- sfree(param->val.u.ptr);
- }
- }
+ _gmx_selelem_free_param(&method->param[i]);
}
sfree(method->param);
sfree(method);
fprintf(fp, " eval=");
_gmx_sel_print_evalfunc_name(fp, sel.evaluate);
}
- if (!(sel.flags & SEL_ALLOCVAL))
+ if (sel.v.nalloc < 0)
{
fprintf(fp, " (ext)");
}
fprintf(fp, "\n");
}
}
+ else if (sel.type == SEL_SUBEXPRREF && sel.u.param != NULL)
+ {
+ fprintf(fp, "%*c param", level*2+1, ' ');
+ if (sel.u.param->name != NULL)
+ {
+ fprintf(fp, " \"%s\"", sel.u.param->name);
+ }
+ if (sel.u.param->val.nalloc < 0)
+ {
+ fprintf(fp, " (ext)");
+ }
+ else
+ {
+ fprintf(fp, " nalloc: %d", sel.u.param->val.nalloc);
+ }
+ fprintf(fp, "\n");
+ }
if (sel.cdata)
{
#include <boost/shared_ptr.hpp>
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/utility/common.h"
+#include "gromacs/selection/indexutil.h"
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/real.h"
-#include "indexutil.h"
#include "selvalue.h"
struct gmx_ana_poscalc_t;
class ExceptionInitializer;
+//! \cond internal
/*! \brief
* Function pointer for evaluating a gmx::SelectionTreeElement.
*/
typedef void (*sel_evalfunc)(struct gmx_sel_evaluate_t *data,
const SelectionTreeElementPointer &sel,
gmx_ana_index_t *g);
+//! \endcond
+
+/*! \internal
+ * \brief
+ * Stores the location of a selection element in the selection text.
+ *
+ * The location is stored as a range in the pretty-printed selection text
+ * (where whitespace has been sanitized), and can be used to extract that text
+ * for error messages and other diagnostic purposes.
+ * During parsing, the extraction is done with _gmx_sel_lexer_get_text().
+ *
+ * This needs to be a plain C struct for Bison to properly deal with it.
+ */
+struct SelectionLocation
+{
+ //! Returns an empty location.
+ static SelectionLocation createEmpty()
+ {
+ SelectionLocation empty = {0, 0};
+ return empty;
+ }
+
+ //! Start index of the string where this element has been parsed from.
+ int startIndex;
+ //! End index of the string where this element has been parsed from.
+ int endIndex;
+};
/*! \internal \brief
* Represents an element of a selection expression.
/*! \brief
* Allocates memory and performs common initialization.
*
- * \param[in] type Type of selection element to create.
+ * \param[in] type Type of selection element to create.
+ * \param[in] location Location of the element.
*
* \a type is set to \p type,
* \a v::type is set to \ref GROUP_VALUE for boolean and comparison
* is also set for \ref SEL_BOOLEAN elements).
* All the pointers are set to NULL.
*/
- explicit SelectionTreeElement(e_selelem_t type);
+ SelectionTreeElement(e_selelem_t type, const SelectionLocation &location);
~SelectionTreeElement();
//! Frees the memory allocated for the \a v union.
//! Returns the name of the element.
const std::string &name() const { return name_; }
+ //! Returns the location of the element.
+ const SelectionLocation &location() const { return location_; }
+
/*! \brief
* Sets the name of the element.
*
void checkUnsortedAtoms(bool bUnsortedAllowed,
ExceptionInitializer *errors) const;
/*! \brief
- * Resolved an unresolved reference to an index group.
+ * Resolves an unresolved reference to an index group.
*
- * \param[in] grps Index groups to use to resolve the reference.
+ * \param[in] grps Index groups to use to resolve the reference.
+ * \param[in] natoms Maximum number of atoms the selections can evaluate to
+ * (zero if the topology/atom count is not set yet).
* \throws std::bad_alloc if out of memory.
* \throws InconsistentInputError if the reference cannot be
* resolved.
*/
- void resolveIndexGroupReference(gmx_ana_indexgrps_t *grps);
+ void resolveIndexGroupReference(gmx_ana_indexgrps_t *grps, int natoms);
+ /*! \brief
+ * Checks that an index group has valid atom indices.
+ *
+ * \param[in] natoms Maximum number of atoms the selections can evaluate to.
+ * \throws std::bad_alloc if out of memory.
+ * \throws InconsistentInputError if there are invalid atom indices.
+ */
+ void checkIndexGroup(int natoms);
//! Type of the element.
e_selelem_t type;
/*! \brief
* Name of the element.
*
- * This field is only used for informative purposes.
+ * This field is only used for diagnostic purposes.
*/
std::string name_;
+ /*! \brief
+ * Location of the element in the selection text.
+ *
+ * This field is only used for diagnostic purposes (including error
+ * messages).
+ */
+ SelectionLocation location_;
GMX_DISALLOW_COPY_AND_ASSIGN(SelectionTreeElement);
};
_gmx_selelem_set_vtype(const gmx::SelectionTreeElementPointer &sel,
e_selvalue_t vtype);
-/** Frees the memory allocated for a selection method. */
+/*! \brief
+ * Frees the memory allocated for a selection method parameter.
+ *
+ * \param[in] param Parameter to free.
+ */
+void
+_gmx_selelem_free_param(struct gmx_ana_selparam_t *param);
+/*! \brief
+ * Frees the memory allocated for a selection method.
+ *
+ * \param[in] method Method to free.
+ * \param[in] mdata Method data to free.
+ */
void
_gmx_selelem_free_method(struct gmx_ana_selmethod_t *method, void *mdata);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
+#include "selhelp.h"
+
#include <string>
-#include <vector>
#include <utility>
+#include <vector>
#include <boost/scoped_ptr.hpp>
#include "gromacs/utility/file.h"
#include "gromacs/utility/stringutil.h"
-#include "selhelp.h"
#include "selmethod.h"
#include "symrec.h"
const char *const CommonHelpText::text[] = {
"Selections are used to select atoms/molecules/residues for analysis.",
"In contrast to traditional index files, selections can be dynamic, i.e.,",
- "select different atoms for different trajectory frames.[PAR]",
+ "select different atoms for different trajectory frames. The GROMACS",
+ "manual contains a short introductory section to selections in the",
+ "Analysis chapter, including suggestions on how to get familiar with",
+ "selections if you are new to the concept. The subtopics listed below",
+ "provide more details on the technical and syntactic aspects of",
+ "selections.[PAR]",
"Each analysis tool requires a different number of selections and the",
"selections are interpreted differently. The general idea is still the",
"can be an atom position or center-of-mass or center-of-geometry of",
"a set of atoms. The tool then uses these positions for its analysis to",
"allow very flexible processing. Some analysis tools may have limitations",
- "on the types of selections allowed.[PAR]",
-
- "To get started with selections, run, e.g., [TT][PROGRAM] select[tt]",
- "without specifying selections on the command-line and use the interactive",
- "prompt to try out different selections.",
- "This tool provides output options that allow one to see what is actually",
- "selected by the given selections, and the interactive prompt reports",
- "syntax errors immediately, allowing one to try again.",
- "The subtopics listed below give more details on different aspects of",
- "selections.",
+ "on the types of selections allowed."
};
struct ArithmeticHelpText
"evaluation order.[BR]",
"3. [TT]ATOM_EXPR[tt] expressions can be converted into [TT]POS_EXPR[tt]",
"expressions in various ways, see the \"positions\" subtopic for more",
- "details.[PAR]",
+ "details.[BR]",
+ "4. [TT]POS_EXPR[tt] can be converted into [TT]NUM_EXPR[tt] using syntax",
+ "like \"x of POS_EXPR\". Currently, this is only supported for single",
+ "positions like in expression \"x of cog of ATOM_EXPR\".[PAR]",
"Some keywords select atoms based on string values such as the atom name.",
"For these keywords, it is possible to use wildcards ([TT]name \"C*\"[tt])",
} // namespace
-/*! \cond internal */
+//! \cond libapi */
HelpTopicPointer createSelectionHelpTopic()
{
CompositeHelpTopicPointer root(new CompositeHelpTopic<CommonHelpText>);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/*! \internal \file
+/*! \libinternal \file
* \brief
* Functions for initializing online help for selections.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
* \ingroup module_selection
*/
#ifndef GMX_SELECTION_SELHELP_H
#define GMX_SELECTION_SELHELP_H
-#include "../onlinehelp/helptopicinterface.h"
+#include "gromacs/onlinehelp/helptopicinterface.h"
namespace gmx
{
-/*! \cond internal */
-/*! \internal \brief
+//! \cond libapi
+/*! \libinternal \brief
* Creates a help tree for selections.
*
* \throws std::bad_alloc if out of memory.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
+#include "selmethod.h"
+
#include <ctype.h>
#include <stdarg.h>
#include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/selection/selmethod.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#ifndef GMX_SELECTION_SELMETHOD_H
#define GMX_SELECTION_SELMETHOD_H
-#include "../legacyheaders/typedefs.h"
-
-#include "indexutil.h"
#include "selparam.h"
#include "selvalue.h"
class SelectionParserSymbolTable;
} // namespace gmx
+struct gmx_ana_index_t;
struct gmx_ana_pos_t;
struct gmx_ana_selcollection_t;
+struct t_pbc;
+struct t_topology;
+struct t_trxframe;
/*! \name Selection method flags
* \anchor selmethod_flags
* For \ref STR_VALUE methods, the pointers stored in \p out->s are discarded
* without freeing; it is the responsibility of this function to provide
* pointers that can be discarded without memory leaks.
+ *
+ * If the method accesses \p fr outside the index group specified in \p g or
+ * what it receives from its parameters, it must check that \p fr actually
+ * contains such an atom in case the \p fr has been loaded from a trajectory
+ * that only contains a subset of the system.
*/
typedef void (*sel_updatefunc)(t_topology *top, t_trxframe *fr, t_pbc *pbc,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out,
* \param data Internal data structure from sel_datafunc().
* \returns 0 on success, a non-zero error code on error.
*
- * This function should evaluate the method for each position in \p g,
+ * This function should evaluate the method for each position in \p pos,
* and write the output values to \p out. The pointer in the union \p out->u
* that corresponds to the type of the method should be used.
* Enough memory has been allocated to store the output values.
* The number of values in \p out should also be updated if necessary.
- * However, \ref POS_VALUE or \ref GROUP_VALUE methods should not touch
- * \p out->nr (it should be 1 anyways).
+ * \ref POS_VALUE or \ref GROUP_VALUE methods should not touch
+ * \p out->nr (it should be 1 anyways). For other types of methods, the number
+ * of output values should equal the number of positions in \p pos.
*
* For \ref STR_VALUE methods, the pointers stored in \p out->s are discarded
* without freeing; it is the responsibility of this function to provide
* pointers that can be discarded without memory leaks.
+ *
+ * If the method accesses \p fr outside the atoms referenced in \p pos or
+ * what it receives from its parameters, it must check that \p fr actually
+ * contains such an atom in case the \p fr has been loaded from a trajectory
+ * that only contains a subset of the system.
*/
typedef void (*sel_updatefunc_pos)(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- struct gmx_ana_pos_t *pos,
- gmx_ana_selvalue_t *out,
+ gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out,
void *data);
/*! \internal
* If some information is not available, the corresponding field can be set to
* 0/NULL.
*/
-typedef struct gmx_ana_selmethod_help_t
+struct gmx_ana_selmethod_help_t
{
/*! \brief
* One-line description of the syntax of the method.
* to NULL.
*/
const char **help;
-} gmx_ana_selmethod_help_t;
+};
/*! \internal
* \brief
* More details on implementing new selection methods can be found on a
* separate page: \ref page_module_selection_custom.
*/
-typedef struct gmx_ana_selmethod_t
+struct gmx_ana_selmethod_t
{
/** Name of the method. */
const char *name;
/** Help data for the method. */
gmx_ana_selmethod_help_t help;
-} gmx_ana_selmethod_t;
+};
/** Registers a selection method. */
int
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_SELECTION_SELPARAM_H
#define GMX_SELECTION_SELPARAM_H
-#include "indexutil.h"
+#include "gromacs/selection/indexutil.h"
+
#include "selvalue.h"
/*! \name Parameter flags
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
+#include "selvalue.h"
+
#include "gromacs/selection/indexutil.h"
#include "gromacs/selection/position.h"
-#include "gromacs/selection/selvalue.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
-/*!
- * \param[out] val Output structure
- *
- * The type of \p val is not touched.
- * Any contents of \p val are discarded without freeing.
- */
void
_gmx_selvalue_clear(gmx_ana_selvalue_t *val)
{
val->nalloc = 0;
}
-/*!
- * \param[in,out] val Value structure to allocate.
- * \param[in] n Maximum number of values needed.
- * \returns Zero on success.
- *
- * Reserves memory for the values within \p val to store at least \p n values,
- * of the type specified in the \p val structure.
- *
- * If the type is \ref POS_VALUE or \ref GROUP_VALUE, memory is reserved for
- * the data structures, but no memory is reserved inside these newly allocated
- * data structures.
- * Similarly, for \ref STR_VALUE values, the pointers are set to NULL.
- * For other values, the memory is uninitialized.
- */
-int
+void
+_gmx_selvalue_free(gmx_ana_selvalue_t *val)
+{
+ if (val->nalloc > 0)
+ {
+ if (val->type == POS_VALUE)
+ {
+ delete[] val->u.p;
+ }
+ else
+ {
+ sfree(val->u.ptr);
+ }
+ }
+ // TODO: It causes a memory leak somewhere if val->nr is assigned zero here...
+ val->u.ptr = NULL;
+ val->nalloc = 0;
+}
+
+void
_gmx_selvalue_reserve(gmx_ana_selvalue_t *val, int n)
{
int i;
if (val->nalloc == -1)
{
- return 0;
+ return;
}
if (!val->u.ptr || val->nalloc < n)
}
val->nalloc = n;
}
- return 0;
}
-/*!
- * \param[in,out] val Value structure to allocate.
- * \param[in] ptr Pointer where the values should be stored.
- * \returns Zero on success.
- *
- * Automatic memory management is disabled for \p ptr, unless \p ptr is NULL.
- */
-int
+void
+_gmx_selvalue_getstore_and_release(gmx_ana_selvalue_t *val, void **ptr, int *nalloc)
+{
+ *ptr = val->u.ptr;
+ *nalloc = val->nalloc;
+ val->u.ptr = NULL;
+ val->nalloc = 0;
+}
+
+void
_gmx_selvalue_setstore(gmx_ana_selvalue_t *val, void *ptr)
{
+ GMX_ASSERT(val->nalloc <= 0,
+ "Memory leak from discarding an existing value");
val->u.ptr = ptr;
val->nalloc = (ptr ? -1 : 0);
- return 0;
}
-/*!
- * \param[in,out] val Value structure to allocate.
- * \param[in] ptr Pointer where the values should be stored.
- * \param[in] nalloc Number of values allocated for \p ptr.
- * \returns Zero on success.
- */
-int
+void
_gmx_selvalue_setstore_alloc(gmx_ana_selvalue_t *val, void *ptr, int nalloc)
{
+ GMX_ASSERT(val->nalloc <= 0 || (ptr == val->u.ptr && nalloc == val->nalloc),
+ "Memory leak from discarding an existing value");
val->u.ptr = ptr;
val->nalloc = nalloc;
- return 0;
}
#ifndef GMX_SELECTION_SELVALUE_H
#define GMX_SELECTION_SELVALUE_H
-#include "../legacyheaders/types/simple.h"
+#include "gromacs/utility/real.h"
/** Defines the value type of a different selection objects. */
typedef enum
int nalloc;
} gmx_ana_selvalue_t;
-/** Initializes an empty selection value structure. */
+/*! \brief
+ * Initializes an empty selection value structure.
+ *
+ * \param[out] val Output structure
+ *
+ * The type of \p val is not touched.
+ * Any contents of \p val are discarded without freeing.
+ */
void
_gmx_selvalue_clear(gmx_ana_selvalue_t *val);
-/** Reserve memory for storing selection values. */
-int
+/*! \brief
+ * Frees memory allocated for a selection value structure.
+ *
+ * \param[in,out] val Values to free.
+ *
+ * The type of \p val is not touched.
+ * If memory is not allocated, the value pointers are simply cleared without
+ * freeing.
+ */
+void
+_gmx_selvalue_free(gmx_ana_selvalue_t *val);
+/*! \brief
+ * Reserve memory for storing selection values.
+ *
+ * \param[in,out] val Value structure to allocate.
+ * \param[in] n Maximum number of values needed.
+ *
+ * Reserves memory for the values within \p val to store at least \p n values,
+ * of the type specified in the \p val structure.
+ *
+ * If the type is \ref POS_VALUE or \ref GROUP_VALUE, memory is reserved for
+ * the data structures, but no memory is reserved inside these newly allocated
+ * data structures.
+ * Similarly, for \ref STR_VALUE values, the pointers are set to NULL.
+ * For other values, the memory is uninitialized.
+ */
+void
_gmx_selvalue_reserve(gmx_ana_selvalue_t *val, int n);
-/** Sets the memory for storing selection values. */
-int
+/*! \brief
+ * Gets and releases the memory pointer for storing selection values.
+ *
+ * \param[in,out] val Value structure to release.
+ * \param[out] ptr Pointer where the values are stored.
+ * \param[out] nalloc Pointer where the values are stored.
+ *
+ * Returns the pointer where values of \p val were stored in \p ptr and
+ * \p nalloc, and clears the memory in \p val.
+ */
+void
+_gmx_selvalue_getstore_and_release(gmx_ana_selvalue_t *val, void **ptr, int *nalloc);
+/*! \brief
+ * Sets the memory for storing selection values.
+ *
+ * \param[in,out] val Value structure to set storage for.
+ * \param[in] ptr Pointer where the values should be stored.
+ *
+ * Automatic memory management is disabled for \p ptr.
+ * Asserts if \p val had a previous storage that it owned, as that would result
+ * in a memory leak.
+ */
+void
_gmx_selvalue_setstore(gmx_ana_selvalue_t *val, void *ptr);
-/** Sets the memory for storing selection values and marks it for automatic freeing. */
-int
+/*! \brief
+ * Sets the memory for storing selection values and marks it for automatic freeing.
+ *
+ * \param[in,out] val Value structure to set storage for.
+ * \param[in] ptr Pointer where the values should be stored.
+ * \param[in] nalloc Number of values allocated for \p ptr.
+ *
+ * Asserts if \p val had a previous storage that it owned, as that would result
+ * in a memory leak.
+ */
+void
_gmx_selvalue_setstore_alloc(gmx_ana_selvalue_t *val, void *ptr, int nalloc);
#endif
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
#include <cmath>
#include "gromacs/legacyheaders/macros.h"
-
#include "gromacs/math/utilities.h"
-#include "gromacs/selection/selmethod.h"
-#include "gromacs/utility/common.h"
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/smalloc.h"
+#include "selmethod.h"
+
/** Defines the comparison operator for comparison expressions. */
typedef enum
{
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/vec.h"
+#include "gmxpre.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
#include "gromacs/selection/nbsearch.h"
#include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
#include "gromacs/utility/exceptions.h"
+#include "selmethod.h"
+
/*! \internal
* \brief
* Data structure for distance-based selection method.
static void
init_common(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
{
- t_methoddata_distance *d = (t_methoddata_distance *)data;
+ t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
if ((param[0].flags & SPAR_SET) && d->cutoff <= 0)
{
static void
init_frame_common(t_topology * /* top */, t_trxframe * /* fr */, t_pbc *pbc, void *data)
{
- t_methoddata_distance *d = (t_methoddata_distance *)data;
+ t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
d->nbsearch.reset();
gmx::AnalysisNeighborhoodPositions pos(d->p.x, d->p.count());
evaluate_distance(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
{
- t_methoddata_distance *d = (t_methoddata_distance *)data;
+ t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
- out->nr = pos->m.mapb.nra;
- for (int b = 0; b < pos->count(); ++b)
+ out->nr = pos->count();
+ for (int i = 0; i < pos->count(); ++i)
{
- real dist = d->nbsearch.minimumDistance(pos->x[b]);
- for (int i = pos->m.mapb.index[b]; i < pos->m.mapb.index[b+1]; ++i)
- {
- out->u.r[i] = dist;
- }
+ out->u.r[i] = d->nbsearch.minimumDistance(pos->x[i]);
}
}
evaluate_within(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
{
- t_methoddata_distance *d = (t_methoddata_distance *)data;
+ t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
out->u.g->isize = 0;
for (int b = 0; b < pos->count(); ++b)
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#include <algorithm>
+#include "gmxpre.h"
#include <math.h>
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/physics.h"
-#include "gromacs/legacyheaders/vec.h"
+#include <algorithm>
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/indexutil.h"
#include "gromacs/selection/position.h"
#include "gromacs/selection/selection.h"
-#include "gromacs/selection/selmethod.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/smalloc.h"
#include "selelem.h"
+#include "selmethod.h"
using std::min;
using std::max;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
#include <cctype>
#include <cstring>
#include <boost/shared_ptr.hpp>
#include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/selection/selmethod.h"
+#include "gromacs/selection/position.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxregex.h"
-#include "gromacs/utility/messagestringcollector.h"
-#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
#include "keywords.h"
#include "parsetree.h"
#include "scanner.h"
#include "selelem.h"
+#include "selmethod.h"
/*! \brief
* Allocates data for integer keyword evaluation.
{
if (!gmx::Regex::isSupported())
{
- GMX_THROW(gmx::InvalidInputError(gmx::formatString(
- "No regular expression support, "
- "cannot match \"%s\"", str)));
+ std::string message
+ = gmx::formatString("No regular expression support, "
+ "cannot match \"%s\"", str);
+ GMX_THROW(gmx::InvalidInputError(message));
}
regex_.reset(new gmx::Regex(str));
}
/** Initializes frame evaluation for keyword evaluation in an arbitrary group. */
static void
init_frame_kweval(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data);
-/** Evaluates keywords in an arbitrary group. */
+/*! \brief
+ * Evaluates keywords in an arbitrary group.
+ *
+ * See sel_updatefunc() for description of the parameters.
+ * \p data should point to a \c t_methoddata_kweval.
+ *
+ * Calls the evaluation function of the wrapped keyword with the given
+ * parameters, with the exception of using \c t_methoddata_kweval::g for the
+ * evaluation group.
+ */
static void
-evaluate_kweval(t_topology *top, t_trxframe *fr, t_pbc *pbc, gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data);
+evaluate_kweval(t_topology *top, t_trxframe *fr, t_pbc *pbc, gmx_ana_index_t *g,
+ gmx_ana_selvalue_t *out, void *data);
+/*! \brief
+ * Evaluates keywords in an arbitrary set of positions.
+ *
+ * See sel_updatefunc() for description of the parameters.
+ * \p data should point to a \c t_methoddata_kweval.
+ *
+ * Calls the evaluation function of the wrapped keyword with the given
+ * parameters, with the exception of using \c t_methoddata_kweval::p for the
+ * evaluation positions.
+ */
+static void
+evaluate_kweval_pos(t_topology *top, t_trxframe *fr, t_pbc *pbc, gmx_ana_index_t *g,
+ gmx_ana_selvalue_t *out, void *data);
/*! \internal \brief
* Data structure for keyword evaluation in arbitrary groups.
*/
-typedef struct
+struct t_methoddata_kweval
{
- /** Wrapped keyword method for evaluating the values. */
+ //! Initialize new keyword evaluator for the given keyword.
+ t_methoddata_kweval(gmx_ana_selmethod_t *method, void *data)
+ : kwmethod(method), kwmdata(data)
+ {
+ gmx_ana_index_clear(&g);
+ }
+ ~t_methoddata_kweval()
+ {
+ _gmx_selelem_free_method(kwmethod, kwmdata);
+ }
+
+ //! Wrapped keyword method for evaluating the values.
gmx_ana_selmethod_t *kwmethod;
- /** Method data for \p kwmethod. */
+ //! Method data for \p kwmethod.
void *kwmdata;
- /** Group in which \p kwmethod should be evaluated. */
+ //! Group in which \p kwmethod should be evaluated.
gmx_ana_index_t g;
-} t_methoddata_kweval;
+ //! Positions for which \p kwmethod should be evaluated.
+ gmx_ana_pos_t p;
+};
/** Parameters for keyword evaluation in an arbitrary group. */
-static gmx_ana_selparam_t smparams_kweval[] = {
+static gmx_ana_selparam_t smparams_kweval_group[] = {
{NULL, {GROUP_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
};
+/** Parameters for keyword evaluation from positions. */
+static gmx_ana_selparam_t smparams_kweval_pos[] = {
+ {NULL, {POS_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
+};
/********************************************************************
static void
init_kweval(t_topology *top, int /* npar */, gmx_ana_selparam_t * /* param */, void *data)
{
- t_methoddata_kweval *d = (t_methoddata_kweval *)data;
+ t_methoddata_kweval *d = static_cast<t_methoddata_kweval *>(data);
d->kwmethod->init(top, 0, NULL, d->kwmdata);
}
static void
init_output_kweval(t_topology * /* top */, gmx_ana_selvalue_t *out, void *data)
{
- t_methoddata_kweval *d = (t_methoddata_kweval *)data;
+ t_methoddata_kweval *d = static_cast<t_methoddata_kweval *>(data);
out->nr = d->g.isize;
_gmx_selvalue_reserve(out, out->nr);
static void
free_data_kweval(void *data)
{
- t_methoddata_kweval *d = (t_methoddata_kweval *)data;
+ t_methoddata_kweval *d = static_cast<t_methoddata_kweval *>(data);
- _gmx_selelem_free_method(d->kwmethod, d->kwmdata);
- sfree(d);
+ delete d;
}
/*!
static void
init_frame_kweval(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data)
{
- t_methoddata_kweval *d = (t_methoddata_kweval *)data;
+ t_methoddata_kweval *d = static_cast<t_methoddata_kweval *>(data);
d->kwmethod->init_frame(top, fr, pbc, d->kwmdata);
}
-/*!
- * See sel_updatefunc() for description of the parameters.
- * \p data should point to a \c t_methoddata_kweval.
- *
- * Calls the evaluation function of the wrapped keyword with the given
- * parameters, with the exception of using \c t_methoddata_kweval::g for the
- * evaluation group.
- */
static void
evaluate_kweval(t_topology *top, t_trxframe *fr, t_pbc *pbc,
gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data)
{
- t_methoddata_kweval *d = (t_methoddata_kweval *)data;
+ t_methoddata_kweval *d = static_cast<t_methoddata_kweval *>(data);
d->kwmethod->update(top, fr, pbc, &d->g, out, d->kwmdata);
}
-/*!
+static void
+evaluate_kweval_pos(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+ gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data)
+{
+ t_methoddata_kweval *d = static_cast<t_methoddata_kweval *>(data);
+
+ d->kwmethod->pupdate(top, fr, pbc, &d->p, out, d->kwmdata);
+}
+
+/*! \brief
+ * Initializes a selection element for evaluating a keyword in a given group.
+ *
* \param[in] method Keyword selection method to evaluate.
- * \param[in] params Parameter that gives the group to evaluate \p method in.
+ * \param[in] params Parameters to pass to initialization (the child group).
* \param[in] scanner Scanner data structure.
- * \returns Pointer to the created selection element (NULL on error).
- *
- * Creates a \ref SEL_EXPRESSION selection element that evaluates the keyword
- * method given by \p method in the group given by \p param.
+ * \returns Pointer to the created selection element.
*
- * The name of \p param should be empty.
+ * Implements _gmx_sel_init_keyword_evaluator() for \ref GROUP_VALUE input
+ * selections.
*/
-gmx::SelectionTreeElementPointer
-_gmx_sel_init_keyword_evaluator(gmx_ana_selmethod_t *method,
- const gmx::SelectionParserParameterList ¶ms,
- void *scanner)
+static gmx::SelectionTreeElementPointer
+init_evaluator_group(gmx_ana_selmethod_t *method,
+ const gmx::SelectionParserParameterList ¶ms,
+ void *scanner)
{
- gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
- char buf[1024];
- sprintf(buf, "In evaluation of '%s'", method->name);
- gmx::MessageStringContext context(errors, buf);
-
if ((method->flags & (SMETH_SINGLEVAL | SMETH_VARNUMVAL))
|| method->outinit || method->pupdate)
{
- GMX_THROW(gmx::InternalError(
- "Unsupported keyword method for arbitrary group evaluation"));
+ std::string message
+ = gmx::formatString("Keyword '%s' cannot be evaluated in this context",
+ method->name);
+ GMX_THROW(gmx::InvalidInputError(message));
}
+ // TODO: For same ... as ..., some other location could be more intuitive.
gmx::SelectionTreeElementPointer sel(
- new gmx::SelectionTreeElement(SEL_EXPRESSION));
+ new gmx::SelectionTreeElement(
+ SEL_EXPRESSION, _gmx_sel_lexer_get_current_location(scanner)));
_gmx_selelem_set_method(sel, method, scanner);
- t_methoddata_kweval *data;
- snew(data, 1);
- data->kwmethod = sel->u.expr.method;
- data->kwmdata = sel->u.expr.mdata;
- gmx_ana_index_clear(&data->g);
+ t_methoddata_kweval *data
+ = new t_methoddata_kweval(sel->u.expr.method, sel->u.expr.mdata);
snew(sel->u.expr.method, 1);
- memcpy(sel->u.expr.method, data->kwmethod, sizeof(gmx_ana_selmethod_t));
- sel->u.expr.method->flags |= SMETH_VARNUMVAL;
+ sel->u.expr.method->name = data->kwmethod->name;
+ sel->u.expr.method->type = data->kwmethod->type;
+ sel->u.expr.method->flags = data->kwmethod->flags | SMETH_VARNUMVAL;
sel->u.expr.method->init_data = NULL;
sel->u.expr.method->set_poscoll = NULL;
sel->u.expr.method->init = method->init ? &init_kweval : NULL;
sel->u.expr.method->init_frame = method->init_frame ? &init_frame_kweval : NULL;
sel->u.expr.method->update = &evaluate_kweval;
sel->u.expr.method->pupdate = NULL;
- sel->u.expr.method->nparams = asize(smparams_kweval);
- sel->u.expr.method->param = smparams_kweval;
+ sel->u.expr.method->nparams = asize(smparams_kweval_group);
+ sel->u.expr.method->param = smparams_kweval_group;
_gmx_selelem_init_method_params(sel, scanner);
sel->u.expr.mdata = data;
sel->u.expr.method->param[0].val.u.g = &data->g;
- if (!_gmx_sel_parse_params(params, sel->u.expr.method->nparams,
- sel->u.expr.method->param, sel, scanner))
+ _gmx_sel_parse_params(params, sel->u.expr.method->nparams,
+ sel->u.expr.method->param, sel, scanner);
+ return sel;
+}
+
+/*! \brief
+ * Initializes a selection element for evaluating a keyword in given positions.
+ *
+ * \param[in] method Keyword selection method to evaluate.
+ * \param[in] params Parameters to pass to initialization (the child positions).
+ * \param[in] scanner Scanner data structure.
+ * \returns Pointer to the created selection element.
+ *
+ * Implements _gmx_sel_init_keyword_evaluator() for \ref POS_VALUE input
+ * selections.
+ */
+static gmx::SelectionTreeElementPointer
+init_evaluator_pos(gmx_ana_selmethod_t *method,
+ const gmx::SelectionParserParameterList ¶ms,
+ void *scanner)
+{
+ if ((method->flags & (SMETH_SINGLEVAL | SMETH_VARNUMVAL))
+ || method->outinit || method->pupdate == NULL)
{
- return gmx::SelectionTreeElementPointer();
+ std::string message
+ = gmx::formatString("Keyword '%s' cannot be evaluated in this context",
+ method->name);
+ GMX_THROW(gmx::InvalidInputError(message));
}
+
+ gmx::SelectionTreeElementPointer sel(
+ new gmx::SelectionTreeElement(
+ SEL_EXPRESSION, _gmx_sel_lexer_get_current_location(scanner)));
+ _gmx_selelem_set_method(sel, method, scanner);
+
+ t_methoddata_kweval *data
+ = new t_methoddata_kweval(sel->u.expr.method, sel->u.expr.mdata);
+
+ snew(sel->u.expr.method, 1);
+ sel->u.expr.method->name = data->kwmethod->name;
+ sel->u.expr.method->type = data->kwmethod->type;
+ sel->u.expr.method->flags = data->kwmethod->flags | SMETH_SINGLEVAL;
+ sel->u.expr.method->init_data = NULL;
+ sel->u.expr.method->set_poscoll = NULL;
+ sel->u.expr.method->init = method->init ? &init_kweval : NULL;
+ sel->u.expr.method->outinit = NULL;
+ sel->u.expr.method->free = &free_data_kweval;
+ sel->u.expr.method->init_frame = method->init_frame ? &init_frame_kweval : NULL;
+ sel->u.expr.method->update = &evaluate_kweval_pos;
+ sel->u.expr.method->pupdate = NULL;
+ sel->u.expr.method->nparams = asize(smparams_kweval_pos);
+ sel->u.expr.method->param = smparams_kweval_pos;
+ _gmx_selelem_init_method_params(sel, scanner);
+ sel->u.expr.mdata = data;
+
+ sel->u.expr.method->param[0].val.u.p = &data->p;
+
+ _gmx_sel_parse_params(params, sel->u.expr.method->nparams,
+ sel->u.expr.method->param, sel, scanner);
return sel;
}
+
+gmx::SelectionTreeElementPointer
+_gmx_sel_init_keyword_evaluator(gmx_ana_selmethod_t *method,
+ const gmx::SelectionTreeElementPointer &child,
+ void *scanner)
+{
+ gmx::SelectionParserParameterList params;
+ params.push_back(
+ gmx::SelectionParserParameter::createFromExpression(NULL, child));
+ if (child->v.type == GROUP_VALUE)
+ {
+ return init_evaluator_group(method, params, scanner);
+ }
+ else if (child->v.type == POS_VALUE)
+ {
+ return init_evaluator_pos(method, params, scanner);
+ }
+ else
+ {
+ std::string text(_gmx_sel_lexer_get_text(scanner, child->location()));
+ std::string message
+ = gmx::formatString("Expression '%s' cannot be used to evaluate keywords",
+ text.c_str());
+ GMX_THROW(gmx::InvalidInputError(message));
+ }
+}
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/vec.h"
+#include "gmxpre.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
#include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
-#include "gromacs/utility/common.h"
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/smalloc.h"
+#include "selmethod.h"
+
/*! \internal \brief
* Data structure for the merging selection modifiers.
*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/vec.h"
+#include "gmxpre.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
#include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
+#include "selmethod.h"
+
/*! \internal \brief
* Data structure for the \p permute selection modifier.
*/
static void
evaluate_permute(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
- gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data)
+ gmx_ana_pos_t * /*p*/, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_permute *d = (t_methoddata_permute *)data;
int i, j, b;
/* De-permute the reference ID */
refid = refid - (refid % d->n) + d->perm[refid % d->n];
}
- gmx_ana_pos_append(out->u.p, p, b, refid);
+ gmx_ana_pos_append(out->u.p, &d->p, b, refid);
}
}
gmx_ana_pos_append_finish(out->u.p);
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#include "gromacs/legacyheaders/macros.h"
+#include "gmxpre.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
#include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
#include "keywords.h"
+#include "poscalc.h"
#include "selelem.h"
+#include "selmethod.h"
/*! \internal \brief
* Data structure for position keyword evaluation.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
#include <stdlib.h>
#include "gromacs/legacyheaders/macros.h"
-
-#include "gromacs/selection/selmethod.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/smalloc.h"
#include "keywords.h"
#include "parsetree.h"
#include "selelem.h"
+#include "selmethod.h"
/*! \internal
* \brief
* \param[in,out] method The method to initialize.
* \param[in,out] params Pointer to the first parameter.
* \param[in] scanner Scanner data structure.
- * \returns 0 on success, a non-zero error code on error.
*
- * If \p *method is not a \c same method, this function returns zero
+ * If \p *method is not a \c same method, this function returns
* immediately.
*/
-int
+void
_gmx_selelem_custom_init_same(gmx_ana_selmethod_t **method,
const gmx::SelectionParserParameterListPointer ¶ms,
void *scanner)
/* Do nothing if this is not a same method. */
if (!*method || (*method)->name != sm_same.name || params->empty())
{
- return 0;
+ return;
}
const gmx::SelectionParserValueList &kwvalues = params->front().values();
if (kwvalues.size() != 1 || !kwvalues.front().hasExpressionValue()
|| kwvalues.front().expr->type != SEL_EXPRESSION)
{
- _gmx_selparser_error(scanner, "'same' should be followed by a single keyword");
- return -1;
+ GMX_THROW(gmx::InvalidInputError("'same' should be followed by a single keyword"));
}
gmx_ana_selmethod_t *kwmethod = kwvalues.front().expr->u.expr.method;
if (kwmethod->type == STR_VALUE)
gmx::SelectionParserParameterList::iterator asparam = ++params->begin();
if (asparam != params->end() && asparam->name() == sm_same.param[1].name)
{
- gmx::SelectionParserParameterList kwparams;
- gmx::SelectionParserValueListPointer values(
- new gmx::SelectionParserValueList(asparam->values()));
- kwparams.push_back(
- gmx::SelectionParserParameter::create(NULL, move(values)));
-
+ const gmx::SelectionParserValueList &asvalues = asparam->values();
+ if (asvalues.size() != 1 || !asvalues.front().hasExpressionValue())
+ {
+ // TODO: Think about providing more informative context.
+ GMX_THROW(gmx::InvalidInputError("'same ... as' should be followed by a single expression"));
+ }
+ const gmx::SelectionTreeElementPointer &child = asvalues.front().expr;
/* Create a second keyword evaluation element for the keyword given as
* the first parameter, evaluating the keyword in the group given by the
* second parameter. */
gmx::SelectionTreeElementPointer kwelem
- = _gmx_sel_init_keyword_evaluator(kwmethod, kwparams, scanner);
- // FIXME: Use exceptions.
- if (!kwelem)
- {
- return -1;
- }
+ = _gmx_sel_init_keyword_evaluator(kwmethod, child, scanner);
/* Replace the second parameter with one with a value from \p kwelem. */
std::string pname = asparam->name();
*asparam = gmx::SelectionParserParameter::createFromExpression(pname, kwelem);
}
- return 0;
}
static void
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
#include <cctype>
#include "gromacs/legacyheaders/macros.h"
-
#include "gromacs/selection/position.h"
-#include "gromacs/selection/selmethod.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/utility/exceptions.h"
+#include "selmethod.h"
+
/** Evaluates the \p all selection keyword. */
static void
evaluate_all(t_topology *top, t_trxframe *fr, t_pbc *pbc,
* Internal utility function for position keyword evaluation.
*
* \param[out] out Output array.
- * \param[in] pos Position data to use instead of atomic coordinates
- * (can be NULL).
+ * \param[in] pos Position data to use instead of atomic coordinates.
* \param[in] d Coordinate index to evaluate (\p XX, \p YY or \p ZZ).
*
* This function is used internally by evaluate_x(), evaluate_y() and
static void
evaluate_coord(real out[], gmx_ana_pos_t *pos, int d)
{
- for (int b = 0; b < pos->count(); ++b)
+ for (int i = 0; i < pos->count(); ++i)
{
- const real v = pos->x[b][d];
- for (int i = pos->m.mapb.index[b]; i < pos->m.mapb.index[b+1]; ++i)
- {
- out[i] = v;
- }
+ out[i] = pos->x[i][d];
}
// TODO: Make this more efficient by directly extracting the coordinates
// from the frame coordinates for atomic positions instead of going through
* See sel_updatefunc_pos() for description of the parameters.
* \p data is not used.
*
- * Returns the \p x coordinate for each atom in \p out->u.r.
+ * Returns the \p x coordinate for each position in \p out->u.r.
*/
static void
evaluate_x(t_topology * /*top*/, t_trxframe * /*fr*/, t_pbc * /*pbc*/,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void * /*data*/)
{
- out->nr = pos->m.mapb.nra;
+ out->nr = pos->count();
evaluate_coord(out->u.r, pos, XX);
}
* See sel_updatefunc() for description of the parameters.
* \p data is not used.
*
- * Returns the \p y coordinate for each atom in \p out->u.r.
+ * Returns the \p y coordinate for each position in \p out->u.r.
*/
static void
evaluate_y(t_topology * /*top*/, t_trxframe * /*fr*/, t_pbc * /*pbc*/,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void * /*data*/)
{
- out->nr = pos->m.mapb.nra;
+ out->nr = pos->count();
evaluate_coord(out->u.r, pos, YY);
}
* See sel_updatefunc() for description of the parameters.
* \p data is not used.
*
- * Returns the \p z coordinate for each atom in \p out->u.r.
+ * Returns the \p z coordinate for each position in \p out->u.r.
*/
static void
evaluate_z(t_topology * /*top*/, t_trxframe * /*fr*/, t_pbc * /*pbc*/,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void * /*data*/)
{
- out->nr = pos->m.mapb.nra;
+ out->nr = pos->count();
evaluate_coord(out->u.r, pos, ZZ);
}
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
+#include "symrec.h"
+
#include <map>
#include <string>
#include <utility>
#include "gromacs/legacyheaders/macros.h"
-
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/stringutil.h"
#include "poscalc.h"
#include "selelem.h"
-#include "symrec.h"
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <iterator>
#include <string>
-#include "gromacs/utility/common.h"
+#include "gromacs/utility/classhelpers.h"
#include "selelem.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#include <gtest/gtest.h>
-
-#include "gromacs/legacyheaders/typedefs.h"
+#include "gmxpre.h"
#include "gromacs/selection/indexutil.h"
+#include <gtest/gtest.h>
+
+#include "gromacs/topology/block.h"
+
#include "testutils/refdata.h"
#include "toputils.h"
void testInit(int atomCount, const int atoms[], e_index_t type);
void testUpdate(int atomCount, const int atoms[], bool bMaskOnly,
const char *name);
+ void testOrgIdGroup(e_index_t type, const char *name);
template <int count>
void testInit(const int (&atoms)[count], e_index_t type)
{
}
}
+void IndexMapTest::testOrgIdGroup(e_index_t type, const char *name)
+{
+ gmx::test::TestReferenceChecker compound(
+ checker_.checkCompound("OrgIdGroups", name));
+ const int count
+ = gmx_ana_indexmap_init_orgid_group(&map_, topManager_.topology(), type);
+ compound.checkInteger(count, "GroupCount");
+ compound.checkSequenceArray(map_.mapb.nr, map_.orgid, "OrgId");
+ for (int i = 0; i < map_.mapb.nr; ++i)
+ {
+ EXPECT_EQ(map_.orgid[i], map_.mapid[i]);
+ }
+}
+
void IndexMapTest::checkMapping(int atomCount, const int atoms[],
const char *name)
{
testInit(maxGroup, INDEX_ATOM);
}
+TEST_F(IndexMapTest, InitializesOrgIdGroupAtom)
+{
+ const int maxGroup[] = { 2, 5, 7 };
+ testInit(maxGroup, INDEX_ATOM);
+ testOrgIdGroup(INDEX_ATOM, "Atoms");
+}
+
+TEST_F(IndexMapTest, InitializesOrgIdGroupSingle)
+{
+ const int maxGroup[] = { 3, 4, 7, 8, 13 };
+ topManager_.initAtoms(18);
+ topManager_.initUniformResidues(3);
+ testInit(maxGroup, INDEX_RES);
+ testOrgIdGroup(INDEX_ATOM, "Single");
+}
+
+TEST_F(IndexMapTest, InitializesOrgIdGroupResidue)
+{
+ const int maxGroup[] = { 3, 4, 7, 8, 13 };
+ topManager_.initAtoms(18);
+ topManager_.initUniformResidues(3);
+ testInit(maxGroup, INDEX_ATOM);
+ testOrgIdGroup(INDEX_RES, "Residues");
+}
+
+TEST_F(IndexMapTest, InitializesOrgIdGroupMolecule)
+{
+ const int maxGroup[] = { 1, 2, 3, 4, 7, 8, 13 };
+ topManager_.initAtoms(18);
+ topManager_.initUniformResidues(3);
+ topManager_.initUniformMolecules(6);
+ testInit(maxGroup, INDEX_RES);
+ testOrgIdGroup(INDEX_MOL, "Molecules");
+}
+
+TEST_F(IndexMapTest, InitializesOrgIdGroupAll)
+{
+ const int maxGroup[] = { 3, 4, 7, 8, 13 };
+ testInit(maxGroup, INDEX_ATOM);
+ testOrgIdGroup(INDEX_ALL, "All");
+}
+
TEST_F(IndexMapTest, InitializesMoleculeBlock)
{
const int maxGroup[] = { 3, 4, 7, 8, 13 };
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#include <gtest/gtest.h>
+#include "gmxpre.h"
+
+#include "gromacs/selection/nbsearch.h"
#include <cmath>
+#include <algorithm>
#include <limits>
-#include <set>
+#include <numeric>
#include <vector>
-#include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/vec.h"
+#include <gtest/gtest.h>
-#include "gromacs/selection/nbsearch.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/random/random.h"
+#include "gromacs/topology/block.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
#include "testutils/testasserts.h"
class NeighborhoodSearchTestData
{
public:
+ struct RefPair
+ {
+ RefPair(int refIndex, real distance)
+ : refIndex(refIndex), distance(distance), bFound(false),
+ bExcluded(false), bIndexed(true)
+ {
+ }
+
+ bool operator<(const RefPair &other) const
+ {
+ return refIndex < other.refIndex;
+ }
+
+ int refIndex;
+ real distance;
+ // The variables below are state variables that are only used
+ // during the actual testing after creating a copy of the reference
+ // pair list, not as part of the reference data.
+ // Simpler to have just a single structure for both purposes.
+ bool bFound;
+ bool bExcluded;
+ bool bIndexed;
+ };
+
struct TestPosition
{
explicit TestPosition(const rvec x)
copy_rvec(x, this->x);
}
- rvec x;
- real refMinDist;
- int refNearestPoint;
- std::set<int> refPairs;
+ rvec x;
+ real refMinDist;
+ int refNearestPoint;
+ std::vector<RefPair> refPairs;
};
+
typedef std::vector<TestPosition> TestPositionList;
NeighborhoodSearchTestData(int seed, real cutoff);
gmx::AnalysisNeighborhoodPositions refPositions() const
{
- return gmx::AnalysisNeighborhoodPositions(refPos_, refPosCount_);
+ return gmx::AnalysisNeighborhoodPositions(refPos_);
}
gmx::AnalysisNeighborhoodPositions testPositions() const
{
- if (testPos_ == NULL)
+ if (testPos_.empty())
{
- snew(testPos_, testPositions_.size());
+ testPos_.reserve(testPositions_.size());
for (size_t i = 0; i < testPositions_.size(); ++i)
{
- copy_rvec(testPositions_[i].x, testPos_[i]);
+ testPos_.push_back(testPositions_[i].x);
}
}
- return gmx::AnalysisNeighborhoodPositions(testPos_,
- testPositions_.size());
+ return gmx::AnalysisNeighborhoodPositions(testPos_);
}
gmx::AnalysisNeighborhoodPositions testPosition(int index) const
{
void addTestPosition(const rvec x)
{
- GMX_RELEASE_ASSERT(testPos_ == NULL,
+ GMX_RELEASE_ASSERT(testPos_.empty(),
"Cannot add positions after testPositions() call");
testPositions_.push_back(TestPosition(x));
}
- void generateRandomPosition(rvec x);
+ gmx::RVec generateRandomPosition();
+ std::vector<int> generateIndex(int count) const;
void generateRandomRefPositions(int count);
void generateRandomTestPositions(int count);
- void computeReferences(t_pbc *pbc);
+ void computeReferences(t_pbc *pbc)
+ {
+ computeReferencesInternal(pbc, false);
+ }
+ void computeReferencesXY(t_pbc *pbc)
+ {
+ computeReferencesInternal(pbc, true);
+ }
+
+ bool containsPair(int testIndex, const RefPair &pair) const
+ {
+ const std::vector<RefPair> &refPairs = testPositions_[testIndex].refPairs;
+ std::vector<RefPair>::const_iterator foundRefPair
+ = std::lower_bound(refPairs.begin(), refPairs.end(), pair);
+ if (foundRefPair == refPairs.end() || foundRefPair->refIndex != pair.refIndex)
+ {
+ return false;
+ }
+ return true;
+ }
gmx_rng_t rng_;
real cutoff_;
matrix box_;
t_pbc pbc_;
int refPosCount_;
- rvec *refPos_;
+ std::vector<gmx::RVec> refPos_;
TestPositionList testPositions_;
private:
- mutable rvec *testPos_;
+ void computeReferencesInternal(t_pbc *pbc, bool bXY);
+
+ mutable std::vector<gmx::RVec> testPos_;
};
+//! Shorthand for a collection of reference pairs.
+typedef std::vector<NeighborhoodSearchTestData::RefPair> RefPairList;
+
NeighborhoodSearchTestData::NeighborhoodSearchTestData(int seed, real cutoff)
- : rng_(NULL), cutoff_(cutoff), refPosCount_(0), refPos_(NULL), testPos_(NULL)
+ : rng_(NULL), cutoff_(cutoff), refPosCount_(0)
{
// TODO: Handle errors.
rng_ = gmx_rng_init(seed);
{
gmx_rng_destroy(rng_);
}
- sfree(refPos_);
- sfree(testPos_);
}
-void NeighborhoodSearchTestData::generateRandomPosition(rvec x)
+gmx::RVec NeighborhoodSearchTestData::generateRandomPosition()
{
- rvec fx;
+ rvec fx, x;
fx[XX] = gmx_rng_uniform_real(rng_);
fx[YY] = gmx_rng_uniform_real(rng_);
fx[ZZ] = gmx_rng_uniform_real(rng_);
x[XX] += 0.2 * gmx_rng_uniform_real(rng_) - 0.1;
x[YY] += 0.2 * gmx_rng_uniform_real(rng_) - 0.1;
x[ZZ] += 0.2 * gmx_rng_uniform_real(rng_) - 0.1;
+ return x;
+}
+
+std::vector<int> NeighborhoodSearchTestData::generateIndex(int count) const
+{
+ std::vector<int> result;
+ for (int i = 0; i < count; ++i)
+ {
+ if (gmx_rng_uniform_real(rng_) > 0.5)
+ {
+ result.push_back(i);
+ }
+ }
+ return result;
}
void NeighborhoodSearchTestData::generateRandomRefPositions(int count)
{
refPosCount_ = count;
- snew(refPos_, refPosCount_);
- for (int i = 0; i < refPosCount_; ++i)
+ refPos_.reserve(count);
+ for (int i = 0; i < count; ++i)
{
- generateRandomPosition(refPos_[i]);
+ refPos_.push_back(generateRandomPosition());
}
}
testPositions_.reserve(count);
for (int i = 0; i < count; ++i)
{
- rvec x;
- generateRandomPosition(x);
- addTestPosition(x);
+ addTestPosition(generateRandomPosition());
}
}
-void NeighborhoodSearchTestData::computeReferences(t_pbc *pbc)
+void NeighborhoodSearchTestData::computeReferencesInternal(t_pbc *pbc, bool bXY)
{
real cutoff = cutoff_;
if (cutoff <= 0)
{
rvec_sub(i->x, refPos_[j], dx);
}
- const real dist = norm(dx);
+ // TODO: This may not work intuitively for 2D with the third box
+ // vector not parallel to the Z axis, but neither does the actual
+ // neighborhood search.
+ const real dist =
+ !bXY ? norm(dx) : sqrt(sqr(dx[XX]) + sqr(dx[YY]));
if (dist < i->refMinDist)
{
i->refMinDist = dist;
}
if (dist <= cutoff)
{
- i->refPairs.insert(j);
+ RefPair pair(j, dist);
+ GMX_RELEASE_ASSERT(i->refPairs.empty() || i->refPairs.back() < pair,
+ "Reference pairs should be generated in sorted order");
+ i->refPairs.push_back(pair);
}
}
}
}
+/********************************************************************
+ * ExclusionsHelper
+ */
+
+class ExclusionsHelper
+{
+ public:
+ static void markExcludedPairs(RefPairList *refPairs, int testIndex,
+ const t_blocka *excls);
+
+ ExclusionsHelper(int refPosCount, int testPosCount);
+
+ void generateExclusions();
+
+ const t_blocka *exclusions() const { return &excls_; }
+
+ gmx::ConstArrayRef<int> refPosIds() const
+ {
+ return gmx::constArrayRefFromVector<int>(exclusionIds_.begin(),
+ exclusionIds_.begin() + refPosCount_);
+ }
+ gmx::ConstArrayRef<int> testPosIds() const
+ {
+ return gmx::constArrayRefFromVector<int>(exclusionIds_.begin(),
+ exclusionIds_.begin() + testPosCount_);
+ }
+
+ private:
+ int refPosCount_;
+ int testPosCount_;
+ std::vector<int> exclusionIds_;
+ std::vector<int> exclsIndex_;
+ std::vector<int> exclsAtoms_;
+ t_blocka excls_;
+};
+
+// static
+void ExclusionsHelper::markExcludedPairs(RefPairList *refPairs, int testIndex,
+ const t_blocka *excls)
+{
+ int count = 0;
+ for (int i = excls->index[testIndex]; i < excls->index[testIndex + 1]; ++i)
+ {
+ const int excludedIndex = excls->a[i];
+ NeighborhoodSearchTestData::RefPair searchPair(excludedIndex, 0.0);
+ RefPairList::iterator excludedRefPair
+ = std::lower_bound(refPairs->begin(), refPairs->end(), searchPair);
+ if (excludedRefPair != refPairs->end()
+ && excludedRefPair->refIndex == excludedIndex)
+ {
+ excludedRefPair->bFound = true;
+ excludedRefPair->bExcluded = true;
+ ++count;
+ }
+ }
+}
+
+ExclusionsHelper::ExclusionsHelper(int refPosCount, int testPosCount)
+ : refPosCount_(refPosCount), testPosCount_(testPosCount)
+{
+ // Generate an array of 0, 1, 2, ...
+ // TODO: Make the tests work also with non-trivial exclusion IDs,
+ // and test that.
+ exclusionIds_.resize(std::max(refPosCount, testPosCount), 1);
+ exclusionIds_[0] = 0;
+ std::partial_sum(exclusionIds_.begin(), exclusionIds_.end(),
+ exclusionIds_.begin());
+
+ excls_.nr = 0;
+ excls_.index = NULL;
+ excls_.nra = 0;
+ excls_.a = NULL;
+ excls_.nalloc_index = 0;
+ excls_.nalloc_a = 0;
+}
+
+void ExclusionsHelper::generateExclusions()
+{
+ // TODO: Consider a better set of test data, where the density of the
+ // particles would be higher, or where the exclusions would not be random,
+ // to make a higher percentage of the exclusions to actually be within the
+ // cutoff.
+ exclsIndex_.reserve(testPosCount_ + 1);
+ exclsAtoms_.reserve(testPosCount_ * 20);
+ exclsIndex_.push_back(0);
+ for (int i = 0; i < testPosCount_; ++i)
+ {
+ for (int j = 0; j < 20; ++j)
+ {
+ exclsAtoms_.push_back(i + j*3);
+ }
+ exclsIndex_.push_back(exclsAtoms_.size());
+ }
+ excls_.nr = exclsIndex_.size();
+ excls_.index = &exclsIndex_[0];
+ excls_.nra = exclsAtoms_.size();
+ excls_.a = &exclsAtoms_[0];
+}
+
/********************************************************************
* NeighborhoodSearchTest
*/
const NeighborhoodSearchTestData &data);
void testPairSearch(gmx::AnalysisNeighborhoodSearch *search,
const NeighborhoodSearchTestData &data);
+ void testPairSearchIndexed(gmx::AnalysisNeighborhood *nb,
+ const NeighborhoodSearchTestData &data);
+ void testPairSearchFull(gmx::AnalysisNeighborhoodSearch *search,
+ const NeighborhoodSearchTestData &data,
+ const gmx::AnalysisNeighborhoodPositions &pos,
+ const t_blocka *excls,
+ const gmx::ConstArrayRef<int> &refIndices,
+ const gmx::ConstArrayRef<int> &testIndices);
gmx::AnalysisNeighborhood nb_;
};
{
EXPECT_EQ(i->refNearestPoint, pair.refIndex());
EXPECT_EQ(0, pair.testIndex());
+ EXPECT_REAL_EQ_TOL(i->refMinDist, sqrt(pair.distance2()),
+ gmx::test::ulpTolerance(64));
}
else
{
}
}
+//! Helper function for formatting test failure messages.
+std::string formatVector(const rvec x)
+{
+ return gmx::formatString("[%.3f, %.3f, %.3f]", x[XX], x[YY], x[ZZ]);
+}
+
+/*! \brief
+ * Helper function to check that all expected pairs were found.
+ */
+void checkAllPairsFound(const RefPairList &refPairs,
+ const std::vector<gmx::RVec> &refPos,
+ int testPosIndex, const rvec testPos)
+{
+ // This could be elegantly expressed with Google Mock matchers, but that
+ // has a significant effect on the runtime of the tests...
+ int count = 0;
+ RefPairList::const_iterator first;
+ for (RefPairList::const_iterator i = refPairs.begin(); i != refPairs.end(); ++i)
+ {
+ if (!i->bFound)
+ {
+ ++count;
+ first = i;
+ }
+ }
+ if (count > 0)
+ {
+ ADD_FAILURE()
+ << "Some pairs (" << count << "/" << refPairs.size() << ") "
+ << "within the cutoff were not found. First pair:\n"
+ << " Ref: " << first->refIndex << " at "
+ << formatVector(refPos[first->refIndex]) << "\n"
+ << "Test: " << testPosIndex << " at " << formatVector(testPos) << "\n"
+ << "Dist: " << first->distance;
+ }
+}
+
void NeighborhoodSearchTest::testPairSearch(
gmx::AnalysisNeighborhoodSearch *search,
const NeighborhoodSearchTestData &data)
{
- NeighborhoodSearchTestData::TestPositionList::const_iterator i;
- for (i = data.testPositions_.begin(); i != data.testPositions_.end(); ++i)
+ testPairSearchFull(search, data, data.testPositions(), NULL,
+ gmx::EmptyArrayRef(), gmx::EmptyArrayRef());
+}
+
+void NeighborhoodSearchTest::testPairSearchIndexed(
+ gmx::AnalysisNeighborhood *nb,
+ const NeighborhoodSearchTestData &data)
+{
+ std::vector<int> refIndices(data.generateIndex(data.refPos_.size()));
+ std::vector<int> testIndices(data.generateIndex(data.testPositions_.size()));
+ gmx::AnalysisNeighborhoodSearch search =
+ nb->initSearch(&data.pbc_,
+ data.refPositions().indexed(refIndices));
+ testPairSearchFull(&search, data, data.testPositions(), NULL,
+ refIndices, testIndices);
+}
+
+void NeighborhoodSearchTest::testPairSearchFull(
+ gmx::AnalysisNeighborhoodSearch *search,
+ const NeighborhoodSearchTestData &data,
+ const gmx::AnalysisNeighborhoodPositions &pos,
+ const t_blocka *excls,
+ const gmx::ConstArrayRef<int> &refIndices,
+ const gmx::ConstArrayRef<int> &testIndices)
+{
+ // TODO: Some parts of this code do not work properly if pos does not
+ // initially contain all the test positions.
+ std::set<int> remainingTestPositions;
+ gmx::AnalysisNeighborhoodPositions posCopy(pos);
+ if (testIndices.empty())
{
- std::set<int> checkSet = i->refPairs;
- gmx::AnalysisNeighborhoodPairSearch pairSearch =
- search->startPairSearch(i->x);
- gmx::AnalysisNeighborhoodPair pair;
- while (pairSearch.findNextPair(&pair))
+ for (size_t i = 0; i < data.testPositions_.size(); ++i)
{
- EXPECT_EQ(0, pair.testIndex());
- if (checkSet.erase(pair.refIndex()) == 0)
+ remainingTestPositions.insert(i);
+ }
+ }
+ else
+ {
+ remainingTestPositions.insert(testIndices.begin(), testIndices.end());
+ posCopy.indexed(testIndices);
+ }
+ gmx::AnalysisNeighborhoodPairSearch pairSearch
+ = search->startPairSearch(posCopy);
+ gmx::AnalysisNeighborhoodPair pair;
+ // There is an ordering assumption here that all pairs for a test position
+ // are returned consencutively; with the current optimizations in the
+ // search code, this is reasoable, as the set of grid cell pairs searched
+ // depends on the test position.
+ RefPairList refPairs;
+ int prevTestPos = -1;
+ while (pairSearch.findNextPair(&pair))
+ {
+ const int testIndex =
+ (testIndices.empty() ? pair.testIndex() : testIndices[pair.testIndex()]);
+ const int refIndex =
+ (refIndices.empty() ? pair.refIndex() : refIndices[pair.refIndex()]);
+ if (testIndex != prevTestPos)
+ {
+ if (prevTestPos != -1)
+ {
+ checkAllPairsFound(refPairs, data.refPos_, prevTestPos,
+ data.testPositions_[prevTestPos].x);
+ }
+ if (remainingTestPositions.count(testIndex) == 0)
{
- // TODO: Check whether the same pair was returned more than
- // once and give a better error message if so.
ADD_FAILURE()
- << "Expected: Position " << pair.refIndex()
- << " is within cutoff.\n"
- << " Actual: It is not.";
+ << "Pairs for test position " << testIndex
+ << " are returned more than once.";
+ }
+ remainingTestPositions.erase(testIndex);
+ refPairs = data.testPositions_[testIndex].refPairs;
+ if (excls != NULL)
+ {
+ ExclusionsHelper::markExcludedPairs(&refPairs, testIndex, excls);
}
+ if (!refIndices.empty())
+ {
+ RefPairList::iterator refPair;
+ for (refPair = refPairs.begin(); refPair != refPairs.end(); ++refPair)
+ {
+ refPair->bIndexed = false;
+ }
+ for (size_t i = 0; i < refIndices.size(); ++i)
+ {
+ NeighborhoodSearchTestData::RefPair searchPair(refIndices[i], 0.0);
+ refPair = std::lower_bound(refPairs.begin(), refPairs.end(), searchPair);
+ if (refPair != refPairs.end() && refPair->refIndex == refIndices[i])
+ {
+ refPair->bIndexed = true;
+ }
+ }
+ for (refPair = refPairs.begin(); refPair != refPairs.end(); ++refPair)
+ {
+ if (!refPair->bIndexed)
+ {
+ refPair->bFound = true;
+ }
+ }
+ }
+ prevTestPos = testIndex;
+ }
+
+ NeighborhoodSearchTestData::RefPair searchPair(refIndex,
+ sqrt(pair.distance2()));
+ RefPairList::iterator foundRefPair
+ = std::lower_bound(refPairs.begin(), refPairs.end(), searchPair);
+ if (foundRefPair == refPairs.end() || foundRefPair->refIndex != refIndex)
+ {
+ ADD_FAILURE()
+ << "Expected: Pair (ref: " << refIndex << ", test: " << testIndex
+ << ") is not within the cutoff.\n"
+ << " Actual: It is returned.";
+ }
+ else if (foundRefPair->bExcluded)
+ {
+ ADD_FAILURE()
+ << "Expected: Pair (ref: " << refIndex << ", test: " << testIndex
+ << ") is excluded from the search.\n"
+ << " Actual: It is returned.";
+ }
+ else if (!foundRefPair->bIndexed)
+ {
+ ADD_FAILURE()
+ << "Expected: Pair (ref: " << refIndex << ", test: " << testIndex
+ << ") is not part of the indexed set.\n"
+ << " Actual: It is returned.";
+ }
+ else if (foundRefPair->bFound)
+ {
+ ADD_FAILURE()
+ << "Expected: Pair (ref: " << refIndex << ", test: " << testIndex
+ << ") is returned only once.\n"
+ << " Actual: It is returned multiple times.";
+ return;
+ }
+ else
+ {
+ foundRefPair->bFound = true;
+ EXPECT_REAL_EQ_TOL(foundRefPair->distance, searchPair.distance,
+ gmx::test::ulpTolerance(64))
+ << "Distance computed by the neighborhood search does not match.";
+ }
+ }
+ checkAllPairsFound(refPairs, data.refPos_, prevTestPos,
+ data.testPositions_[prevTestPos].x);
+ for (std::set<int>::const_iterator i = remainingTestPositions.begin();
+ i != remainingTestPositions.end(); ++i)
+ {
+ if (!data.testPositions_[*i].refPairs.empty())
+ {
+ ADD_FAILURE()
+ << "Expected: Pairs would be returned for test position " << *i << ".\n"
+ << " Actual: None were returned.";
+ break;
}
- EXPECT_TRUE(checkSet.empty()) << "Some positions were not returned by the pair search.";
}
}
NeighborhoodSearchTestData data_;
};
+class TrivialNoPBCTestData
+{
+ public:
+ static const NeighborhoodSearchTestData &get()
+ {
+ static TrivialNoPBCTestData singleton;
+ return singleton.data_;
+ }
+
+ TrivialNoPBCTestData() : data_(12345, 1.0)
+ {
+ data_.generateRandomRefPositions(10);
+ data_.generateRandomTestPositions(5);
+ data_.computeReferences(NULL);
+ }
+
+ private:
+ NeighborhoodSearchTestData data_;
+};
+
class RandomBoxFullPBCData
{
public:
NeighborhoodSearchTestData data_;
};
+class RandomBoxXYFullPBCData
+{
+ public:
+ static const NeighborhoodSearchTestData &get()
+ {
+ static RandomBoxXYFullPBCData singleton;
+ return singleton.data_;
+ }
+
+ RandomBoxXYFullPBCData() : data_(54321, 1.0)
+ {
+ data_.box_[XX][XX] = 10.0;
+ data_.box_[YY][YY] = 5.0;
+ data_.box_[ZZ][ZZ] = 7.0;
+ // TODO: Consider whether manually picking some positions would give better
+ // test coverage.
+ data_.generateRandomRefPositions(1000);
+ data_.generateRandomTestPositions(100);
+ set_pbc(&data_.pbc_, epbcXYZ, data_.box_);
+ data_.computeReferencesXY(&data_.pbc_);
+ }
+
+ private:
+ NeighborhoodSearchTestData data_;
+};
+
class RandomTriclinicFullPBCData
{
public:
NeighborhoodSearchTestData data_;
};
+class RandomBoxNoPBCData
+{
+ public:
+ static const NeighborhoodSearchTestData &get()
+ {
+ static RandomBoxNoPBCData singleton;
+ return singleton.data_;
+ }
+
+ RandomBoxNoPBCData() : data_(12345, 1.0)
+ {
+ data_.box_[XX][XX] = 10.0;
+ data_.box_[YY][YY] = 5.0;
+ data_.box_[ZZ][ZZ] = 7.0;
+ // TODO: Consider whether manually picking some positions would give better
+ // test coverage.
+ data_.generateRandomRefPositions(1000);
+ data_.generateRandomTestPositions(100);
+ set_pbc(&data_.pbc_, epbcNONE, data_.box_);
+ data_.computeReferences(NULL);
+ }
+
+ private:
+ NeighborhoodSearchTestData data_;
+};
+
/********************************************************************
* Actual tests
*/
testMinimumDistance(&search, data);
testNearestPoint(&search, data);
testPairSearch(&search, data);
+
+ search.reset();
+ testPairSearchIndexed(&nb_, data);
+}
+
+TEST_F(NeighborhoodSearchTest, SimpleSearchXY)
+{
+ const NeighborhoodSearchTestData &data = RandomBoxXYFullPBCData::get();
+
+ nb_.setCutoff(data.cutoff_);
+ nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Simple);
+ nb_.setXYMode(true);
+ gmx::AnalysisNeighborhoodSearch search =
+ nb_.initSearch(&data.pbc_, data.refPositions());
+ ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Simple, search.mode());
+
+ testIsWithin(&search, data);
+ testMinimumDistance(&search, data);
+ testNearestPoint(&search, data);
+ testPairSearch(&search, data);
}
TEST_F(NeighborhoodSearchTest, GridSearchBox)
testMinimumDistance(&search, data);
testNearestPoint(&search, data);
testPairSearch(&search, data);
+
+ search.reset();
+ testPairSearchIndexed(&nb_, data);
}
TEST_F(NeighborhoodSearchTest, GridSearchTriclinic)
nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Grid);
gmx::AnalysisNeighborhoodSearch search =
nb_.initSearch(&data.pbc_, data.refPositions());
- // Currently, grid searching not supported with 2D PBC.
- //ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Grid, search.mode());
+ ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Grid, search.mode());
+
+ testIsWithin(&search, data);
+ testMinimumDistance(&search, data);
+ testNearestPoint(&search, data);
+ testPairSearch(&search, data);
+}
+
+TEST_F(NeighborhoodSearchTest, GridSearchNoPBC)
+{
+ const NeighborhoodSearchTestData &data = RandomBoxNoPBCData::get();
+
+ nb_.setCutoff(data.cutoff_);
+ nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Grid);
+ gmx::AnalysisNeighborhoodSearch search =
+ nb_.initSearch(&data.pbc_, data.refPositions());
+ ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Grid, search.mode());
+
+ testPairSearch(&search, data);
+}
+
+TEST_F(NeighborhoodSearchTest, GridSearchXYBox)
+{
+ const NeighborhoodSearchTestData &data = RandomBoxXYFullPBCData::get();
+
+ nb_.setCutoff(data.cutoff_);
+ nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Grid);
+ nb_.setXYMode(true);
+ gmx::AnalysisNeighborhoodSearch search =
+ nb_.initSearch(&data.pbc_, data.refPositions());
+ ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Grid, search.mode());
testIsWithin(&search, data);
testMinimumDistance(&search, data);
testPairSearch(&search2, data);
gmx::AnalysisNeighborhoodPair pair;
- pairSearch1.findNextPair(&pair);
+ ASSERT_TRUE(pairSearch1.findNextPair(&pair))
+ << "Test data did not contain any pairs for position 0 (problem in the test).";
EXPECT_EQ(0, pair.testIndex());
- EXPECT_TRUE(data.testPositions_[0].refPairs.count(pair.refIndex()) == 1);
+ {
+ NeighborhoodSearchTestData::RefPair searchPair(pair.refIndex(), sqrt(pair.distance2()));
+ EXPECT_TRUE(data.containsPair(0, searchPair));
+ }
- pairSearch2.findNextPair(&pair);
+ ASSERT_TRUE(pairSearch2.findNextPair(&pair))
+ << "Test data did not contain any pairs for position 1 (problem in the test).";
EXPECT_EQ(1, pair.testIndex());
- EXPECT_TRUE(data.testPositions_[1].refPairs.count(pair.refIndex()) == 1);
+ {
+ NeighborhoodSearchTestData::RefPair searchPair(pair.refIndex(), sqrt(pair.distance2()));
+ EXPECT_TRUE(data.containsPair(1, searchPair));
+ }
+}
+
+TEST_F(NeighborhoodSearchTest, HandlesNoPBC)
+{
+ const NeighborhoodSearchTestData &data = TrivialNoPBCTestData::get();
+
+ nb_.setCutoff(data.cutoff_);
+ gmx::AnalysisNeighborhoodSearch search =
+ nb_.initSearch(&data.pbc_, data.refPositions());
+ ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Simple, search.mode());
+
+ testIsWithin(&search, data);
+ testMinimumDistance(&search, data);
+ testNearestPoint(&search, data);
+ testPairSearch(&search, data);
+}
+
+TEST_F(NeighborhoodSearchTest, HandlesNullPBC)
+{
+ const NeighborhoodSearchTestData &data = TrivialNoPBCTestData::get();
+
+ nb_.setCutoff(data.cutoff_);
+ gmx::AnalysisNeighborhoodSearch search =
+ nb_.initSearch(NULL, data.refPositions());
+ ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Simple, search.mode());
+
+ testIsWithin(&search, data);
+ testMinimumDistance(&search, data);
+ testNearestPoint(&search, data);
+ testPairSearch(&search, data);
}
TEST_F(NeighborhoodSearchTest, HandlesSkippingPairs)
++currentIndex;
}
EXPECT_EQ(currentIndex, pair.testIndex());
- EXPECT_TRUE(data.testPositions_[currentIndex].refPairs.count(pair.refIndex()) == 1);
+ NeighborhoodSearchTestData::RefPair searchPair(pair.refIndex(), sqrt(pair.distance2()));
+ EXPECT_TRUE(data.containsPair(currentIndex, searchPair));
pairSearch.skipRemainingPairsForTestPosition();
++currentIndex;
}
}
+TEST_F(NeighborhoodSearchTest, SimpleSearchExclusions)
+{
+ const NeighborhoodSearchTestData &data = RandomBoxFullPBCData::get();
+
+ ExclusionsHelper helper(data.refPosCount_, data.testPositions_.size());
+ helper.generateExclusions();
+
+ nb_.setCutoff(data.cutoff_);
+ nb_.setTopologyExclusions(helper.exclusions());
+ nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Simple);
+ gmx::AnalysisNeighborhoodSearch search =
+ nb_.initSearch(&data.pbc_,
+ data.refPositions().exclusionIds(helper.refPosIds()));
+ ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Simple, search.mode());
+
+ testPairSearchFull(&search, data,
+ data.testPositions().exclusionIds(helper.testPosIds()),
+ helper.exclusions(), gmx::EmptyArrayRef(), gmx::EmptyArrayRef());
+}
+
+TEST_F(NeighborhoodSearchTest, GridSearchExclusions)
+{
+ const NeighborhoodSearchTestData &data = RandomBoxFullPBCData::get();
+
+ ExclusionsHelper helper(data.refPosCount_, data.testPositions_.size());
+ helper.generateExclusions();
+
+ nb_.setCutoff(data.cutoff_);
+ nb_.setTopologyExclusions(helper.exclusions());
+ nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Grid);
+ gmx::AnalysisNeighborhoodSearch search =
+ nb_.initSearch(&data.pbc_,
+ data.refPositions().exclusionIds(helper.refPosIds()));
+ ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Grid, search.mode());
+
+ testPairSearchFull(&search, data,
+ data.testPositions().exclusionIds(helper.testPosIds()),
+ helper.exclusions(), gmx::EmptyArrayRef(), gmx::EmptyArrayRef());
+}
+
} // namespace
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
-#include <gtest/gtest.h>
+#include "gmxpre.h"
+
+#include "gromacs/selection/poscalc.h"
#include <vector>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vec.h"
+#include <gtest/gtest.h>
+#include "gromacs/fileio/trx.h"
+#include "gromacs/math/vec.h"
#include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/poscalc.h"
#include "gromacs/selection/position.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/uniqueptr.h"
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
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+ <IndexMapping Name="Initialized">
+ <Sequence Name="Input">
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+ <Int Name="MapId">3</Int>
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+ <Block>
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+ <Int>0</Int>
+ <Int>0</Int>
+ <Int>0</Int>
+ </Sequence>
+ </OrgIdGroups>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
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+ <Int>2</Int>
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+ </OrgIdGroups>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
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+ <Int Name="RefId">3</Int>
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+ </Block>
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+ <OrgIdGroups Name="Molecules">
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+ <Int>0</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ </Sequence>
+ </OrgIdGroups>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <IndexMapping Name="Initialized">
+ <Sequence Name="Input">
+ <Int Name="Length">5</Int>
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+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>13</Int>
+ </Sequence>
+ <Int Name="Count">5</Int>
+ <Block>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>3</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ <Int Name="MapId">3</Int>
+ </Block>
+ <Block>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ <Int Name="MapId">4</Int>
+ </Block>
+ <Block>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>7</Int>
+ </Sequence>
+ <Int Name="RefId">2</Int>
+ <Int Name="MapId">7</Int>
+ </Block>
+ <Block>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>8</Int>
+ </Sequence>
+ <Int Name="RefId">3</Int>
+ <Int Name="MapId">8</Int>
+ </Block>
+ <Block>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>13</Int>
+ </Sequence>
+ <Int Name="RefId">4</Int>
+ <Int Name="MapId">13</Int>
+ </Block>
+ </IndexMapping>
+ <OrgIdGroups Name="Residues">
+ <Int Name="GroupCount">3</Int>
+ <Sequence Name="OrgId">
+ <Int Name="Length">5</Int>
+ <Int>0</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ </Sequence>
+ </OrgIdGroups>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <IndexMapping Name="Initialized">
+ <Sequence Name="Input">
+ <Int Name="Length">5</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>13</Int>
+ </Sequence>
+ <Int Name="Count">3</Int>
+ <Block>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ </Sequence>
+ <Int Name="RefId">0</Int>
+ <Int Name="MapId">1</Int>
+ </Block>
+ <Block>
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ </Sequence>
+ <Int Name="RefId">1</Int>
+ <Int Name="MapId">2</Int>
+ </Block>
+ <Block>
+ <Sequence Name="Atoms">
+ <Int Name="Length">1</Int>
+ <Int>13</Int>
+ </Sequence>
+ <Int Name="RefId">2</Int>
+ <Int Name="MapId">4</Int>
+ </Block>
+ </IndexMapping>
+ <OrgIdGroups Name="Single">
+ <Int Name="GroupCount">3</Int>
+ <Sequence Name="OrgId">
+ <Int Name="Length">3</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ </Sequence>
+ </OrgIdGroups>
+</ReferenceData>
<Sequence Name="Atoms">
<Int Name="Length">0</Int>
</Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">1</Int>
+ <Position>
+ <Int Name="RefId">0</Int>
+ <Int Name="MappedId">0</Int>
+ </Position>
+ </Sequence>
</Selection>
</CompiledSelections>
<EvaluatedSelections Name="Frame1">
<Real Name="Y">-2</Real>
<Real Name="Z">3.5</Real>
</Vector>
+ <Int Name="RefId">0</Int>
+ <Int Name="MappedId">0</Int>
</Position>
</Sequence>
</Selection>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <ParsedSelections Name="Parsed">
+ <ParsedSelection Name="Selection1">
+ <String Name="Input">[0, 0, 0] plus [0, 1, 0]</String>
+ <String Name="Text">[0, 0, 0] plus [0, 1, 0]</String>
+ <Bool Name="Dynamic">false</Bool>
+ </ParsedSelection>
+ </ParsedSelections>
+ <CompiledSelections Name="Compiled">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">0</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">2</Int>
+ <Position>
+ <Int Name="RefId">0</Int>
+ <Int Name="MappedId">0</Int>
+ </Position>
+ <Position>
+ <Int Name="RefId">1</Int>
+ <Int Name="MappedId">0</Int>
+ </Position>
+ </Sequence>
+ </Selection>
+ </CompiledSelections>
+ <EvaluatedSelections Name="Frame1">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">0</Int>
+ </Sequence>
+ <Sequence Name="Positions">
+ <Int Name="Length">2</Int>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Int Name="RefId">0</Int>
+ <Int Name="MappedId">0</Int>
+ </Position>
+ <Position>
+ <Vector Name="Coordinates">
+ <Real Name="X">0</Real>
+ <Real Name="Y">1</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Int Name="RefId">1</Int>
+ <Int Name="MappedId">0</Int>
+ </Position>
+ </Sequence>
+ </Selection>
+ </EvaluatedSelections>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <ParsedSelections Name="Parsed">
+ <ParsedSelection Name="Selection1">
+ <String Name="Input">x < y of cog of resnr 2</String>
+ <String Name="Text">x < y of cog of resnr 2</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ </ParsedSelections>
+ <CompiledSelections Name="Compiled">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ </CompiledSelections>
+ <EvaluatedSelections Name="Frame1">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">8</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ </Sequence>
+ </Selection>
+ </EvaluatedSelections>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <ParsedSelections Name="Parsed">
+ <ParsedSelection Name="Selection1">
+ <String Name="Input">x - y of cog of resnr 2 < 0</String>
+ <String Name="Text">x - y of cog of resnr 2 < 0</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ </ParsedSelections>
+ <CompiledSelections Name="Compiled">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ </CompiledSelections>
+ <EvaluatedSelections Name="Frame1">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">8</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ </Sequence>
+ </Selection>
+ </EvaluatedSelections>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <ParsedSelections Name="Parsed">
+ <ParsedSelection Name="Selection1">
+ <String Name="Input">res_cog x > 2</String>
+ <String Name="Text">res_cog x > 2</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection2">
+ <String Name="Input">name CB and res_cog y > 2.5</String>
+ <String Name="Text">name CB and res_cog y > 2.5</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ </ParsedSelections>
+ <CompiledSelections Name="Compiled">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection2">
+ <Sequence Name="Atoms">
+ <Int Name="Length">5</Int>
+ <Int>0</Int>
+ <Int>3</Int>
+ <Int>6</Int>
+ <Int>9</Int>
+ <Int>12</Int>
+ </Sequence>
+ </Selection>
+ </CompiledSelections>
+ <EvaluatedSelections Name="Frame1">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">9</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection2">
+ <Sequence Name="Atoms">
+ <Int Name="Length">2</Int>
+ <Int>6</Int>
+ <Int>9</Int>
+ </Sequence>
+ </Selection>
+ </EvaluatedSelections>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <ParsedSelections Name="Parsed">
+ <ParsedSelection Name="Selection1">
+ <String Name="Input">res_cog distance from cog of resnr 1 < 2</String>
+ <String Name="Text">res_cog distance from cog of resnr 1 < 2</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ <ParsedSelection Name="Selection2">
+ <String Name="Input">res_cog within 2 of cog of resnr 1</String>
+ <String Name="Text">res_cog within 2 of cog of resnr 1</String>
+ <Bool Name="Dynamic">true</Bool>
+ </ParsedSelection>
+ </ParsedSelections>
+ <CompiledSelections Name="Compiled">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection2">
+ <Sequence Name="Atoms">
+ <Int Name="Length">15</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ <Int>9</Int>
+ <Int>10</Int>
+ <Int>11</Int>
+ <Int>12</Int>
+ <Int>13</Int>
+ <Int>14</Int>
+ </Sequence>
+ </Selection>
+ </CompiledSelections>
+ <EvaluatedSelections Name="Frame1">
+ <Selection Name="Selection1">
+ <Sequence Name="Atoms">
+ <Int Name="Length">9</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ </Sequence>
+ </Selection>
+ <Selection Name="Selection2">
+ <Sequence Name="Atoms">
+ <Int Name="Length">9</Int>
+ <Int>0</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ <Int>4</Int>
+ <Int>5</Int>
+ <Int>6</Int>
+ <Int>7</Int>
+ <Int>8</Int>
+ </Sequence>
+ </Selection>
+ </EvaluatedSelections>
+</ReferenceData>
</table>
</xsl:template>
+<xsl:template match="OrgIdGroups">
+ <h2>Groups: <xsl:value-of select="@Name"/></h2>
+ <table>
+ <tr>
+ <td>Group count:</td>
+ <td><xsl:value-of select="Int[@Name='GroupCount']"/></td>
+ </tr>
+ <tr>
+ <td>OrgId</td>
+ <td>
+ <xsl:call-template name="SequenceAsCSV">
+ <xsl:with-param name="root" select="Sequence[@Name='OrgId']"/>
+ </xsl:call-template>
+ </td>
+ </tr>
+ </table>
+</xsl:template>
+
<!-- Position calculation reference data -->
<xsl:template match="InitializedPositions">
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
+#include "gromacs/selection/selectioncollection.h"
+
#include <gtest/gtest.h>
+#include "gromacs/fileio/trx.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
#include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/selectioncollection.h"
#include "gromacs/selection/selection.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/flags.h"
// EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
}
+TEST_F(SelectionCollectionTest, HandlesOutOfRangeAtomIndexInGroup)
+{
+ ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, 5));
+ ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
+ EXPECT_THROW_GMX(sc_.parseFromString("group \"GrpB\""), gmx::InconsistentInputError);
+}
+
+TEST_F(SelectionCollectionTest, HandlesOutOfRangeAtomIndexInGroupDelayed)
+{
+ ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
+ ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"GrpB\""));
+ EXPECT_THROW_GMX(sc_.setTopology(NULL, 5), gmx::InconsistentInputError);
+}
+
+TEST_F(SelectionCollectionTest, HandlesOutOfRangeAtomIndexInGroupDelayed2)
+{
+ ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, 5));
+ ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"GrpB\""));
+ EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
+}
+
TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
{
ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
}
-// TODO: Tests for evaluation errors
+TEST_F(SelectionCollectionTest, HandlesFramesWithTooSmallAtomSubsets)
+{
+ ASSERT_NO_THROW_GMX(sc_.parseFromString("atomnr 3 to 10"));
+ ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
+ ASSERT_NO_THROW_GMX(sc_.compile());
+ frame_->natoms = 8;
+ EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
+}
+
+TEST_F(SelectionCollectionTest, HandlesFramesWithTooSmallAtomSubsets2)
+{
+ // Evaluating the positions will require atoms 1-9.
+ ASSERT_NO_THROW_GMX(sc_.parseFromString("whole_res_com of atomnr 2 5 7"));
+ ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
+ ASSERT_NO_THROW_GMX(sc_.compile());
+ frame_->natoms = 8;
+ EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
+}
+
+TEST_F(SelectionCollectionTest, HandlesFramesWithTooSmallAtomSubsets3)
+{
+ ASSERT_NO_THROW_GMX(sc_.parseFromString("mindistance from atomnr 1 to 5 < 2"));
+ ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
+ ASSERT_NO_THROW_GMX(sc_.compile());
+ frame_->natoms = 10;
+ EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
+}
+
+// TODO: Tests for more evaluation errors
/********************************************************************
ASSERT_NO_FATAL_FAILURE(runCompiler());
}
+
TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
{
static const char * const selections[] = {
"[1, -2, 3.5]"
};
- setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
+ setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
+ | efTestPositionMapping);
+ runTest("simple.gro", selections);
+}
+
+
+TEST_F(SelectionCollectionDataTest, HandlesConstantPositionsWithModifiers)
+{
+ static const char * const selections[] = {
+ "[0, 0, 0] plus [0, 1, 0]"
+ };
+ setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
+ | efTestPositionMapping);
runTest("simple.gro", selections);
}
}
+TEST_F(SelectionCollectionDataTest, HandlesPositionModifiersForKeywords)
+{
+ static const char * const selections[] = {
+ "res_cog x > 2",
+ "name CB and res_cog y > 2.5"
+ };
+ setFlags(TestFlags() | efTestEvaluation);
+ runTest("simple.gro", selections);
+}
+
+
+TEST_F(SelectionCollectionDataTest, HandlesPositionModifiersForMethods)
+{
+ static const char * const selections[] = {
+ "res_cog distance from cog of resnr 1 < 2",
+ "res_cog within 2 of cog of resnr 1"
+ };
+ setFlags(TestFlags() | efTestEvaluation);
+ runTest("simple.gro", selections);
+}
+
+
+TEST_F(SelectionCollectionDataTest, HandlesKeywordOfPositions)
+{
+ static const char * const selections[] = {
+ "x < y of cog of resnr 2"
+ };
+ setFlags(TestFlags() | efTestEvaluation);
+ runTest("simple.gro", selections);
+}
+
+TEST_F(SelectionCollectionDataTest, HandlesKeywordOfPositionsInArithmetic)
+{
+ static const char * const selections[] = {
+ "x - y of cog of resnr 2 < 0"
+ };
+ setFlags(TestFlags() | efTestEvaluation);
+ runTest("simple.gro", selections);
+}
+
+
TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
{
static const char * const selections[] = {
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
+#include "gromacs/selection/selectionoption.h"
+
#include <gtest/gtest.h>
#include "gromacs/options/options.h"
#include "gromacs/selection/selection.h"
#include "gromacs/selection/selectioncollection.h"
#include "gromacs/selection/selectionfileoption.h"
-#include "gromacs/selection/selectionoption.h"
#include "gromacs/selection/selectionoptionmanager.h"
#include "gromacs/utility/exceptions.h"
public:
SelectionOptionTestBase();
- void setManager();
void loadTopology(const char *filename);
gmx::SelectionCollection sc_;
SelectionOptionTestBase::SelectionOptionTestBase()
: manager_(&sc_), options_(NULL, NULL)
{
+ options_.addManager(&manager_);
sc_.setReferencePosType("atom");
sc_.setOutputPosType("atom");
}
-void SelectionOptionTestBase::setManager()
-{
- setManagerForSelectionOptions(&options_, &manager_);
-}
-
void SelectionOptionTestBase::loadTopology(const char *filename)
{
topManager_.loadTopology(filename);
gmx::Selection sel;
using gmx::SelectionOption;
ASSERT_NO_THROW_GMX(options_.addOption(SelectionOption("sel").store(&sel)));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
using gmx::SelectionOption;
ASSERT_NO_THROW_GMX(options_.addOption(
SelectionOption("sel").store(&sel).onlyStatic()));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
using gmx::SelectionOption;
ASSERT_NO_THROW_GMX(options_.addOption(
SelectionOption("sel").store(&sel).onlyAtoms()));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
using gmx::SelectionOption;
ASSERT_NO_THROW_GMX(options_.addOption(
SelectionOption("sel").store(&sel)));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
using gmx::SelectionOption;
ASSERT_NO_THROW_GMX(options_.addOption(
SelectionOption("sel").store(&sel)));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
gmx::Selection sel;
using gmx::SelectionOption;
ASSERT_NO_THROW_GMX(options_.addOption(SelectionOption("sel").store(&sel)));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
using gmx::SelectionOption;
ASSERT_NO_THROW_GMX(options_.addOption(
SelectionOption("sel").store(sel).valueCount(2)));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
using gmx::SelectionOption;
options_.addOption(SelectionOption("sel").store(&sel)
.defaultSelectionText("all"));
- setManager();
EXPECT_NO_THROW_GMX(options_.finish());
using gmx::SelectionOption;
gmx::SelectionOptionInfo *info = options_.addOption(
SelectionOption("sel").storeVector(&sel).multiValue());
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
using gmx::SelectionOption;
gmx::SelectionOptionInfo *info = options_.addOption(
SelectionOption("sel").store(&sel));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
using gmx::SelectionOption;
gmx::SelectionOptionInfo *info = options_.addOption(
SelectionOption("sel").storeVector(&sel).multiValue());
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
using gmx::SelectionOption;
gmx::SelectionOptionInfo *info = options_.addOption(
SelectionOption("sel").storeVector(&sel).multiValue());
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
using gmx::SelectionOption;
ASSERT_NO_THROW_GMX(options_.addOption(
SelectionOption("sel").store(&sel).required()));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
ASSERT_NO_THROW_GMX(options_.addOption(
SelectionOption("sel").store(sel).required()
.valueCount(2)));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
gmx::Selection sel;
using gmx::SelectionOption;
ASSERT_NO_THROW_GMX(options_.addOption(SelectionOption("sel").store(&sel)));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
using gmx::SelectionOption;
gmx::SelectionOptionInfo *info = options_.addOption(
SelectionOption("sel").storeVector(&sel).valueCount(3));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
ASSERT_NO_THROW_GMX(options_.addOption(
SelectionOption("reqsel").storeVector(&reqsel)
.multiValue().required()));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
SelectionOption("sel1").storeVector(&sel1).multiValue()));
ASSERT_NO_THROW_GMX(options_.addOption(
SelectionOption("sel2").storeVector(&sel2).multiValue()));
- setManager();
gmx::OptionsAssigner assigner(&options_);
std::string value(TestFileManager::getInputFilePath("selfile.dat"));
SelectionOption("sel1").storeVector(&sel1)));
ASSERT_NO_THROW_GMX(options_.addOption(
SelectionOption("sel2").storeVector(&sel2)));
- setManager();
gmx::OptionsAssigner assigner(&options_);
std::string value(TestFileManager::getInputFilePath("selfile.dat"));
ASSERT_NO_THROW_GMX(options_.addOption(
SelectionOption("optsel").storeVector(&optsel)
.multiValue()));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
ASSERT_NO_THROW_GMX(options_.addOption(
SelectionOption("sel2").storeVector(&sel2)
.multiValue().required()));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
SelectionOption("sel1").storeVector(&sel1).required()));
ASSERT_NO_THROW_GMX(options_.addOption(
SelectionOption("sel2").storeVector(&sel2).required()));
- setManager();
gmx::OptionsAssigner assigner(&options_);
std::string value(TestFileManager::getInputFilePath("selfile.dat"));
using gmx::SelectionOption;
ASSERT_NO_THROW_GMX(options_.addOption(
SelectionOption("sel").storeVector(&sel).multiValue()));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
using gmx::SelectionOption;
ASSERT_NO_THROW_GMX(options_.addOption(
SelectionOption("sel").storeVector(&sel).multiValue()));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
using gmx::SelectionOption;
ASSERT_NO_THROW_GMX(options_.addOption(
SelectionOption("sel").storeVector(&sel).multiValue()));
- setManager();
gmx::OptionsAssigner assigner(&options_);
EXPECT_NO_THROW_GMX(assigner.start());
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
#include "toputils.h"
#include <cstring>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vec.h"
-
#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trx.h"
#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
atomtypes_.reserve(count);
for (int i = 0; i < count; ++i)
{
- atomtypes_.push_back(strdup(types[i]));
+ atomtypes_.push_back(gmx_strdup(types[i]));
}
snew(top_->atoms.atomtype, top_->atoms.nr);
for (int i = 0, j = 0; i < top_->atoms.nr; ++i, ++j)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
-#include "gromacs/legacyheaders/typedefs.h"
+struct t_topology;
+struct t_trxframe;
namespace gmx
{
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GMX_SIMD_IMPL_ARM_NEON_H
+#define GMX_SIMD_IMPL_ARM_NEON_H
+
+#include <math.h>
+
+#include <arm_neon.h>
+
+/* ARM 32-bit NEON SIMD instruction wrappers
+ *
+ * Please see documentation in gromacs/simd/simd.h for defines.
+ */
+
+/* Capability definitions for ARM 32-bit NEON */
+#define GMX_SIMD_HAVE_FLOAT
+#undef GMX_SIMD_HAVE_DOUBLE
+#define GMX_SIMD_HAVE_HARDWARE
+#define GMX_SIMD_HAVE_LOADU
+#define GMX_SIMD_HAVE_STOREU
+#define GMX_SIMD_HAVE_LOGICAL
+#define GMX_SIMD_HAVE_FMA
+#undef GMX_SIMD_HAVE_FRACTION
+#define GMX_SIMD_HAVE_FINT32
+#define GMX_SIMD_HAVE_FINT32_EXTRACT
+#define GMX_SIMD_HAVE_FINT32_LOGICAL
+#define GMX_SIMD_HAVE_FINT32_ARITHMETICS
+#undef GMX_SIMD_HAVE_DINT32
+#undef GMX_SIMD_HAVE_DINT32_EXTRACT
+#undef GMX_SIMD_HAVE_DINT32_LOGICAL
+#undef GMX_SIMD_HAVE_DINT32_ARITHMETICS
+#define GMX_SIMD4_HAVE_FLOAT
+#undef GMX_SIMD4_HAVE_DOUBLE
+
+/* Implementation details */
+#define GMX_SIMD_FLOAT_WIDTH 4
+#undef GMX_SIMD_DOUBLE_WIDTH
+#define GMX_SIMD_FINT32_WIDTH 4
+#undef GMX_SIMD_DINT32_WIDTH
+#define GMX_SIMD_RSQRT_BITS 8
+#define GMX_SIMD_RCP_BITS 8
+
+/****************************************************
+ * SINGLE PRECISION SIMD IMPLEMENTATION *
+ ****************************************************/
+#define gmx_simd_float_t float32x4_t
+#define gmx_simd_load_f vld1q_f32
+#define gmx_simd_load1_f vld1q_dup_f32
+#define gmx_simd_set1_f vdupq_n_f32
+#define gmx_simd_store_f vst1q_f32
+#define gmx_simd_loadu_f vld1q_f32
+#define gmx_simd_storeu_f vst1q_f32
+#define gmx_simd_setzero_f() vdupq_n_f32(0.0f)
+#define gmx_simd_add_f vaddq_f32
+#define gmx_simd_sub_f vsubq_f32
+#define gmx_simd_mul_f vmulq_f32
+#ifdef __ARM_FEATURE_FMA
+# define gmx_simd_fmadd_f(a, b, c) vfmaq_f32(c, b, a)
+# define gmx_simd_fmsub_f(a, b, c) vnegq_f32(vfmsq_f32(c, b, a))
+# define gmx_simd_fnmadd_f(a, b, c) vfmaq_f32(c, b, a)
+# define gmx_simd_fnmsub_f(a, b, c) vnegq_f32(vfmaq_f32(c, b, a))
+#else
+# define gmx_simd_fmadd_f(a, b, c) vmlaq_f32(c, b, a)
+# define gmx_simd_fmsub_f(a, b, c) vnegq_f32(vmlsq_f32(c, b, a))
+# define gmx_simd_fnmadd_f(a, b, c) vmlsq_f32(c, b, a)
+# define gmx_simd_fnmsub_f(a, b, c) vnegq_f32(vmlaq_f32(c, b, a))
+#endif
+#define gmx_simd_and_f(a, b) vreinterpretq_f32_s32(vandq_s32(vreinterpretq_s32_f32(a), vreinterpretq_s32_f32(b)))
+#define gmx_simd_andnot_f(a, b) vreinterpretq_f32_s32(vbicq_s32(vreinterpretq_s32_f32(b), vreinterpretq_s32_f32(a)))
+#define gmx_simd_or_f(a, b) vreinterpretq_f32_s32(vorrq_s32(vreinterpretq_s32_f32(a), vreinterpretq_s32_f32(b)))
+#define gmx_simd_xor_f(a, b) vreinterpretq_f32_s32(veorq_s32(vreinterpretq_s32_f32(a), vreinterpretq_s32_f32(b)))
+#define gmx_simd_rsqrt_f vrsqrteq_f32
+#define gmx_simd_rsqrt_iter_f(lu, x) vmulq_f32(lu, vrsqrtsq_f32(vmulq_f32(lu, lu), x))
+#define gmx_simd_rcp_f vrecpeq_f32
+#define gmx_simd_rcp_iter_f(lu, x) vmulq_f32(lu, vrecpsq_f32(lu, x))
+#define gmx_simd_fabs_f(x) vabsq_f32(x)
+#define gmx_simd_fneg_f(x) vnegq_f32(x)
+#define gmx_simd_max_f vmaxq_f32
+#define gmx_simd_min_f vminq_f32
+#define gmx_simd_round_f(x) gmx_simd_cvt_i2f(gmx_simd_cvt_f2i(x))
+#define gmx_simd_trunc_f(x) gmx_simd_cvt_i2f(gmx_simd_cvtt_f2i(x))
+#define gmx_simd_fraction_f(x) vsubq_f32(x, gmx_simd_trunc_f(x))
+#define gmx_simd_get_exponent_f gmx_simd_get_exponent_f_arm_neon
+#define gmx_simd_get_mantissa_f gmx_simd_get_mantissa_f_arm_neon
+#define gmx_simd_set_exponent_f gmx_simd_set_exponent_f_arm_neon
+/* integer datatype corresponding to float: gmx_simd_fint32_t */
+#define gmx_simd_fint32_t int32x4_t
+#define gmx_simd_load_fi(m) vld1q_s32(m)
+#define gmx_simd_set1_fi vdupq_n_s32
+#define gmx_simd_store_fi(m, x) vst1q_s32(m, x)
+#define gmx_simd_loadu_fi(m) vld1q_s32(m)
+#define gmx_simd_storeu_fi(m, x) vst1q_s32(m, x)
+#define gmx_simd_setzero_fi() vdupq_n_s32(0)
+#define gmx_simd_cvtt_f2i vcvtq_s32_f32
+#define gmx_simd_cvt_f2i(x) vcvtq_s32_f32(gmx_simd_add_f(gmx_simd_or_f(gmx_simd_and_f(vdupq_n_f32(-0.0f), x), vdupq_n_f32(0.5f)), x))
+#define gmx_simd_cvt_i2f vcvtq_f32_s32
+#define gmx_simd_extract_fi(x, i) vgetq_lane_s32(x, i)
+/* Integer logical ops on gmx_simd_fint32_t */
+#define gmx_simd_slli_fi vshlq_n_s32
+#define gmx_simd_srli_fi vshrq_n_s32
+#define gmx_simd_and_fi vandq_s32
+#define gmx_simd_andnot_fi(a, b) vbicq_s32(b, a)
+#define gmx_simd_or_fi vorrq_s32
+#define gmx_simd_xor_fi veorq_s32
+/* Integer arithmetic ops on gmx_simd_fint32_t */
+#define gmx_simd_add_fi vaddq_s32
+#define gmx_simd_sub_fi vsubq_s32
+#define gmx_simd_mul_fi vmulq_s32
+/* Boolean & comparison operations on gmx_simd_float_t */
+#define gmx_simd_fbool_t uint32x4_t
+#define gmx_simd_cmpeq_f vceqq_f32
+#define gmx_simd_cmplt_f vcltq_f32
+#define gmx_simd_cmple_f vcleq_f32
+#define gmx_simd_and_fb vandq_u32
+#define gmx_simd_or_fb vorrq_u32
+#define gmx_simd_anytrue_fb gmx_simd_anytrue_fb_arm_neon
+#define gmx_simd_blendzero_f(a, sel) vreinterpretq_f32_u32(vandq_u32(vreinterpretq_u32_f32(a), sel))
+#define gmx_simd_blendnotzero_f(a, sel) vreinterpretq_f32_u32(vbicq_u32(vreinterpretq_u32_f32(a), sel))
+#define gmx_simd_blendv_f(a, b, sel) vbslq_f32(sel, b, a)
+#define gmx_simd_reduce_f(a) gmx_simd_reduce_f_arm_neon(a)
+/* Boolean & comparison operations on gmx_simd_fint32_t */
+#define gmx_simd_fibool_t uint32x4_t
+#define gmx_simd_cmpeq_fi vceqq_s32
+#define gmx_simd_cmplt_fi vcltq_s32
+#define gmx_simd_and_fib vandq_u32
+#define gmx_simd_or_fib vorrq_u32
+#define gmx_simd_anytrue_fib gmx_simd_anytrue_fb
+#define gmx_simd_blendzero_fi(a, sel) vandq_s32(a, vreinterpretq_s32_u32(sel))
+#define gmx_simd_blendnotzero_fi(a, sel) vbicq_s32(a, vreinterpretq_s32_u32(sel))
+#define gmx_simd_blendv_fi(a, b, sel) vbslq_s32(sel, b, a)
+/* Conversions between different booleans */
+#define gmx_simd_cvt_fb2fib(x) (x)
+#define gmx_simd_cvt_fib2fb(x) (x)
+
+/****************************************************
+ * NO DOUBLE PRECISION SIMD AVAILABLE *
+ ****************************************************/
+
+
+/****************************************************
+ * SINGLE PRECISION IMPLEMENTATION HELPER FUNCTIONS *
+ ****************************************************/
+static gmx_inline gmx_simd_float_t
+gmx_simd_get_exponent_f_arm_neon(gmx_simd_float_t x)
+{
+ const float32x4_t expmask = vreinterpretq_f32_s32( vdupq_n_s32(0x7F800000) );
+ int32x4_t iexp;
+
+ iexp = vreinterpretq_s32_f32(gmx_simd_and_f(x, expmask));
+ iexp = vsubq_s32(vshrq_n_s32(iexp, 23), vdupq_n_s32(127));
+ return vcvtq_f32_s32(iexp);
+}
+
+
+static gmx_inline gmx_simd_float_t
+gmx_simd_get_mantissa_f_arm_neon(gmx_simd_float_t x)
+{
+ const float32x4_t mantmask = vreinterpretq_f32_s32( vdupq_n_s32(0x007FFFFF) );
+ const float32x4_t one = vdupq_n_f32(1.0f);
+
+ /* Get mantissa */
+ x = gmx_simd_and_f(mantmask, x);
+ /* Reset zero (but correctly biased) exponent */
+ return gmx_simd_or_f(x, one);
+}
+
+
+static gmx_inline gmx_simd_float_t
+gmx_simd_set_exponent_f_arm_neon(gmx_simd_float_t x)
+{
+ int32x4_t iexp = gmx_simd_cvt_f2i(x);
+
+ iexp = vshlq_n_s32(vaddq_s32(iexp, vdupq_n_s32(127)), 23);
+ return vreinterpretq_f32_s32(iexp);
+}
+
+static gmx_inline float
+gmx_simd_reduce_f_arm_neon(gmx_simd_float_t a)
+{
+ float32x4_t b = vextq_f32(a, a, 2);
+
+ a = vaddq_f32(a, b);
+ b = vextq_f32(a, a, 1);
+ a = vaddq_f32(a, b);
+ return vgetq_lane_f32(a, 0);
+}
+
+static gmx_inline int
+gmx_simd_anytrue_fb_arm_neon(gmx_simd_fbool_t a)
+{
+ uint32x4_t b = vextq_u32(a, a, 2);
+
+ a = gmx_simd_or_fb(a, b);
+ b = vextq_u32(a, a, 1);
+ a = gmx_simd_or_fb(a, b);
+ return (vgetq_lane_u32(a, 0) != 0);
+}
+
+
+/* ARM 32-bit Neon is already 4-wide in single, so just reuse float type for SIMD4 */
+#define gmx_simd4_float_t gmx_simd_float_t
+#define gmx_simd4_load_f gmx_simd_load_f
+#define gmx_simd4_load1_f gmx_simd_load1_f
+#define gmx_simd4_set1_f gmx_simd_set1_f
+#define gmx_simd4_store_f gmx_simd_store_f
+#define gmx_simd4_loadu_f gmx_simd_loadu_f
+#define gmx_simd4_storeu_f gmx_simd_storeu_f
+#define gmx_simd4_setzero_f gmx_simd_setzero_f
+#define gmx_simd4_add_f gmx_simd_add_f
+#define gmx_simd4_sub_f gmx_simd_sub_f
+#define gmx_simd4_mul_f gmx_simd_mul_f
+#define gmx_simd4_fmadd_f gmx_simd_fmadd_f
+#define gmx_simd4_fmsub_f gmx_simd_fmsub_f
+#define gmx_simd4_fnmadd_f gmx_simd_fnmadd_f
+#define gmx_simd4_fnmsub_f gmx_simd_fnmsub_f
+#define gmx_simd4_and_f gmx_simd_and_f
+#define gmx_simd4_andnot_f gmx_simd_andnot_f
+#define gmx_simd4_or_f gmx_simd_or_f
+#define gmx_simd4_xor_f gmx_simd_xor_f
+#define gmx_simd4_rsqrt_f gmx_simd_rsqrt_f
+#define gmx_simd4_fabs_f gmx_simd_fabs_f
+#define gmx_simd4_fneg_f gmx_simd_fneg_f
+#define gmx_simd4_max_f gmx_simd_max_f
+#define gmx_simd4_min_f gmx_simd_min_f
+#define gmx_simd4_round_f gmx_simd_round_f
+#define gmx_simd4_trunc_f gmx_simd_trunc_f
+#define gmx_simd4_dotproduct3_f gmx_simd4_dotproduct3_f_arm_neon
+#define gmx_simd4_fbool_t gmx_simd_fbool_t
+#define gmx_simd4_cmpeq_f gmx_simd_cmpeq_f
+#define gmx_simd4_cmplt_f gmx_simd_cmplt_f
+#define gmx_simd4_cmple_f gmx_simd_cmple_f
+#define gmx_simd4_and_fb gmx_simd_and_fb
+#define gmx_simd4_or_fb gmx_simd_or_fb
+#define gmx_simd4_anytrue_fb gmx_simd_anytrue_fb
+#define gmx_simd4_blendzero_f gmx_simd_blendzero_f
+#define gmx_simd4_blendnotzero_f gmx_simd_blendnotzero_f
+#define gmx_simd4_blendv_f gmx_simd_blendv_f
+#define gmx_simd4_reduce_f gmx_simd_reduce_f
+
+/* SIMD4 Dotproduct helper function */
+static gmx_inline float
+gmx_simd4_dotproduct3_f_arm_neon(gmx_simd_float_t a, gmx_simd_float_t b)
+{
+ gmx_simd_float_t c;
+ c = gmx_simd_mul_f(a, b);
+ /* set 4th element to 0, then add all of them */
+ c = vsetq_lane_f32(0.0f, c, 3);
+ return gmx_simd_reduce_f_arm_neon(c);
+}
+
+#endif /* GMX_SIMD_IMPL_ARM_NEON_H */
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GMX_SIMD_IMPL_ARM_NEON_ASIMD_H
+#define GMX_SIMD_IMPL_ARM_NEON_ASIMD_H
+
+#include <math.h>
+
+#include <arm_neon.h>
+
+/* ARM (AArch64) NEON Advanced SIMD instruction wrappers
+ *
+ * Please see documentation in gromacs/simd/simd.h for defines.
+ */
+
+/* Inherit single-precision and integer part from 32-bit arm */
+#include "gromacs/simd/impl_arm_neon/impl_arm_neon.h"
+
+/* Override some capability definitions from ARM 32-bit NEON - we now have double */
+#define GMX_SIMD_HAVE_DOUBLE
+#define GMX_SIMD_HAVE_DINT32
+#define GMX_SIMD_HAVE_DINT32_EXTRACT
+#define GMX_SIMD_HAVE_DINT32_LOGICAL
+#define GMX_SIMD_HAVE_DINT32_ARITHMETICS
+
+/* Implementation details */
+#define GMX_SIMD_DOUBLE_WIDTH 2
+#define GMX_SIMD_DINT32_WIDTH 2
+
+/* NEON ASIMD always has FMA support, so make sure we use that for single too. */
+#undef gmx_simd_fmadd_f
+#define gmx_simd_fmadd_f(a, b, c) vfmaq_f32(c, b, a)
+#undef gmx_simd_fmsub_f
+#define gmx_simd_fmsub_f(a, b, c) vnegq_f32(vfmsq_f32(c, b, a))
+#undef gmx_simd_fnmadd_f
+#define gmx_simd_fnmadd_f(a, b, c) vfmsq_f32(c, b, a)
+#undef gmx_simd_fnmsub_f
+#define gmx_simd_fnmsub_f(a, b, c) vnegq_f32(vfmaq_f32(c, b, a))
+
+/* The rounding instructions were actually added already in ARMv8, but most
+ * compilers did not add intrinsics for them. Make sure we use them for single
+ * precision too when enabling NEON Advanced SIMD.
+ */
+#undef gmx_simd_round_f
+#define gmx_simd_round_f(x) vrndnq_f32(x)
+#undef gmx_simd_trunc_f
+#define gmx_simd_trunc_f(x) vrndq_f32(x)
+
+/* NEON Advanced SIMD has a real rounding conversion instruction */
+#undef gmx_simd_cvt_f2i
+#define gmx_simd_cvt_f2i(x) vcvtnq_s32_f32(x)
+
+/* Since we redefine rounding/conversion-with-rounding, make
+ * sure we use the new operations by redefining the routine
+ * to set the exponent too.
+ */
+#undef gmx_simd_set_exponent_f
+#define gmx_simd_set_exponent_f gmx_simd_set_exponent_f_arm_neon_asimd
+
+/* We can do more efficient reduce with vector pairwise arithmetic */
+#undef gmx_simd_reduce_f
+#define gmx_simd_reduce_f(a) gmx_simd_reduce_f_arm_neon_asimd(a)
+
+/* Pick the largest unsigned integer as a shortcut for any-true */
+#undef gmx_simd_anytrue_fb
+#define gmx_simd_anytrue_fb(x) (vmaxvq_u32(x) != 0)
+#undef gmx_simd_anytrue_fib
+#define gmx_simd_anytrue_fib(x) (vmaxvq_u32(x) != 0)
+
+/* gcc-4.8 is missing the proper vreinterpretq casts
+ * for 64-bit operands. However, since these datatypes
+ * are opaque to the compiler we can safely cast one
+ * to the other without any conversion happening.
+ */
+
+/****************************************************
+ * DOUBLE PRECISION SIMD IMPLEMENTATION *
+ ****************************************************/
+#define gmx_simd_double_t float64x2_t
+#define gmx_simd_load_d vld1q_f64
+#define gmx_simd_load1_d vld1q_dup_f64
+#define gmx_simd_set1_d vdupq_n_f64
+#define gmx_simd_store_d vst1q_f64
+#define gmx_simd_loadu_d vld1q_f64
+#define gmx_simd_storeu_d vst1q_f64
+#define gmx_simd_setzero_d() vdupq_n_f64(0.0)
+#define gmx_simd_add_d vaddq_f64
+#define gmx_simd_sub_d vsubq_f64
+#define gmx_simd_mul_d vmulq_f64
+#define gmx_simd_fmadd_d(a, b, c) vfmaq_f64(c, b, a)
+#define gmx_simd_fmsub_d(a, b, c) vnegq_f64(vfmsq_f64(c, b, a))
+#define gmx_simd_fnmadd_d(a, b, c) vfmsq_f64(c, b, a)
+#define gmx_simd_fnmsub_d(a, b, c) vnegq_f64(vfmaq_f64(c, b, a))
+#define gmx_simd_and_d(a, b) (float64x2_t)(vandq_s64((int64x2_t)(a), (int64x2_t)(b)))
+#define gmx_simd_andnot_d(a, b) (float64x2_t)(vbicq_s64((int64x2_t)(b), (int64x2_t)(a)))
+#define gmx_simd_or_d(a, b) (float64x2_t)(vorrq_s64((int64x2_t)(a), (int64x2_t)(b)))
+#define gmx_simd_xor_d(a, b) (float64x2_t)(veorq_s64((int64x2_t)(a), (int64x2_t)(b)))
+#define gmx_simd_rsqrt_d vrsqrteq_f64
+#define gmx_simd_rsqrt_iter_d(lu, x) vmulq_f64(lu, vrsqrtsq_f64(vmulq_f64(lu, lu), x))
+#define gmx_simd_rcp_d vrecpeq_f64
+#define gmx_simd_rcp_iter_d(lu, x) vmulq_f64(lu, vrecpsq_f64(lu, x))
+#define gmx_simd_fabs_d(x) vabsq_f64(x)
+#define gmx_simd_fneg_d(x) vnegq_f64(x)
+#define gmx_simd_max_d vmaxq_f64
+#define gmx_simd_min_d vminq_f64
+#define gmx_simd_round_d(x) vrndnq_f64(x)
+#define gmx_simd_trunc_d(x) vrndq_f64(x)
+#define gmx_simd_fraction_d(x) vsubq_f64(x, gmx_simd_trunc_d(x))
+#define gmx_simd_get_exponent_d gmx_simd_get_exponent_d_arm_neon_asimd
+#define gmx_simd_get_mantissa_d gmx_simd_get_mantissa_d_arm_neon_asimd
+#define gmx_simd_set_exponent_d gmx_simd_set_exponent_d_arm_neon_asimd
+/* integer datatype corresponding to double: gmx_simd_dint32_t */
+#define gmx_simd_dint32_t int32x2_t
+#define gmx_simd_load_di(m) vld1_s32(m)
+#define gmx_simd_set1_di vdup_n_s32
+#define gmx_simd_store_di(m, x) vst1_s32(m, x)
+#define gmx_simd_loadu_di(m) vld1_s32(m)
+#define gmx_simd_storeu_di(m, x) vst1_s32(m, x)
+#define gmx_simd_setzero_di() vdup_n_s32(0)
+#define gmx_simd_cvtt_d2i(x) vmovn_s64(vcvtq_s64_f64(x))
+#define gmx_simd_cvt_d2i(x) vmovn_s64(vcvtnq_s64_f64(x))
+#define gmx_simd_cvt_i2d(x) vcvtq_f64_s64(vmovl_s32(x))
+#define gmx_simd_extract_di(x, i) vget_lane_s32(x, i)
+/* Integer logical ops on gmx_simd_dint32_t */
+#define gmx_simd_slli_di vshl_n_s32
+#define gmx_simd_srli_di vshr_n_s32
+#define gmx_simd_and_di vand_s32
+#define gmx_simd_andnot_di(a, b) vbic_s32(b, a)
+#define gmx_simd_or_di vorr_s32
+#define gmx_simd_xor_di veor_s32
+/* Integer arithmetic ops on gmx_simd_dint32_t */
+#define gmx_simd_add_di vadd_s32
+#define gmx_simd_sub_di vsub_s32
+#define gmx_simd_mul_di vmul_s32
+/* Boolean & comparison operations on gmx_simd_double_t */
+#define gmx_simd_dbool_t uint64x2_t
+#define gmx_simd_cmpeq_d vceqq_f64
+#define gmx_simd_cmplt_d vcltq_f64
+#define gmx_simd_cmple_d vcleq_f64
+#define gmx_simd_and_db vandq_u64
+#define gmx_simd_or_db vorrq_u64
+#define gmx_simd_anytrue_db(x) (vmaxvq_u32((uint32x4_t)(x)) != 0)
+#define gmx_simd_blendzero_d(a, sel) (float64x2_t)(vandq_u64((uint64x2_t)(a), sel))
+#define gmx_simd_blendnotzero_d(a, sel) (float64x2_t)(vbicq_u64((uint64x2_t)(a), sel))
+#define gmx_simd_blendv_d(a, b, sel) vbslq_f64(sel, b, a)
+#define gmx_simd_reduce_d(a) gmx_simd_reduce_d_arm_neon_asimd(a)
+/* Boolean & comparison operations on gmx_simd_dint32_t */
+#define gmx_simd_dibool_t uint32x2_t
+#define gmx_simd_cmpeq_di vceq_s32
+#define gmx_simd_cmplt_di vclt_s32
+#define gmx_simd_and_dib vand_u32
+#define gmx_simd_or_dib vorr_u32
+#define gmx_simd_anytrue_dib(x) (vmaxv_u32(x) != 0)
+#define gmx_simd_blendzero_di(a, sel) vand_s32(a, vreinterpret_s32_u32(sel))
+#define gmx_simd_blendnotzero_di(a, sel) vbic_s32(a, vreinterpret_s32_u32(sel))
+#define gmx_simd_blendv_di(a, b, sel) vbsl_s32(sel, b, a)
+/* Conversions between different booleans */
+#define gmx_simd_cvt_db2dib(x) vqmovn_u64(x)
+#define gmx_simd_cvt_dib2db(x) vorrq_u64(vmovl_u32(x), vshlq_n_u64(vmovl_u32(x), 32))
+
+/* Float/double conversion */
+#define gmx_simd_cvt_f2dd(f, d0, d1) { *d0 = vcvt_f64_f32(vget_low_f32(f)); *d1 = vcvt_high_f64_f32(f); }
+#define gmx_simd_cvt_dd2f(d0, d1) vcvt_high_f32_f64(vcvt_f32_f64(d0), d1)
+
+/****************************************************
+ * SINGLE PRECISION IMPLEMENTATION HELPER FUNCTIONS *
+ ****************************************************/
+static gmx_inline gmx_simd_float_t
+gmx_simd_set_exponent_f_arm_neon_asimd(gmx_simd_float_t x)
+{
+ int32x4_t iexp = vcvtnq_s32_f32(x);
+
+ iexp = vshlq_n_s32(vaddq_s32(iexp, vdupq_n_s32(127)), 23);
+ return vreinterpretq_f32_s32(iexp);
+}
+
+static gmx_inline float
+gmx_simd_reduce_f_arm_neon_asimd(gmx_simd_float_t a)
+{
+ a = vpaddq_f32(a, a);
+ a = vpaddq_f32(a, a);
+ return vgetq_lane_f32(a, 0);
+}
+
+
+/****************************************************
+ * DOUBLE PRECISION IMPLEMENTATION HELPER FUNCTIONS *
+ ****************************************************/
+static gmx_inline gmx_simd_double_t
+gmx_simd_get_exponent_d_arm_neon_asimd(gmx_simd_double_t x)
+{
+ const float64x2_t expmask = (float64x2_t)( vdupq_n_s64(0x7FF0000000000000LL) );
+ int64x2_t iexp;
+
+ iexp = (int64x2_t)(gmx_simd_and_d(x, expmask));
+ iexp = vsubq_s64(vshrq_n_s64(iexp, 52), vdupq_n_s64(1023));
+ return vcvtq_f64_s64(iexp);
+}
+
+
+static gmx_inline gmx_simd_double_t
+gmx_simd_get_mantissa_d_arm_neon_asimd(gmx_simd_double_t x)
+{
+ const float64x2_t mantmask = (float64x2_t)( vdupq_n_s64(0x000FFFFFFFFFFFFFLL) );
+ const float64x2_t one = vdupq_n_f64(1.0);
+
+ /* Get mantissa */
+ x = gmx_simd_and_d(mantmask, x);
+ /* Reset zero (but correctly biased) exponent */
+ return gmx_simd_or_d(x, one);
+}
+
+
+static gmx_inline gmx_simd_double_t
+gmx_simd_set_exponent_d_arm_neon_asimd(gmx_simd_double_t x)
+{
+ int64x2_t iexp = vcvtnq_s64_f64(x);
+
+ iexp = vshlq_n_s64(vaddq_s64(iexp, vdupq_n_s64(1023)), 52);
+ return (float64x2_t)(iexp);
+}
+
+static gmx_inline double
+gmx_simd_reduce_d_arm_neon_asimd(gmx_simd_double_t a)
+{
+ a = vpaddq_f64(a, a);
+ return vgetq_lane_f64(a, 0);
+}
+
+#endif /* GMX_SIMD_IMPL_ARM_NEON_ASIMD_H */
#include <qpxmath.h>
#endif
+#include "config.h"
+
/* IBM QPX SIMD instruction wrappers
*
* Please see documentation in gromacs/simd/simd.h for the available
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GMX_SIMD_IMPLEMENTATION_IBM_VMX_H
+#define GMX_SIMD_IMPLEMENTATION_IBM_VMX_H
+
+#include <math.h>
+
+#include <altivec.h>
+
+/* Make sure we do not screw up c++ - undefine vector/bool, and rely on __vector and __bool */
+#undef vector
+#undef bool
+
+/* IBM VMX SIMD instruction wrappers. Power6 and later.
+ *
+ * Please see documentation in gromacs/simd/simd.h for the available
+ * defines.
+ */
+/* Capability definitions for IBM VMX */
+#define GMX_SIMD_HAVE_FLOAT
+#undef GMX_SIMD_HAVE_DOUBLE
+#define GMX_SIMD_HAVE_HARDWARE
+#undef GMX_SIMD_HAVE_LOADU
+#undef GMX_SIMD_HAVE_STOREU
+#define GMX_SIMD_HAVE_LOGICAL
+/* VMX only provides fmadd/fnmadd (our definitions), but not fmsub/fnmsub.
+ * However, fnmadd is what we need for 1/sqrt(x).
+ */
+#define GMX_SIMD_HAVE_FMA
+#undef GMX_SIMD_HAVE_FRACTION
+#define GMX_SIMD_HAVE_FINT32
+#undef GMX_SIMD_HAVE_FINT32_EXTRACT
+#define GMX_SIMD_HAVE_FINT32_LOGICAL
+#define GMX_SIMD_HAVE_FINT32_ARITHMETICS
+#undef GMX_SIMD_HAVE_DINT32
+#undef GMX_SIMD_HAVE_DINT32_EXTRACT
+#undef GMX_SIMD_HAVE_DINT32_LOGICAL
+#undef GMX_SIMD_HAVE_DINT32_ARITHMETICS
+#define GMX_SIMD4_HAVE_FLOAT
+#undef GMX_SIMD4_HAVE_DOUBLE
+
+/* Implementation details */
+#define GMX_SIMD_FLOAT_WIDTH 4
+#undef GMX_SIMD_DOUBLE_WIDTH
+#define GMX_SIMD_FINT32_WIDTH 4
+#undef GMX_SIMD_DINT32_WIDTH
+#define GMX_SIMD_RSQRT_BITS 14
+#define GMX_SIMD_RCP_BITS 14
+
+/****************************************************
+ * SINGLE PRECISION SIMD IMPLEMENTATION *
+ ****************************************************/
+#define gmx_simd_float_t __vector float
+#define gmx_simd_load_f(m) vec_ld(0, (const __vector float *)m)
+#define gmx_simd_load1_f(m) gmx_simd_load1_f_ibm_vmx(m)
+#define gmx_simd_set1_f(x) gmx_simd_set1_f_ibm_vmx(x)
+#define gmx_simd_store_f(m, x) vec_st(x, 0, (__vector float *)m)
+#undef gmx_simd_loadu_f
+#undef gmx_simd_storeu_f
+#define gmx_simd_setzero_f() ((__vector float)vec_splat_u32(0))
+#define gmx_simd_add_f(a, b) vec_add(a, b)
+#define gmx_simd_sub_f(a, b) vec_sub(a, b)
+#define gmx_simd_mul_f(a, b) vec_mul(a, b)
+#define gmx_simd_fmadd_f(a, b, c) vec_madd(a, b, c)
+#define gmx_simd_fmsub_f(a, b, c) vec_sub(vec_mul(a, b), c)
+/* IBM uses an alternative FMA definition, so -a*b+c=-(a*b-c) is "nmsub" */
+#define gmx_simd_fnmadd_f(a, b, c) vec_nmsub(a, b, c)
+/* IBM uses an alternative FMA definition, so -a*b-c=-(a*b+c) is "nmadd" */
+#define gmx_simd_fnmsub_f(a, b, c) vec_sub(gmx_simd_setzero_f(), vec_madd(a, b, c))
+#define gmx_simd_and_f(a, b) vec_and(a, b)
+#define gmx_simd_andnot_f(a, b) vec_andc(b, a)
+#define gmx_simd_or_f(a, b) vec_or(a, b)
+#define gmx_simd_xor_f(a, b) vec_xor(a, b)
+#define gmx_simd_rsqrt_f(a) vec_rsqrte(a)
+#define gmx_simd_rcp_f(a) vec_re(a)
+#define gmx_simd_fabs_f(a) vec_abs(a)
+#define gmx_simd_fneg_f(a) vec_xor(a, (__vector float)vec_sl(vec_splat_u32(-1), vec_splat_u32(-1)))
+#define gmx_simd_max_f(a, b) vec_max(a, b)
+#define gmx_simd_min_f(a, b) vec_min(a, b)
+#define gmx_simd_round_f(a) vec_round(a)
+#define gmx_simd_trunc_f(a) vec_trunc(a)
+#define gmx_simd_fraction_f(x) vec_sub(x, vec_trunc(x))
+#define gmx_simd_get_exponent_f(a) gmx_simd_get_exponent_f_ibm_vmx(a)
+#define gmx_simd_get_mantissa_f(a) gmx_simd_get_mantissa_f_ibm_vmx(a)
+#define gmx_simd_set_exponent_f(a) gmx_simd_set_exponent_f_ibm_vmx(a)
+/* integer datatype corresponding to float: gmx_simd_fint32_t */
+#define gmx_simd_fint32_t __vector int
+#define gmx_simd_load_fi(m) vec_ld(0, (const __vector int *)m)
+#define gmx_simd_set1_fi(i) gmx_simd_set1_fi_ibm_vmx((int)i)
+#define gmx_simd_store_fi(m, x) vec_st(x, 0, (__vector int *)m)
+#undef gmx_simd_loadu_fi
+#undef gmx_simd_storeu_fi
+#define gmx_simd_setzero_fi() vec_splat_s32(0)
+#define gmx_simd_cvt_f2i(a) vec_cts(vec_round(a), 0)
+#define gmx_simd_cvtt_f2i(a) vec_cts(a, 0)
+#define gmx_simd_cvt_i2f(a) vec_ctf(a, 0)
+#undef gmx_simd_extract_fi
+/* Integer logical ops on gmx_simd_fint32_t */
+/* The shift constant magic requires an explanation:
+ * VMX only allows literals up to 15 to be created directly with vec_splat_u32,
+ * and we need to be able to shift up to 31 bits. The code on the right hand
+ * side splits the constant in three parts with values in the range 0..15.
+ * Since the argument has to be a constant (but our and VMX requirement), these
+ * constants will be evaluated at compile-time, and if one or two parts evaluate
+ * to zero they will be removed with -O2 or higher optimization (checked).
+ */
+#define gmx_simd_slli_fi(a, i) vec_sl(a, vec_add(vec_add(vec_splat_u32( (((i&0xF)+(i/16))&0xF)+i/31 ), vec_splat_u32( (i/16)*15 )), vec_splat_u32( (i/31)*15 )))
+#define gmx_simd_srli_fi(a, i) vec_sr(a, vec_add(vec_add(vec_splat_u32( (((i&0xF)+(i/16))&0xF)+i/31 ), vec_splat_u32( (i/16)*15 )), vec_splat_u32( (i/31)*15 )))
+#define gmx_simd_and_fi(a, b) vec_and(a, b)
+#define gmx_simd_andnot_fi(a, b) vec_andc(b, a)
+#define gmx_simd_or_fi(a, b) vec_or(a, b)
+#define gmx_simd_xor_fi(a, b) vec_xor(a, b)
+/* Integer arithmetic ops on gmx_simd_fint32_t */
+#define gmx_simd_add_fi(a, b) vec_add(a, b)
+#define gmx_simd_sub_fi(a, b) vec_sub(a, b)
+#define gmx_simd_mul_fi(a, b) vec_mule((__vector short)a, (__vector short)b)
+/* Boolean & comparison operations on gmx_simd_float_t */
+#define gmx_simd_fbool_t __vector __bool int
+#define gmx_simd_cmpeq_f(a, b) vec_cmpeq(a, b)
+#define gmx_simd_cmplt_f(a, b) vec_cmplt(a, b)
+#define gmx_simd_cmple_f(a, b) vec_cmple(a, b)
+#define gmx_simd_and_fb(a, b) vec_and(a, b)
+#define gmx_simd_or_fb(a, b) vec_or(a, b)
+#define gmx_simd_anytrue_fb(a) vec_any_ne(a, (__vector __bool int)vec_splat_u32(0))
+#define gmx_simd_blendzero_f(a, sel) vec_and(a, (__vector float)sel)
+#define gmx_simd_blendnotzero_f(a, sel) vec_andc(a, (__vector float)sel)
+#define gmx_simd_blendv_f(a, b, sel) vec_sel(a, b, sel)
+#define gmx_simd_reduce_f(a) gmx_simd_reduce_f_ibm_vmx(a)
+/* Boolean & comparison operations on gmx_simd_fint32_t */
+#define gmx_simd_fibool_t __vector __bool int
+#define gmx_simd_cmpeq_fi(a, b) vec_cmpeq(a, b)
+#define gmx_simd_cmplt_fi(a, b) vec_cmplt(a, b)
+#define gmx_simd_and_fib(a, b) vec_and(a, b)
+#define gmx_simd_or_fib(a, b) vec_or(a, b)
+#define gmx_simd_anytrue_fib(a) vec_any_ne(a, (__vector __bool int)vec_splat_u32(0))
+#define gmx_simd_blendzero_fi(a, sel) vec_and(a, (__vector int)sel)
+#define gmx_simd_blendnotzero_fi(a, sel) vec_andc(a, (__vector int)sel)
+#define gmx_simd_blendv_fi(a, b, sel) vec_sel(a, b, sel)
+/* Conversions between different booleans */
+#define gmx_simd_cvt_fb2fib(x) (x)
+#define gmx_simd_cvt_fib2fb(x) (x)
+
+/* Double is not available with VMX SIMD */
+
+/****************************************************
+ * IMPLEMENTATION HELPER FUNCTIONS *
+ ****************************************************/
+static gmx_inline gmx_simd_float_t
+gmx_simd_set1_f_ibm_vmx(const float x)
+{
+ /* In the old days when PPC was all big endian we could
+ * use the vec_lvsl() instruction to permute bytes based on
+ * a load adress. However, at least with gcc-4.8.2 the bytes
+ * end up reversed on Power8 running little endian (Linux).
+ * Since this is not a critical instruction we work around
+ * it by first putting the data in an aligned position before
+ * loading, so we can avoid vec_lvsl() entirely. We can
+ * do this slightly faster on GCC with alignment attributes.
+ */
+ __vector float vx;
+#ifdef __GNUC__
+ float alignedx __attribute ((aligned (16)));
+ alignedx = x;
+ vx = vec_lde(0, &alignedx);
+#else
+ struct {
+ vector float vx; float x[4];
+ } conv;
+ conv.x[0] = x;
+ vx = vec_lde(0, conv.x);
+#endif
+ return vec_splat(vx, 0);
+}
+
+static gmx_inline gmx_simd_float_t
+gmx_simd_load1_f_ibm_vmx(const float * m)
+{
+ return gmx_simd_set1_f_ibm_vmx(*m);
+}
+
+static gmx_inline gmx_simd_fint32_t
+gmx_simd_set1_fi_ibm_vmx(const int x)
+{
+ /* See comment in gmx_simd_set1_f_ibm_vmx why we
+ * cannot use vec_lvsl().
+ */
+ __vector int vx;
+#ifdef __GNUC__
+ int alignedx __attribute ((aligned (16)));
+ alignedx = x;
+ vx = vec_lde(0, &alignedx);
+#else
+ struct {
+ vector int vx; int x[4];
+ } conv;
+ conv.x[0] = x;
+ vx = vec_lde(0, conv.x);
+#endif
+ return vec_splat(vx, 0);
+}
+
+
+static gmx_inline gmx_simd_float_t
+gmx_simd_get_exponent_f_ibm_vmx(gmx_simd_float_t x)
+{
+ /* Generate 0x7F800000 without memory operations */
+ gmx_simd_float_t expmask = (__vector float)gmx_simd_slli_fi(vec_add(vec_splat_s32(15), vec_sl(vec_splat_s32(15), vec_splat_u32(4))), 23);
+ gmx_simd_fint32_t i127 = vec_sub(vec_sl(vec_splat_s32(1), vec_splat_u32(7)), vec_splat_s32(1));
+ gmx_simd_fint32_t iexp;
+
+ iexp = (__vector int)gmx_simd_and_f(x, expmask);
+ iexp = vec_sub(gmx_simd_srli_fi(iexp, 23), i127);
+ return vec_ctf(iexp, 0);
+}
+
+static gmx_inline gmx_simd_float_t
+gmx_simd_get_mantissa_f_ibm_vmx(gmx_simd_float_t x)
+{
+ gmx_simd_float_t expmask = (__vector float)gmx_simd_slli_fi(vec_add(vec_splat_s32(15), vec_sl(vec_splat_s32(15), vec_splat_u32(4))), 23);
+
+ /* Get mantissa. By taking the absolute value (to get rid of the sign bit) we can
+ * use the same mask as for gmx_simd_get_exponent_f() (but complement it). Since
+ * these two routines are typically called together, this will save a few operations.
+ */
+ x = gmx_simd_andnot_f(expmask, vec_abs(x));
+ /* Reset zero (but correctly biased) exponent */
+ return gmx_simd_or_f(x, vec_ctf(vec_splat_s32(1), 0));
+}
+
+static gmx_inline gmx_simd_float_t
+gmx_simd_set_exponent_f_ibm_vmx(gmx_simd_float_t x)
+{
+ gmx_simd_fint32_t iexp = gmx_simd_cvt_f2i(x);
+ gmx_simd_fint32_t i127 = vec_sub(vec_sl(vec_splat_s32(1), vec_splat_u32(7)), vec_splat_s32(1));
+
+ iexp = gmx_simd_slli_fi(vec_add(iexp, i127), 23);
+ return (__vector float)iexp;
+}
+
+static gmx_inline float
+gmx_simd_reduce_f_ibm_vmx(gmx_simd_float_t x)
+{
+ float res;
+ x = vec_add(x, vec_sld(x, x, 8));
+ x = vec_add(x, vec_sld(x, x, 4));
+ vec_ste(x, 0, &res);
+ return res;
+}
+
+
+
+/* SINGLE */
+#define gmx_simd4_float_t gmx_simd_float_t
+#define gmx_simd4_load_f gmx_simd_load_f
+#define gmx_simd4_load1_f gmx_simd_load1_f
+#define gmx_simd4_set1_f gmx_simd_set1_f
+#define gmx_simd4_store_f gmx_simd_store_f
+#define gmx_simd4_loadu_f gmx_simd_loadu_f
+#define gmx_simd4_storeu_f gmx_simd_storeu_f
+#define gmx_simd4_setzero_f gmx_simd_setzero_f
+#define gmx_simd4_add_f gmx_simd_add_f
+#define gmx_simd4_sub_f gmx_simd_sub_f
+#define gmx_simd4_mul_f gmx_simd_mul_f
+#define gmx_simd4_fmadd_f gmx_simd_fmadd_f
+#define gmx_simd4_fmsub_f gmx_simd_fmsub_f
+#define gmx_simd4_fnmadd_f gmx_simd_fnmadd_f
+#define gmx_simd4_fnmsub_f gmx_simd_fnmsub_f
+#define gmx_simd4_and_f gmx_simd_and_f
+#define gmx_simd4_andnot_f gmx_simd_andnot_f
+#define gmx_simd4_or_f gmx_simd_or_f
+#define gmx_simd4_xor_f gmx_simd_xor_f
+#define gmx_simd4_rsqrt_f gmx_simd_rsqrt_f
+#define gmx_simd4_rcp_f gmx_simd_rcp_f
+#define gmx_simd4_fabs_f gmx_simd_fabs_f
+#define gmx_simd4_fneg_f gmx_simd_fneg_f
+#define gmx_simd4_max_f gmx_simd_max_f
+#define gmx_simd4_min_f gmx_simd_min_f
+#define gmx_simd4_round_f gmx_simd_round_f
+#define gmx_simd4_trunc_f gmx_simd_trunc_f
+#define gmx_simd4_fraction_f gmx_simd_fraction_f
+#define gmx_simd4_get_exponent_f gmx_simd_get_exponent_f
+#define gmx_simd4_get_mantissa_f gmx_simd_get_mantissa_f
+#define gmx_simd4_set_exponent_f gmx_simd_set_exponent_f
+#define gmx_simd4_dotproduct3_f gmx_simd4_dotproduct3_f_ibm_vmx
+#define gmx_simd4_fint32_t gmx_simd_fint32_t
+#define gmx_simd4_load_fi gmx_simd_load_fi
+#define gmx_simd4_load1_fi gmx_simd_load1_fi
+#define gmx_simd4_set1_fi gmx_simd_set1_fi
+#define gmx_simd4_store_fi gmx_simd_store_fi
+#define gmx_simd4_loadu_fi gmx_simd_loadu_fi
+#define gmx_simd4_storeu_fi gmx_simd_storeu_fi
+#define gmx_simd4_setzero_fi gmx_simd_setzero_fi
+#define gmx_simd4_cvt_f2i gmx_simd_cvt_f2i
+#define gmx_simd4_cvtt_f2i gmx_simd_cvtt_f2i
+#define gmx_simd4_cvt_i2f gmx_simd_cvt_i2f
+#define gmx_simd4_fbool_t gmx_simd_fbool_t
+#define gmx_simd4_cmpeq_f gmx_simd_cmpeq_f
+#define gmx_simd4_cmplt_f gmx_simd_cmplt_f
+#define gmx_simd4_cmple_f gmx_simd_cmple_f
+#define gmx_simd4_and_fb gmx_simd_and_fb
+#define gmx_simd4_or_fb gmx_simd_or_fb
+#define gmx_simd4_anytrue_fb gmx_simd_anytrue_fb
+#define gmx_simd4_blendzero_f gmx_simd_blendzero_f
+#define gmx_simd4_blendnotzero_f gmx_simd_blendnotzero_f
+#define gmx_simd4_blendv_f gmx_simd_blendv_f
+#define gmx_simd4_reduce_f gmx_simd_reduce_f
+
+static gmx_inline float
+gmx_simd4_dotproduct3_f_ibm_vmx(gmx_simd4_float_t a, gmx_simd4_float_t b)
+{
+ gmx_simd4_float_t c = vec_mul(a, b);
+ /* Keep only elements 0,1,2 by shifting in zero from right */
+ c = vec_sld(c, gmx_simd_setzero_f(), 4);
+ /* calculate sum */
+ return gmx_simd_reduce_f_ibm_vmx(c);
+}
+
+/* Function to check whether SIMD operations have resulted in overflow.
+ * For now, this is unfortunately a dummy for this architecture.
+ */
+static int
+gmx_simd_check_and_reset_overflow(void)
+{
+ return 0;
+}
+
+#endif /* GMX_SIMD_IMPLEMENTATION_IBM_VMX_H */
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GMX_SIMD_IMPLEMENTATION_IBM_VSX_H
+#define GMX_SIMD_IMPLEMENTATION_IBM_VSX_H
+
+#include <math.h>
+
+#include <altivec.h>
+
+/* IBM VSX SIMD instruction wrappers. Power7 and later.
+ *
+ * While this instruction set is similar to VMX, there are quite a few differences
+ * that make it easier to understand if we start from scratch rather than by
+ * including the VMX implementation and changing lots of things.
+ */
+
+
+/* Make sure we do not screw up c++ - undefine vector/bool, and rely on __vector,
+ * which is present both on gcc and xlc.
+ */
+#undef vector
+
+/* g++ is also unhappy with the clash of vector bool and the C++ reserved 'bool',
+ * which is solved by undefining bool and reyling on __bool. However, that does
+ * not work with xlc, which requires us to use bool. Solve the conflict by
+ * defining a new vsx_bool.
+ */
+#ifdef __GNUC__
+# define vsx_bool __bool
+# undef bool
+#else
+# define vsx_bool bool
+#endif
+
+/* Since we've had to use quite a few compiler and endian defines in this code
+ * it might not 'just work' when e.g. clang provides VSX support. If you are
+ * reading this because you saw the error below for a new compiler, try removing
+ * the checks, but then make sure you run 'make test'.
+ */
+#if !(defined __GNUC__) && !(defined __IBMC__) && !(defined __IBMCPP__)
+# error VSX acceleration is very compiler-dependent, and only tested for gcc & xlc.
+#endif
+
+#if !(defined __BIG_ENDIAN__) && !(defined __LITTLE_ENDIAN__)
+# error VSX platform not recognized - both gcc & xlc should define big or little endian!
+#endif
+
+/* Capability definitions for IBM VSX */
+#define GMX_SIMD_HAVE_FLOAT
+#define GMX_SIMD_HAVE_DOUBLE
+#define GMX_SIMD_HAVE_HARDWARE
+#define GMX_SIMD_HAVE_LOADU
+#define GMX_SIMD_HAVE_STOREU
+#define GMX_SIMD_HAVE_LOGICAL
+#define GMX_SIMD_HAVE_FMA
+#undef GMX_SIMD_HAVE_FRACTION
+#define GMX_SIMD_HAVE_FINT32
+#define GMX_SIMD_HAVE_FINT32_EXTRACT
+#define GMX_SIMD_HAVE_FINT32_LOGICAL
+#define GMX_SIMD_HAVE_FINT32_ARITHMETICS
+#define GMX_SIMD_HAVE_DINT32
+#define GMX_SIMD_HAVE_DINT32_EXTRACT
+#define GMX_SIMD_HAVE_DINT32_LOGICAL
+#define GMX_SIMD_HAVE_DINT32_ARITHMETICS
+#define GMX_SIMD4_HAVE_FLOAT
+#undef GMX_SIMD4_HAVE_DOUBLE
+
+/* Implementation details */
+#define GMX_SIMD_FLOAT_WIDTH 4
+#define GMX_SIMD_DOUBLE_WIDTH 2
+#define GMX_SIMD_FINT32_WIDTH 4
+#define GMX_SIMD_DINT32_WIDTH 2
+#define GMX_SIMD_RSQRT_BITS 14
+#define GMX_SIMD_RCP_BITS 14
+
+/****************************************************
+ * SINGLE PRECISION SIMD IMPLEMENTATION *
+ ****************************************************/
+#define gmx_simd_float_t __vector float
+#ifdef __GNUC__
+# define gmx_simd_load_f(m) vec_vsx_ld(0, (const float *)m)
+# define gmx_simd_store_f(m, x) vec_vsx_st(x, 0, (float *)m)
+#else
+/* IBM xlC */
+# define gmx_simd_load_f(m) vec_xlw4(0, (float *)(m))
+# define gmx_simd_store_f(m, x) vec_xstw4(x, 0, (float *)(m))
+#endif
+#define gmx_simd_load1_f(m) vec_splats((float)(*m))
+#define gmx_simd_set1_f(x) vec_splats((float)(x))
+#define gmx_simd_loadu_f gmx_simd_load_f
+#define gmx_simd_storeu_f gmx_simd_store_f
+#define gmx_simd_setzero_f() vec_splats(0.0f)
+#define gmx_simd_add_f(a, b) vec_add(a, b)
+#define gmx_simd_sub_f(a, b) vec_sub(a, b)
+#define gmx_simd_mul_f(a, b) vec_mul(a, b)
+#define gmx_simd_fmadd_f(a, b, c) vec_madd(a, b, c)
+#define gmx_simd_fmsub_f(a, b, c) vec_msub(a, b, c)
+/* IBM uses an alternative FMA definition, so -a*b+c=-(a*b-c) is "nmsub" */
+#define gmx_simd_fnmadd_f(a, b, c) vec_nmsub(a, b, c)
+/* IBM uses an alternative FMA definition, so -a*b-c=-(a*b+c) is "nmadd" */
+#define gmx_simd_fnmsub_f(a, b, c) vec_nmadd(a, b, c)
+#define gmx_simd_and_f(a, b) vec_and(a, b)
+#define gmx_simd_andnot_f(a, b) vec_andc(b, a)
+#define gmx_simd_or_f(a, b) vec_or(a, b)
+#define gmx_simd_xor_f(a, b) vec_xor(a, b)
+#define gmx_simd_rsqrt_f(a) vec_rsqrte(a)
+#define gmx_simd_rcp_f(a) vec_re(a)
+#define gmx_simd_fabs_f(a) vec_abs(a)
+#ifdef __GNUC__
+/* gcc up to at least version 4.9 is missing intrinsics for vec_neg(), use inline asm. */
+# define gmx_simd_fneg_f(a) ({ __vector float res; __asm__ ("xvnegsp %0,%1" : \
+ "=ww" ((__vector float)res) : "ww" ((__vector float)(a))); res; })
+#else
+/* IBM xlC */
+# define gmx_simd_fneg_f(a) vec_neg(a)
+#endif
+#define gmx_simd_max_f(a, b) vec_max(a, b)
+#define gmx_simd_min_f(a, b) vec_min(a, b)
+#define gmx_simd_round_f(a) vec_round(a)
+#define gmx_simd_trunc_f(a) vec_trunc(a)
+#define gmx_simd_fraction_f(x) vec_sub(x, vec_trunc(x))
+#define gmx_simd_get_exponent_f(a) gmx_simd_get_exponent_f_ibm_vsx(a)
+#define gmx_simd_get_mantissa_f(a) gmx_simd_get_mantissa_f_ibm_vsx(a)
+#define gmx_simd_set_exponent_f(a) gmx_simd_set_exponent_f_ibm_vsx(a)
+/* integer datatype corresponding to float: gmx_simd_fint32_t */
+#define gmx_simd_fint32_t __vector signed int
+#ifdef __GNUC__
+# define gmx_simd_load_fi(m) vec_vsx_ld(0, (const int *)m)
+# define gmx_simd_store_fi(m, x) vec_vsx_st(x, 0, (int *)m)
+#else
+/* IBM xlC */
+# define gmx_simd_load_fi(m) vec_xlw4(0, (int *)m)
+# define gmx_simd_store_fi(m, x) vec_xstw4(x, 0, (int *)m)
+#endif
+#define gmx_simd_set1_fi(i) vec_splats((int)(i))
+#define gmx_simd_loadu_fi gmx_simd_load_fi
+#define gmx_simd_storeu_fi gmx_simd_store_fi
+#define gmx_simd_setzero_fi() vec_splats((int)0)
+#define gmx_simd_cvt_f2i(a) vec_cts(vec_round(a), 0)
+#define gmx_simd_cvtt_f2i(a) vec_cts(a, 0)
+#define gmx_simd_cvt_i2f(a) vec_ctf(a, 0)
+#define gmx_simd_extract_fi(a, i) gmx_simd_extract_fi_ibm_vsx(a, i)
+/* Integer logical ops on gmx_simd_fint32_t */
+#define gmx_simd_slli_fi(a, i) vec_sl(a, vec_splats((unsigned int)i))
+#define gmx_simd_srli_fi(a, i) vec_sr(a, vec_splats((unsigned int)i))
+#define gmx_simd_and_fi(a, b) vec_and(a, b)
+#define gmx_simd_andnot_fi(a, b) vec_andc(b, a)
+#define gmx_simd_or_fi(a, b) vec_or(a, b)
+#define gmx_simd_xor_fi(a, b) vec_xor(a, b)
+/* Integer arithmetic ops on gmx_simd_fint32_t */
+#define gmx_simd_add_fi(a, b) vec_add(a, b)
+#define gmx_simd_sub_fi(a, b) vec_sub(a, b)
+#ifdef __GNUC__
+/* gcc-4.9 does not provide vec_mul() for integers */
+# ifdef __BIG_ENDIAN__
+# define gmx_simd_mul_fi(a, b) vec_mulo((__vector short)a, (__vector short)b)
+# else
+# define gmx_simd_mul_fi(a, b) vec_mule((__vector short)a, (__vector short)b)
+# endif
+#else
+/* IBM xlC */
+# define gmx_simd_mul_fi(a, b) vec_mul(a, b)
+#endif
+/* Boolean & comparison operations on gmx_simd_float_t */
+#define gmx_simd_fbool_t __vector vsx_bool int
+#define gmx_simd_cmpeq_f(a, b) vec_cmpeq(a, b)
+#define gmx_simd_cmplt_f(a, b) vec_cmplt(a, b)
+#define gmx_simd_cmple_f(a, b) vec_cmple(a, b)
+#define gmx_simd_and_fb(a, b) vec_and(a, b)
+#define gmx_simd_or_fb(a, b) vec_or(a, b)
+#define gmx_simd_anytrue_fb(a) vec_any_ne(a, (__vector vsx_bool int)vec_splats(0))
+#define gmx_simd_blendzero_f(a, sel) vec_and(a, (__vector float)sel)
+#define gmx_simd_blendnotzero_f(a, sel) vec_andc(a, (__vector float)sel)
+#define gmx_simd_blendv_f(a, b, sel) vec_sel(a, b, sel)
+#define gmx_simd_reduce_f(a) gmx_simd_reduce_f_ibm_vsx(a)
+/* Boolean & comparison operations on gmx_simd_fint32_t */
+#define gmx_simd_fibool_t __vector vsx_bool int
+#define gmx_simd_cmpeq_fi(a, b) vec_cmpeq(a, b)
+#define gmx_simd_cmplt_fi(a, b) vec_cmplt(a, b)
+#define gmx_simd_and_fib(a, b) vec_and(a, b)
+#define gmx_simd_or_fib(a, b) vec_or(a, b)
+#define gmx_simd_anytrue_fib(a) vec_any_ne(a, (__vector vsx_bool int)vec_splats(0))
+#define gmx_simd_blendzero_fi(a, sel) vec_and(a, (__vector signed int)sel)
+#define gmx_simd_blendnotzero_fi(a, sel) vec_andc(a, (__vector signed int)sel)
+#define gmx_simd_blendv_fi(a, b, sel) vec_sel(a, b, sel)
+/* Conversions between different booleans */
+#define gmx_simd_cvt_fb2fib(x) (x)
+#define gmx_simd_cvt_fib2fb(x) (x)
+
+/****************************************************
+ * DOUBLE PRECISION SIMD IMPLEMENTATION *
+ ****************************************************/
+#define gmx_simd_double_t __vector double
+#ifdef __GNUC__
+# define gmx_simd_load_d(m) vec_vsx_ld(0, (const __vector double *)(m))
+# define gmx_simd_store_d(m, x) vec_vsx_st(x, 0, (__vector double *)(m))
+#else
+/* IBM xlC */
+# define gmx_simd_load_d(m) vec_xld2(0, (double *)(m))
+# define gmx_simd_store_d(m, x) vec_xstd2(x, 0, (double *)(m))
+#endif
+#define gmx_simd_load1_d(m) vec_splats((double)(*m))
+#define gmx_simd_set1_d(x) vec_splats((double)(x))
+#define gmx_simd_loadu_d gmx_simd_load_d
+#define gmx_simd_storeu_d gmx_simd_store_d
+#define gmx_simd_setzero_d() vec_splats(0.0)
+#define gmx_simd_add_d(a, b) vec_add(a, b)
+#define gmx_simd_sub_d(a, b) vec_sub(a, b)
+#define gmx_simd_mul_d(a, b) vec_mul(a, b)
+#define gmx_simd_fmadd_d(a, b, c) vec_madd(a, b, c)
+#define gmx_simd_fmsub_d(a, b, c) vec_msub(a, b, c)
+/* IBM uses an alternative FMA definition, so -a*b+c=-(a*b-c) is "nmsub" */
+#define gmx_simd_fnmadd_d(a, b, c) vec_nmsub(a, b, c)
+/* IBM uses an alternative FMA definition, so -a*b-c=-(a*b+c) is "nmadd" */
+#define gmx_simd_fnmsub_d(a, b, c) vec_nmadd(a, b, c)
+#define gmx_simd_and_d(a, b) vec_and(a, b)
+#define gmx_simd_andnot_d(a, b) vec_andc(b, a)
+#define gmx_simd_or_d(a, b) vec_or(a, b)
+#define gmx_simd_xor_d(a, b) vec_xor(a, b)
+#define gmx_simd_rsqrt_d(a) vec_rsqrte(a)
+#define gmx_simd_rcp_d(a) vec_re(a)
+#define gmx_simd_fabs_d(a) vec_abs(a)
+#ifdef __GNUC__
+/* gcc up to at least version 4.9 is missing intrinsics for vec_neg(), use inline asm. */
+# define gmx_simd_fneg_d(a) ({ __vector double res; __asm__ ("xvnegdp %0,%1" : \
+ "=ww" (res) : "ww" ((__vector double) (a))); res; })
+#else
+/* IBM xlC */
+# define gmx_simd_fneg_d(a) vec_neg(a)
+#endif
+#define gmx_simd_max_d(a, b) vec_max(a, b)
+#define gmx_simd_min_d(a, b) vec_min(a, b)
+#ifdef __GNUC__
+/* gcc up to at least version 4.9 does not support vec_round() in double precision. */
+# define gmx_simd_round_d(a) ({ __vector double res; __asm__ ("xvrdpi %0,%1" : \
+ "=ww" (res) : "ww" ((__vector double) (a))); res; })
+#else
+/* IBM xlC */
+# define gmx_simd_round_d(a) vec_round(a)
+#endif
+#define gmx_simd_trunc_d(a) vec_trunc(a)
+#define gmx_simd_fraction_d(x) vec_sub(x, vec_trunc(x))
+#define gmx_simd_get_exponent_d(a) gmx_simd_get_exponent_d_ibm_vsx(a)
+#define gmx_simd_get_mantissa_d(a) gmx_simd_get_mantissa_d_ibm_vsx(a)
+#define gmx_simd_set_exponent_d(a) gmx_simd_set_exponent_d_ibm_vsx(a)
+/* integer datatype corresponding to double: gmx_simd_dint32_t */
+#define gmx_simd_dint32_t __vector signed int
+#define gmx_simd_load_di(m) gmx_simd_load_di_ibm_vsx(m)
+#define gmx_simd_store_di(m, x) gmx_simd_store_di_ibm_vsx(m, x)
+#define gmx_simd_set1_di(i) vec_splats((int)(i))
+#define gmx_simd_loadu_di gmx_simd_load_di
+#define gmx_simd_storeu_di gmx_simd_store_di
+#define gmx_simd_setzero_di() vec_splats((int)0)
+#ifdef __GNUC__
+/* gcc up to at least version 4.9 is missing intrinsics for double precision
+ * to integer conversion, use inline asm instead.
+ */
+# define gmx_simd_cvtt_d2i(a) ({ __vector signed int res; __asm__ ("xvcvdpsxws %0,%1" : \
+ "=ww" (res) : "ww" ((__vector double) (a))); res; })
+# define gmx_simd_cvt_i2d(a) ({ __vector double res; __asm__ ("xvcvsxwdp %0,%1" : \
+ "=ww" (res) : "ww" ((__vector signed int) (a))); res; })
+#else
+/* IBM xlC */
+# define gmx_simd_cvtt_d2i(a) vec_cts(a, 0)
+# define gmx_simd_cvt_i2d(a) vec_ctd(a, 0)
+#endif
+#define gmx_simd_cvt_d2i(a) gmx_simd_cvtt_d2i(gmx_simd_round_d(a))
+#define gmx_simd_extract_di(a, i) gmx_simd_extract_fi_ibm_vsx(a, (i)*2)
+/* Integer logical ops on gmx_simd_dint32_t */
+#define gmx_simd_slli_di(a, i) vec_sl(a, vec_splats((unsigned int)i))
+#define gmx_simd_srli_di(a, i) vec_sr(a, vec_splats((unsigned int)i))
+#define gmx_simd_and_di(a, b) vec_and(a, b)
+#define gmx_simd_andnot_di(a, b) vec_andc(b, a)
+#define gmx_simd_or_di(a, b) vec_or(a, b)
+#define gmx_simd_xor_di(a, b) vec_xor(a, b)
+/* Integer arithmetic ops on gmx_simd_dint32_t */
+#define gmx_simd_add_di(a, b) vec_add(a, b)
+#define gmx_simd_sub_di(a, b) vec_sub(a, b)
+#ifdef __GNUC__
+/* gcc 4.9 does not provide vec_mul() for integers */
+# ifdef __BIG_ENDIAN__
+# define gmx_simd_mul_di(a, b) vec_mulo((__vector short)a, (__vector short)b)
+# else
+# define gmx_simd_mul_di(a, b) vec_mule((__vector short)a, (__vector short)b)
+# endif
+#else
+/* IBM xlC */
+# define gmx_simd_mul_di(a, b) vec_mul(a, b)
+#endif
+/* Boolean & comparison operations on gmx_simd_double_t */
+#define gmx_simd_dbool_t __vector vsx_bool long long
+#define gmx_simd_cmpeq_d(a, b) vec_cmpeq(a, b)
+#define gmx_simd_cmplt_d(a, b) vec_cmplt(a, b)
+#define gmx_simd_cmple_d(a, b) vec_cmple(a, b)
+#define gmx_simd_and_db(a, b) (__vector vsx_bool long long)vec_and((__vector signed int)a, (__vector signed int)b)
+#define gmx_simd_or_db(a, b) (__vector vsx_bool long long)vec_or((__vector signed int)a, (__vector signed int)b)
+#define gmx_simd_anytrue_db(a) vec_any_ne((__vector vsx_bool int)a, (__vector vsx_bool int)vec_splats(0))
+#define gmx_simd_blendzero_d(a, sel) vec_and(a, (__vector double)sel)
+#define gmx_simd_blendnotzero_d(a, sel) vec_andc(a, (__vector double)sel)
+#define gmx_simd_blendv_d(a, b, sel) vec_sel(a, b, sel)
+#define gmx_simd_reduce_d(a) gmx_simd_reduce_d_ibm_vsx(a)
+/* Boolean & comparison operations on gmx_simd_fint32_t */
+#define gmx_simd_dibool_t __vector vsx_bool int
+#define gmx_simd_cmpeq_di(a, b) vec_cmpeq(a, b)
+#define gmx_simd_cmplt_di(a, b) vec_cmplt(a, b)
+#define gmx_simd_and_dib(a, b) vec_and(a, b)
+#define gmx_simd_or_dib(a, b) vec_or(a, b)
+/* Since we have applied all operations to pairs of elements we can work on all elements here */
+#define gmx_simd_anytrue_dib(a) vec_any_ne(a, (__vector vsx_bool int)vec_splats(0))
+#define gmx_simd_blendzero_di(a, sel) vec_and(a, (__vector signed int)sel)
+#define gmx_simd_blendnotzero_di(a, sel) vec_andc(a, (__vector signed int)sel)
+#define gmx_simd_blendv_di(a, b, sel) vec_sel(a, b, sel)
+/* Conversions between different booleans */
+#define gmx_simd_cvt_db2dib(x) (__vector vsx_bool int)(x)
+#define gmx_simd_cvt_dib2db(x) (__vector vsx_bool long long)(x)
+/* Float/double conversion */
+#define gmx_simd_cvt_f2dd(f, d0, d1) gmx_simd_cvt_f2dd_ibm_vsx(f, d0, d1)
+#define gmx_simd_cvt_dd2f(d0, d1) gmx_simd_cvt_dd2f_ibm_vsx(d0, d1)
+
+/* Convenience defines to work around GCC/xlc compiler differences */
+
+#ifdef __GNUC__
+/* vec_xxsldwi() and vec_xxpermdi() were missing from altivec.h
+ * in gcc-4.8, but the builtins are available. This was fixed in gcc-4.9.
+ */
+# ifndef vec_xxsldwi
+# define vec_xxsldwi __builtin_vsx_xxsldwi
+# endif
+# ifndef vec_xxpermdi
+# define vec_xxpermdi __builtin_vsx_xxpermdi
+# endif
+/* gcc up to at least 4.9 is missing intrinsics for
+ * double-to-float and float-to-double conversions. Use inline asm.
+ */
+# define gmx_vsx_f2d(x) ({ __vector double res; __asm__ ("xvcvspdp %0,%1" : \
+ "=ww" (res) : "ww" ((__vector float) (x))); res; })
+# define gmx_vsx_d2f(x) ({ __vector float res; __asm__ ("xvcvdpsp %0,%1" : \
+ "=ww" (res) : "ww" ((__vector double) (x))); res; })
+#else
+/* IBM xlC */
+# define vec_xxsldwi vec_sldw
+# define vec_xxpermdi vec_permi
+/* f2d and d2f are indeed identical on xlC; it is selected by the argument and result type. */
+# define gmx_vsx_f2d(x) vec_cvf(x)
+# define gmx_vsx_d2f(x) vec_cvf(x)
+#endif
+
+
+/****************************************************
+ * SINGLE PREC. IMPLEMENTATION HELPER FUNCTIONS *
+ ****************************************************/
+static gmx_inline gmx_simd_float_t
+gmx_simd_get_exponent_f_ibm_vsx(gmx_simd_float_t x)
+{
+ /* Generate 0x7F800000 without memory operations */
+ gmx_simd_float_t expmask = (__vector float)vec_splats(0x7F800000);
+ gmx_simd_fint32_t i127 = vec_splats(127);
+ gmx_simd_fint32_t iexp;
+
+ iexp = (__vector signed int)gmx_simd_and_f(x, expmask);
+ iexp = vec_sub(gmx_simd_srli_fi(iexp, 23), i127);
+ return vec_ctf(iexp, 0);
+}
+
+static gmx_inline gmx_simd_float_t
+gmx_simd_get_mantissa_f_ibm_vsx(gmx_simd_float_t x)
+{
+ gmx_simd_float_t expmask = (__vector float)vec_splats(0x7F800000);
+
+ x = gmx_simd_andnot_f(expmask, vec_abs(x));
+ /* Reset zero (but correctly biased) exponent */
+ return gmx_simd_or_f(x, vec_splats(1.0f));
+}
+
+static gmx_inline gmx_simd_float_t
+gmx_simd_set_exponent_f_ibm_vsx(gmx_simd_float_t x)
+{
+ gmx_simd_fint32_t iexp = gmx_simd_cvt_f2i(x);
+ gmx_simd_fint32_t i127 = vec_splats(127);
+
+ iexp = gmx_simd_slli_fi(vec_add(iexp, i127), 23);
+ return (__vector float)iexp;
+}
+
+static gmx_inline float
+gmx_simd_reduce_f_ibm_vsx(gmx_simd_float_t x)
+{
+ x = vec_add(x, vec_xxsldwi(x, x, 2));
+ x = vec_add(x, vec_xxsldwi(x, x, 1));
+ return vec_extract(x, 0);
+}
+
+static gmx_inline int
+gmx_simd_extract_fi_ibm_vsx(gmx_simd_fint32_t gmx_unused x, unsigned int i)
+{
+ /* For some reason gcc-4.9 warns about x being unused, which it isn't. */
+#if (defined __GNUC__) && (defined __LITTLE_ENDIAN__)
+ /* On Power7 and earlier big-endian architecture the GNU version of vec_extract()
+ * works fine, but it appears to be buggy on Power8 running in little-endian mode.
+ * Use inline assembly instead. Since this can only happen on Power8 and later,
+ * we can use a Power8-specific direct move instruction.
+ */
+ int res;
+ __asm__ ("mfvsrwz %0,%1" : "=r" (res) : \
+ "ww" ((vec_xxsldwi((x), (x), (((2-(i))&0x3 ))))));
+ return res;
+#else
+ /* IBM xlC, and GNU when running in big-endian mode */
+ return vec_extract(x, i);
+#endif
+}
+
+/****************************************************
+ * DOUBLE PREC. IMPLEMENTATION HELPER FUNCTIONS *
+ ****************************************************/
+static gmx_inline gmx_simd_dint32_t
+gmx_simd_load_di_ibm_vsx(const int *m)
+{
+ __vector signed int vi;
+ __vector signed int d0 = vec_splats(m[0]);
+ __vector signed int d1 = vec_splats(m[1]);
+#ifdef __LITTLE_ENDIAN__
+ vi = (__vector signed int)vec_xxpermdi((__vector double)d1, (__vector double)d0, 0x0);
+#else
+ vi = (__vector signed int)vec_xxpermdi((__vector double)d0, (__vector double)d1, 0x0);
+#endif
+ return vi;
+}
+
+static gmx_inline void
+gmx_simd_store_di_ibm_vsx(int *m, gmx_simd_dint32_t x)
+{
+ m[0] = gmx_simd_extract_di(x, 0);
+ m[1] = gmx_simd_extract_di(x, 1);
+}
+
+static gmx_inline gmx_simd_double_t
+gmx_simd_get_exponent_d_ibm_vsx(gmx_simd_double_t x)
+{
+ gmx_simd_double_t expmask = (__vector double)vec_mergel(vec_splats((int)0x7FF00000), vec_splats((int)0));
+ gmx_simd_dint32_t i1023 = vec_splats(1023);
+ gmx_simd_dint32_t iexp;
+
+ iexp = (__vector signed int)gmx_simd_and_d(x, expmask);
+ /* The upper half of each double is already in positions 0/2, so we only need
+ * to shift by another 52-32=20 bits.
+ */
+ iexp = gmx_simd_srli_fi(iexp, 20);
+ iexp = vec_sub(iexp, i1023);
+ /* Now we have the correct integer in elements 0 & 2. Never mind about elements 1,3 */
+ return gmx_simd_cvt_i2d(iexp);
+}
+
+static gmx_inline gmx_simd_double_t
+gmx_simd_get_mantissa_d_ibm_vsx(gmx_simd_double_t x)
+{
+ gmx_simd_double_t expmask = (__vector double)vec_mergel(vec_splats((int)0x7FF00000), vec_splats((int)0));
+
+ x = gmx_simd_andnot_d(expmask, vec_abs(x));
+ /* Reset zero (but correctly biased) exponent */
+ return gmx_simd_or_d(x, vec_splats(1.0));
+}
+
+static gmx_inline gmx_simd_double_t
+gmx_simd_set_exponent_d_ibm_vsx(gmx_simd_double_t x)
+{
+ gmx_simd_dint32_t iexp = gmx_simd_cvt_d2i(x);
+ gmx_simd_dint32_t i1023 = vec_splats(1023);
+ gmx_simd_dint32_t tmp;
+
+ iexp = vec_add(iexp, i1023);
+ /* exponent is now present in pairs of integers; 0011.
+ * Elements 0/2 already correspond to the upper half of each double,
+ * so we only need to shift by another 52-32=20 bits.
+ * The remaining elements 1/3 are shifted by 32 bits to make them zero.
+ */
+ iexp = vec_sl(iexp, (__vector unsigned int)vec_splats((int)20));
+ tmp = vec_mergeh(iexp, iexp);
+ iexp = vec_mergel(tmp, iexp);
+ iexp = vec_mergel(iexp, gmx_simd_setzero_di());
+ return (__vector double)iexp;
+}
+
+static gmx_inline double
+gmx_simd_reduce_d_ibm_vsx(gmx_simd_double_t x)
+{
+ x = vec_add(x, vec_xxsldwi(x, x, 2));
+ return vec_extract(x, 0);
+}
+
+
+/****************************************************
+ * CONVERSION IMPLEMENTATION HELPER FUNCTIONS *
+ ****************************************************/
+static gmx_inline void
+gmx_simd_cvt_f2dd_ibm_vsx(gmx_simd_float_t f0,
+ gmx_simd_double_t * d0, gmx_simd_double_t * d1)
+{
+ __vector float fA, fB;
+ fA = vec_mergel(f0, f0); /* 0011 */
+ fB = vec_mergeh(f0, f0); /* 2233 */
+ *d0 = gmx_vsx_f2d(fA); /* 01 */
+ *d1 = gmx_vsx_f2d(fB); /* 23 */
+}
+
+
+static gmx_inline gmx_simd_float_t
+gmx_simd_cvt_dd2f_ibm_vsx(gmx_simd_double_t d0, gmx_simd_double_t d1)
+{
+ __vector float fA, fB, fC, fD, fE;
+ fA = gmx_vsx_d2f(d0); /* 0x1x */
+ fB = gmx_vsx_d2f(d1); /* 2x3x */
+ fC = vec_mergel(fA, fB); /* 02xx */
+ fD = vec_mergeh(fA, fB); /* 13xx */
+ fE = vec_mergel(fD, fC); /* 0123 */
+ return fE;
+}
+
+/* Single precision VSX is 4 elements wide, use for SIMD4 */
+#define gmx_simd4_float_t gmx_simd_float_t
+#define gmx_simd4_load_f gmx_simd_load_f
+#define gmx_simd4_load1_f gmx_simd_load1_f
+#define gmx_simd4_set1_f gmx_simd_set1_f
+#define gmx_simd4_store_f gmx_simd_store_f
+#define gmx_simd4_loadu_f gmx_simd_loadu_f
+#define gmx_simd4_storeu_f gmx_simd_storeu_f
+#define gmx_simd4_setzero_f gmx_simd_setzero_f
+#define gmx_simd4_add_f gmx_simd_add_f
+#define gmx_simd4_sub_f gmx_simd_sub_f
+#define gmx_simd4_mul_f gmx_simd_mul_f
+#define gmx_simd4_fmadd_f gmx_simd_fmadd_f
+#define gmx_simd4_fmsub_f gmx_simd_fmsub_f
+#define gmx_simd4_fnmadd_f gmx_simd_fnmadd_f
+#define gmx_simd4_fnmsub_f gmx_simd_fnmsub_f
+#define gmx_simd4_and_f gmx_simd_and_f
+#define gmx_simd4_andnot_f gmx_simd_andnot_f
+#define gmx_simd4_or_f gmx_simd_or_f
+#define gmx_simd4_xor_f gmx_simd_xor_f
+#define gmx_simd4_rsqrt_f gmx_simd_rsqrt_f
+#define gmx_simd4_rcp_f gmx_simd_rcp_f
+#define gmx_simd4_fabs_f gmx_simd_fabs_f
+#define gmx_simd4_fneg_f gmx_simd_fneg_f
+#define gmx_simd4_max_f gmx_simd_max_f
+#define gmx_simd4_min_f gmx_simd_min_f
+#define gmx_simd4_round_f gmx_simd_round_f
+#define gmx_simd4_trunc_f gmx_simd_trunc_f
+#define gmx_simd4_fraction_f gmx_simd_fraction_f
+#define gmx_simd4_get_exponent_f gmx_simd_get_exponent_f
+#define gmx_simd4_get_mantissa_f gmx_simd_get_mantissa_f
+#define gmx_simd4_set_exponent_f gmx_simd_set_exponent_f
+#define gmx_simd4_dotproduct3_f gmx_simd4_dotproduct3_f_ibm_vsx
+#define gmx_simd4_fint32_t gmx_simd_fint32_t
+#define gmx_simd4_load_fi gmx_simd_load_fi
+#define gmx_simd4_load1_fi gmx_simd_load1_fi
+#define gmx_simd4_set1_fi gmx_simd_set1_fi
+#define gmx_simd4_store_fi gmx_simd_store_fi
+#define gmx_simd4_loadu_fi gmx_simd_loadu_fi
+#define gmx_simd4_storeu_fi gmx_simd_storeu_fi
+#define gmx_simd4_setzero_fi gmx_simd_setzero_fi
+#define gmx_simd4_cvt_f2i gmx_simd_cvt_f2i
+#define gmx_simd4_cvtt_f2i gmx_simd_cvtt_f2i
+#define gmx_simd4_cvt_i2f gmx_simd_cvt_i2f
+#define gmx_simd4_fbool_t gmx_simd_fbool_t
+#define gmx_simd4_cmpeq_f gmx_simd_cmpeq_f
+#define gmx_simd4_cmplt_f gmx_simd_cmplt_f
+#define gmx_simd4_cmple_f gmx_simd_cmple_f
+#define gmx_simd4_and_fb gmx_simd_and_fb
+#define gmx_simd4_or_fb gmx_simd_or_fb
+#define gmx_simd4_anytrue_fb gmx_simd_anytrue_fb
+#define gmx_simd4_blendzero_f gmx_simd_blendzero_f
+#define gmx_simd4_blendnotzero_f gmx_simd_blendnotzero_f
+#define gmx_simd4_blendv_f gmx_simd_blendv_f
+#define gmx_simd4_reduce_f gmx_simd_reduce_f
+
+static gmx_inline float
+gmx_simd4_dotproduct3_f_ibm_vsx(gmx_simd4_float_t a, gmx_simd4_float_t b)
+{
+ gmx_simd4_float_t c = gmx_simd_mul_f(a, b);
+ gmx_simd4_float_t sum;
+ sum = vec_add(c, vec_xxsldwi(c, c, 2));
+ sum = vec_add(sum, vec_xxsldwi(c, c, 1));
+ return vec_extract(sum, 0);
+}
+
+/* Function to check whether SIMD operations have resulted in overflow.
+ * For now, this is unfortunately a dummy for this architecture.
+ */
+static int
+gmx_simd_check_and_reset_overflow(void)
+{
+ return 0;
+}
+
+/* Undefine our temporary work-arounds so they are not used by mistake */
+#undef gmx_vsx_f2d
+#undef gmx_vsx_d2f
+
+#endif /* GMX_SIMD_IMPLEMENTATION_IBM_VSX_H */
#ifndef GMX_SIMD_IMPL_INTEL_MIC_H
#define GMX_SIMD_IMPL_INTEL_MIC_H
+#include "config.h"
+
#include <math.h>
+
#include <immintrin.h>
/* Intel Xeon Phi, or
static gmx_inline __m512 gmx_simdcall
gmx_simd_exp_f_mic(__m512 x)
{
- /* only 59ulp accuracy so we need to do extra an iteration
- Using: http://yacas.sourceforge.net/Algochapter5.html 5.4 Method 3 */
- __m512 r = gmx_simd_exp2_f(_mm512_mul_ps(x, _mm512_set1_ps(1.44269504088896341)));
- __mmask16 m = _mm512_cmpneq_ps_mask(r, _mm512_setzero_ps());
- __m512 t = _mm512_mask_fnmadd_ps(_mm512_mask_log2ae23_ps(_mm512_undefined_ps(), m, r), m, _mm512_set1_ps(0.693147180559945286226764), x);
- return _mm512_mask_fmadd_ps(r, m, t, r);
+ const gmx_simd_float_t argscale = gmx_simd_set1_f(1.44269504088896341f);
+ const gmx_simd_float_t invargscale = gmx_simd_set1_f(-0.69314718055994528623f);
+ __m512 xscaled = _mm512_mul_ps(x, argscale);
+ __m512 r = gmx_simd_exp2_f_mic(xscaled);
+
+ /* gmx_simd_exp2_f_mic() provides 23 bits of accuracy, but we ruin some of that
+ * with the argument scaling due to single-precision rounding, where the
+ * rounding error is amplified exponentially. To correct this, we find the
+ * difference between the scaled argument and the true one (extended precision
+ * arithmetics does not appear to be necessary to fulfill our accuracy requirements)
+ * and then multiply by the exponent of this correction since exp(a+b)=exp(a)*exp(b).
+ * Note that this only adds two instructions (and maybe some constant loads).
+ */
+ x = gmx_simd_fmadd_f(invargscale, xscaled, x);
+ /* x will now be a _very_ small number, so approximate exp(x)=1+x.
+ * We should thus apply the correction as r'=r*(1+x)=r+r*x
+ */
+ r = gmx_simd_fmadd_f(r, x, r);
+ return r;
}
static gmx_inline __m512 gmx_simdcall
#include <math.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
/*! \cond libapi */
/*! \addtogroup module_simd */
#ifndef GMX_SIMD_IMPL_X86_AVX2_256_H
#define GMX_SIMD_IMPL_X86_AVX2_256_H
+#include "config.h"
+
#include <math.h>
+
#include <immintrin.h>
/* x86 256-bit AVX2 SIMD instruction wrappers
#ifndef GMX_SIMD_IMPL_X86_AVX_128_FMA_H
#define GMX_SIMD_IMPL_X86_AVX_128_FMA_H
+#include "config.h"
+
#include <math.h>
+
#include <immintrin.h>
#include <x86intrin.h>
#ifndef GMX_SIMD_IMPL_X86_AVX_256_H
#define GMX_SIMD_IMPL_X86_AVX_256_H
-#include <math.h>
+#include "config.h"
+
#include <immintrin.h>
/* It is cleaner to start the AVX implementation from scratch rather than
#define gmx_simd_set_exponent_f gmx_simd_set_exponent_f_avx_256
/* integer datatype corresponding to float: gmx_simd_fint32_t */
#define gmx_simd_fint32_t __m256i
-#define gmx_simd_load_fi(m) _mm256_castps_si256(_mm256_load_ps((const float *)m))
+#define gmx_simd_load_fi(m) _mm256_load_si256((__m256i const*)m)
#define gmx_simd_set1_fi _mm256_set1_epi32
-#define gmx_simd_store_fi(m, x) _mm256_store_ps((float *)m, _mm256_castsi256_ps(x))
-#define gmx_simd_loadu_fi(m) _mm256_castps_si256(_mm256_loadu_ps((const float *)m))
-#define gmx_simd_storeu_fi(m, x) _mm256_storeu_ps((float *)m, _mm256_castsi256_ps(x))
+#define gmx_simd_store_fi(m, x) _mm256_store_si256((__m256i *)m, x)
+#define gmx_simd_loadu_fi(m) _mm256_loadu_si256((__m256i const*)m)
+#define gmx_simd_storeu_fi(m, x) _mm256_storeu_si256((__m256i *)m, x)
#define gmx_simd_setzero_fi _mm256_setzero_si256
#define gmx_simd_cvt_f2i _mm256_cvtps_epi32
#define gmx_simd_cvtt_f2i _mm256_cvttps_epi32
#ifndef GMX_SIMD_IMPL_X86_SSE2_H
#define GMX_SIMD_IMPL_X86_SSE2_H
+#include "config.h"
+
#include <math.h>
+
#include <emmintrin.h>
/* Set capabilities that can be inherited */
#ifndef GMX_SIMD_IMPL_X86_SSE4_1_H
#define GMX_SIMD_IMPL_X86_SSE4_1_H
+#include "config.h"
+
#include <math.h>
-#include <smmintrin.h>
+#include <smmintrin.h>
/* x86 SSE4.1 SIMD instruction wrappers
*
#ifndef GMX_SIMD_MATH_AVX_128_FMA_DOUBLE_H
#define GMX_SIMD_MATH_AVX_128_FMA_DOUBLE_H
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
/* Temporary:
* Alias some old SSE definitions to new SIMD definitions so we don't need
#ifndef GMX_SIMD_MATH_AVX_128_FMA_SINGLE_H
#define GMX_SIMD_MATH_AVX_128_FMA_SINGLE_H
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
/* Temporary:
* Alias some old SSE definitions to new SIMD definitions so we don't need
#ifndef GMX_SIMD_MATH_AVX_256_DOUBLE_H
#define GMX_SIMD_MATH_AVX_256_DOUBLE_H
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
/* Temporary:
* Alias some old SSE definitions to new SIMD definitions so we don't need
#ifndef GMX_SIMD_MATH_AVX_256_SINGLE_H
#define GMX_SIMD_MATH_AVX_256_SINGLE_H
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
/* Temporary:
* Alias some old SSE definitions to new SIMD definitions so we don't need
#ifndef GMX_SIMD_MATH_SSE2_DOUBLE_H
#define GMX_SIMD_MATH_SSE2_DOUBLE_H
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
/* Temporary:
* Alias some old SSE definitions to new SIMD definitions so we don't need
#ifndef GMX_SIMD_MATH_SSE2_SINGLE_H
#define GMX_SIMD_MATH_SSE2_SINGLE_H
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
/* Temporary:
* Alias some old SSE definitions to new SIMD definitions so we don't need
#ifndef GMX_SIMD_MATH_SSE4_1_DOUBLE_H
#define GMX_SIMD_MATH_SSE4_1_DOUBLE_H
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
/* Temporary:
* Alias some old SSE definitions to new SIMD definitions so we don't need
#ifndef GMX_SIMD_MATH_SSE4_1_SINGLE_H
#define GMX_SIMD_MATH_SSE4_1_SINGLE_H
-#include "simd_math.h"
+#include "gromacs/simd/simd_math.h"
/* Temporary:
* Alias some old SSE definitions to new SIMD definitions so we don't need
* \ingroup module_simd
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "config.h"
#include <stddef.h>
-#include "gromacs/legacyheaders/types/simple.h"
+
+#include "gromacs/utility/basedefinitions.h"
/* Forward declarations so memory allocation can be used in implementations */
static gmx_inline float * gmx_simd_align_f(float *p);
* this SIMD module are static, so it will work perfectly fine to include this
* file with different SIMD definitions for different files.
*/
-#if defined __MIC__
-# include "gromacs/simd/impl_intel_mic/impl_intel_mic.h"
+#if defined GMX_SIMD_X86_MIC
+# include "impl_intel_mic/impl_intel_mic.h"
#elif defined GMX_SIMD_X86_AVX2_256
-# include "gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h"
+# include "impl_x86_avx2_256/impl_x86_avx2_256.h"
#elif defined GMX_SIMD_X86_AVX_256
-# include "gromacs/simd/impl_x86_avx_256/impl_x86_avx_256.h"
+# include "impl_x86_avx_256/impl_x86_avx_256.h"
#elif defined GMX_SIMD_X86_AVX_128_FMA
-# include "gromacs/simd/impl_x86_avx_128_fma/impl_x86_avx_128_fma.h"
+# include "impl_x86_avx_128_fma/impl_x86_avx_128_fma.h"
#elif defined GMX_SIMD_X86_SSE4_1
-# include "gromacs/simd/impl_x86_sse4_1/impl_x86_sse4_1.h"
+# include "impl_x86_sse4_1/impl_x86_sse4_1.h"
#elif defined GMX_SIMD_X86_SSE2
-# include "gromacs/simd/impl_x86_sse2/impl_x86_sse2.h"
+# include "impl_x86_sse2/impl_x86_sse2.h"
+#elif defined GMX_SIMD_ARM_NEON
+# include "impl_arm_neon/impl_arm_neon.h"
+#elif defined GMX_SIMD_ARM_NEON_ASIMD
+# include "impl_arm_neon_asimd/impl_arm_neon_asimd.h"
#elif defined GMX_SIMD_IBM_QPX
-# include "gromacs/simd/impl_ibm_qpx/impl_ibm_qpx.h"
+# include "impl_ibm_qpx/impl_ibm_qpx.h"
+#elif defined GMX_SIMD_IBM_VMX
+# include "impl_ibm_vmx/impl_ibm_vmx.h"
+#elif defined GMX_SIMD_IBM_VSX
+# include "impl_ibm_vsx/impl_ibm_vsx.h"
#elif defined GMX_SIMD_SPARC64_HPC_ACE
-# include "gromacs/simd/impl_sparc64_hpc_ace/impl_sparc64_hpc_ace.h"
+# include "impl_sparc64_hpc_ace/impl_sparc64_hpc_ace.h"
#elif (defined GMX_SIMD_REFERENCE) || (defined DOXYGEN)
/* Plain C SIMD reference implementation, also serves as documentation.
* For now this code path will also be taken for Sparc64_HPC_ACE since we have
* not yet added the verlet kernel extensions there. The group kernels do not
* depend on this file, so they will still be accelerated with SIMD.
*/
-# include "gromacs/simd/impl_reference/impl_reference.h"
+# include "impl_reference/impl_reference.h"
#else
/* Turn off the GMX_SIMD flag if we do not even have reference support */
# undef GMX_SIMD
* \ingroup module_simd
*/
+#include "config.h"
+
#include <math.h>
#include "gromacs/math/utilities.h"
#endif
}
+#ifndef gmx_simd_rsqrt_iter_f
/*! \brief Perform one Newton-Raphson iteration to improve 1/sqrt(x) for SIMD float.
*
* This is a low-level routine that should only be used by SIMD math routine
return gmx_simd_mul_f(gmx_simd_set1_f(0.5f), gmx_simd_mul_f(gmx_simd_sub_f(gmx_simd_set1_f(3.0f), gmx_simd_mul_f(gmx_simd_mul_f(lu, lu), x)), lu));
# endif
}
+#endif
/*! \brief Calculate 1/sqrt(x) for SIMD float.
*
return lu;
}
+/*! \brief Calculate 1/sqrt(x) for masked entries of SIMD float.
+ *
+ * Identical to gmx_simd_invsqrt_f but avoids fp-exception for non-masked entries.
+ * The result for the non-masked entries is undefined and the user has to use blend
+ * with the same mask to obtain a defined result.
+ *
+ * \param x Argument that must be >0 for masked entries
+ * \param m Masked entries
+ * \return 1/sqrt(x). Result is undefined if your argument was invalid or entry was not masked.
+ */
+#ifdef NDEBUG
+#define gmx_simd_invsqrt_maskfpe_f(x, m) gmx_simd_invsqrt_f(x)
+#else
+static gmx_inline gmx_simd_float_t
+gmx_simd_invsqrt_maskfpe_f(gmx_simd_float_t x, gmx_simd_fbool_t m)
+{
+ return gmx_simd_invsqrt_f(gmx_simd_blendv_f(gmx_simd_set1_f(1.0f), x, m));
+}
+#endif
+
+/*! \brief Calculate 1/sqrt(x) for non-masked entries of SIMD float.
+ *
+ * Identical to gmx_simd_invsqrt_f but avoids fp-exception for masked entries.
+ * The result for the non-masked entries is undefined and the user has to use blend
+ * with the same mask to obtain a defined result.
+ *
+ * \param x Argument that must be >0 for non-masked entries
+ * \param m Masked entries
+ * \return 1/sqrt(x). Result is undefined if your argument was invalid or entry was masked.
+ */
+#ifdef NDEBUG
+#define gmx_simd_invsqrt_notmaskfpe_f(x, m) gmx_simd_invsqrt_f(x)
+#else
+static gmx_inline gmx_simd_float_t
+gmx_simd_invsqrt_notmaskfpe_f(gmx_simd_float_t x, gmx_simd_fbool_t m)
+{
+ return gmx_simd_invsqrt_f(gmx_simd_blendv_f(x, gmx_simd_set1_f(1.0f), m));
+}
+#endif
+
/*! \brief Calculate 1/sqrt(x) for two SIMD floats.
*
* You should normally call the real-precision routine \ref gmx_simd_invsqrt_pair_r.
*out1 = gmx_simd_invsqrt_f(x1);
}
+#ifndef gmx_simd_rcp_iter_f
/*! \brief Perform one Newton-Raphson iteration to improve 1/x for SIMD float.
*
* This is a low-level routine that should only be used by SIMD math routine
{
return gmx_simd_mul_f(lu, gmx_simd_fnmadd_f(lu, x, gmx_simd_set1_f(2.0f)));
}
+#endif
/*! \brief Calculate 1/x for SIMD float.
*
return lu;
}
+/*! \brief Calculate 1/x for masked entries of SIMD float.
+ *
+ * Identical to gmx_simd_inv_f but avoids fp-exception for non-masked entries.
+ * The result for the non-masked entries is undefined and the user has to use blend
+ * with the same mask to obtain a defined result.
+ *
+ * \param x Argument that must be nonzero for masked entries
+ * \param m Masked entries
+ * \return 1/x. Result is undefined if your argument was invalid or entry was not masked.
+ */
+#ifdef NDEBUG
+#define gmx_simd_inv_maskfpe_f(x, m) gmx_simd_inv_f(x)
+#else
+static gmx_inline gmx_simd_float_t
+gmx_simd_inv_maskfpe_f(gmx_simd_float_t x, gmx_simd_fbool_t m)
+{
+ return gmx_simd_inv_f(gmx_simd_blendv_f(gmx_simd_set1_f(1.0f), x, m));
+}
+#endif
+
+/*! \brief Calculate 1/x for non-masked entries of SIMD float.
+ *
+ * Identical to gmx_simd_inv_f but avoids fp-exception for masked entries.
+ * The result for the non-masked entries is undefined and the user has to use blend
+ * with the same mask to obtain a defined result.
+ *
+ * \param x Argument that must be nonzero for non-masked entries
+ * \param m Masked entries
+ * \return 1/x. Result is undefined if your argument was invalid or entry was masked.
+ */
+#ifdef NDEBUG
+#define gmx_simd_inv_notmaskfpe_f(x, m) gmx_simd_inv_f(x)
+#else
+static gmx_inline gmx_simd_float_t
+gmx_simd_inv_notmaskfpe_f(gmx_simd_float_t x, gmx_simd_fbool_t m)
+{
+ return gmx_simd_inv_f(gmx_simd_blendv_f(x, gmx_simd_set1_f(1.0f), m));
+}
+#endif
+
/*! \brief Calculate sqrt(x) correctly for SIMD floats, including argument 0.0.
*
* You should normally call the real-precision routine \ref gmx_simd_sqrt_r.
gmx_simd_float_t res;
mask = gmx_simd_cmpeq_f(x, gmx_simd_setzero_f());
- res = gmx_simd_blendnotzero_f(gmx_simd_invsqrt_f(x), mask);
+ res = gmx_simd_blendnotzero_f(gmx_simd_invsqrt_notmaskfpe_f(x, mask), mask);
return gmx_simd_mul_f(res, x);
}
const gmx_simd_float_t argscale = gmx_simd_set1_f(1.44269504088896341f);
/* Lower bound: Disallow numbers that would lead to an IEEE fp exponent reaching +-127. */
const gmx_simd_float_t arglimit = gmx_simd_set1_f(126.0f);
- const gmx_simd_float_t invargscale0 = gmx_simd_set1_f(0.693145751953125f);
- const gmx_simd_float_t invargscale1 = gmx_simd_set1_f(1.428606765330187045e-06f);
+ const gmx_simd_float_t invargscale0 = gmx_simd_set1_f(-0.693145751953125f);
+ const gmx_simd_float_t invargscale1 = gmx_simd_set1_f(-1.428606765330187045e-06f);
const gmx_simd_float_t CC4 = gmx_simd_set1_f(0.00136324646882712841033936f);
const gmx_simd_float_t CC3 = gmx_simd_set1_f(0.00836596917361021041870117f);
const gmx_simd_float_t CC2 = gmx_simd_set1_f(0.0416710823774337768554688f);
fexppart = gmx_simd_blendzero_f(fexppart, valuemask);
/* Extended precision arithmetics */
- x = gmx_simd_fnmadd_f(invargscale0, intpart, x);
- x = gmx_simd_fnmadd_f(invargscale1, intpart, x);
+ x = gmx_simd_fmadd_f(invargscale0, intpart, x);
+ x = gmx_simd_fmadd_f(invargscale1, intpart, x);
p = gmx_simd_fmadd_f(CC4, x, CC3);
p = gmx_simd_fmadd_f(p, x, CC2);
gmx_simd_float_t pA0, pA1, pB0, pB1, pC0, pC1;
gmx_simd_float_t expmx2;
gmx_simd_float_t res_erf, res_erfc, res;
- gmx_simd_fbool_t mask;
+ gmx_simd_fbool_t mask, msk_erf;
/* Calculate erf() */
x2 = gmx_simd_mul_f(x, x);
/* Calculate erfc */
y = gmx_simd_fabs_f(x);
- t = gmx_simd_inv_f(y);
+ msk_erf = gmx_simd_cmplt_f(y, gmx_simd_set1_f(0.75f));
+ t = gmx_simd_inv_notmaskfpe_f(y, msk_erf);
w = gmx_simd_sub_f(t, one);
t2 = gmx_simd_mul_f(t, t);
w2 = gmx_simd_mul_f(w, w);
res_erfc = gmx_simd_blendv_f(res_erfc, gmx_simd_sub_f(two, res_erfc), mask);
/* Select erf() or erfc() */
- mask = gmx_simd_cmplt_f(y, gmx_simd_set1_f(0.75f));
- res = gmx_simd_blendv_f(gmx_simd_sub_f(one, res_erfc), res_erf, mask);
+ res = gmx_simd_blendv_f(gmx_simd_sub_f(one, res_erfc), res_erf, msk_erf);
return res;
}
gmx_simd_float_t pA0, pA1, pB0, pB1, pC0, pC1;
gmx_simd_float_t expmx2, corr;
gmx_simd_float_t res_erf, res_erfc, res;
- gmx_simd_fbool_t mask;
+ gmx_simd_fbool_t mask, msk_erf;
/* Calculate erf() */
x2 = gmx_simd_mul_f(x, x);
/* Calculate erfc */
y = gmx_simd_fabs_f(x);
- t = gmx_simd_inv_f(y);
+ msk_erf = gmx_simd_cmplt_f(y, gmx_simd_set1_f(0.75f));
+ t = gmx_simd_inv_notmaskfpe_f(y, msk_erf);
w = gmx_simd_sub_f(t, one);
t2 = gmx_simd_mul_f(t, t);
w2 = gmx_simd_mul_f(w, w);
res_erfc = gmx_simd_blendv_f(res_erfc, gmx_simd_sub_f(two, res_erfc), mask);
/* Select erf() or erfc() */
- mask = gmx_simd_cmplt_f(y, gmx_simd_set1_f(0.75f));
- res = gmx_simd_blendv_f(res_erfc, gmx_simd_sub_f(one, res_erf), mask);
+ res = gmx_simd_blendv_f(res_erfc, gmx_simd_sub_f(one, res_erf), msk_erf);
return res;
}
gmx_simd_sincos_f(gmx_simd_float_t x, gmx_simd_float_t *sinval, gmx_simd_float_t *cosval)
{
/* Constants to subtract Pi/4*x from y while minimizing precision loss */
- const gmx_simd_float_t argred0 = gmx_simd_set1_f(1.5703125);
- const gmx_simd_float_t argred1 = gmx_simd_set1_f(4.83751296997070312500e-04f);
- const gmx_simd_float_t argred2 = gmx_simd_set1_f(7.54953362047672271729e-08f);
- const gmx_simd_float_t argred3 = gmx_simd_set1_f(2.56334406825708960298e-12f);
+ const gmx_simd_float_t argred0 = gmx_simd_set1_f(-1.5703125);
+ const gmx_simd_float_t argred1 = gmx_simd_set1_f(-4.83751296997070312500e-04f);
+ const gmx_simd_float_t argred2 = gmx_simd_set1_f(-7.54953362047672271729e-08f);
+ const gmx_simd_float_t argred3 = gmx_simd_set1_f(-2.56334406825708960298e-12f);
const gmx_simd_float_t two_over_pi = gmx_simd_set1_f(2.0f/M_PI);
const gmx_simd_float_t const_sin2 = gmx_simd_set1_f(-1.9515295891e-4f);
const gmx_simd_float_t const_sin1 = gmx_simd_set1_f( 8.3321608736e-3f);
/* where mask is FALSE, set sign. */
csign = gmx_simd_xor_sign_f(csign, gmx_simd_blendv_f(gmx_simd_set1_f(-1.0f), one, mask));
#endif
- x = gmx_simd_fnmadd_f(y, argred0, x);
- x = gmx_simd_fnmadd_f(y, argred1, x);
- x = gmx_simd_fnmadd_f(y, argred2, x);
- x = gmx_simd_fnmadd_f(y, argred3, x);
+ x = gmx_simd_fmadd_f(y, argred0, x);
+ x = gmx_simd_fmadd_f(y, argred1, x);
+ x = gmx_simd_fmadd_f(y, argred2, x);
+ x = gmx_simd_fmadd_f(y, argred3, x);
x2 = gmx_simd_mul_f(x, x);
psin = gmx_simd_fmadd_f(const_sin2, x2, const_sin1);
static gmx_inline gmx_simd_float_t gmx_simdcall
gmx_simd_tan_f(gmx_simd_float_t x)
{
- const gmx_simd_float_t argred0 = gmx_simd_set1_f(1.5703125);
- const gmx_simd_float_t argred1 = gmx_simd_set1_f(4.83751296997070312500e-04f);
- const gmx_simd_float_t argred2 = gmx_simd_set1_f(7.54953362047672271729e-08f);
- const gmx_simd_float_t argred3 = gmx_simd_set1_f(2.56334406825708960298e-12f);
+ const gmx_simd_float_t argred0 = gmx_simd_set1_f(-1.5703125);
+ const gmx_simd_float_t argred1 = gmx_simd_set1_f(-4.83751296997070312500e-04f);
+ const gmx_simd_float_t argred2 = gmx_simd_set1_f(-7.54953362047672271729e-08f);
+ const gmx_simd_float_t argred3 = gmx_simd_set1_f(-2.56334406825708960298e-12f);
const gmx_simd_float_t two_over_pi = gmx_simd_set1_f(2.0f/M_PI);
const gmx_simd_float_t CT6 = gmx_simd_set1_f(0.009498288995810566122993911);
const gmx_simd_float_t CT5 = gmx_simd_set1_f(0.002895755790837379295226923);
y = gmx_simd_round_f(z);
mask = gmx_simd_cvt_fib2fb(gmx_simd_cmpeq_fi(gmx_simd_and_fi(iy, ione), ione));
- x = gmx_simd_fnmadd_f(y, argred0, x);
- x = gmx_simd_fnmadd_f(y, argred1, x);
- x = gmx_simd_fnmadd_f(y, argred2, x);
- x = gmx_simd_fnmadd_f(y, argred3, x);
+ x = gmx_simd_fmadd_f(y, argred0, x);
+ x = gmx_simd_fmadd_f(y, argred1, x);
+ x = gmx_simd_fmadd_f(y, argred2, x);
+ x = gmx_simd_fmadd_f(y, argred3, x);
x = gmx_simd_xor_f(gmx_simd_blendzero_f(gmx_simd_set1_f(GMX_FLOAT_NEGZERO), mask), x);
#else
const gmx_simd_float_t quarter = gmx_simd_set1_f(0.25f);
m3 = gmx_simd_cmple_f(threequarter, q);
m1 = gmx_simd_and_fb(m1, m2);
mask = gmx_simd_or_fb(m1, m3);
- w = gmx_simd_fnmadd_f(y, argred0, w);
- w = gmx_simd_fnmadd_f(y, argred1, w);
- w = gmx_simd_fnmadd_f(y, argred2, w);
- w = gmx_simd_fnmadd_f(y, argred3, w);
+ w = gmx_simd_fmadd_f(y, argred0, w);
+ w = gmx_simd_fmadd_f(y, argred1, w);
+ w = gmx_simd_fmadd_f(y, argred2, w);
+ w = gmx_simd_fmadd_f(y, argred3, w);
w = gmx_simd_blendv_f(w, gmx_simd_fneg_f(w), mask);
x = gmx_simd_xor_sign_f(w, x);
p = gmx_simd_fmadd_f(p, x2, CT1);
p = gmx_simd_fmadd_f(x2, gmx_simd_mul_f(p, x), x);
- p = gmx_simd_blendv_f( p, gmx_simd_inv_f(p), mask);
+ p = gmx_simd_blendv_f( p, gmx_simd_inv_maskfpe_f(p, mask), mask);
return p;
}
gmx_simd_float_t xabs;
gmx_simd_float_t z, z1, z2, q, q1, q2;
gmx_simd_float_t pA, pB;
- gmx_simd_fbool_t mask;
+ gmx_simd_fbool_t mask, mask2;
xabs = gmx_simd_fabs_f(x);
mask = gmx_simd_cmplt_f(half, xabs);
z1 = gmx_simd_mul_f(half, gmx_simd_sub_f(one, xabs));
- q1 = gmx_simd_mul_f(z1, gmx_simd_invsqrt_f(z1));
- q1 = gmx_simd_blendnotzero_f(q1, gmx_simd_cmpeq_f(xabs, one));
+ mask2 = gmx_simd_cmpeq_f(xabs, one);
+ q1 = gmx_simd_mul_f(z1, gmx_simd_invsqrt_notmaskfpe_f(z1, mask2));
+ q1 = gmx_simd_blendnotzero_f(q1, mask2);
q2 = xabs;
z2 = gmx_simd_mul_f(q2, q2);
z = gmx_simd_blendv_f(z2, z1, mask);
const gmx_simd_float_t halfpi = gmx_simd_set1_f((float)M_PI/2.0f);
gmx_simd_float_t xabs;
gmx_simd_float_t z, z1, z2, z3;
- gmx_simd_fbool_t mask1, mask2;
+ gmx_simd_fbool_t mask1, mask2, mask3;
xabs = gmx_simd_fabs_f(x);
mask1 = gmx_simd_cmplt_f(half, xabs);
mask2 = gmx_simd_cmplt_f(gmx_simd_setzero_f(), x);
z = gmx_simd_mul_f(half, gmx_simd_sub_f(one, xabs));
- z = gmx_simd_mul_f(z, gmx_simd_invsqrt_f(z));
- z = gmx_simd_blendnotzero_f(z, gmx_simd_cmpeq_f(xabs, one));
+ mask3 = gmx_simd_cmpeq_f(xabs, one);
+ z = gmx_simd_mul_f(z, gmx_simd_invsqrt_notmaskfpe_f(z, mask3));
+ z = gmx_simd_blendnotzero_f(z, mask3);
z = gmx_simd_blendv_f(x, z, mask1);
z = gmx_simd_asin_f(z);
const gmx_simd_float_t CA7 = gmx_simd_set1_f(-0.1420273631811141967773f);
const gmx_simd_float_t CA5 = gmx_simd_set1_f(0.1999269574880599975585f);
const gmx_simd_float_t CA3 = gmx_simd_set1_f(-0.3333310186862945556640f);
+ const gmx_simd_float_t one = gmx_simd_set1_f(1.0f);
gmx_simd_float_t x2, x3, x4, pA, pB;
gmx_simd_fbool_t mask, mask2;
mask = gmx_simd_cmplt_f(x, gmx_simd_setzero_f());
x = gmx_simd_fabs_f(x);
- mask2 = gmx_simd_cmplt_f(gmx_simd_set1_f(1.0f), x);
- x = gmx_simd_blendv_f(x, gmx_simd_inv_f(x), mask2);
+ mask2 = gmx_simd_cmplt_f(one, x);
+ x = gmx_simd_blendv_f(x, gmx_simd_inv_maskfpe_f(x, mask2), mask2);
x2 = gmx_simd_mul_f(x, x);
x3 = gmx_simd_mul_f(x2, x);
aoffset = gmx_simd_blendv_f(aoffset, pi, mask_xlt0);
aoffset = gmx_simd_blendv_f(aoffset, gmx_simd_fneg_f(aoffset), mask_ylt0);
- xinv = gmx_simd_blendnotzero_f(gmx_simd_inv_f(x), mask_x0);
+ xinv = gmx_simd_blendnotzero_f(gmx_simd_inv_notmaskfpe_f(x, mask_x0), mask_x0);
p = gmx_simd_mul_f(y, xinv);
p = gmx_simd_atan_f(p);
p = gmx_simd_add_f(p, aoffset);
#endif
}
+#ifndef gmx_simd_rsqrt_iter_d
/*! \brief Perform one Newton-Raphson iteration to improve 1/sqrt(x) for SIMD double.
*
* \copydetails gmx_simd_rsqrt_iter_f
return gmx_simd_mul_d(gmx_simd_set1_d(0.5), gmx_simd_mul_d(gmx_simd_sub_d(gmx_simd_set1_d(3.0), gmx_simd_mul_d(gmx_simd_mul_d(lu, lu), x)), lu));
#endif
}
-
+#endif
/*! \brief Calculate 1/sqrt(x) for SIMD double
*
return lu;
}
+/*! \brief Calculate 1/sqrt(x) for masked entries of SIMD double.
+ *
+ * \copydetails gmx_simd_invsqrt_maskfpe_f
+ */
+#ifdef NDEBUG
+#define gmx_simd_invsqrt_maskfpe_d(x, m) gmx_simd_invsqrt_d(x)
+#else
+static gmx_inline gmx_simd_double_t
+gmx_simd_invsqrt_maskfpe_d(gmx_simd_double_t x, gmx_simd_dbool_t m)
+{
+ return gmx_simd_invsqrt_d(gmx_simd_blendv_d(gmx_simd_set1_d(1.0f), x, m));
+}
+#endif
+
+/*! \brief Calculate 1/sqrt(x) for non-masked entries of SIMD double.
+ *
+ * \copydetails gmx_simd_invsqrt_notmaskfpe_f
+ */
+#ifdef NDEBUG
+#define gmx_simd_invsqrt_notmaskfpe_d(x, m) gmx_simd_invsqrt_d(x)
+#else
+static gmx_inline gmx_simd_double_t
+gmx_simd_invsqrt_notmaskfpe_d(gmx_simd_double_t x, gmx_simd_dbool_t m)
+{
+ return gmx_simd_invsqrt_d(gmx_simd_blendv_d(x, gmx_simd_set1_d(1.0f), m));
+}
+#endif
+
/*! \brief Calculate 1/sqrt(x) for two SIMD doubles.
*
* \copydetails gmx_simd_invsqrt_pair_f
#endif
}
+#ifndef gmx_simd_rcp_iter_d
/*! \brief Perform one Newton-Raphson iteration to improve 1/x for SIMD double.
*
* \copydetails gmx_simd_rcp_iter_f
{
return gmx_simd_mul_d(lu, gmx_simd_fnmadd_d(lu, x, gmx_simd_set1_d(2.0)));
}
+#endif
/*! \brief Calculate 1/x for SIMD double.
*
return lu;
}
+/*! \brief Calculate 1/x for masked entries of SIMD double.
+ *
+ * \copydetails gmx_simd_inv_maskfpe_f
+ */
+#ifdef NDEBUG
+#define gmx_simd_inv_maskfpe_d(x, m) gmx_simd_inv_d(x)
+#else
+static gmx_inline gmx_simd_double_t
+gmx_simd_inv_maskfpe_d(gmx_simd_double_t x, gmx_simd_dbool_t m)
+{
+ return gmx_simd_inv_d(gmx_simd_blendv_d(gmx_simd_set1_d(1.0f), x, m));
+}
+#endif
+
+/*! \brief Calculate 1/x for non-masked entries of SIMD double.
+ *
+ * \copydetails gmx_simd_inv_notmaskfpe_f
+ */
+#ifdef NDEBUG
+#define gmx_simd_inv_notmaskfpe_d(x, m) gmx_simd_inv_d(x)
+#else
+static gmx_inline gmx_simd_double_t
+gmx_simd_inv_notmaskfpe_d(gmx_simd_double_t x, gmx_simd_dbool_t m)
+{
+ return gmx_simd_inv_d(gmx_simd_blendv_d(x, gmx_simd_set1_d(1.0f), m));
+}
+#endif
+
/*! \brief Calculate sqrt(x) correctly for SIMD doubles, including argument 0.0.
*
* \copydetails gmx_simd_sqrt_f
gmx_simd_double_t res;
mask = gmx_simd_cmpeq_d(x, gmx_simd_setzero_d());
- res = gmx_simd_blendnotzero_d(gmx_simd_invsqrt_d(x), mask);
+ res = gmx_simd_blendnotzero_d(gmx_simd_invsqrt_notmaskfpe_d(x, mask), mask);
return gmx_simd_mul_d(res, x);
}
{
const gmx_simd_double_t argscale = gmx_simd_set1_d(1.44269504088896340735992468100);
const gmx_simd_double_t arglimit = gmx_simd_set1_d(1022.0);
- const gmx_simd_double_t invargscale0 = gmx_simd_set1_d(0.69314718055966295651160180568695068359375);
- const gmx_simd_double_t invargscale1 = gmx_simd_set1_d(2.8235290563031577122588448175013436025525412068e-13);
+ const gmx_simd_double_t invargscale0 = gmx_simd_set1_d(-0.69314718055966295651160180568695068359375);
+ const gmx_simd_double_t invargscale1 = gmx_simd_set1_d(-2.8235290563031577122588448175013436025525412068e-13);
const gmx_simd_double_t CE12 = gmx_simd_set1_d(2.078375306791423699350304e-09);
const gmx_simd_double_t CE11 = gmx_simd_set1_d(2.518173854179933105218635e-08);
const gmx_simd_double_t CE10 = gmx_simd_set1_d(2.755842049600488770111608e-07);
fexppart = gmx_simd_blendzero_d(fexppart, valuemask);
/* Extended precision arithmetics */
- x = gmx_simd_fnmadd_d(invargscale0, intpart, x);
- x = gmx_simd_fnmadd_d(invargscale1, intpart, x);
+ x = gmx_simd_fmadd_d(invargscale0, intpart, x);
+ x = gmx_simd_fmadd_d(invargscale1, intpart, x);
p = gmx_simd_fmadd_d(CE12, x, CE11);
p = gmx_simd_fmadd_d(p, x, CE10);
gmx_simd_double_t PolyCP0, PolyCP1, PolyCQ0, PolyCQ1;
gmx_simd_double_t res_erf, res_erfcB, res_erfcC, res_erfc, res;
gmx_simd_double_t expmx2;
- gmx_simd_dbool_t mask;
+ gmx_simd_dbool_t mask, mask_erf;
/* Calculate erf() */
xabs = gmx_simd_fabs_d(x);
+ mask_erf = gmx_simd_cmplt_d(xabs, one);
x2 = gmx_simd_mul_d(x, x);
x4 = gmx_simd_mul_d(x2, x2);
PolyAQ1 = gmx_simd_mul_d(PolyAQ1, x2);
PolyAQ0 = gmx_simd_add_d(PolyAQ0, PolyAQ1);
- res_erf = gmx_simd_mul_d(PolyAP0, gmx_simd_inv_d(PolyAQ0));
+ res_erf = gmx_simd_mul_d(PolyAP0, gmx_simd_inv_maskfpe_d(PolyAQ0, mask_erf));
res_erf = gmx_simd_add_d(CAoffset, res_erf);
res_erf = gmx_simd_mul_d(x, res_erf);
PolyBQ1 = gmx_simd_mul_d(PolyBQ1, t);
PolyBQ0 = gmx_simd_add_d(PolyBQ0, PolyBQ1);
- res_erfcB = gmx_simd_mul_d(PolyBP0, gmx_simd_inv_d(PolyBQ0));
+ res_erfcB = gmx_simd_mul_d(PolyBP0, gmx_simd_inv_notmaskfpe_d(PolyBQ0, mask_erf));
res_erfcB = gmx_simd_mul_d(res_erfcB, xabs);
/* Calculate erfc() in range [4.5,inf] */
- w = gmx_simd_inv_d(xabs);
+ w = gmx_simd_inv_notmaskfpe_d(xabs, mask_erf);
w2 = gmx_simd_mul_d(w, w);
PolyCP0 = gmx_simd_mul_d(CCP6, w2);
expmx2 = gmx_simd_exp_d( gmx_simd_fneg_d(x2) );
- res_erfcC = gmx_simd_mul_d(PolyCP0, gmx_simd_inv_d(PolyCQ0));
+ res_erfcC = gmx_simd_mul_d(PolyCP0, gmx_simd_inv_notmaskfpe_d(PolyCQ0, mask_erf));
res_erfcC = gmx_simd_add_d(res_erfcC, CCoffset);
res_erfcC = gmx_simd_mul_d(res_erfcC, w);
res_erfc = gmx_simd_blendv_d(res_erfc, gmx_simd_sub_d(two, res_erfc), mask);
/* Select erf() or erfc() */
- mask = gmx_simd_cmplt_d(xabs, one);
- res = gmx_simd_blendv_d(gmx_simd_sub_d(one, res_erfc), res_erf, mask);
+ res = gmx_simd_blendv_d(gmx_simd_sub_d(one, res_erfc), res_erf, mask_erf);
return res;
}
gmx_simd_double_t PolyCP0, PolyCP1, PolyCQ0, PolyCQ1;
gmx_simd_double_t res_erf, res_erfcB, res_erfcC, res_erfc, res;
gmx_simd_double_t expmx2;
- gmx_simd_dbool_t mask;
+ gmx_simd_dbool_t mask, mask_erf;
/* Calculate erf() */
xabs = gmx_simd_fabs_d(x);
+ mask_erf = gmx_simd_cmplt_d(xabs, one);
x2 = gmx_simd_mul_d(x, x);
x4 = gmx_simd_mul_d(x2, x2);
PolyAQ1 = gmx_simd_mul_d(PolyAQ1, x2);
PolyAQ0 = gmx_simd_add_d(PolyAQ0, PolyAQ1);
- res_erf = gmx_simd_mul_d(PolyAP0, gmx_simd_inv_d(PolyAQ0));
+ res_erf = gmx_simd_mul_d(PolyAP0, gmx_simd_inv_maskfpe_d(PolyAQ0, mask_erf));
res_erf = gmx_simd_add_d(CAoffset, res_erf);
res_erf = gmx_simd_mul_d(x, res_erf);
PolyBQ1 = gmx_simd_mul_d(PolyBQ1, t);
PolyBQ0 = gmx_simd_add_d(PolyBQ0, PolyBQ1);
- res_erfcB = gmx_simd_mul_d(PolyBP0, gmx_simd_inv_d(PolyBQ0));
+ res_erfcB = gmx_simd_mul_d(PolyBP0, gmx_simd_inv_notmaskfpe_d(PolyBQ0, mask_erf));
res_erfcB = gmx_simd_mul_d(res_erfcB, xabs);
/* Calculate erfc() in range [4.5,inf] */
- w = gmx_simd_inv_d(xabs);
+ w = gmx_simd_inv_notmaskfpe_d(xabs, mask_erf);
w2 = gmx_simd_mul_d(w, w);
PolyCP0 = gmx_simd_mul_d(CCP6, w2);
expmx2 = gmx_simd_exp_d( gmx_simd_fneg_d(x2) );
- res_erfcC = gmx_simd_mul_d(PolyCP0, gmx_simd_inv_d(PolyCQ0));
+ res_erfcC = gmx_simd_mul_d(PolyCP0, gmx_simd_inv_notmaskfpe_d(PolyCQ0, mask_erf));
res_erfcC = gmx_simd_add_d(res_erfcC, CCoffset);
res_erfcC = gmx_simd_mul_d(res_erfcC, w);
res_erfc = gmx_simd_blendv_d(res_erfc, gmx_simd_sub_d(two, res_erfc), mask);
/* Select erf() or erfc() */
- mask = gmx_simd_cmplt_d(xabs, one);
- res = gmx_simd_blendv_d(res_erfc, gmx_simd_sub_d(one, res_erf), mask);
+ res = gmx_simd_blendv_d(res_erfc, gmx_simd_sub_d(one, res_erf), mask_erf);
return res;
}
gmx_simd_sincos_d(gmx_simd_double_t x, gmx_simd_double_t *sinval, gmx_simd_double_t *cosval)
{
/* Constants to subtract Pi/4*x from y while minimizing precision loss */
- const gmx_simd_double_t argred0 = gmx_simd_set1_d(2*0.78539816290140151978);
- const gmx_simd_double_t argred1 = gmx_simd_set1_d(2*4.9604678871439933374e-10);
- const gmx_simd_double_t argred2 = gmx_simd_set1_d(2*1.1258708853173288931e-18);
- const gmx_simd_double_t argred3 = gmx_simd_set1_d(2*1.7607799325916000908e-27);
+ const gmx_simd_double_t argred0 = gmx_simd_set1_d(-2*0.78539816290140151978);
+ const gmx_simd_double_t argred1 = gmx_simd_set1_d(-2*4.9604678871439933374e-10);
+ const gmx_simd_double_t argred2 = gmx_simd_set1_d(-2*1.1258708853173288931e-18);
+ const gmx_simd_double_t argred3 = gmx_simd_set1_d(-2*1.7607799325916000908e-27);
const gmx_simd_double_t two_over_pi = gmx_simd_set1_d(2.0/M_PI);
const gmx_simd_double_t const_sin5 = gmx_simd_set1_d( 1.58938307283228937328511e-10);
const gmx_simd_double_t const_sin4 = gmx_simd_set1_d(-2.50506943502539773349318e-08);
/* where mask is FALSE, set sign. */
csign = gmx_simd_xor_sign_d(csign, gmx_simd_blendv_d(gmx_simd_set1_d(-1.0), one, mask));
#endif
- x = gmx_simd_fnmadd_d(y, argred0, x);
- x = gmx_simd_fnmadd_d(y, argred1, x);
- x = gmx_simd_fnmadd_d(y, argred2, x);
- x = gmx_simd_fnmadd_d(y, argred3, x);
+ x = gmx_simd_fmadd_d(y, argred0, x);
+ x = gmx_simd_fmadd_d(y, argred1, x);
+ x = gmx_simd_fmadd_d(y, argred2, x);
+ x = gmx_simd_fmadd_d(y, argred3, x);
x2 = gmx_simd_mul_d(x, x);
psin = gmx_simd_fmadd_d(const_sin5, x2, const_sin4);
static gmx_inline gmx_simd_double_t gmx_simdcall
gmx_simd_tan_d(gmx_simd_double_t x)
{
- const gmx_simd_double_t argred0 = gmx_simd_set1_d(2*0.78539816290140151978);
- const gmx_simd_double_t argred1 = gmx_simd_set1_d(2*4.9604678871439933374e-10);
- const gmx_simd_double_t argred2 = gmx_simd_set1_d(2*1.1258708853173288931e-18);
- const gmx_simd_double_t argred3 = gmx_simd_set1_d(2*1.7607799325916000908e-27);
+ const gmx_simd_double_t argred0 = gmx_simd_set1_d(-2*0.78539816290140151978);
+ const gmx_simd_double_t argred1 = gmx_simd_set1_d(-2*4.9604678871439933374e-10);
+ const gmx_simd_double_t argred2 = gmx_simd_set1_d(-2*1.1258708853173288931e-18);
+ const gmx_simd_double_t argred3 = gmx_simd_set1_d(-2*1.7607799325916000908e-27);
const gmx_simd_double_t two_over_pi = gmx_simd_set1_d(2.0/M_PI);
const gmx_simd_double_t CT15 = gmx_simd_set1_d(1.01419718511083373224408e-05);
const gmx_simd_double_t CT14 = gmx_simd_set1_d(-2.59519791585924697698614e-05);
y = gmx_simd_round_d(z);
mask = gmx_simd_cvt_dib2db(gmx_simd_cmpeq_di(gmx_simd_and_di(iy, ione), ione));
- x = gmx_simd_fnmadd_d(y, argred0, x);
- x = gmx_simd_fnmadd_d(y, argred1, x);
- x = gmx_simd_fnmadd_d(y, argred2, x);
- x = gmx_simd_fnmadd_d(y, argred3, x);
+ x = gmx_simd_fmadd_d(y, argred0, x);
+ x = gmx_simd_fmadd_d(y, argred1, x);
+ x = gmx_simd_fmadd_d(y, argred2, x);
+ x = gmx_simd_fmadd_d(y, argred3, x);
x = gmx_simd_xor_d(gmx_simd_blendzero_d(gmx_simd_set1_d(GMX_DOUBLE_NEGZERO), mask), x);
#else
const gmx_simd_double_t quarter = gmx_simd_set1_d(0.25);
m3 = gmx_simd_cmple_d(threequarter, q);
m1 = gmx_simd_and_db(m1, m2);
mask = gmx_simd_or_db(m1, m3);
- w = gmx_simd_fnmadd_d(y, argred0, w);
- w = gmx_simd_fnmadd_d(y, argred1, w);
- w = gmx_simd_fnmadd_d(y, argred2, w);
- w = gmx_simd_fnmadd_d(y, argred3, w);
+ w = gmx_simd_fmadd_d(y, argred0, w);
+ w = gmx_simd_fmadd_d(y, argred1, w);
+ w = gmx_simd_fmadd_d(y, argred2, w);
+ w = gmx_simd_fmadd_d(y, argred3, w);
w = gmx_simd_blendv_d(w, gmx_simd_fneg_d(w), mask);
x = gmx_simd_xor_sign_d(w, x);
p = gmx_simd_fmadd_d(p, x2, CT1);
p = gmx_simd_fmadd_d(x2, gmx_simd_mul_d(p, x), x);
- p = gmx_simd_blendv_d( p, gmx_simd_inv_d(p), mask);
+ p = gmx_simd_blendv_d( p, gmx_simd_inv_maskfpe_d(p, mask), mask);
return p;
}
gmx_simd_double_t RA, RB;
gmx_simd_double_t SA, SB;
gmx_simd_double_t nom, denom;
- gmx_simd_dbool_t mask;
+ gmx_simd_dbool_t mask, mask2;
xabs = gmx_simd_fabs_d(x);
nom = gmx_simd_blendv_d( PA, RA, mask );
denom = gmx_simd_blendv_d( QA, SA, mask );
- q = gmx_simd_mul_d( nom, gmx_simd_inv_d(denom) );
+ mask2 = gmx_simd_cmplt_d(limit2, xabs);
+ q = gmx_simd_mul_d( nom, gmx_simd_inv_maskfpe_d(denom, mask2) );
zz = gmx_simd_add_d(zz, zz);
zz = gmx_simd_sqrt_d(zz);
z = gmx_simd_blendv_d( w, z, mask );
- mask = gmx_simd_cmplt_d(limit2, xabs);
- z = gmx_simd_blendv_d( xabs, z, mask );
+ z = gmx_simd_blendv_d( xabs, z, mask2 );
z = gmx_simd_xor_sign_d(z, x);
mask1 = gmx_simd_cmplt_d(limit1, xabs);
mask2 = gmx_simd_cmplt_d(limit2, xabs);
- t1 = gmx_simd_mul_d(gmx_simd_add_d(xabs, mone), gmx_simd_inv_d(gmx_simd_sub_d(xabs, mone)));
- t2 = gmx_simd_mul_d(mone, gmx_simd_inv_d(xabs));
+ t1 = gmx_simd_mul_d(gmx_simd_add_d(xabs, mone),
+ gmx_simd_inv_maskfpe_d(gmx_simd_sub_d(xabs, mone), mask1));
+ t2 = gmx_simd_mul_d(mone, gmx_simd_inv_maskfpe_d(xabs, mask2));
y = gmx_simd_blendzero_d(quarterpi, mask1);
y = gmx_simd_blendv_d(y, halfpi, mask2);
aoffset = gmx_simd_blendv_d(aoffset, pi, mask_xlt0);
aoffset = gmx_simd_blendv_d(aoffset, gmx_simd_fneg_d(aoffset), mask_ylt0);
- xinv = gmx_simd_blendnotzero_d(gmx_simd_inv_d(x), mask_x0);
+ xinv = gmx_simd_blendnotzero_d(gmx_simd_inv_notmaskfpe_d(x, mask_x0), mask_x0);
p = gmx_simd_mul_d(y, xinv);
p = gmx_simd_atan_d(p);
p = gmx_simd_add_d(p, aoffset);
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "base.h"
#include <math.h>
-#include "testutils/testoptions.h"
-#include "gromacs/options/options.h"
#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/options.h"
-#include "base.h"
+#include "testutils/testoptions.h"
namespace gmx
{
* \ingroup module_simd
*/
#include <vector>
+
#include <gtest/gtest.h>
-#include "gromacs/simd/simd.h"
+#include "gromacs/simd/simd.h"
+#include "gromacs/utility/real.h"
namespace gmx
{
* conservative so it works with (inverse) square root, division,
* exponentials, logarithms, and error functions.
*/
- SimdBaseTest()
- {
+ SimdBaseTest() :
#ifdef GMX_DOUBLE
- ulpTol_ = 255LL; // Aim for roughly twice the precision we have in single.
+ ulpTol_(255LL), // Aim for roughly twice the precision we have in single.
#else
- ulpTol_ = 10LL; // Be a bit liberal so compiler optimization doesn't bite us.
+ ulpTol_(10LL), // Be a bit liberal so compiler optimization doesn't bite us.
#endif
- absTol_ = 0;
- range_ = std::pair<real, real>(1, 10);
+ absTol_(0), range_(std::pair<real, real>(1, 10))
+ {
}
/*! \brief Adjust ulp tolerance from the default 10 (float) or 255 (double). */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
/*! \internal \file
* \brief
*/
#include <gtest/gtest.h>
+
#include "gromacs/simd/simd.h"
+#include "gromacs/utility/real.h"
namespace
{
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include "simd.h"
* \ingroup module_simd
*/
#include <vector>
+
#include <gtest/gtest.h>
+
#include "gromacs/simd/simd.h"
#include "base.h"
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include "simd4.h"
*/
#include <vector>
+
#include <gtest/gtest.h>
+
#include "gromacs/simd/simd.h"
-#include "gromacs/simd/tests/base.h"
+
+#include "base.h"
namespace gmx
{
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
+
#include "gromacs/math/utilities.h"
#include "simd4.h"
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <vector>
+
#include "gromacs/math/utilities.h"
+#include "gromacs/options/basicoptions.h"
#include "gromacs/simd/simd.h"
#include "gromacs/simd/simd_math.h"
-#include "gromacs/options/basicoptions.h"
#include "simd4.h"
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
+
#include "gromacs/simd/simd.h"
#include "gromacs/simd/vector_operations.h"
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
+
#include "gromacs/math/utilities.h"
#include "simd.h"
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include "simd.h"
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/simd/simd_math.h"
+
+#include "config.h"
#include <vector>
+
#include "gromacs/math/utilities.h"
-#include "gromacs/simd/simd.h"
-#include "gromacs/simd/simd_math.h"
#include "gromacs/options/basicoptions.h"
+#include "gromacs/simd/simd.h"
#include "simd.h"
{
absDiff = fabs(vref[i]-vtst[i]);
absOk = absOk && ( absDiff < absTol_ );
- signOk = signOk && ( vref[i]*vtst[i] >= 0 );
+ signOk = signOk && ( (vref[i] >= 0 && vtst[i] >= 0) ||
+ (vref[i] <= 0 && vtst[i] <= 0));
if (absDiff >= absTol_)
{
/*! \brief Evaluate reference version of PME force correction. */
real ref_pmecorrF(real x)
{
- real y = sqrt(x);
- return 2*exp(-x)/(sqrt(M_PI)*x) - gmx_erfd(y)/(x*y);
+ if (x != 0)
+ {
+ real y = sqrt(x);
+ return 2*exp(-x)/(sqrt(M_PI)*x) - gmx_erfd(y)/(x*y);
+ }
+ else
+ {
+ return -4/(3*sqrt(M_PI));
+ }
}
// The PME corrections will be added to ~1/r2, so absolute tolerance of EPS is fine.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
+
#include "gromacs/simd/simd.h"
#include "gromacs/simd/vector_operations.h"
#ifndef GMX_SIMD_VECTOR_OPERATIONS_H
#define GMX_SIMD_VECTOR_OPERATIONS_H
+#include "config.h"
+
#include "gromacs/simd/simd.h"
/*! \cond libapi */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
#include "statistics.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+
#include <math.h>
-#include "typedefs.h"
+
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
-#include "vec.h"
static int gmx_dnint(double x)
{
#ifndef GMX_STATISTICS_H
#define GMX_STATISTICS_H
+#include <stdio.h>
+
+#include "gromacs/utility/real.h"
+
/*! \libinternal \file
*
* \brief
#ifdef __cplusplus
extern "C" {
#endif
-#include <stdio.h>
-#include "types/simple.h"
//! Abstract container type
typedef struct gmx_stats *gmx_stats_t;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <stdio.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
+
+#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
-#include "statistics.h"
+#include "gromacs/statistics/statistics.h"
+#include "gromacs/utility/real.h"
+#include "gromacs/utility/smalloc.h"
static void horizontal()
{
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-file(GLOB SWAP_SOURCES *.cpp *.c)
+file(GLOB SWAP_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${SWAP_SOURCES} PARENT_SCOPE)
-gmx_install_headers(swap enums.h)
+gmx_install_headers(enums.h)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Carsten Kutzner <ckutzne@gwdg.de>
* \ingroup module_swap
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "swapcoords.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
-#include "typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/mdlib/groupcoord.h"
-#include "mtop_util.h"
-#include "macros.h"
-#include "vec.h"
-#include "names.h"
-#include "network.h"
-#include "mdrun.h"
-#include "xvgr.h"
-#include "copyrite.h"
+
#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/groupcoord.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
-#include "swapcoords.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
-static char *SwS = {"SWAP:"}; /**< For output that comes from the swap module */
-static char *SwSEmpty = {" "}; /**< Placeholder for multi-line output */
-static char* IonString[eIonNR] = {"anion", "cation" }; /**< Type of ion, used for verbose output */
-static char* IonStr[eIonNR] = {"-", "+" }; /**< Type of ion, used for short output */
-static char* CompStr[eCompNR] = {"A", "B" }; /**< Compartment name */
-static char *SwapStr[eSwapTypesNR+1] = { "", "X-", "Y-", "Z-", NULL}; /**< Name for the swap types. */
-static char *DimStr[DIM+1] = { "X", "Y", "Z", NULL}; /**< Name for the swap dimension. */
+static const char *SwS = {"SWAP:"}; /**< For output that comes from the swap module */
+static const char *SwSEmpty = {" "}; /**< Placeholder for multi-line output */
+static const char* IonString[eIonNR] = {"anion", "cation" }; /**< Type of ion, used for verbose output */
+static const char* IonStr[eIonNR] = {"-", "+" }; /**< Type of ion, used for short output */
+static const char* CompStr[eCompNR] = {"A", "B" }; /**< Compartment name */
+static const char *SwapStr[eSwapTypesNR+1] = { "", "X-", "Y-", "Z-", NULL}; /**< Name for the swap types. */
+static const char *DimStr[DIM+1] = { "X", "Y", "Z", NULL}; /**< Name for the swap dimension. */
/* eGrpSplit0 and eGrpSplit1 _must_ be neighbors in this list because
* we sometimes loop from eGrpSplit0 to eGrpSplit1 */
enum {
eGrpIons, eGrpSplit0, eGrpSplit1, eGrpSolvent, eGrpNr
-}; /**< Group identifier */
-static char* GrpString[eGrpNr] = { "ion", "split0", "split1", "solvent" }; /**< Group name */
+}; /**< Group identifier */
+static const char* GrpString[eGrpNr] = { "ion", "split0", "split1", "solvent" }; /**< Group name */
/** Keep track of through which channel the ions have passed */
enum eChannelHistory {
eChHistPassedNone, eChHistPassedCh0, eChHistPassedCh1, eChHistNr
};
-static char* ChannelString[eChHistNr] = { "none", "channel0", "channel1" }; /**< Name for the channels */
+static const char* ChannelString[eChHistNr] = { "none", "channel0", "channel1" }; /**< Name for the channels */
/*! \brief Domain identifier.
*
enum eDomain {
eDomainNotset, eDomainA, eDomainB, eDomainNr
};
-static char* DomainString[eDomainNr] = { "not_assigned", "Domain_A", "Domain_B" }; /**< Name for the domains */
+static const char* DomainString[eDomainNr] = { "not_assigned", "Domain_A", "Domain_B" }; /**< Name for the domains */
/*! \internal \brief
* Main (private) data structure for the position swapping protocol.
*/
-typedef struct swap
+typedef struct t_swap
{
int swapdim; /**< One of XX, YY, ZZ */
t_pbc *pbc; /**< Needed to make molecules whole. */
/*! \brief Prints to swap output file which ions are in which compartment. */
static void print_ionlist(
- t_swap *s,
- double time,
- char comment[])
+ t_swap *s,
+ double time,
+ const char comment[])
{
int itype, icomp, i, j;
t_compartment *comp;
{
fprintf(stderr, "\n"
"%s Warning: %d atoms were detected as being in both channels! Probably your split\n"
- "%s cylinder is way too large, or one compartment has collapsed (step %"GMX_PRId64 ")\n",
+ "%s cylinder is way too large, or one compartment has collapsed (step %" GMX_PRId64 ")\n",
SwS, s->cyl0and1, SwS, step);
fprintf(s->fpout, "Warning: %d atoms were assigned to both channels!\n", s->cyl0and1);
}
/* Now actually correct the number of ions */
- g = &(s->group[eGrpSolvent]);
nswaps = 0;
alook = gmx_mtop_atomlookup_init(mtop);
for (ic = 0; ic < eCompNR; ic++)
if (bVerbose)
{
- fprintf(stderr, "%s Performed %d swap%s in step %"GMX_PRId64 ".\n", SwS, nswaps, nswaps > 1 ? "s" : "", step);
+ fprintf(stderr, "%s Performed %d swap%s in step %" GMX_PRId64 ".\n", SwS, nswaps, nswaps > 1 ? "s" : "", step);
}
if (s->fpout != NULL)
{
#ifndef GMX_SWAP_SWAPCOORDS_H
#define GMX_SWAP_SWAPCOORDS_H
-#include "typedefs.h"
-#include "types/commrec.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/timing/wallcycle.h"
#ifdef __cplusplus
extern "C" {
file(GLOB TIMING_SOURCES *.cpp *.c)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TIMING_SOURCES} PARENT_SCOPE)
-set(TIMING_PUBLIC_HEADERS
- walltime_accounting.h)
-gmx_install_headers(timing ${TIMING_PUBLIC_HEADERS})
+gmx_install_headers(
+ wallcycle.h
+ walltime_accounting.h
+ )
if (BUILD_TESTING)
# add_subdirectory(tests)
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2006 David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "gromacs/timing/cyclecounter.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "cyclecounter.h"
+
+#include "config.h"
#include <time.h>
+
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
-
#ifdef _MSC_VER
#include <windows.h>
#endif
* define HAVE_RDTSCP to use the serializing rdtscp instruction instead of rdtsc.
* This is only supported on newer Intel/AMD hardware, but provides better accuracy.
*/
-#ifdef HAVE_CONFIG_H
#include "config.h"
-#endif
#ifdef _MSC_VER
#include <intrin.h>
#elif defined(__xlC__) && defined (_AIX)
/* AIX compilers */
-#include <sys/time.h>
#include <sys/systemcfg.h>
+#include <sys/time.h>
typedef unsigned long long
gmx_cycles_t;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "gromacs/timing/wallcycle.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "wallcycle.h"
-#include <string.h>
+#include "config.h"
-#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "md_logging.h"
-#include "gromacs/utility/cstringutil.h"
+#include <stdlib.h>
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/timing/cyclecounter.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/snprintf.h"
/* DEBUG_WCYCLE adds consistency checking for the counters.
* It checks if you stop a counter different from the last
*/
/* #define DEBUG_WCYCLE */
+#ifdef DEBUG_WCYCLE
+#include "gromacs/utility/fatalerror.h"
+#endif
+
typedef struct
{
int n;
"DD redist.", "DD NS grid + sort", "DD setup comm.",
"DD make top.", "DD make constr.", "DD top. other",
"NS grid local", "NS grid non-loc.", "NS search local", "NS search non-loc.",
- "Bonded F", "Nonbonded F", "Ewald F correction",
+ "Listed F", "Nonbonded F", "Ewald F correction",
"NB X buffer ops.", "NB F buffer ops."
};
char nthreads_str[6];
char ncalls_str[11];
double wallt;
+ double percentage = (tot > 0.) ? (100. * c_sum / tot) : 0.;
if (c_sum > 0)
{
fprintf(fplog, " %-19.19s %4s %4s %10s %10.3f %14.3f %5.1f\n",
name, nnodes_str, nthreads_str, ncalls_str, wallt,
- c_sum*1e-9, 100*c_sum/tot);
+ c_sum*1e-9, percentage);
}
}
{
double *cyc_sum;
double tot, tot_for_pp, tot_for_rest, tot_gpu, tot_cpu_overlap, gpu_cpu_ratio, tot_k;
- double c2t, c2t_pp, c2t_pme;
+ double c2t, c2t_pp, c2t_pme = 0;
int i, j, npp, nth_pp, nth_pme, nth_tot;
char buf[STRLEN];
const char *hline = "-----------------------------------------------------------------------------";
{
c2t = realtime/tot;
c2t_pp = c2t * nth_tot / (double) (npp*nth_pp);
- c2t_pme = c2t * nth_tot / (double) (npme*nth_pme);
+ if (npme > 0)
+ {
+ c2t_pme = c2t * nth_tot / (double) (npme*nth_pme);
+ }
}
else
{
#define GMX_TIMING_WALLCYCLE_H
#include <stdio.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
+
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
#endif
+typedef struct gmx_wallcycle *gmx_wallcycle_t;
+
enum {
ewcRUN, ewcSTEP, ewcPPDURINGPME, ewcDOMDEC, ewcDDCOMMLOAD,
ewcDDCOMMBOUND, ewcVSITECONSTR, ewcPP_PMESENDX, ewcNS, ewcLAUNCH_GPU_NB,
ewcsDD_MAKETOP, ewcsDD_MAKECONSTR, ewcsDD_TOPOTHER,
ewcsNBS_GRID_LOCAL, ewcsNBS_GRID_NONLOCAL,
ewcsNBS_SEARCH_LOCAL, ewcsNBS_SEARCH_NONLOCAL,
- ewcsBONDED, ewcsNONBONDED, ewcsEWALD_CORRECTION,
+ ewcsLISTED, ewcsNONBONDED, ewcsEWALD_CORRECTION,
ewcsNB_X_BUF_OPS, ewcsNB_F_BUF_OPS,
ewcsNR
};
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "gromacs/timing/walltime_accounting.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "walltime_accounting.h"
+
+#include "config.h"
#include <time.h>
+
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
#include <sys/time.h>
#endif
-#include "gromacs/legacyheaders/types/simple.h"
-
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/smalloc.h"
/* TODO in future: convert gmx_walltime_accounting to a class,
return walltime_accounting->start_time_stamp;
}
-double
+gmx_int64_t
walltime_accounting_get_nsteps_done(gmx_walltime_accounting_t walltime_accounting)
{
return walltime_accounting->nsteps_done;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TIMING_WALLTIME_ACCOUNTING_H
#define GMX_TIMING_WALLTIME_ACCOUNTING_H
-#include "../legacyheaders/types/simple.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
}
#endif
-/*! Contains per-process and per-thread data about elapsed wall-clock
- * times and integration steps performed. */
+/*! \brief
+ * Contains per-process and per-thread data about elapsed wall-clock
+ * times and integration steps performed. */
typedef struct gmx_walltime_accounting *gmx_walltime_accounting_t;
//! Constructor
void
walltime_accounting_destroy(gmx_walltime_accounting_t walltime_accounting);
-/*! Record initial time stamps, e.g. at run end or counter
- * re-initalization time */
+/*! \brief
+ * Record initial time stamps, e.g. at run end or counter re-initalization time
+ */
void
walltime_accounting_start(gmx_walltime_accounting_t walltime_accounting);
-/*! Measure and cache the elapsed wall-clock time since
- * walltime_accounting_start */
+/*! \brief
+ * Measure and cache the elapsed wall-clock time since
+ * walltime_accounting_start() */
void
walltime_accounting_end(gmx_walltime_accounting_t walltime_accounting);
-/*! Measure and return the elapsed wall-clock time since
- * walltime_accounting_start */
+/*! \brief
+ * Measure and return the elapsed wall-clock time since
+ * walltime_accounting_start() */
double
walltime_accounting_get_current_elapsed_time(gmx_walltime_accounting_t walltime_accounting);
walltime_accounting_get_start_time_stamp(gmx_walltime_accounting_t walltime_accounting);
//! Get the number of integration steps done
-double
+gmx_int64_t
walltime_accounting_get_nsteps_done(gmx_walltime_accounting_t walltime_accounting);
-/*! Set the number of integration steps done
+/*! \brief Set the number of integration steps done
*
* TODO consider whether this should get done in walltime_accounting_end */
void
walltime_accounting_set_nsteps_done(gmx_walltime_accounting_t walltime_accounting,
gmx_int64_t nsteps_done);
-/*! \brief Calls system timing routines (e.g. clock_gettime) to get the
- * (fractional) number of seconds elapsed since the epoch.
+/*! \brief
+ * Calls system timing routines (e.g. clock_gettime) to get the (fractional)
+ * number of seconds elapsed since the epoch.
*
* Resolution is implementation-dependent, but typically nanoseconds
* or microseconds. */
file(GLOB TOOLS_SOURCES *.cpp *.c)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TOOLS_SOURCES} PARENT_SCOPE)
-set(TOOLS_PUBLIC_HEADERS
- )
-gmx_install_headers(tools ${TOOLS_PUBLIC_HEADERS})
-
if (BUILD_TESTING)
# add_subdirectory(tests)
endif()
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <stdio.h>
#include <string.h>
-#include "main.h"
-#include "macros.h"
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "gmx_fatal.h"
-#include "atomprop.h"
-#include "vec.h"
-#include "pbc.h"
-#include "physics.h"
-#include "index.h"
-#include "gromacs/utility/smalloc.h"
-#include "names.h"
-#include "mtop_util.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/xtcio.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/trxio.h"
-
-#include "compare.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/tools/compare.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
int bStep;
int gmx_check(int argc, char *argv[])
{
const char *desc[] = {
- "[THISMODULE] reads a trajectory ([TT].trj[tt], [TT].trr[tt] or ",
- "[TT].xtc[tt]), an energy file ([TT].ene[tt] or [TT].edr[tt])",
+ "[THISMODULE] reads a trajectory ([TT].tng[tt], [TT].trr[tt] or ",
+ "[TT].xtc[tt]), an energy file ([TT].edr[tt])",
"or an index file ([TT].ndx[tt])",
"and prints out useful information about them.[PAR]",
"Option [TT]-c[tt] checks for presence of coordinates,",
"file are indeed correct in the trajectory. If not you may have",
"non-matching files due to e.g. deshuffling or due to problems with",
"virtual sites. With these flags, [TT]gmx check[tt] provides a quick check for such problems.[PAR]",
- "The program can compare two run input ([TT].tpr[tt], [TT].tpb[tt] or",
- "[TT].tpa[tt]) files",
+ "The program can compare two run input ([TT].tpr[tt])",
+ "files",
"when both [TT]-s1[tt] and [TT]-s2[tt] are supplied.",
"Similarly a pair of trajectory files can be compared (using the [TT]-f2[tt]",
"option), or a pair of energy files (using the [TT]-e2[tt] option).[PAR]",
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffOPTRD },
{ efTRX, "-f2", NULL, ffOPTRD },
- { efTPX, "-s1", "top1", ffOPTRD },
- { efTPX, "-s2", "top2", ffOPTRD },
+ { efTPR, "-s1", "top1", ffOPTRD },
+ { efTPR, "-s2", "top2", ffOPTRD },
{ efTPS, "-c", NULL, ffOPTRD },
{ efEDR, "-e", NULL, ffOPTRD },
{ efEDR, "-e2", "ener2", ffOPTRD },
}
else if (fn2)
{
- fprintf(stderr, "Please give me TWO trajectory (.xtc/.trr/.trj) files!\n");
+ fprintf(stderr, "Please give me TWO trajectory (.xtc/.trr/.tng) files!\n");
}
fn1 = opt2fn_null("-s1", NFILE, fnm);
}
else if ((fn1 && !opt2fn_null("-f", NFILE, fnm)) || (!fn1 && fn2))
{
- fprintf(stderr, "Please give me TWO run input (.tpr/.tpa/.tpb) files\n"
+ fprintf(stderr, "Please give me TWO run input (.tpr) files\n"
"or specify the -m flag to generate a methods.tex file\n");
}
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <stdio.h>
#include <string.h>
-#include "main.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/futil.h"
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "gmx_fatal.h"
-#include "names.h"
+
+#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/enxio.h"
-#include "mtop_util.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void cmp_int(FILE *fp, const char *s, int index, int i1, int i2)
{
{
if (index != -1)
{
- fprintf(fp, "%s[%d] (%u - %u)\n", s, index, i1, i2);
+ fprintf(fp, "%s[%d] (%hu - %hu)\n", s, index, i1, i2);
}
else
{
- fprintf(fp, "%s (%u - %u)\n", s, i1, i2);
+ fprintf(fp, "%s (%hu - %hu)\n", s, i1, i2);
}
}
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "index.h"
-#include "gmx_fatal.h"
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "names.h"
-#include "typedefs.h"
-#include "gromacs/gmxpreprocess/readir.h"
+
#include "gromacs/commandline/pargs.h"
-#include "vec.h"
-#include "mtop_util.h"
-#include "checkpoint.h"
+#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/enxio.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/state.h"
+#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define RANGECHK(i, n) if ((i) >= (n)) gmx_fatal(FARGS, "Your index file contains atomnumbers (e.g. %d)\nthat are larger than the number of atoms in the tpr file (%d)", (i), (n))
char buf[200], buf2[200];
output_env_t oenv;
t_filenm fnm[] = {
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efTRN, "-f", NULL, ffOPTRD },
{ efEDR, "-e", NULL, ffOPTRD },
{ efNDX, NULL, NULL, ffOPTRD },
- { efTPX, "-o", "tpxout", ffWRITE }
+ { efTPR, "-o", "tprout", ffWRITE }
};
#define NFILE asize(fnm)
bTime = opt2parg_bSet("-time", asize(pa), pa);
bTraj = (opt2bSet("-f", NFILE, fnm) || bTime);
- top_fn = ftp2fn(efTPX, NFILE, fnm);
+ top_fn = ftp2fn(efTPR, NFILE, fnm);
fprintf(stderr, "Reading toplogy and stuff from %s\n", top_fn);
snew(ir, 1);
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
+#include <assert.h>
+#include <math.h>
#include <stdio.h>
#include <string.h>
-#include <math.h>
-#include <assert.h>
-#include "main.h"
-#include "macros.h"
+
#include "gromacs/commandline/pargs.h"
-#include "sysstuff.h"
-#include "txtdump.h"
-#include "gmx_fatal.h"
-#include "gromacs/utility/smalloc.h"
-#include "names.h"
-#include "txtdump.h"
-#include "gromacs/gmxpreprocess/gmxcpp.h"
-#include "checkpoint.h"
-#include "mtop_util.h"
-#include "gromacs/fileio/xtcio.h"
#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/fileio/mtxio.h"
#include "gromacs/fileio/tngio.h"
#include "gromacs/fileio/tngio_for_tools.h"
-
-#ifdef HAVE_UNISTD_H
-#include <unistd.h>
-#endif
-
-#include "gromacs/linearalgebra/mtxio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/gmxpreprocess/gmxcpp.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
#include "gromacs/linearalgebra/sparsematrix.h"
-
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static void list_tpx(const char *fn, gmx_bool bShowNumbers, const char *mdpfn,
gmx_bool bSysTop)
void list_trx(const char *fn)
{
- int ftp;
-
- ftp = fn2ftp(fn);
- if (ftp == efXTC)
- {
- list_xtc(fn);
- }
- else if ((ftp == efTRR) || (ftp == efTRJ))
- {
- list_trn(fn);
- }
- else if (ftp == efTNG)
- {
- list_tng(fn);
- }
- else
+ switch (fn2ftp(fn))
{
- fprintf(stderr, "File %s is of an unsupported type. Try using the command\n 'less %s'\n",
- fn, fn);
+ case efXTC:
+ list_xtc(fn);
+ break;
+ case efTRR:
+ list_trn(fn);
+ break;
+ case efTNG:
+ list_tng(fn);
+ break;
+ default:
+ fprintf(stderr, "File %s is of an unsupported type. Try using the command\n 'less %s'\n",
+ fn, fn);
}
}
int gmx_dump(int argc, char *argv[])
{
const char *desc[] = {
- "[THISMODULE] reads a run input file ([TT].tpa[tt]/[TT].tpr[tt]/[TT].tpb[tt]),",
- "a trajectory ([TT].trj[tt]/[TT].trr[tt]/[TT].xtc[tt]), an energy",
- "file ([TT].ene[tt]/[TT].edr[tt]), or a checkpoint file ([TT].cpt[tt])",
+ "[THISMODULE] reads a run input file ([TT].tpr[tt]),",
+ "a trajectory ([TT].trr[tt]/[TT].xtc[tt]/[TT]/tng[tt]), an energy",
+ "file ([TT].edr[tt]) or a checkpoint file ([TT].cpt[tt])",
"and prints that to standard output in a readable format.",
"This program is essential for checking your run input file in case of",
"problems.[PAR]",
"Position restraint output from -sys -s is broken"
};
t_filenm fnm[] = {
- { efTPX, "-s", NULL, ffOPTRD },
+ { efTPR, "-s", NULL, ffOPTRD },
{ efTRX, "-f", NULL, ffOPTRD },
{ efEDR, "-e", NULL, ffOPTRD },
{ efCPT, NULL, NULL, ffOPTRD },
}
- if (ftp2bSet(efTPX, NFILE, fnm))
+ if (ftp2bSet(efTPR, NFILE, fnm))
{
- list_tpx(ftp2fn(efTPX, NFILE, fnm), bShowNumbers,
+ list_tpx(ftp2fn(efTPR, NFILE, fnm), bShowNumbers,
ftp2fn_null(efMDP, NFILE, fnm), bSysTop);
}
else if (ftp2bSet(efTRX, NFILE, fnm))
#ifndef GMX_TOOLS_DUMP_H
#define GMX_TOOLS_DUMP_H
-#include "gromacs/legacyheaders/types/simple.h"
-
#ifdef __cplusplus
extern "C" {
#endif
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+file(GLOB TOPOLOGY_SOURCES *.cpp *.c)
+set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TOPOLOGY_SOURCES} PARENT_SCOPE)
+
+gmx_install_headers(
+ atomprop.h
+ atoms.h
+ block.h
+ idef.h
+ index.h
+ mtop_util.h
+ symtab.h
+ topology.h
+ )
+
+if (BUILD_TESTING)
+# add_subdirectory(tests)
+endif()
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "atomprop.h"
#include <ctype.h>
+#include <stdio.h>
#include <string.h>
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
-#include "atomprop.h"
-#include "macros.h"
-#include "index.h"
-#include "copyrite.h"
-
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/strdb.h"
+#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/math/utilities.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
gmx_bool bSet;
} aprop_t;
typedef struct gmx_atomprop {
- gmx_bool bWarned, bWarnVDW;
- aprop_t prop[epropNR];
- gmx_residuetype_t restype;
+ gmx_bool bWarned, bWarnVDW;
+ aprop_t prop[epropNR];
+ gmx_residuetype_t *restype;
} gmx_atomprop;
return i;
}
-static int get_prop_index(aprop_t *ap, gmx_residuetype_t restype,
+static int get_prop_index(aprop_t *ap, gmx_residuetype_t *restype,
char *resnm, char *atomnm,
gmx_bool *bExact)
{
return j;
}
-static void add_prop(aprop_t *ap, gmx_residuetype_t restype,
+static void add_prop(aprop_t *ap, gmx_residuetype_t *restype,
char *resnm, char *atomnm,
real p, int line)
{
ap->bAvail[i] = FALSE;
}
}
- ap->atomnm[ap->nprop] = strdup(atomnm);
- ap->resnm[ap->nprop] = strdup(resnm);
+ ap->atomnm[ap->nprop] = gmx_strdup(atomnm);
+ ap->resnm[ap->nprop] = gmx_strdup(resnm);
j = ap->nprop;
ap->nprop++;
}
while (get_a_line(fp, line, STRLEN))
{
line_no++;
- if (sscanf(line, "%s %s %lf", resnm, atomnm, &pp) == 3)
+ if (sscanf(line, "%31s %31s %20lf", resnm, atomnm, &pp) == 3)
{
pp *= factor;
add_prop(ap, aps->restype, resnm, atomnm, pp, line_no);
ap = &ap2->prop[eprop];
if (!ap->bSet)
{
- ap->db = strdup(fns[eprop]);
+ ap->db = gmx_strdup(fns[eprop]);
ap->def = def[eprop];
read_prop(aps, eprop, fac[eprop]);
gmx_atomprop_t gmx_atomprop_init(void)
{
gmx_atomprop *aps;
- int p;
snew(aps, 1);
real *value)
{
gmx_atomprop *ap = (gmx_atomprop*) aps;
- size_t i;
int j;
#define MAXQ 32
char atomname[MAXQ], resname[MAXQ];
}
if (isdigit(atomnm[0]))
{
+ int i;
/* put digit after atomname */
- for (i = 1; (i < min(MAXQ-1, strlen(atomnm))); i++)
+ for (i = 1; i < MAXQ-1 && atomnm[i] != '\0'; i++)
{
atomname[i-1] = atomnm[i];
}
return gmx_nint(ap->prop[epropElement].value[i]);
}
}
- return NOTSET;
+ return -1;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_TOPOLOGY_ATOMPROP_H
+#define GMX_TOPOLOGY_ATOMPROP_H
-#ifndef _atomprop_h
-#define _atomprop_h
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#endif
-#include "index.h"
-
/* Abstract type for the atom property database */
typedef struct gmx_atomprop *gmx_atomprop_t;
}
#endif
-
#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "atoms.h"
+
+#include <cstring>
+
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/smalloc.h"
+
+void init_atom(t_atoms *at)
+{
+ at->nr = 0;
+ at->nres = 0;
+ at->atom = NULL;
+ at->resinfo = NULL;
+ at->atomname = NULL;
+ at->atomtype = NULL;
+ at->atomtypeB = NULL;
+ at->pdbinfo = NULL;
+}
+
+void init_atomtypes(t_atomtypes *at)
+{
+ at->nr = 0;
+ at->radius = NULL;
+ at->vol = NULL;
+ at->atomnumber = NULL;
+ at->gb_radius = NULL;
+ at->S_hct = NULL;
+}
+
+void done_atom(t_atoms *at)
+{
+ at->nr = 0;
+ at->nres = 0;
+ sfree(at->atom);
+ sfree(at->resinfo);
+ sfree(at->atomname);
+ sfree(at->atomtype);
+ sfree(at->atomtypeB);
+ if (at->pdbinfo)
+ {
+ sfree(at->pdbinfo);
+ }
+}
+
+void done_atomtypes(t_atomtypes *atype)
+{
+ atype->nr = 0;
+ sfree(atype->radius);
+ sfree(atype->vol);
+ sfree(atype->surftens);
+ sfree(atype->atomnumber);
+ sfree(atype->gb_radius);
+ sfree(atype->S_hct);
+}
+
+void add_t_atoms(t_atoms *atoms, int natom_extra, int nres_extra)
+{
+ int i;
+
+ if (natom_extra > 0)
+ {
+ srenew(atoms->atomname, atoms->nr+natom_extra);
+ srenew(atoms->atom, atoms->nr+natom_extra);
+ if (NULL != atoms->pdbinfo)
+ {
+ srenew(atoms->pdbinfo, atoms->nr+natom_extra);
+ }
+ if (NULL != atoms->atomtype)
+ {
+ srenew(atoms->atomtype, atoms->nr+natom_extra);
+ }
+ if (NULL != atoms->atomtypeB)
+ {
+ srenew(atoms->atomtypeB, atoms->nr+natom_extra);
+ }
+ for (i = atoms->nr; (i < atoms->nr+natom_extra); i++)
+ {
+ atoms->atomname[i] = NULL;
+ memset(&atoms->atom[i], 0, sizeof(atoms->atom[i]));
+ if (NULL != atoms->pdbinfo)
+ {
+ std::memset(&atoms->pdbinfo[i], 0, sizeof(atoms->pdbinfo[i]));
+ }
+ if (NULL != atoms->atomtype)
+ {
+ atoms->atomtype[i] = NULL;
+ }
+ if (NULL != atoms->atomtypeB)
+ {
+ atoms->atomtypeB[i] = NULL;
+ }
+ }
+ atoms->nr += natom_extra;
+ }
+ if (nres_extra > 0)
+ {
+ srenew(atoms->resinfo, atoms->nres+nres_extra);
+ for (i = atoms->nres; (i < atoms->nres+nres_extra); i++)
+ {
+ std::memset(&atoms->resinfo[i], 0, sizeof(atoms->resinfo[i]));
+ }
+ atoms->nres += nres_extra;
+ }
+}
+
+void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo)
+{
+ atoms->nr = natoms;
+ atoms->nres = 0;
+ snew(atoms->atomname, natoms);
+ atoms->atomtype = NULL;
+ atoms->atomtypeB = NULL;
+ snew(atoms->resinfo, natoms);
+ snew(atoms->atom, natoms);
+ if (bPdbinfo)
+ {
+ snew(atoms->pdbinfo, natoms);
+ }
+ else
+ {
+ atoms->pdbinfo = NULL;
+ }
+}
+
+t_atoms *copy_t_atoms(t_atoms *src)
+{
+ t_atoms *dst;
+ int i;
+
+ snew(dst, 1);
+ init_t_atoms(dst, src->nr, (NULL != src->pdbinfo));
+ dst->nr = src->nr;
+ if (NULL != src->atomname)
+ {
+ snew(dst->atomname, src->nr);
+ }
+ if (NULL != src->atomtype)
+ {
+ snew(dst->atomtype, src->nr);
+ }
+ if (NULL != src->atomtypeB)
+ {
+ snew(dst->atomtypeB, src->nr);
+ }
+ for (i = 0; (i < src->nr); i++)
+ {
+ dst->atom[i] = src->atom[i];
+ if (NULL != src->pdbinfo)
+ {
+ dst->pdbinfo[i] = src->pdbinfo[i];
+ }
+ if (NULL != src->atomname)
+ {
+ dst->atomname[i] = src->atomname[i];
+ }
+ if (NULL != src->atomtype)
+ {
+ dst->atomtype[i] = src->atomtype[i];
+ }
+ if (NULL != src->atomtypeB)
+ {
+ dst->atomtypeB[i] = src->atomtypeB[i];
+ }
+ }
+ dst->nres = src->nres;
+ for (i = 0; (i < src->nres); i++)
+ {
+ dst->resinfo[i] = src->resinfo[i];
+ }
+ return dst;
+}
+
+void t_atoms_set_resinfo(t_atoms *atoms, int atom_ind, t_symtab *symtab,
+ const char *resname, int resnr, unsigned char ic,
+ int chainnum, char chainid)
+{
+ t_resinfo *ri;
+
+ ri = &atoms->resinfo[atoms->atom[atom_ind].resind];
+ ri->name = put_symtab(symtab, resname);
+ ri->rtp = NULL;
+ ri->nr = resnr;
+ ri->ic = ic;
+ ri->chainnum = chainnum;
+ ri->chainid = chainid;
+}
+
+void free_t_atoms(t_atoms *atoms, gmx_bool bFreeNames)
+{
+ int i;
+
+ if (bFreeNames && atoms->atomname != NULL)
+ {
+ for (i = 0; i < atoms->nr; i++)
+ {
+ if (atoms->atomname[i] != NULL)
+ {
+ sfree(*atoms->atomname[i]);
+ *atoms->atomname[i] = NULL;
+ }
+ }
+ }
+ if (bFreeNames && atoms->resinfo != NULL)
+ {
+ for (i = 0; i < atoms->nres; i++)
+ {
+ if (atoms->resinfo[i].name != NULL)
+ {
+ sfree(*atoms->resinfo[i].name);
+ *atoms->resinfo[i].name = NULL;
+ }
+ }
+ }
+ if (bFreeNames && atoms->atomtype != NULL)
+ {
+ for (i = 0; i < atoms->nr; i++)
+ {
+ if (atoms->atomtype[i] != NULL)
+ {
+ sfree(*atoms->atomtype[i]);
+ *atoms->atomtype[i] = NULL;
+ }
+ }
+ }
+ if (bFreeNames && atoms->atomtypeB != NULL)
+ {
+ for (i = 0; i < atoms->nr; i++)
+ {
+ if (atoms->atomtypeB[i] != NULL)
+ {
+ sfree(*atoms->atomtypeB[i]);
+ *atoms->atomtypeB[i] = NULL;
+ }
+ }
+ }
+ sfree(atoms->atomname);
+ sfree(atoms->atomtype);
+ sfree(atoms->atomtypeB);
+ sfree(atoms->resinfo);
+ sfree(atoms->atom);
+ sfree(atoms->pdbinfo);
+ atoms->nr = 0;
+ atoms->nres = 0;
+ atoms->atomname = NULL;
+ atoms->atomtype = NULL;
+ atoms->atomtypeB = NULL;
+ atoms->resinfo = NULL;
+ atoms->atom = NULL;
+ atoms->pdbinfo = NULL;
+}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _atoms_h
-#define _atoms_h
+#ifndef GMX_TOPOLOGY_ATOMS_H
+#define GMX_TOPOLOGY_ATOMS_H
-
-#include "simple.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_symtab;
+
enum {
eptAtom, eptNucleus, eptShell, eptBond, eptVSite, eptNR
};
/* The particle type */
-typedef struct {
+typedef struct t_atom
+{
real m, q; /* Mass and charge */
real mB, qB; /* Mass and charge for Free Energy calc */
unsigned short type; /* Atom type */
char elem[4]; /* Element name */
} t_atom;
-typedef struct {
+typedef struct t_resinfo
+{
char **name; /* Pointer to the residue name */
int nr; /* Residue number */
unsigned char ic; /* Code for insertion of residues */
char **rtp; /* rtp building block name (optional) */
} t_resinfo;
-typedef struct {
+typedef struct t_pdbinfo
+{
int type; /* PDB record name */
int atomnr; /* PDB atom number */
char altloc; /* Alternate location indicator */
int uij[6]; /* Anisotropic B-factor */
} t_pdbinfo;
-typedef struct {
+typedef struct t_grps
+{
int nr; /* Number of different groups */
int *nm_ind; /* Index in the group names */
} t_grps;
-typedef struct {
+typedef struct t_atoms
+{
int nr; /* Nr of atoms */
t_atom *atom; /* Array of atoms (dim: nr) */
/* The following entries will not */
t_pdbinfo *pdbinfo; /* PDB Information, such as aniso. Bfac */
} t_atoms;
-typedef struct {
+typedef struct t_atomtypes
+{
int nr; /* number of atomtypes */
real *radius; /* GBSA radius for each atomtype */
real *vol; /* GBSA efective volume for each atomtype */
int *atomnumber; /* Atomic number, used for QM/MM */
} t_atomtypes;
-
#define PERTURBED(a) (((a).mB != (a).m) || ((a).qB != (a).q) || ((a).typeB != (a).type))
+void init_atom(t_atoms *at);
+void init_atomtypes(t_atomtypes *at);
+void done_atom(t_atoms *at);
+void done_atomtypes(t_atomtypes *at);
+
+void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo);
+/* allocate memory for the arrays, set nr to natoms and nres to 0
+ * set pdbinfo to NULL or allocate memory for it */
+
+t_atoms *copy_t_atoms(t_atoms *src);
+/* copy an atoms struct from src to a new one */
+
+void add_t_atoms(t_atoms *atoms, int natom_extra, int nres_extra);
+/* allocate extra space for more atoms and or residues */
+
+void t_atoms_set_resinfo(t_atoms *atoms, int atom_ind, struct t_symtab *symtab,
+ const char *resname, int resnr, unsigned char ic,
+ int chainnum, char chainid);
+/* Set the residue name, number, insertion code and chain identifier
+ * of atom index atom_ind.
+ */
+
+void free_t_atoms(t_atoms *atoms, gmx_bool bFreeNames);
+/* Free all the arrays and set the nr and nres to 0.
+ * bFreeNames tells if to free the atom and residue name strings,
+ * don't free them if they still need to be used in e.g. the topology struct.
+ */
+
#ifdef __cplusplus
}
#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements classes from atomsbuilder.h.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ */
+#include "gmxpre.h"
+
+#include "atomsbuilder.h"
+
+#include <algorithm>
+
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/utility/smalloc.h"
+
+namespace gmx
+{
+
+/********************************************************************
+ * AtomsBuilder
+ */
+
+AtomsBuilder::AtomsBuilder(t_atoms *atoms)
+ : atoms_(atoms), nrAlloc_(atoms->nr), nresAlloc_(atoms->nres),
+ currentResidueIndex_(atoms->nres), nextResidueNumber_(-1)
+{
+ if (atoms->nres > 0)
+ {
+ nextResidueNumber_ = atoms->resinfo[atoms->nres - 1].nr + 1;
+ }
+}
+
+AtomsBuilder::~AtomsBuilder()
+{
+}
+
+void AtomsBuilder::reserve(int atomCount, int residueCount)
+{
+ srenew(atoms_->atom, atomCount);
+ srenew(atoms_->atomname, atomCount);
+ srenew(atoms_->resinfo, residueCount);
+ nrAlloc_ = atomCount;
+ nresAlloc_ = residueCount;
+}
+
+void AtomsBuilder::clearAtoms()
+{
+ atoms_->nr = 0;
+ atoms_->nres = 0;
+ currentResidueIndex_ = 0;
+ nextResidueNumber_ = -1;
+}
+
+int AtomsBuilder::currentAtomCount() const
+{
+ return atoms_->nr;
+}
+
+void AtomsBuilder::setNextResidueNumber(int number)
+{
+ nextResidueNumber_ = number;
+}
+
+void AtomsBuilder::addAtom(const t_atoms &atoms, int i)
+{
+ const int index = atoms_->nr;
+ atoms_->atom[index] = atoms.atom[i];
+ atoms_->atomname[index] = atoms.atomname[i];
+ atoms_->atom[index].resind = currentResidueIndex_;
+ ++atoms_->nr;
+}
+
+void AtomsBuilder::startResidue(const t_resinfo &resinfo)
+{
+ if (nextResidueNumber_ == -1)
+ {
+ nextResidueNumber_ = resinfo.nr;
+ }
+ const int index = atoms_->nres;
+ atoms_->resinfo[index] = resinfo;
+ atoms_->resinfo[index].nr = nextResidueNumber_;
+ ++nextResidueNumber_;
+ currentResidueIndex_ = index;
+ ++atoms_->nres;
+}
+
+void AtomsBuilder::finishResidue(const t_resinfo &resinfo)
+{
+ if (nextResidueNumber_ == -1)
+ {
+ nextResidueNumber_ = resinfo.nr;
+ }
+ const int index = currentResidueIndex_;
+ atoms_->resinfo[index] = resinfo;
+ atoms_->resinfo[index].nr = nextResidueNumber_;
+ ++nextResidueNumber_;
+ currentResidueIndex_ = index + 1;
+ if (index >= atoms_->nres)
+ {
+ ++atoms_->nres;
+ }
+}
+
+void AtomsBuilder::discardCurrentResidue()
+{
+ int index = atoms_->nr - 1;
+ while (index > 0 && atoms_->atom[index - 1].resind == currentResidueIndex_)
+ {
+ --index;
+ }
+ atoms_->nr = index;
+ atoms_->nres = currentResidueIndex_;
+}
+
+void AtomsBuilder::mergeAtoms(const t_atoms &atoms)
+{
+ if (atoms_->nr + atoms.nr > nrAlloc_
+ || atoms_->nres + atoms.nres > nresAlloc_)
+ {
+ reserve(atoms_->nr + atoms.nr, atoms_->nres + atoms.nres);
+ }
+ int prevResInd = -1;
+ for (int i = 0; i < atoms.nr; ++i)
+ {
+ const int resind = atoms.atom[i].resind;
+ if (resind != prevResInd)
+ {
+ startResidue(atoms.resinfo[resind]);
+ prevResInd = resind;
+ }
+ addAtom(atoms, i);
+ }
+}
+
+/********************************************************************
+ * AtomsRemover
+ */
+
+AtomsRemover::AtomsRemover(const t_atoms &atoms)
+ : removed_(atoms.nr, 0)
+{
+}
+
+AtomsRemover::~AtomsRemover()
+{
+}
+
+void AtomsRemover::markAll()
+{
+ std::fill(removed_.begin(), removed_.end(), 1);
+}
+
+void AtomsRemover::markResidue(const t_atoms &atoms, int atomIndex, bool bStatus)
+{
+ const int resind = atoms.atom[atomIndex].resind;
+ while (atomIndex > 0 && resind == atoms.atom[atomIndex - 1].resind)
+ {
+ --atomIndex;
+ }
+ while (atomIndex < atoms.nr && resind == atoms.atom[atomIndex].resind)
+ {
+ removed_[atomIndex] = (bStatus ? 1 : 0);
+ ++atomIndex;
+ }
+}
+
+void AtomsRemover::removeMarkedVectors(rvec array[]) const
+{
+ for (size_t i = 0, j = 0; i < removed_.size(); ++i)
+ {
+ if (!removed_[i])
+ {
+ copy_rvec(array[i], array[j]);
+ ++j;
+ }
+ }
+}
+
+void AtomsRemover::removeMarkedValues(real array[]) const
+{
+ for (size_t i = 0, j = 0; i < removed_.size(); ++i)
+ {
+ if (!removed_[i])
+ {
+ array[j] = array[i];
+ ++j;
+ }
+ }
+}
+
+void AtomsRemover::removeMarkedAtoms(t_atoms *atoms) const
+{
+ const int originalAtomCount = atoms->nr;
+ AtomsBuilder builder(atoms);
+ if (atoms->nr > 0)
+ {
+ builder.setNextResidueNumber(atoms->resinfo[0].nr);
+ }
+ builder.clearAtoms();
+ int prevResInd = -1;
+ for (int i = 0; i < originalAtomCount; ++i)
+ {
+ if (!removed_[i])
+ {
+ const int resind = atoms->atom[i].resind;
+ if (resind != prevResInd)
+ {
+ builder.startResidue(atoms->resinfo[resind]);
+ prevResInd = resind;
+ }
+ builder.addAtom(*atoms, i);
+ }
+ }
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Utility classes for manipulating \c t_atoms structures.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ */
+#ifndef GMX_TOPOLOGY_ATOMSBUILDER_H
+#define GMX_TOPOLOGY_ATOMSBUILDER_H
+
+#include <vector>
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/real.h"
+
+struct t_atoms;
+struct t_resinfo;
+
+namespace gmx
+{
+
+class AtomsBuilder
+{
+ public:
+ explicit AtomsBuilder(t_atoms *atoms);
+ ~AtomsBuilder();
+
+ void reserve(int atomCount, int residueCount);
+ void clearAtoms();
+
+ int currentAtomCount() const;
+
+ void setNextResidueNumber(int number);
+ void addAtom(const t_atoms &atoms, int i);
+ void startResidue(const t_resinfo &resinfo);
+ void finishResidue(const t_resinfo &resinfo);
+ void discardCurrentResidue();
+
+ void mergeAtoms(const t_atoms &atoms);
+
+ private:
+ t_atoms *atoms_;
+ int nrAlloc_;
+ int nresAlloc_;
+ int currentResidueIndex_;
+ int nextResidueNumber_;
+
+ GMX_DISALLOW_COPY_AND_ASSIGN(AtomsBuilder);
+};
+
+class AtomsRemover
+{
+ public:
+ explicit AtomsRemover(const t_atoms &atoms);
+ ~AtomsRemover();
+
+ void markAll();
+ void markResidue(const t_atoms &atoms, int atomIndex, bool bStatus);
+ bool isMarked(int atomIndex) const { return removed_[atomIndex] != 0; }
+
+ void removeMarkedVectors(rvec array[]) const;
+ void removeMarkedValues(real array[]) const;
+ void removeMarkedAtoms(t_atoms *atoms) const;
+
+ private:
+ std::vector<char> removed_;
+
+ GMX_DISALLOW_COPY_AND_ASSIGN(AtomsRemover);
+};
+
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "block.h"
+
+#include <algorithm>
+
+#include "gromacs/utility/smalloc.h"
+
+void init_block(t_block *block)
+{
+ block->nr = 0;
+ block->nalloc_index = 1;
+ snew(block->index, block->nalloc_index);
+ block->index[0] = 0;
+}
+
+void init_blocka(t_blocka *block)
+{
+ block->nr = 0;
+ block->nra = 0;
+ block->nalloc_index = 1;
+ snew(block->index, block->nalloc_index);
+ block->index[0] = 0;
+ block->nalloc_a = 0;
+ block->a = NULL;
+}
+
+t_blocka *new_blocka(void)
+{
+ t_blocka *block;
+
+ snew(block, 1);
+ snew(block->index, 1);
+
+ return block;
+}
+
+void done_block(t_block *block)
+{
+ block->nr = 0;
+ sfree(block->index);
+ block->nalloc_index = 0;
+}
+
+void done_blocka(t_blocka *block)
+{
+ block->nr = 0;
+ block->nra = 0;
+ sfree(block->index);
+ sfree(block->a);
+ block->index = NULL;
+ block->a = NULL;
+ block->nalloc_index = 0;
+ block->nalloc_a = 0;
+}
+
+void stupid_fill_block(t_block *grp, int natom, gmx_bool bOneIndexGroup)
+{
+ if (bOneIndexGroup)
+ {
+ grp->nalloc_index = 2;
+ snew(grp->index, grp->nalloc_index);
+ grp->index[0] = 0;
+ grp->index[1] = natom;
+ grp->nr = 1;
+ }
+ else
+ {
+ grp->nalloc_index = natom+1;
+ snew(grp->index, grp->nalloc_index);
+ snew(grp->index, natom+1);
+ for (int i = 0; i <= natom; ++i)
+ {
+ grp->index[i] = i;
+ }
+ grp->nr = natom;
+ }
+}
+
+void stupid_fill_blocka(t_blocka *grp, int natom)
+{
+ grp->nalloc_a = natom;
+ snew(grp->a, grp->nalloc_a);
+ for (int i = 0; i < natom; ++i)
+ {
+ grp->a[i] = i;
+ }
+ grp->nra = natom;
+
+ grp->nalloc_index = natom + 1;
+ snew(grp->index, grp->nalloc_index);
+ for (int i = 0; i <= natom; ++i)
+ {
+ grp->index[i] = i;
+ }
+ grp->nr = natom;
+}
+
+void copy_blocka(const t_blocka *src, t_blocka *dest)
+{
+ dest->nr = src->nr;
+ /* Workaround for inconsistent handling of nalloc_index in
+ * other parts of the code. Often nalloc_index and nalloc_a
+ * are not set.
+ */
+ dest->nalloc_index = std::max(src->nalloc_index, dest->nr + 1);
+ snew(dest->index, dest->nalloc_index);
+ for (int i = 0; i < dest->nr+1; ++i)
+ {
+ dest->index[i] = src->index[i];
+ }
+ dest->nra = src->nra;
+ /* See above. */
+ dest->nalloc_a = std::max(src->nalloc_a, dest->nra);
+ snew(dest->a, dest->nalloc_a);
+ for (int i = 0; i < dest->nra; ++i)
+ {
+ dest->a[i] = src->a[i];
+ }
+}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _block_h
-#define _block_h
+#ifndef GMX_TOPOLOGY_BLOCK_H
+#define GMX_TOPOLOGY_BLOCK_H
-
-#include "idef.h"
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef __cplusplus
extern "C" {
This makes the mapping from atoms to molecules O(Nmolecules) instead
of O(Natoms) in size. */
-typedef struct {
- int nr; /* The number of blocks */
+typedef struct t_block
+{
+ int nr; /* The number of blocks */
atom_id *index; /* Array of indices (dim: nr+1) */
- int nalloc_index; /* The allocation size for index */
+ int nalloc_index; /* The allocation size for index */
} t_block;
-typedef struct {
- int nr; /* The number of blocks */
- atom_id *index; /* Array of indices in a (dim: nr+1) */
- int nra; /* The number of atoms */
+typedef struct t_blocka
+{
+ int nr; /* The number of blocks */
+ atom_id *index; /* Array of indices in a (dim: nr+1) */
+ int nra; /* The number of atoms */
atom_id *a; /* Array of atom numbers in each group */
- /* (dim: nra) */
- /* Block i (0<=i<nr) runs from */
+ /* (dim: nra) */
+ /* Block i (0<=i<nr) runs from */
/* index[i] to index[i+1]-1. There will */
- /* allways be an extra entry in index */
- /* to terminate the table */
+ /* allways be an extra entry in index */
+ /* to terminate the table */
int nalloc_index; /* The allocation size for index */
int nalloc_a; /* The allocation size for a */
} t_blocka;
+void init_block(t_block *block);
+void init_blocka(t_blocka *block);
+t_blocka *new_blocka(void);
+/* allocate new block */
+
+void done_block(t_block *block);
+void done_blocka(t_blocka *block);
+
+void copy_blocka(const t_blocka *src, t_blocka *dest);
+
+void stupid_fill_block(t_block *grp, int natom, gmx_bool bOneIndexGroup);
+/* Fill a block structure with numbers identical to the index
+ * (0, 1, 2, .. natom-1)
+ * If bOneIndexGroup, then all atoms are lumped in one index group,
+ * otherwise there is one atom per index entry
+ */
+
+void stupid_fill_blocka(t_blocka *grp, int natom);
+/* Fill a block structure with numbers identical to the index
+ * (0, 1, 2, .. natom-1)
+ * There is one atom per index entry
+ */
#ifdef __cplusplus
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_TOPOLOGY_IDEF_H
+#define GMX_TOPOLOGY_IDEF_H
-
-#ifndef _idef_h
-#define _idef_h
-
-#include "simple.h"
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef __cplusplus
extern "C" {
F_DVDL_BONDED,
F_DVDL_RESTRAINT,
F_DVDL_TEMPERATURE, /* not calculated for now, but should just be the energy (NVT) or enthalpy (NPT), or 0 (NVE) */
- F_NRE /* This number is for the total number of energies */
+ F_NRE /* This number is for the total number of energies */
};
#define IS_RESTRAINT_TYPE(ifunc) (((ifunc == F_POSRES) || (ifunc == F_FBPOSRES) || (ifunc == F_DISRES) || (ifunc == F_RESTRBONDS) || (ifunc == F_DISRESVIOL) || (ifunc == F_ORIRES) || (ifunc == F_ORIRESDEV) || (ifunc == F_ANGRES) || (ifunc == F_ANGRESZ) || (ifunc == F_DIHRES)))
-/* A macro for checking if ftype is an explicit pair-listed LJ or COULOMB
- * interaction type:
- * bonded LJ (usually 1-4), or special listed non-bonded for FEP.
- */
-#define IS_LISTED_LJ_C(ftype) ((ftype) >= F_LJ14 && (ftype) <= F_LJC_PAIRS_NB)
-
-typedef union
+typedef union t_iparams
{
/* Some parameters have A and B values for free energy calculations.
* The B values are not used for regular simulations of course.
* the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
* interactions.
*/
-typedef struct
+typedef struct t_ilist
{
int nr;
int nr_nonperturbed;
* The struct t_ilist defines a list of atoms with their interactions.
* General field description:
* int nr
- * the size (nr elements) of the interactions array (iatoms[]).
+ * the size (nr elements) of the interactions array (iatoms[]).
* t_iatom *iatoms
* specifies which atoms are involved in an interaction of a certain
* type. The layout of this array is as follows:
*
- * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
- * |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
- * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
+ * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
+ * |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
+ * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
*
* So for interaction type type1 3 atoms are needed, and for type2 and
* type3 only 2. The type identifier is used to select the function to
- * calculate the interaction and its actual parameters. This type
- * identifier is an index in a params[] and functype[] array.
+ * calculate the interaction and its actual parameters. This type
+ * identifier is an index in a params[] and functype[] array.
*/
typedef struct
{
real *cmap; /* Has length 4*grid_spacing*grid_spacing, */
/* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
-} cmapdata_t;
+} gmx_cmapdata_t;
-typedef struct
+typedef struct gmx_cmap_t
{
- int ngrid; /* Number of allocated cmap (cmapdata_t ) grids */
- int grid_spacing; /* Grid spacing */
- cmapdata_t *cmapdata; /* Pointer to grid with actual, pre-interpolated data */
+ int ngrid; /* Number of allocated cmap (cmapdata_t ) grids */
+ int grid_spacing; /* Grid spacing */
+ gmx_cmapdata_t *cmapdata; /* Pointer to grid with actual, pre-interpolated data */
} gmx_cmap_t;
-typedef struct
+typedef struct gmx_ffparams_t
{
int ntypes;
int atnr;
ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
};
-typedef struct
+typedef struct t_idef
{
int ntypes;
int atnr;
* version of the program can use it as easy as the single node version.
* General field description:
* int ntypes
- * defines the number of elements in functype[] and param[].
+ * defines the number of elements in functype[] and param[].
* int nodeid
* the node id (if parallel machines)
* int atnr
* the number of atomtypes
* t_functype *functype
- * array of length ntypes, defines for every force type what type of
+ * array of length ntypes, defines for every force type what type of
* function to use. Every "bond" with the same function but different
- * force parameters is a different force type. The type identifier in the
- * forceatoms[] array is an index in this array.
+ * force parameters is a different force type. The type identifier in the
+ * forceatoms[] array is an index in this array.
* t_iparams *iparams
- * array of length ntypes, defines the parameters for every interaction
+ * array of length ntypes, defines the parameters for every interaction
* type. The type identifier in the actual interaction list
* (ilist[ftype].iatoms[]) is an index in this array.
* gmx_cmap_t cmap_grid
* the grid for the dihedral pair correction maps.
* t_iparams *iparams_posres, *iparams_fbposres
- * defines the parameters for position restraints only.
+ * defines the parameters for position restraints only.
* Position restraints are the only interactions that have different
* parameters (reference positions) for different molecules
* of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
* should be at least F_NRE*(nthreads+1).
*/
-typedef struct {
- int n; /* n+1 is the number of points */
- real scale; /* distance between two points */
- real *data; /* the actual table data, per point there are 4 numbers */
-} bondedtable_t;
-
#ifdef __cplusplus
}
#endif
-
#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "index.h"
+
+#include <assert.h>
#include <ctype.h>
+#include <stdlib.h>
#include <string.h>
-#include <assert.h>
-#include "sysstuff.h"
-#include "macros.h"
-#include "names.h"
-#include "gromacs/utility/cstringutil.h"
-#include "main.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "invblock.h"
-#include "macros.h"
-#include "index.h"
-#include "txtdump.h"
-#include "gromacs/fileio/futil.h"
+#include <algorithm>
+
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/strdb.h"
-#include "gmx_fatal.h"
-
-const char gmx_residuetype_undefined[] = "Other";
-
-struct gmx_residuetype
-{
- int n;
- char ** resname;
- char ** restype;
-
-};
-
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/invblock.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static gmx_bool gmx_ask_yesno(gmx_bool bASK)
{
}
}
-t_blocka *new_blocka(void)
-{
- t_blocka *block;
-
- snew(block, 1);
- snew(block->index, 1);
-
- return block;
-}
-
void write_index(const char *outf, t_blocka *b, char **gnames, gmx_bool bDuplicate, int natoms)
{
FILE *out;
srenew(b->index, b->nr+2);
srenew(*gnames, b->nr+1);
- (*gnames)[b->nr] = strdup(name);
+ (*gnames)[b->nr] = gmx_strdup(name);
srenew(b->a, b->nra+nra);
for (i = 0; (i < nra); i++)
}
static void
-p_status(const char **restype, int nres, const char **typenames, int ntypes)
+p_status(const char *const *restype, int nres,
+ const char *const *typenames, int ntypes)
{
int i, j;
- int found;
-
int * counter;
snew(counter, ntypes);
}
for (i = 0; i < nres; i++)
{
- found = 0;
for (j = 0; j < ntypes; j++)
{
if (!gmx_strcasecmp(restype[i], typenames[j]))
}
-atom_id *
+static atom_id *
mk_aid(t_atoms *atoms, const char ** restype, const char * typestring, int *nra, gmx_bool bMatch)
/* Make an array of atom_ids for all atoms with residuetypes matching typestring, or the opposite if bMatch is false */
{
restp_t *restp = NULL;
char **attp = NULL;
char *rname, *aname;
- atom_id *other_ndx, *aid, *aaid;
+ atom_id *aid, *aaid;
int i, j, k, l, resind, naid, naaid, natp, nrestp = 0;
for (i = 0; (i < atoms->nres); i++)
{
printf("Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...\n");
}
- snew(other_ndx, atoms->nr);
for (k = 0; (k < atoms->nr); k++)
{
resind = atoms->atom[k].resind;
if (l == nrestp)
{
srenew(restp, nrestp+1);
- restp[nrestp].rname = strdup(rname);
+ restp[nrestp].rname = gmx_strdup(rname);
restp[nrestp].bNeg = FALSE;
- restp[nrestp].gname = strdup(rname);
+ restp[nrestp].gname = gmx_strdup(rname);
nrestp++;
-
}
}
}
sfree(attp);
attp = NULL;
}
- sfree(aid);
}
+ sfree(aid);
+ sfree(restp[i].rname);
+ sfree(restp[i].gname);
}
- sfree(other_ndx);
+ sfree(restp);
}
}
/** The set of atom names that will be used to form this index group */
const char **defining_atomnames;
/** Size of the defining_atomnames array */
- const int num_defining_atomnames;
+ int num_defining_atomnames;
/** Name of this index group */
const char *group_name;
/** Whether the above atom names name the atoms in the group, or
int n, j;
atom_id *aid;
- int nra, nnpres, npres;
+ int nra, npres;
gmx_bool match;
char ndx_name[STRLEN], *atnm;
int i;
if (nra > 0)
{
add_grp(gb, gn, nra, aid, "SwapSC-CO");
- nra = 0;
}
}
}
}
-
-
-/* Return 0 if the name was found, otherwise -1.
- * p_restype is set to a pointer to the type name, or 'Other' if we did not find it.
- */
-int
-gmx_residuetype_get_type(gmx_residuetype_t rt, const char * resname, const char ** p_restype)
-{
- int i, rc;
-
- rc = -1;
- for (i = 0; i < rt->n && rc; i++)
- {
- rc = gmx_strcasecmp(rt->resname[i], resname);
- }
-
- *p_restype = (rc == 0) ? rt->restype[i-1] : gmx_residuetype_undefined;
-
- return rc;
-}
-
-int
-gmx_residuetype_add(gmx_residuetype_t rt, const char *newresname, const char *newrestype)
-{
- int i;
- int found;
- const char * p_oldtype;
-
- found = !gmx_residuetype_get_type(rt, newresname, &p_oldtype);
-
- if (found && gmx_strcasecmp(p_oldtype, newrestype))
- {
- fprintf(stderr, "Warning: Residue '%s' already present with type '%s' in database, ignoring new type '%s'.",
- newresname, p_oldtype, newrestype);
- }
-
- if (found == 0)
- {
- srenew(rt->resname, rt->n+1);
- srenew(rt->restype, rt->n+1);
- rt->resname[rt->n] = strdup(newresname);
- rt->restype[rt->n] = strdup(newrestype);
- rt->n++;
- }
-
- return 0;
-}
-
-
-int
-gmx_residuetype_init(gmx_residuetype_t *prt)
-{
- FILE * db;
- char line[STRLEN];
- char resname[STRLEN], restype[STRLEN], dum[STRLEN];
- char * p;
- int i;
- struct gmx_residuetype *rt;
-
- snew(rt, 1);
- *prt = rt;
-
- rt->n = 0;
- rt->resname = NULL;
- rt->restype = NULL;
-
- db = libopen("residuetypes.dat");
-
- while (get_a_line(db, line, STRLEN))
- {
- strip_comment(line);
- trim(line);
- if (line[0] != '\0')
- {
- if (sscanf(line, "%s %s %s", resname, restype, dum) != 2)
- {
- gmx_fatal(FARGS, "Incorrect number of columns (2 expected) for line in residuetypes.dat");
- }
- gmx_residuetype_add(rt, resname, restype);
- }
- }
-
- fclose(db);
-
- return 0;
-}
-
-
-
-int
-gmx_residuetype_destroy(gmx_residuetype_t rt)
-{
- int i;
-
- for (i = 0; i < rt->n; i++)
- {
- sfree(rt->resname[i]);
- sfree(rt->restype[i]);
- }
- sfree(rt->resname);
- sfree(rt->restype);
- sfree(rt);
-
- return 0;
-}
-
-int
-gmx_residuetype_get_alltypes(gmx_residuetype_t rt,
- const char *** p_typenames,
- int * ntypes)
-{
- int i, j, n;
- int found;
- const char ** my_typename;
- char * p;
-
- n = 0;
-
- my_typename = NULL;
- for (i = 0; i < rt->n; i++)
- {
- p = rt->restype[i];
- found = 0;
- for (j = 0; j < n && !found; j++)
- {
- found = !gmx_strcasecmp(p, my_typename[j]);
- }
-
- if (!found)
- {
- srenew(my_typename, n+1);
- my_typename[n] = p;
- n++;
- }
- }
- *ntypes = n;
- *p_typenames = my_typename;
-
- return 0;
-}
-
-
-
-gmx_bool
-gmx_residuetype_is_protein(gmx_residuetype_t rt, const char *resnm)
-{
- gmx_bool rc;
- const char *p_type;
-
- if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
- gmx_strcasecmp(p_type, "Protein") == 0)
- {
- rc = TRUE;
- }
- else
- {
- rc = FALSE;
- }
- return rc;
-}
-
-gmx_bool
-gmx_residuetype_is_dna(gmx_residuetype_t rt, const char *resnm)
-{
- gmx_bool rc;
- const char *p_type;
-
- if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
- gmx_strcasecmp(p_type, "DNA") == 0)
- {
- rc = TRUE;
- }
- else
- {
- rc = FALSE;
- }
- return rc;
-}
-
-gmx_bool
-gmx_residuetype_is_rna(gmx_residuetype_t rt, const char *resnm)
-{
- gmx_bool rc;
- const char *p_type;
-
- if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
- gmx_strcasecmp(p_type, "RNA") == 0)
- {
- rc = TRUE;
- }
- else
- {
- rc = FALSE;
- }
- return rc;
-}
-
-/* Return the size of the arrays */
-int
-gmx_residuetype_get_size(gmx_residuetype_t rt)
-{
- return rt->n;
-}
-
-/* Search for a residuetype with name resnm within the
- * gmx_residuetype database. Return the index if found,
- * otherwise -1.
- */
-int
-gmx_residuetype_get_index(gmx_residuetype_t rt, const char *resnm)
-{
- int i, rc;
-
- rc = -1;
- for (i = 0; i < rt->n && rc; i++)
- {
- rc = gmx_strcasecmp(rt->resname[i], resnm);
- }
-
- return (0 == rc) ? i-1 : -1;
-}
-
-/* Return the name of the residuetype with the given index, or
- * NULL if not found. */
-const char *
-gmx_residuetype_get_name(gmx_residuetype_t rt, int index)
-{
- if (index >= 0 && index < rt->n)
- {
- return rt->resname[index];
- }
- else
- {
- return NULL;
- }
-}
-
-
-
void analyse(t_atoms *atoms, t_blocka *gb, char ***gn, gmx_bool bASK, gmx_bool bVerb)
{
- gmx_residuetype_t rt = NULL;
+ gmx_residuetype_t*rt = NULL;
char *resnm;
atom_id *aid;
const char ** restype;
int nra;
int i, k;
- size_t j;
int ntypes;
- char * p;
- const char ** p_typename;
+ char ** p_typename;
int iwater, iion;
int nwater, nion;
int found;
found = 0;
for (k = 0; k < ntypes && !found; k++)
{
+ assert(p_typename != NULL);
found = !strcmp(restype[i], p_typename[k]);
}
if (!found)
{
srenew(p_typename, ntypes+1);
- p_typename[ntypes++] = strdup(restype[i]);
+ p_typename[ntypes++] = gmx_strdup(restype[i]);
}
}
sfree(aid);
analyse_other(restype, atoms, gb, gn, bASK, bVerb);
}
+ sfree(p_typename[k]);
}
sfree(p_typename);
{
srenew(gb->index, gb->nr+2);
srenew(*gn, gb->nr+1);
- (*gn)[gb->nr] = strdup("Water_and_ions");
+ (*gn)[gb->nr] = gmx_strdup("Water_and_ions");
srenew(gb->a, gb->nra+nwater+nion);
if (nwater > 0)
{
{
FILE *in;
t_blocka *b;
- int a, maxentries;
- int i, j, ng, nread;
+ int maxentries;
+ int i, j;
char line[STRLEN], *pt, str[STRLEN];
in = gmx_fio_fopen(gfile, "r");
snew(b, 1);
- get_a_line(in, line, STRLEN);
- if (line[0] == '[')
+ b->nr = 0;
+ b->index = NULL;
+ b->nra = 0;
+ b->a = NULL;
+ *grpname = NULL;
+ maxentries = 0;
+ while (get_a_line(in, line, STRLEN))
{
- /* new format */
- b->nr = 0;
- b->index = NULL;
- b->nra = 0;
- b->a = NULL;
- *grpname = NULL;
- maxentries = 0;
- do
+ if (get_header(line, str))
{
- if (get_header(line, str))
+ b->nr++;
+ srenew(b->index, b->nr+1);
+ srenew(*grpname, b->nr);
+ if (b->nr == 1)
{
- b->nr++;
- srenew(b->index, b->nr+1);
- srenew(*grpname, b->nr);
- if (b->nr == 1)
- {
- b->index[0] = 0;
- }
- b->index[b->nr] = b->index[b->nr-1];
- (*grpname)[b->nr-1] = strdup(str);
- }
- else
- {
- if (b->nr == 0)
- {
- gmx_fatal(FARGS, "The first header of your indexfile is invalid");
- }
- pt = line;
- while (sscanf(pt, "%s", str) == 1)
- {
- i = b->index[b->nr];
- if (i >= maxentries)
- {
- maxentries += 1024;
- srenew(b->a, maxentries);
- }
- b->a[i] = strtol(str, NULL, 10)-1;
- b->index[b->nr]++;
- (b->nra)++;
- pt = strstr(pt, str)+strlen(str);
- }
+ b->index[0] = 0;
}
+ b->index[b->nr] = b->index[b->nr-1];
+ (*grpname)[b->nr-1] = gmx_strdup(str);
}
- while (get_a_line(in, line, STRLEN));
- }
- else
- {
- /* old format */
- sscanf(line, "%d%d", &b->nr, &b->nra);
- snew(b->index, b->nr+1);
- snew(*grpname, b->nr);
- b->index[0] = 0;
- snew(b->a, b->nra);
- for (i = 0; (i < b->nr); i++)
+ else
{
- nread = fscanf(in, "%s%d", str, &ng);
- (*grpname)[i] = strdup(str);
- b->index[i+1] = b->index[i]+ng;
- if (b->index[i+1] > b->nra)
+ if (b->nr == 0)
{
- gmx_fatal(FARGS, "Something wrong in your indexfile at group %s", str);
+ gmx_fatal(FARGS, "The first header of your indexfile is invalid");
}
- for (j = 0; (j < ng); j++)
+ pt = line;
+ while (sscanf(pt, "%s", str) == 1)
{
- nread = fscanf(in, "%d", &a);
- b->a[b->index[i]+j] = a;
+ i = b->index[b->nr];
+ if (i >= maxentries)
+ {
+ maxentries += 1024;
+ srenew(b->a, maxentries);
+ }
+ assert(b->a != NULL); // for clang analyzer
+ b->a[i] = strtol(str, NULL, 10)-1;
+ b->index[b->nr]++;
+ (b->nra)++;
+ pt = strstr(pt, str)+strlen(str);
}
}
}
for (i = 0; (i < b->nr); i++)
{
+ assert(b->a != NULL); // for clang analyzer
for (j = b->index[i]; (j < b->index[i+1]); j++)
{
if (b->a[j] < 0)
fprintf(stderr, "There is one group in the index\n");
gnr1 = 0;
}
- gnames[i] = strdup(grpname[gnr1]);
+ gnames[i] = gmx_strdup(grpname[gnr1]);
isize[i] = grps->index[gnr1+1]-grps->index[gnr1];
snew(index[i], isize[i]);
for (j = 0; (j < isize[i]); j++)
c->maxframe = -1;
for (i = 0; (i < c->clust->nra); i++)
{
- c->maxframe = max(c->maxframe, c->clust->a[i]);
+ c->maxframe = std::max(c->maxframe, c->clust->a[i]);
}
fprintf(fplog ? fplog : stdout,
"There are %d clusters containing %d structures, highest framenr is %d\n",
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_TOPOLOGY_INDEX_H
+#define GMX_TOPOLOGY_INDEX_H
-#ifndef _index_h
-#define _index_h
+#include <stdio.h>
-#include "typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct t_atoms;
+struct t_blocka;
+
void check_index(char *gname, int n, atom_id index[],
char *traj, int natoms);
/* Checks if any index is smaller than zero or larger than natoms,
* and traj (if traj=NULL, "the trajectory" is used).
*/
-t_blocka *init_index(const char *gfile, char ***grpname);
+struct t_blocka *init_index(const char *gfile, char ***grpname);
/* Lower level routine than the next */
void rd_index(const char *statfile, int ngrps, int isize[],
atom_id *index[], char *grpnames[], int grpnr[]);
/* the same but also reads the number of the selected group*/
-void get_index(t_atoms *atoms, const char *fnm, int ngrps,
+void get_index(struct t_atoms *atoms, const char *fnm, int ngrps,
int isize[], atom_id *index[], char *grpnames[]);
/* Does the same as rd_index, but if the fnm pointer is NULL it
* will not read from fnm, but it will make default index groups
*/
typedef struct {
- int maxframe;
- char **grpname;
- t_blocka *clust;
- atom_id *inv_clust;
+ int maxframe;
+ char **grpname;
+ struct t_blocka *clust;
+ atom_id *inv_clust;
} t_cluster_ndx;
t_cluster_ndx *cluster_index(FILE *fplog, const char *ndx);
-typedef struct {
- int n;
- char **name;
-} t_names;
-
-typedef struct gmx_residuetype *
- gmx_residuetype_t;
-
-int
-gmx_residuetype_init(gmx_residuetype_t *rt);
-
-int
-gmx_residuetype_destroy(gmx_residuetype_t rt);
-
-int
-gmx_residuetype_get_type(gmx_residuetype_t rt, const char * resname, const char ** p_restype);
-
-int
-gmx_residuetype_add(gmx_residuetype_t rt, const char *newresname, const char *newrestype);
-
-int
-gmx_residuetype_get_alltypes(gmx_residuetype_t rt,
- const char *** p_typenames,
- int * ntypes);
-
-gmx_bool
-gmx_residuetype_is_protein(gmx_residuetype_t rt, const char *resnm);
-
-gmx_bool
-gmx_residuetype_is_dna(gmx_residuetype_t rt, const char *resnm);
-
-gmx_bool
-gmx_residuetype_is_rna(gmx_residuetype_t rt, const char *resnm);
-int
-gmx_residuetype_get_size(gmx_residuetype_t rt);
-
-int
-gmx_residuetype_get_index(gmx_residuetype_t rt, const char *resnm);
-
-const char *
-gmx_residuetype_get_name(gmx_residuetype_t rt, int index);
-
-
-
-
-
-
-t_blocka *new_blocka(void);
-/* allocate new block */
-
-void write_index(const char *outf, t_blocka *b, char **gnames, gmx_bool bDuplicate, int natoms);
+void write_index(const char *outf, struct t_blocka *b, char **gnames, gmx_bool bDuplicate, int natoms);
/* Writes index blocks to outf (writes an indexfile) */
-void add_grp(t_blocka *b, char ***gnames, int nra, atom_id a[], const char *name);
+void add_grp(struct t_blocka *b, char ***gnames, int nra, atom_id a[], const char *name);
/* Ads group a with name name to block b and namelist gnames */
-void analyse(t_atoms *atoms, t_blocka *gb, char ***gn,
+void analyse(struct t_atoms *atoms, struct t_blocka *gb, char ***gn,
gmx_bool bASK, gmx_bool bVerb);
/* Makes index groups gb with names gn for atoms in atoms.
* bASK=FALSE gives default groups.
}
#endif
-#endif /* _index_h */
+#endif
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
#include "invblock.h"
-#include "gmx_fatal.h"
+
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
atom_id *make_invblock(const t_block *block, int nr)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_TOPOLOGY_INVBLOCK_H
+#define GMX_TOPOLOGY_INVBLOCK_H
-#ifndef _invblock_h
-#define _invblock_h
-
-#include "typedefs.h"
+#include "gromacs/legacyheaders/types/simple.h"
#ifdef __cplusplus
extern "C" {
#endif
-atom_id *make_invblock(const t_block *block, int nr);
+struct t_block;
+struct t_blocka;
+
+atom_id *make_invblock(const struct t_block *block, int nr);
/* Inverse the block structure. nr is the maximum entry in the inversed
* array, and therefore the dimension of the returned array
*/
-atom_id *make_invblocka(const t_blocka *block, int nr);
+atom_id *make_invblocka(const struct t_blocka *block, int nr);
/* Inverse the block structure. nr is the maximum entry in the inversed
* array, and therefore the dimension of the returned array
*/
}
#endif
-#endif /* _invblock_h */
+#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "mtop_util.h"
+#include <limits.h>
+#include <stddef.h>
+#include <stdio.h>
+#include <stdlib.h>
#include <string.h>
+
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/ifunc.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/topology/topsort.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "mtop_util.h"
-#include "topsort.h"
-#include "symtab.h"
-#include "gmx_fatal.h"
static int gmx_mtop_maxresnr(const gmx_mtop_t *mtop, int maxres_renum)
{
{
if (mb >= 0)
{
+ /* cppcheck-suppress nullPointer #6330*/
if (atoms->nres <= mtop->maxres_renum)
{
/* Single residue molecule, keep counting */
+ /* cppcheck-suppress nullPointer #6330*/
maxresnr += mtop->molblock[mb].nmol*atoms->nres;
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "typedefs.h"
+#ifndef GMX_TOPOLOGY_MTOP_UTIL_H
+#define GMX_TOPOLOGY_MTOP_UTIL_H
+
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct gmx_localtop_t;
+struct gmx_moltype_t;
+struct gmx_mtop_t;
+struct t_atom;
+struct t_atoms;
+struct t_block;
+struct t_ilist;
+struct t_topology;
+
/* Should be called after generating or reading mtop,
* to set some compute intesive variables to avoid
* N^2 operations later on.
*/
void
-gmx_mtop_finalize(gmx_mtop_t *mtop);
+gmx_mtop_finalize(struct gmx_mtop_t *mtop);
/* Counts the number of atoms of each type. State should be 0 for
* state A and 1 for state B types. typecount should have at
* least mtop->ffparams.atnr elements.
*/
void
-gmx_mtop_count_atomtypes(const gmx_mtop_t *mtop, int state, int typecount[]);
+gmx_mtop_count_atomtypes(const struct gmx_mtop_t *mtop, int state, int typecount[]);
/* Returns the total number of charge groups in mtop */
int
-ncg_mtop(const gmx_mtop_t *mtop);
+ncg_mtop(const struct gmx_mtop_t *mtop);
/* Removes the charge groups, i.e. makes single atom charge groups, in mtop */
-void gmx_mtop_remove_chargegroups(gmx_mtop_t *mtop);
+void gmx_mtop_remove_chargegroups(struct gmx_mtop_t *mtop);
/* Abstract data type for looking up atoms by global atom number */
/* Initialize atom lookup by global atom number */
gmx_mtop_atomlookup_t
-gmx_mtop_atomlookup_init(const gmx_mtop_t *mtop);
+gmx_mtop_atomlookup_init(const struct gmx_mtop_t *mtop);
/* As gmx_mtop_atomlookup_init, but optimized for atoms involved in settle */
gmx_mtop_atomlookup_t
-gmx_mtop_atomlookup_settle_init(const gmx_mtop_t *mtop);
+gmx_mtop_atomlookup_settle_init(const struct gmx_mtop_t *mtop);
/* Destroy a gmx_mtop_atomlookup_t data structure */
void
void
gmx_mtop_atomnr_to_atom(const gmx_mtop_atomlookup_t alook,
int atnr_global,
- t_atom **atom);
+ struct t_atom **atom);
/* Returns a pointer to the molecule interaction array ilist_mol[F_NRE]
void
gmx_mtop_atomnr_to_ilist(const gmx_mtop_atomlookup_t alook,
int atnr_global,
- t_ilist **ilist_mol, int *atnr_offset);
+ struct t_ilist **ilist_mol, int *atnr_offset);
/* Returns the molecule block index
/* Returns atom name, global resnr and residue name of atom atnr_global */
void
-gmx_mtop_atominfo_global(const gmx_mtop_t *mtop, int atnr_global,
+gmx_mtop_atominfo_global(const struct gmx_mtop_t *mtop, int atnr_global,
char **atomname, int *resnr, char **resname);
* otherwise use gmx_mtop_atomloop_block.
*/
gmx_mtop_atomloop_all_t
-gmx_mtop_atomloop_all_init(const gmx_mtop_t *mtop);
+gmx_mtop_atomloop_all_init(const struct gmx_mtop_t *mtop);
/* Loop to the next atom.
* When not at the end:
*/
gmx_bool
gmx_mtop_atomloop_all_next(gmx_mtop_atomloop_all_t aloop,
- int *at_global, t_atom **atom);
+ int *at_global, struct t_atom **atom);
/* Return the atomname, the residue number and residue name
* of the current atom in the loop.
*/
void
gmx_mtop_atomloop_all_moltype(gmx_mtop_atomloop_all_t aloop,
- gmx_moltype_t **moltype, int *at_mol);
+ struct gmx_moltype_t **moltype, int *at_mol);
/* Abstract type for atom loop over atoms in all molecule blocks */
/* Initialize an atom loop over atoms in all molecule blocks the system.
*/
gmx_mtop_atomloop_block_t
-gmx_mtop_atomloop_block_init(const gmx_mtop_t *mtop);
+gmx_mtop_atomloop_block_init(const struct gmx_mtop_t *mtop);
/* Loop to the next atom.
* When not at the end:
*/
gmx_bool
gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop,
- t_atom **atom, int *nmol);
+ struct t_atom **atom, int *nmol);
/* Abstract type for ilist loop over all ilists */
/* Initialize an ilist loop over all molecule types in the system. */
gmx_mtop_ilistloop_t
-gmx_mtop_ilistloop_init(const gmx_mtop_t *mtop);
+gmx_mtop_ilistloop_init(const struct gmx_mtop_t *mtop);
/* Loop to the next molecule,
*/
gmx_bool
gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop,
- t_ilist **ilist_mol, int *nmol);
+ struct t_ilist **ilist_mol, int *nmol);
/* Abstract type for ilist loop over all ilists of all molecules */
* otherwise use gmx_mtop_ilistloop.
*/
gmx_mtop_ilistloop_all_t
-gmx_mtop_ilistloop_all_init(const gmx_mtop_t *mtop);
+gmx_mtop_ilistloop_all_init(const struct gmx_mtop_t *mtop);
/* Loop to the next molecule,
* When not at the end:
*/
gmx_bool
gmx_mtop_ilistloop_all_next(gmx_mtop_ilistloop_all_t iloop,
- t_ilist **ilist_mol, int *atnr_offset);
+ struct t_ilist **ilist_mol, int *atnr_offset);
/* Returns the total number of interactions in the system of type ftype */
int
-gmx_mtop_ftype_count(const gmx_mtop_t *mtop, int ftype);
+gmx_mtop_ftype_count(const struct gmx_mtop_t *mtop, int ftype);
/* Returns a charge group index for the whole system */
-t_block
-gmx_mtop_global_cgs(const gmx_mtop_t *mtop);
+struct t_block
+gmx_mtop_global_cgs(const struct gmx_mtop_t *mtop);
/* Returns a single t_atoms struct for the whole system */
-t_atoms
-gmx_mtop_global_atoms(const gmx_mtop_t *mtop);
+struct t_atoms
+gmx_mtop_global_atoms(const struct gmx_mtop_t *mtop);
/* Make all charge groups the size of one atom.
* that consist of a single charge group.
*/
void
-gmx_mtop_make_atomic_charge_groups(gmx_mtop_t *mtop, gmx_bool bKeepSingleMolCG);
+gmx_mtop_make_atomic_charge_groups(struct gmx_mtop_t *mtop, gmx_bool bKeepSingleMolCG);
/* Generate a 'local' topology for the whole system.
* When ir!=NULL the free energy interactions will be sorted to the end.
*/
-gmx_localtop_t *
-gmx_mtop_generate_local_top(const gmx_mtop_t *mtop, const t_inputrec *ir);
+struct gmx_localtop_t *
+gmx_mtop_generate_local_top(const struct gmx_mtop_t *mtop, const t_inputrec *ir);
/* Converts a gmx_mtop_t struct to t_topology.
* All memory relating only to mtop will be freed.
*/
-t_topology
-gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop);
+struct t_topology
+gmx_mtop_t_to_t_topology(struct gmx_mtop_t *mtop);
#ifdef __cplusplus
}
#endif
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2010,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "residuetypes.h"
+
+#include <cassert>
+#include <cstdio>
+
+#include "gromacs/fileio/strdb.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
+
+const char gmx_residuetype_undefined[] = "Other";
+
+struct gmx_residuetype_t
+{
+ int n;
+ char ** resname;
+ char ** restype;
+};
+
+int
+gmx_residuetype_init(gmx_residuetype_t **prt)
+{
+ FILE * db;
+ char line[STRLEN];
+ char resname[STRLEN], restype[STRLEN], dum[STRLEN];
+ gmx_residuetype_t *rt;
+
+ snew(rt, 1);
+ *prt = rt;
+
+ rt->n = 0;
+ rt->resname = NULL;
+ rt->restype = NULL;
+
+ db = libopen("residuetypes.dat");
+
+ while (get_a_line(db, line, STRLEN))
+ {
+ strip_comment(line);
+ trim(line);
+ if (line[0] != '\0')
+ {
+ if (sscanf(line, "%1000s %1000s %1000s", resname, restype, dum) != 2)
+ {
+ gmx_fatal(FARGS, "Incorrect number of columns (2 expected) for line in residuetypes.dat");
+ }
+ gmx_residuetype_add(rt, resname, restype);
+ }
+ }
+
+ fclose(db);
+
+ return 0;
+}
+
+int
+gmx_residuetype_destroy(gmx_residuetype_t *rt)
+{
+ int i;
+
+ for (i = 0; i < rt->n; i++)
+ {
+ sfree(rt->resname[i]);
+ sfree(rt->restype[i]);
+ }
+ sfree(rt->resname);
+ sfree(rt->restype);
+ sfree(rt);
+
+ return 0;
+}
+
+/* Return 0 if the name was found, otherwise -1.
+ * p_restype is set to a pointer to the type name, or 'Other' if we did not find it.
+ */
+int
+gmx_residuetype_get_type(gmx_residuetype_t *rt, const char * resname, const char ** p_restype)
+{
+ int i, rc;
+
+ rc = -1;
+ for (i = 0; i < rt->n && rc; i++)
+ {
+ rc = gmx_strcasecmp(rt->resname[i], resname);
+ }
+
+ *p_restype = (rc == 0) ? rt->restype[i-1] : gmx_residuetype_undefined;
+
+ return rc;
+}
+
+int
+gmx_residuetype_add(gmx_residuetype_t *rt, const char *newresname, const char *newrestype)
+{
+ int found;
+ const char * p_oldtype;
+
+ found = !gmx_residuetype_get_type(rt, newresname, &p_oldtype);
+
+ if (found && gmx_strcasecmp(p_oldtype, newrestype))
+ {
+ fprintf(stderr, "Warning: Residue '%s' already present with type '%s' in database, ignoring new type '%s'.",
+ newresname, p_oldtype, newrestype);
+ }
+
+ if (found == 0)
+ {
+ srenew(rt->resname, rt->n+1);
+ srenew(rt->restype, rt->n+1);
+ rt->resname[rt->n] = gmx_strdup(newresname);
+ rt->restype[rt->n] = gmx_strdup(newrestype);
+ rt->n++;
+ }
+
+ return 0;
+}
+
+int
+gmx_residuetype_get_alltypes(gmx_residuetype_t *rt,
+ const char *** p_typenames,
+ int * ntypes)
+{
+ int i, n;
+ const char ** my_typename;
+
+ n = 0;
+ my_typename = NULL;
+ for (i = 0; i < rt->n; i++)
+ {
+ const char *const p = rt->restype[i];
+ bool bFound = false;
+ for (int j = 0; j < n && !bFound; j++)
+ {
+ assert(my_typename != NULL);
+ bFound = !gmx_strcasecmp(p, my_typename[j]);
+ }
+ if (!bFound)
+ {
+ srenew(my_typename, n+1);
+ my_typename[n] = p;
+ n++;
+ }
+ }
+ *ntypes = n;
+ *p_typenames = my_typename;
+
+ return 0;
+}
+
+gmx_bool
+gmx_residuetype_is_protein(gmx_residuetype_t *rt, const char *resnm)
+{
+ gmx_bool rc;
+ const char *p_type;
+
+ if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
+ gmx_strcasecmp(p_type, "Protein") == 0)
+ {
+ rc = TRUE;
+ }
+ else
+ {
+ rc = FALSE;
+ }
+ return rc;
+}
+
+gmx_bool
+gmx_residuetype_is_dna(gmx_residuetype_t *rt, const char *resnm)
+{
+ gmx_bool rc;
+ const char *p_type;
+
+ if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
+ gmx_strcasecmp(p_type, "DNA") == 0)
+ {
+ rc = TRUE;
+ }
+ else
+ {
+ rc = FALSE;
+ }
+ return rc;
+}
+
+gmx_bool
+gmx_residuetype_is_rna(gmx_residuetype_t *rt, const char *resnm)
+{
+ gmx_bool rc;
+ const char *p_type;
+
+ if (gmx_residuetype_get_type(rt, resnm, &p_type) == 0 &&
+ gmx_strcasecmp(p_type, "RNA") == 0)
+ {
+ rc = TRUE;
+ }
+ else
+ {
+ rc = FALSE;
+ }
+ return rc;
+}
+
+/* Return the size of the arrays */
+int
+gmx_residuetype_get_size(gmx_residuetype_t *rt)
+{
+ return rt->n;
+}
+
+/* Search for a residuetype with name resnm within the
+ * gmx_residuetype database. Return the index if found,
+ * otherwise -1.
+ */
+int
+gmx_residuetype_get_index(gmx_residuetype_t *rt, const char *resnm)
+{
+ int i, rc;
+
+ rc = -1;
+ for (i = 0; i < rt->n && rc; i++)
+ {
+ rc = gmx_strcasecmp(rt->resname[i], resnm);
+ }
+
+ return (0 == rc) ? i-1 : -1;
+}
+
+/* Return the name of the residuetype with the given index, or
+ * NULL if not found. */
+const char *
+gmx_residuetype_get_name(gmx_residuetype_t *rt, int index)
+{
+ if (index >= 0 && index < rt->n)
+ {
+ return rt->resname[index];
+ }
+ else
+ {
+ return NULL;
+ }
+}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _iteratedconstraints_h
-#define _iteratedconstraints_h
+#ifndef GMX_TOPOLOGY_RESIDUETYPES_H
+#define GMX_TOPOLOGY_RESIDUETYPES_H
+
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
-extern "C" {
+extern "C"
+{
#endif
-#if 0
-}
-/* Hack to make automatic indenting work */
-#endif
+typedef struct gmx_residuetype_t gmx_residuetype_t;
-/* Definitions for convergence of iterated constraints */
+int
+gmx_residuetype_init(gmx_residuetype_t **rt);
-/* iterate constraints up to 50 times */
-#define MAXITERCONST 50
+int
+gmx_residuetype_destroy(gmx_residuetype_t *rt);
-/* data type */
-typedef struct
-{
- real f, fprev, x, xprev;
- int iter_i;
- gmx_bool bIterationActive;
- real allrelerr[MAXITERCONST+2];
- int num_close; /* number of "close" violations, caused by limited precision. */
-} gmx_iterate_t;
+int
+gmx_residuetype_get_type(gmx_residuetype_t *rt, const char *resname, const char **p_restype);
+
+int
+gmx_residuetype_add(gmx_residuetype_t *rt, const char *newresname, const char *newrestype);
+
+int
+gmx_residuetype_get_alltypes(gmx_residuetype_t *rt,
+ const char ***p_typenames,
+ int *ntypes);
+
+gmx_bool
+gmx_residuetype_is_protein(gmx_residuetype_t *rt, const char *resnm);
+
+gmx_bool
+gmx_residuetype_is_dna(gmx_residuetype_t *rt, const char *resnm);
+
+gmx_bool
+gmx_residuetype_is_rna(gmx_residuetype_t *rt, const char *resnm);
+
+int
+gmx_residuetype_get_size(gmx_residuetype_t *rt);
-void gmx_iterate_init(gmx_iterate_t *iterate, gmx_bool bIterate);
+int
+gmx_residuetype_get_index(gmx_residuetype_t *rt, const char *resnm);
-gmx_bool done_iterating(const t_commrec *cr, FILE *fplog, int nsteps, gmx_iterate_t *iterate, gmx_bool bFirstIterate, real fom, real *newf);
+const char *
+gmx_residuetype_get_name(gmx_residuetype_t *rt, int index);
#ifdef __cplusplus
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "symtab.h"
#include <stdio.h>
#include <string.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gmx_fatal.h"
+
+#include <algorithm>
+
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "txtdump.h"
-#include "symtab.h"
-#include "macros.h"
#define BUFSIZE 1024
#define TABLESIZE 5
int lookup_symtab(t_symtab *symtab, char **name)
{
- int base, index;
+ int base;
t_symbuf *symbuf;
base = 0;
- index = 0;
symbuf = symtab->symbuf;
while (symbuf != NULL)
{
- index = name-symbuf->buf;
+ const int index = name-symbuf->buf;
if ( ( index >= 0 ) && ( index < symbuf->bufsize ) )
{
return index+base;
if (symbuf->buf[i] == NULL)
{
symtab->nr++;
- symbuf->buf[i] = strdup(name);
+ symbuf->buf[i] = gmx_strdup(name);
return &(symbuf->buf[i]);
}
else if (strcmp(symbuf->buf[i], name) == 0)
symbuf = symbuf->next;
symtab->nr++;
- symbuf->buf[0] = strdup(name);
+ symbuf->buf[0] = gmx_strdup(name);
return &(symbuf->buf[0]);
}
symbuf = symtab->symbuf;
while (symbuf != NULL)
{
- symtab->nr -= min(symbuf->bufsize, symtab->nr);
+ symtab->nr -= std::min(symbuf->bufsize, symtab->nr);
freeptr = symbuf;
symbuf = symbuf->next;
sfree(freeptr);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-#ifndef _symtab_h
-#define _symtab_h
+#ifndef GMX_TOPOLOGY_SYMTAB_H
+#define GMX_TOPOLOGY_SYMTAB_H
#include <stdio.h>
-#include "typedefs.h"
#ifdef __cplusplus
extern "C" {
#endif
+typedef struct t_symbuf
+{
+ int bufsize;
+ char **buf;
+ struct t_symbuf *next;
+} t_symbuf;
+
+typedef struct t_symtab
+{
+ int nr;
+ t_symbuf *symbuf;
+} t_symtab;
+
/*
* This module handles symbol table manipulation. All text strings
* needed by an application are allocated only once. All references
}
#endif
-#endif /* _symtab_h */
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "topology.h"
+
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/smalloc.h"
+
+static void init_groups(gmx_groups_t *groups)
+{
+ groups->ngrpname = 0;
+ groups->grpname = NULL;
+ for (int g = 0; g < egcNR; g++)
+ {
+ groups->grps[g].nm_ind = NULL;
+ groups->ngrpnr[g] = 0;
+ groups->grpnr[g] = NULL;
+ }
+
+}
+
+void init_mtop(gmx_mtop_t *mtop)
+{
+ mtop->name = NULL;
+ mtop->nmoltype = 0;
+ mtop->moltype = NULL;
+ mtop->nmolblock = 0;
+ mtop->molblock = NULL;
+ mtop->maxres_renum = 0;
+ mtop->maxresnr = -1;
+ init_groups(&mtop->groups);
+ init_block(&mtop->mols);
+ open_symtab(&mtop->symtab);
+}
+
+void init_top(t_topology *top)
+{
+ top->name = NULL;
+ init_atom(&(top->atoms));
+ init_atomtypes(&(top->atomtypes));
+ init_block(&top->cgs);
+ init_block(&top->mols);
+ init_blocka(&top->excls);
+ open_symtab(&top->symtab);
+}
+
+
+void done_moltype(gmx_moltype_t *molt)
+{
+ done_atom(&molt->atoms);
+ done_block(&molt->cgs);
+ done_blocka(&molt->excls);
+
+ for (int f = 0; f < F_NRE; f++)
+ {
+ sfree(molt->ilist[f].iatoms);
+ molt->ilist[f].nalloc = 0;
+ }
+}
+
+void done_molblock(gmx_molblock_t *molb)
+{
+ if (molb->nposres_xA > 0)
+ {
+ molb->nposres_xA = 0;
+ sfree(molb->posres_xA);
+ }
+ if (molb->nposres_xB > 0)
+ {
+ molb->nposres_xB = 0;
+ sfree(molb->posres_xB);
+ }
+}
+
+void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab)
+{
+ if (bDoneSymtab)
+ {
+ done_symtab(&mtop->symtab);
+ }
+
+ sfree(mtop->ffparams.functype);
+ sfree(mtop->ffparams.iparams);
+
+ for (int i = 0; i < mtop->nmoltype; i++)
+ {
+ done_moltype(&mtop->moltype[i]);
+ }
+ sfree(mtop->moltype);
+ for (int i = 0; i < mtop->nmolblock; i++)
+ {
+ done_molblock(&mtop->molblock[i]);
+ }
+ sfree(mtop->molblock);
+ done_block(&mtop->mols);
+}
+
+void done_top(t_topology *top)
+{
+ sfree(top->idef.functype);
+ sfree(top->idef.iparams);
+ for (int f = 0; f < F_NRE; ++f)
+ {
+ sfree(top->idef.il[f].iatoms);
+ top->idef.il[f].iatoms = NULL;
+ top->idef.il[f].nalloc = 0;
+ }
+
+ done_atom(&(top->atoms));
+
+ /* For GB */
+ done_atomtypes(&(top->atomtypes));
+
+ done_symtab(&(top->symtab));
+ done_block(&(top->cgs));
+ done_block(&(top->mols));
+ done_blocka(&(top->excls));
+}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef GMX_LEGACYHEADERS_TOPOLOGY_H
-#define GMX_LEGACYHEADERS_TOPOLOGY_H
+#ifndef GMX_TOPOLOGY_TOPOLOGY_H
+#define GMX_TOPOLOGY_TOPOLOGY_H
-#include "atoms.h"
-#include "idef.h"
-#include "block.h"
-#include "simple.h"
-#include "symtab.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/symtab.h"
#ifdef __cplusplus
extern "C" {
egcNR
};
-typedef struct {
+typedef struct gmx_moltype_t
+{
char **name; /* Name of the molecule type */
t_atoms atoms; /* The atoms */
t_ilist ilist[F_NRE];
t_blocka excls; /* The exclusions */
} gmx_moltype_t;
-typedef struct {
+typedef struct gmx_molblock_t
+{
int type; /* The molcule type index in mtop.moltype */
int nmol; /* The number of molecules in this block */
int natoms_mol; /* The number of atoms in one molecule */
rvec *posres_xB; /* The posres coords for top B */
} gmx_molblock_t;
-typedef struct {
+typedef struct gmx_groups_t
+{
t_grps grps[egcNR]; /* Groups of things */
int ngrpname; /* Number of groupnames */
char ***grpname; /* Names of the groups */
/* The global, complete system topology struct, based on molecule types.
This structure should contain no data that is O(natoms) in memory. */
-typedef struct {
+typedef struct gmx_mtop_t
+{
char **name; /* Name of the topology */
gmx_ffparams_t ffparams;
int nmoltype;
} gmx_mtop_t;
/* The mdrun node-local topology struct, completely written out */
-typedef struct {
- t_idef idef; /* The interaction function definition */
+typedef struct gmx_localtop_t
+{
+ t_idef idef; /* The interaction function definition */
t_atomtypes atomtypes; /* Atomtype properties */
t_block cgs; /* The charge groups */
t_blocka excls; /* The exclusions */
} gmx_localtop_t;
/* The old topology struct, completely written out, used in analysis tools */
-typedef struct {
+typedef struct t_topology
+{
char **name; /* Name of the topology */
- t_idef idef; /* The interaction function definition */
+ t_idef idef; /* The interaction function definition */
t_atoms atoms; /* The atoms */
t_atomtypes atomtypes; /* Atomtype properties */
t_block cgs; /* The charge groups */
t_symtab symtab; /* The symbol table */
} t_topology;
+void init_mtop(gmx_mtop_t *mtop);
+void init_top(t_topology *top);
+void done_moltype(gmx_moltype_t *molt);
+void done_molblock(gmx_molblock_t *molb);
+void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab);
+void done_top(t_topology *top);
+
+t_atoms *mtop2atoms(gmx_mtop_t *mtop);
+/* generate a t_atoms struct for the system from gmx_mtop_t */
+
#ifdef __cplusplus
}
#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "typedefs.h"
#include "topsort.h"
+
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/types/ifunc.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
static gmx_bool ip_pert(int ftype, const t_iparams *ip)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2008,2009,2010,2013, by the GROMACS development team, led by
+ * Copyright (c) 2008,2009,2010,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _topsort_h
-#define _topsort_h
+#ifndef GMX_TOPOLOGY_TOPSORT_H
+#define GMX_TOPOLOGY_TOPSORT_H
-
-#include "typedefs.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
#ifdef __cplusplus
extern "C" {
#endif
+struct gmx_mtop_t;
+struct t_idef;
/* Returns if there are perturbed bonded interactions */
-gmx_bool gmx_mtop_bondeds_free_energy(const gmx_mtop_t *mtop);
+gmx_bool gmx_mtop_bondeds_free_energy(const struct gmx_mtop_t *mtop);
/* Sort all the bonded ilists in idef to have the perturbed ones at the end
* and set nr_nr_nonperturbed in ilist.
*/
-void gmx_sort_ilist_fe(t_idef *idef, const real *qA, const real *qB);
+void gmx_sort_ilist_fe(struct t_idef *idef, const real *qA, const real *qB);
#ifdef __cplusplus
}
* analysis module at appropriate points to perform the module-specific tasks.
* The analysis module is responsible for creating and managing
* gmx::AnalysisData objects, and the chart shows the most important
- * interactions with this module as well. Interactions with options (for
- * command-line option processing) and selections is not shown for brevity: see
- * \ref module_options for an overview of how options work, and the second
- * chart for a more detailed view of how selections are accessed from an
- * analysis module.
+ * interactions with this module as well. However, the runner takes
+ * responsibility of calling gmx::AnalysisData::finishFrameSerial().
+ * Interactions with options (for command-line option processing) and
+ * selections is not shown for brevity: see \ref module_options for an overview
+ * of how options work, and the second chart for a more detailed view of how
+ * selections are accessed from an analysis module.
* \msc
* runner,
* module [ URL="\ref gmx::TrajectoryAnalysisModule" ],
* URL="\ref gmx::AnalysisDataHandle" ];
* module => data [ label="finishFrame()",
* URL="\ref gmx::AnalysisDataHandle::finishFrame()" ];
- * data => data [ label="process frame 0" ];
+ * runner => data [ label="finishFrameSerial()",
+ * URL="\ref gmx::AnalysisData::finishFrameSerial()" ];
* runner => runner [ label="read and initialize frame 1" ];
* runner => module [ label="analyzeFrame(1)",
* URL="\ref gmx::TrajectoryAnalysisModule::analyzeFrame()" ];
* together with the appropriate thread-local data object.
* The gmx::TrajectoryAnalysisModule::analyzeFrame() calls are only allowed to modify
* the thread-local data object; everything else is read-only. For any output,
- * they pass the information to gmx::AnalysisData, which takes care of ordering
- * the data from different frames such that it gets processed in the right
- * order.
+ * they pass the information to gmx::AnalysisData, which together with the
+ * runner takes care of ordering the data from different frames such that it
+ * gets processed in the right order.
* When all frames are analyzed, gmx::TrajectoryAnalysisModule::finishFrames()
* is called for each thread-local data object to destroy them and to
* accumulate possible results from them into the main
* URL="\ref gmx::TrajectoryAnalysisModule::analyzeFrame()" ];
* thread1 => data [ label="finishFrame(0)",
* URL="\ref gmx::AnalysisDataHandle::finishFrame()" ];
- * data => data [ label="process frame 0" ];
- * data => data [ label="process frame 1" ];
* runner << thread1 [ label="analyzeFrame() (frame 0)" ];
+ * runner => data [ label="finishFrameSerial() (frame 0)",
+ * URL="\ref gmx::AnalysisData::finishFrameSerial()" ];
+ * runner => data [ label="finishFrameSerial() (frame 1)",
+ * URL="\ref gmx::AnalysisData::finishFrameSerial()" ];
* ...;
* runner => thread1 [ label="finishFrames(pdata1)",
* URL="\ref gmx::TrajectoryAnalysisModule::finishFrames()" ];
#ifndef GMX_TRAJECTORYANALYSIS_H
#define GMX_TRAJECTORYANALYSIS_H
-#include "analysisdata.h"
-#include "options.h"
-#include "selection.h"
-
-#include "selection/nbsearch.h"
-#include "trajectoryanalysis/analysismodule.h"
-#include "trajectoryanalysis/analysissettings.h"
-#include "trajectoryanalysis/cmdlinerunner.h"
-#include "utility/arrayref.h"
-#include "utility/exceptions.h"
+#include "gromacs/analysisdata.h"
+#include "gromacs/options.h"
+#include "gromacs/selection.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/selection/nbsearch.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysissettings.h"
+#include "gromacs/trajectoryanalysis/cmdlinerunner.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/exceptions.h"
#endif
file(GLOB TRAJECTORYANALYSIS_SOURCES *.cpp modules/*.cpp modules/*.c)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TRAJECTORYANALYSIS_SOURCES} PARENT_SCOPE)
-set(TRAJECTORYANALYSIS_PUBLIC_HEADERS
+gmx_install_headers(
analysismodule.h
analysissettings.h
- cmdlinerunner.h)
-gmx_install_headers(trajectoryanalysis ${TRAJECTORYANALYSIS_PUBLIC_HEADERS})
+ cmdlinerunner.h
+ )
if (BUILD_TESTING)
add_subdirectory(tests)
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
-#include "gromacs/trajectoryanalysis/analysismodule.h"
+#include "gmxpre.h"
+
+#include "analysismodule.h"
#include <utility>
}
-void TrajectoryAnalysisModule::initAfterFirstFrame(const t_trxframe & /*fr*/)
+void TrajectoryAnalysisModule::initAfterFirstFrame(
+ const TrajectoryAnalysisSettings & /*settings*/,
+ const t_trxframe & /*fr*/)
{
}
impl_->analysisDatasets_[name] = data;
}
+
+void TrajectoryAnalysisModule::finishFrameSerial(int frameIndex)
+{
+ Impl::AnalysisDatasetContainer::const_iterator data;
+ for (data = impl_->analysisDatasets_.begin();
+ data != impl_->analysisDatasets_.end();
+ ++data)
+ {
+ data->second->finishFrameSerial(frameIndex);
+ }
+}
+
} // namespace gmx
#include <string>
#include <vector>
-#include "../legacyheaders/typedefs.h"
+#include <boost/shared_ptr.hpp>
-#include "../selection/selection.h" // For gmx::SelectionList
-#include "../utility/common.h"
-#include "../utility/uniqueptr.h"
+#include "gromacs/selection/selection.h" // For gmx::SelectionList
+#include "gromacs/utility/classhelpers.h"
+
+struct t_pbc;
+struct t_trxframe;
namespace gmx
{
};
//! Smart pointer to manage a TrajectoryAnalysisModuleData object.
-typedef gmx_unique_ptr<TrajectoryAnalysisModuleData>::type
+typedef boost::shared_ptr<TrajectoryAnalysisModuleData>
TrajectoryAnalysisModuleDataPointer;
/*! \brief
*
* The default implementation does nothing.
*/
- virtual void initAfterFirstFrame(const t_trxframe &fr);
+ virtual void initAfterFirstFrame(const TrajectoryAnalysisSettings &settings,
+ const t_trxframe &fr);
/*! \brief
* Starts the analysis of frames.
* care about external modifications.
*/
AbstractAnalysisData &datasetFromName(const char *name) const;
+ /*! \brief
+ * Processes data in AnalysisData objects in serial for each frame.
+ *
+ * \param[in] frameIndex Index of the frame that has been finished.
+ *
+ * This method is called by the framework in order for each frame,
+ * after the analysis for that frame has been finished. These calls
+ * always execute in serial and in sequential frame order, even during
+ * parallel analysis where multiple analyzeFrame() calls may be
+ * executing concurrently.
+ *
+ * \see AnalysisData::finishFrameSerial()
+ */
+ void finishFrameSerial(int frameIndex);
protected:
/*! \brief
};
//! Smart pointer to manage a TrajectoryAnalysisModule.
-typedef gmx_unique_ptr<TrajectoryAnalysisModule>::type
+typedef boost::shared_ptr<TrajectoryAnalysisModule>
TrajectoryAnalysisModulePointer;
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_IMPL_H
#define GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_IMPL_H
-#include "analysissettings.h"
-
-#include "../analysisdata/modules/plot.h"
-#include "../options/timeunitmanager.h"
+#include "gromacs/analysisdata/modules/plot.h"
+#include "gromacs/options/timeunitmanager.h"
+#include "gromacs/trajectoryanalysis/analysissettings.h"
namespace gmx
{
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
-#include "analysissettings.h"
+#include "gmxpre.h"
-#include "gromacs/legacyheaders/vec.h"
+#include "analysissettings.h"
#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/smalloc.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_H
#define GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_H
-#include "../legacyheaders/typedefs.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/options/timeunitmanager.h"
+#include "gromacs/utility/classhelpers.h"
-#include "../options/timeunitmanager.h"
-#include "../utility/common.h"
+struct t_topology;
namespace gmx
{
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
-#include "cmdlinerunner.h"
-
-#ifdef HAVE_CONFIG_H
-#include "config.h"
-#endif
+#include "gmxpre.h"
-#include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/rmpbc.h"
+#include "cmdlinerunner.h"
#include "gromacs/analysisdata/paralleloptions.h"
#include "gromacs/commandline/cmdlinehelpcontext.h"
#include "gromacs/commandline/cmdlinemodule.h"
#include "gromacs/commandline/cmdlinemodulemanager.h"
#include "gromacs/commandline/cmdlineparser.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/options/filenameoptionmanager.h"
#include "gromacs/options/options.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/selectioncollection.h"
#include "gromacs/selection/selectionoptionmanager.h"
#include "gromacs/trajectoryanalysis/analysismodule.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
-#include "gromacs/trajectoryanalysis/runnercommon.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/file.h"
#include "gromacs/utility/gmxassert.h"
+#include "runnercommon.h"
+
namespace gmx
{
SelectionCollection *selections,
int *argc, char *argv[])
{
- Options options(NULL, NULL);
- Options moduleOptions(module_->name(), module_->description());
- Options commonOptions("common", "Common analysis control");
- Options selectionOptions("selection", "Common selection control");
- module_->initOptions(&moduleOptions, settings);
- common->initOptions(&commonOptions);
- selections->initOptions(&selectionOptions);
+ FileNameOptionManager fileoptManager;
+ SelectionOptionManager seloptManager(selections);
+ Options options(NULL, NULL);
+ Options moduleOptions(module_->name(), module_->description());
+ Options commonOptions("common", "Common analysis control");
+ Options selectionOptions("selection", "Common selection control");
+ options.addManager(&fileoptManager);
+ options.addManager(&seloptManager);
options.addSubSection(&commonOptions);
options.addSubSection(&selectionOptions);
options.addSubSection(&moduleOptions);
- SelectionOptionManager seloptManager(selections);
- setManagerForSelectionOptions(&options, &seloptManager);
+ module_->initOptions(&moduleOptions, settings);
+ common->initOptions(&commonOptions);
+ selections->initOptions(&selectionOptions);
{
CommandLineParser parser(&options);
// Load first frame.
common.initFirstFrame();
- module->initAfterFirstFrame(common.frame());
+ module->initAfterFirstFrame(settings, common.frame());
t_pbc pbc;
t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
selections.evaluate(&frame, ppbc);
module->analyzeFrame(nframes, frame, ppbc, pdata.get());
+ module->finishFrameSerial(nframes);
- nframes++;
+ ++nframes;
}
while (common.readNextFrame());
module->finishFrames(pdata.get());
TrajectoryAnalysisSettings settings;
TrajectoryAnalysisRunnerCommon common(&settings);
- Options options(NULL, NULL);
- Options moduleOptions(impl_->module_->name(), impl_->module_->description());
- Options commonOptions("common", "Common analysis control");
- Options selectionOptions("selection", "Common selection control");
-
- impl_->module_->initOptions(&moduleOptions, &settings);
- common.initOptions(&commonOptions);
- selections.initOptions(&selectionOptions);
+ SelectionOptionManager seloptManager(&selections);
+ Options options(NULL, NULL);
+ Options moduleOptions(impl_->module_->name(), impl_->module_->description());
+ Options commonOptions("common", "Common analysis control");
+ Options selectionOptions("selection", "Common selection control");
+ options.addManager(&seloptManager);
options.addSubSection(&commonOptions);
options.addSubSection(&selectionOptions);
options.addSubSection(&moduleOptions);
- SelectionOptionManager seloptManager(&selections);
- setManagerForSelectionOptions(&options, &seloptManager);
+ impl_->module_->initOptions(&moduleOptions, &settings);
+ common.initOptions(&commonOptions);
+ selections.initOptions(&selectionOptions);
CommandLineHelpWriter(options)
.setShowDescriptions(true)
virtual const char *name() const { return name_; }
virtual const char *shortDescription() const { return description_; };
+ virtual void init(CommandLineModuleSettings *settings);
virtual int run(int argc, char *argv[]);
virtual void writeHelp(const CommandLineHelpContext &context) const;
GMX_DISALLOW_COPY_AND_ASSIGN(RunnerCommandLineModule);
};
+void TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::init(
+ CommandLineModuleSettings * /*settings*/)
+{
+}
+
int TrajectoryAnalysisCommandLineRunner::Impl::RunnerCommandLineModule::run(
int argc, char *argv[])
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TRAJECTORYANALYSIS_CMDLINERUNNER_H
#define GMX_TRAJECTORYANALYSIS_CMDLINERUNNER_H
-#include "analysismodule.h"
-#include "../utility/common.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
-#include "gromacs/trajectoryanalysis/modules.h"
+#include "gmxpre.h"
+
+#include "modules.h"
#include "gromacs/commandline/cmdlinemodulemanager.h"
#include "gromacs/trajectoryanalysis/cmdlinerunner.h"
#include "modules/angle.h"
#include "modules/distance.h"
#include "modules/freevolume.h"
+#include "modules/pairdist.h"
+#include "modules/rdf.h"
#include "modules/sasa.h"
#include "modules/select.h"
registerModule<AngleInfo>(manager, group);
registerModule<DistanceInfo>(manager, group);
registerModule<FreeVolumeInfo>(manager, group);
+ registerModule<PairDistanceInfo>(manager, group);
+ registerModule<RdfInfo>(manager, group);
registerModule<SasaInfo>(manager, group);
registerModule<SelectInfo>(manager, group);
}
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
+#include "gmxpre.h"
+
#include "angle.h"
#include <algorithm>
#include <string>
#include <vector>
-#include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/vec.h"
-
#include "gromacs/analysisdata/analysisdata.h"
#include "gromacs/analysisdata/modules/average.h"
#include "gromacs/analysisdata/modules/histogram.h"
#include "gromacs/analysisdata/modules/plot.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/math/vec.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/options/options.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/selection.h"
#include "gromacs/selection/selectionoption.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
{
public:
Angle();
- virtual ~Angle();
virtual void initOptions(Options *options,
TrajectoryAnalysisSettings *settings);
std::vector<int> angleCount_;
int natoms1_;
int natoms2_;
- // TODO: It is not possible to put rvec into a container.
- std::vector<rvec *> vt0_;
+ std::vector<std::vector<RVec> > vt0_;
// Copy and assign disallowed by base.
};
}
-Angle::~Angle()
-{
- for (size_t g = 0; g < vt0_.size(); ++g)
- {
- delete [] vt0_[g];
- }
-}
-
-
void
Angle::initOptions(Options *options, TrajectoryAnalysisSettings * /*settings*/)
{
vt0_.resize(sel1_.size());
for (size_t g = 0; g < sel1_.size(); ++g)
{
- vt0_[g] = new rvec[sel1_[g].posCount() / natoms1_];
+ vt0_[g].resize(sel1_[g].posCount() / natoms1_);
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TRAJECTORYANALYSIS_MODULES_ANGLE_H
#define GMX_TRAJECTORYANALYSIS_MODULES_ANGLE_H
-#include "../analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
namespace gmx
{
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
+#include "gmxpre.h"
+
#include "distance.h"
#include <string>
-#include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/vec.h"
-
#include "gromacs/analysisdata/analysisdata.h"
#include "gromacs/analysisdata/modules/average.h"
#include "gromacs/analysisdata/modules/histogram.h"
#include "gromacs/analysisdata/modules/plot.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/math/vec.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/options/options.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/selection.h"
#include "gromacs/selection/selectionoption.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
"The location of the histogram is set with [TT]-len[tt] and",
"[TT]-tol[tt]. Bin width is set with [TT]-binw[tt].",
"[TT]-oallstat[tt] writes out the average and standard deviation for",
- "each individual distance, calculated over the frames."
+ "each individual distance, calculated over the frames.[PAR]",
+ "Note that [THISMODULE] calculates distances between fixed pairs",
+ "(1-2, 3-4, etc.) within a single selection. To calculate distances",
+ "between two selections, including minimum, maximum, and pairwise",
+ "distances, use [gmx-pairdist]."
};
options->setDescription(desc);
printf("%s:\n", sel->name());
printf(" Number of samples: %d\n",
summaryStatsModule_->sampleCount(index, 0));
- printf(" Average distance: %-6.3f nm\n",
+ printf(" Average distance: %-8.5f nm\n",
summaryStatsModule_->average(index, 0));
- printf(" Standard deviation: %-6.3f nm\n",
+ printf(" Standard deviation: %-8.5f nm\n",
summaryStatsModule_->standardDeviation(index, 0));
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TRAJECTORYANALYSIS_MODULES_DISTANCE_H
#define GMX_TRAJECTORYANALYSIS_MODULES_DISTANCE_H
-#include "../analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
namespace gmx
{
* \author David van der Spoel <david.vanderspoel@icm.uu.se>
* \ingroup module_trajectoryanalysis
*/
+#include "gmxpre.h"
+
#include "freevolume.h"
#include <string>
-#include "gromacs/legacyheaders/atomprop.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/random/random.h"
-#include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/vec.h"
-
#include "gromacs/analysisdata/analysisdata.h"
#include "gromacs/analysisdata/modules/average.h"
#include "gromacs/analysisdata/modules/plot.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/math/vec.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/options/options.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/random/random.h"
#include "gromacs/selection/nbsearch.h"
#include "gromacs/selection/selection.h"
#include "gromacs/selection/selectionoption.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TRAJECTORYANALYSIS_MODULES_FREEVOLUME_H
#define GMX_TRAJECTORYANALYSIS_MODULES_FREEVOLUME_H
-#include "../analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
namespace gmx
{
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2007, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <stdio.h>
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
-#include <stdarg.h>
-/* Modified DvdS */
-#include "pbc.h"
-#include "macros.h"
-#include "vec.h"
-#include "gromacs/utility/smalloc.h"
-#include "nsc.h"
-
-#define TEST_NSC 0
-
-#define TEST_ARC 0
-#define TEST_DOD 0
-#define TEST_CUBE 0
-
-#define UNSP_ICO_DOD 9
-#define UNSP_ICO_ARC 10
-
-real *xpunsp = NULL;
-real del_cube;
-int n_dot, ico_cube, last_n_dot = 0, last_densit = 0, last_unsp = 0;
-int last_cubus = 0;
-
-#define FOURPI (4.*M_PI)
-#define TORAD(A) ((A)*0.017453293)
-#define DP_TOL 0.001
-
-#define UPDATE_FL __file__ = __FILE__, __line__ = __LINE__
-const char * __file__; /* declared versions of macros */
-int __line__; /* __FILE__ and __LINE__ */
-
-#ifdef ERROR
-#undef ERROR
-#endif
-#define ERROR UPDATE_FL, error
-void error(const char *fmt, ...)
-{
- va_list args;
- fprintf(stderr,
- "\n---> ERROR when executing line %i in file %s !\n",
- __line__, __file__);
- va_start(args, fmt);
- vfprintf(stderr, fmt, args);
- va_end(args);
- fprintf(stderr, "\n---> Execution stopped !\n\n");
-}
-
-#define WARNING UPDATE_FL, warning2
-void warning2(const char *fmt, ...)
-{
- va_list args;
- fprintf(stderr,
- "\n---> WARNING : line %i in file %s\n",
- __line__, __file__);
- va_start(args, fmt);
- vfprintf(stderr, fmt, args);
- va_end(args);
- fprintf(stderr, " ...!\n\n");
- fflush(stderr);
- fflush(stdout);
-}
-
-#define ASIN safe_asin
-real safe_asin(real f)
-{
- if ( (fabs(f) < 1.00) )
- {
- return( asin(f) );
- }
- if ( (fabs(f) - 1.00) <= DP_TOL)
- {
- ERROR("ASIN : invalid argument %f", f);
- }
- return(M_PI_2);
-}
-
-
-
-
-/* routines for dot distributions on the surface of the unit sphere */
-real rg, rh;
-
-void icosaeder_vertices(real *xus)
-{
- rh = sqrt(1.-2.*cos(TORAD(72.)))/(1.-cos(TORAD(72.)));
- rg = cos(TORAD(72.))/(1.-cos(TORAD(72.)));
- /* icosaeder vertices */
- xus[ 0] = 0.; xus[ 1] = 0.; xus[ 2] = 1.;
- xus[ 3] = rh*cos(TORAD(72.)); xus[ 4] = rh*sin(TORAD(72.)); xus[ 5] = rg;
- xus[ 6] = rh*cos(TORAD(144.)); xus[ 7] = rh*sin(TORAD(144.)); xus[ 8] = rg;
- xus[ 9] = rh*cos(TORAD(216.)); xus[10] = rh*sin(TORAD(216.)); xus[11] = rg;
- xus[12] = rh*cos(TORAD(288.)); xus[13] = rh*sin(TORAD(288.)); xus[14] = rg;
- xus[15] = rh; xus[16] = 0; xus[17] = rg;
- xus[18] = rh*cos(TORAD(36.)); xus[19] = rh*sin(TORAD(36.)); xus[20] = -rg;
- xus[21] = rh*cos(TORAD(108.)); xus[22] = rh*sin(TORAD(108.)); xus[23] = -rg;
- xus[24] = -rh; xus[25] = 0; xus[26] = -rg;
- xus[27] = rh*cos(TORAD(252.)); xus[28] = rh*sin(TORAD(252.)); xus[29] = -rg;
- xus[30] = rh*cos(TORAD(324.)); xus[31] = rh*sin(TORAD(324.)); xus[32] = -rg;
- xus[33] = 0.; xus[34] = 0.; xus[35] = -1.;
-}
-
-
-void divarc(real x1, real y1, real z1,
- real x2, real y2, real z2,
- int div1, int div2, real *xr, real *yr, real *zr)
-{
-
- real xd, yd, zd, dd, d1, d2, s, x, y, z;
- real phi, sphi, cphi;
-
- xd = y1*z2-y2*z1;
- yd = z1*x2-z2*x1;
- zd = x1*y2-x2*y1;
- dd = sqrt(xd*xd+yd*yd+zd*zd);
- if (dd < DP_TOL)
- {
- ERROR("divarc: rotation axis of length %f", dd);
- }
-
- d1 = x1*x1+y1*y1+z1*z1;
- if (d1 < 0.5)
- {
- ERROR("divarc: vector 1 of sq.length %f", d1);
- }
- d2 = x2*x2+y2*y2+z2*z2;
- if (d2 < 0.5)
- {
- ERROR("divarc: vector 2 of sq.length %f", d2);
- }
-
- phi = ASIN(dd/sqrt(d1*d2));
- phi = phi*((real)div1)/((real)div2);
- sphi = sin(phi); cphi = cos(phi);
- s = (x1*xd+y1*yd+z1*zd)/dd;
-
- x = xd*s*(1.-cphi)/dd + x1 * cphi + (yd*z1-y1*zd)*sphi/dd;
- y = yd*s*(1.-cphi)/dd + y1 * cphi + (zd*x1-z1*xd)*sphi/dd;
- z = zd*s*(1.-cphi)/dd + z1 * cphi + (xd*y1-x1*yd)*sphi/dd;
- dd = sqrt(x*x+y*y+z*z);
- *xr = x/dd; *yr = y/dd; *zr = z/dd;
-}
-
-int ico_dot_arc(int densit) /* densit...required dots per unit sphere */
-{
- /* dot distribution on a unit sphere based on an icosaeder *
- * great circle average refining of icosahedral face */
-
- int i, j, k, tl, tl2, tn, tess;
- real a, d, x, y, z, x2, y2, z2, x3, y3, z3;
- real xij, yij, zij, xji, yji, zji, xik, yik, zik, xki, yki, zki,
- xjk, yjk, zjk, xkj, ykj, zkj;
- real *xus = NULL;
-
- /* calculate tessalation level */
- a = sqrt((((real) densit)-2.)/10.);
- tess = (int) ceil(a);
- n_dot = 10*tess*tess+2;
- if (n_dot < densit)
- {
- ERROR("ico_dot_arc: error in formula for tessalation level (%d->%d, %d)",
- tess, n_dot, densit);
- }
-
- snew(xus, 3*n_dot);
- xpunsp = xus;
- icosaeder_vertices(xus);
-
- if (tess > 1)
- {
- tn = 12;
- a = rh*rh*2.*(1.-cos(TORAD(72.)));
- /* calculate tessalation of icosaeder edges */
- for (i = 0; i < 11; i++)
- {
- for (j = i+1; j < 12; j++)
- {
- x = xus[3*i]-xus[3*j];
- y = xus[1+3*i]-xus[1+3*j]; z = xus[2+3*i]-xus[2+3*j];
- d = x*x+y*y+z*z;
- if (fabs(a-d) > DP_TOL)
- {
- continue;
- }
- for (tl = 1; tl < tess; tl++)
- {
- if (tn >= n_dot)
- {
- ERROR("ico_dot: tn exceeds dimension of xus");
- }
- divarc(xus[3*i], xus[1+3*i], xus[2+3*i],
- xus[3*j], xus[1+3*j], xus[2+3*j],
- tl, tess, &xus[3*tn], &xus[1+3*tn], &xus[2+3*tn]);
- tn++;
- }
- }
- }
- /* calculate tessalation of icosaeder faces */
- for (i = 0; i < 10; i++)
- {
- for (j = i+1; j < 11; j++)
- {
- x = xus[3*i]-xus[3*j];
- y = xus[1+3*i]-xus[1+3*j]; z = xus[2+3*i]-xus[2+3*j];
- d = x*x+y*y+z*z;
- if (fabs(a-d) > DP_TOL)
- {
- continue;
- }
-
- for (k = j+1; k < 12; k++)
- {
- x = xus[3*i]-xus[3*k];
- y = xus[1+3*i]-xus[1+3*k]; z = xus[2+3*i]-xus[2+3*k];
- d = x*x+y*y+z*z;
- if (fabs(a-d) > DP_TOL)
- {
- continue;
- }
- x = xus[3*j]-xus[3*k];
- y = xus[1+3*j]-xus[1+3*k]; z = xus[2+3*j]-xus[2+3*k];
- d = x*x+y*y+z*z;
- if (fabs(a-d) > DP_TOL)
- {
- continue;
- }
- for (tl = 1; tl < tess-1; tl++)
- {
- divarc(xus[3*j], xus[1+3*j], xus[2+3*j],
- xus[3*i], xus[1+3*i], xus[2+3*i],
- tl, tess, &xji, &yji, &zji);
- divarc(xus[3*k], xus[1+3*k], xus[2+3*k],
- xus[3*i], xus[1+3*i], xus[2+3*i],
- tl, tess, &xki, &yki, &zki);
-
- for (tl2 = 1; tl2 < tess-tl; tl2++)
- {
- divarc(xus[3*i], xus[1+3*i], xus[2+3*i],
- xus[3*j], xus[1+3*j], xus[2+3*j],
- tl2, tess, &xij, &yij, &zij);
- divarc(xus[3*k], xus[1+3*k], xus[2+3*k],
- xus[3*j], xus[1+3*j], xus[2+3*j],
- tl2, tess, &xkj, &ykj, &zkj);
- divarc(xus[3*i], xus[1+3*i], xus[2+3*i],
- xus[3*k], xus[1+3*k], xus[2+3*k],
- tess-tl-tl2, tess, &xik, &yik, &zik);
- divarc(xus[3*j], xus[1+3*j], xus[2+3*j],
- xus[3*k], xus[1+3*k], xus[2+3*k],
- tess-tl-tl2, tess, &xjk, &yjk, &zjk);
- if (tn >= n_dot)
- {
- ERROR("ico_dot: tn exceeds dimension of xus");
- }
- divarc(xki, yki, zki, xji, yji, zji, tl2, tess-tl,
- &x, &y, &z);
- divarc(xkj, ykj, zkj, xij, yij, zij, tl, tess-tl2,
- &x2, &y2, &z2);
- divarc(xjk, yjk, zjk, xik, yik, zik, tl, tl+tl2,
- &x3, &y3, &z3);
- x = x+x2+x3; y = y+y2+y3; z = z+z2+z3;
- d = sqrt(x*x+y*y+z*z);
- xus[3*tn] = x/d;
- xus[1+3*tn] = y/d;
- xus[2+3*tn] = z/d;
- tn++;
- } /* cycle tl2 */
- } /* cycle tl */
- } /* cycle k */
- } /* cycle j */
- } /* cycle i */
- if (n_dot != tn)
- {
- ERROR("ico_dot: n_dot(%d) and tn(%d) differ", n_dot, tn);
- }
- } /* end of if (tess > 1) */
-
- return n_dot;
-} /* end of routine ico_dot_arc */
-
-int ico_dot_dod(int densit) /* densit...required dots per unit sphere */
-{
- /* dot distribution on a unit sphere based on an icosaeder *
- * great circle average refining of icosahedral face */
-
- int i, j, k, tl, tl2, tn, tess, j1, j2;
- real a, d, x, y, z, x2, y2, z2, x3, y3, z3, ai_d, adod;
- real xij, yij, zij, xji, yji, zji, xik, yik, zik, xki, yki, zki,
- xjk, yjk, zjk, xkj, ykj, zkj;
- real *xus = NULL;
- /* calculate tesselation level */
- a = sqrt((((real) densit)-2.)/30.);
- tess = max((int) ceil(a), 1);
- n_dot = 30*tess*tess+2;
- if (n_dot < densit)
- {
- ERROR("ico_dot_dod: error in formula for tessalation level (%d->%d, %d)",
- tess, n_dot, densit);
- }
-
- snew(xus, 3*n_dot);
- xpunsp = xus;
- icosaeder_vertices(xus);
-
- tn = 12;
- /* square of the edge of an icosaeder */
- a = rh*rh*2.*(1.-cos(TORAD(72.)));
- /* dodecaeder vertices */
- for (i = 0; i < 10; i++)
- {
- for (j = i+1; j < 11; j++)
- {
- x = xus[3*i]-xus[3*j];
- y = xus[1+3*i]-xus[1+3*j]; z = xus[2+3*i]-xus[2+3*j];
- d = x*x+y*y+z*z;
- if (fabs(a-d) > DP_TOL)
- {
- continue;
- }
- for (k = j+1; k < 12; k++)
- {
- x = xus[3*i]-xus[3*k];
- y = xus[1+3*i]-xus[1+3*k]; z = xus[2+3*i]-xus[2+3*k];
- d = x*x+y*y+z*z;
- if (fabs(a-d) > DP_TOL)
- {
- continue;
- }
- x = xus[3*j]-xus[3*k];
- y = xus[1+3*j]-xus[1+3*k]; z = xus[2+3*j]-xus[2+3*k];
- d = x*x+y*y+z*z;
- if (fabs(a-d) > DP_TOL)
- {
- continue;
- }
- x = xus[ 3*i]+xus[ 3*j]+xus[ 3*k];
- y = xus[1+3*i]+xus[1+3*j]+xus[1+3*k];
- z = xus[2+3*i]+xus[2+3*j]+xus[2+3*k];
- d = sqrt(x*x+y*y+z*z);
- xus[3*tn] = x/d; xus[1+3*tn] = y/d; xus[2+3*tn] = z/d;
- tn++;
- }
- }
- }
-
- if (tess > 1)
- {
- tn = 32;
- /* square of the edge of an dodecaeder */
- adod = 4.*(cos(TORAD(108.))-cos(TORAD(120.)))/(1.-cos(TORAD(120.)));
- /* square of the distance of two adjacent vertices of ico- and dodecaeder */
- ai_d = 2.*(1.-sqrt(1.-a/3.));
-
- /* calculate tessalation of mixed edges */
- for (i = 0; i < 31; i++)
- {
- j1 = 12; j2 = 32; a = ai_d;
- if (i >= 12)
- {
- j1 = i+1; a = adod;
- }
- for (j = j1; j < j2; j++)
- {
- x = xus[3*i]-xus[3*j];
- y = xus[1+3*i]-xus[1+3*j]; z = xus[2+3*i]-xus[2+3*j];
- d = x*x+y*y+z*z;
- if (fabs(a-d) > DP_TOL)
- {
- continue;
- }
- for (tl = 1; tl < tess; tl++)
- {
- if (tn >= n_dot)
- {
- ERROR("ico_dot: tn exceeds dimension of xus");
- }
- divarc(xus[3*i], xus[1+3*i], xus[2+3*i],
- xus[3*j], xus[1+3*j], xus[2+3*j],
- tl, tess, &xus[3*tn], &xus[1+3*tn], &xus[2+3*tn]);
- tn++;
- }
- }
- }
- /* calculate tessalation of pentakisdodecahedron faces */
- for (i = 0; i < 12; i++)
- {
- for (j = 12; j < 31; j++)
- {
- x = xus[3*i]-xus[3*j];
- y = xus[1+3*i]-xus[1+3*j]; z = xus[2+3*i]-xus[2+3*j];
- d = x*x+y*y+z*z;
- if (fabs(ai_d-d) > DP_TOL)
- {
- continue;
- }
-
- for (k = j+1; k < 32; k++)
- {
- x = xus[3*i]-xus[3*k];
- y = xus[1+3*i]-xus[1+3*k]; z = xus[2+3*i]-xus[2+3*k];
- d = x*x+y*y+z*z;
- if (fabs(ai_d-d) > DP_TOL)
- {
- continue;
- }
- x = xus[3*j]-xus[3*k];
- y = xus[1+3*j]-xus[1+3*k]; z = xus[2+3*j]-xus[2+3*k];
- d = x*x+y*y+z*z;
- if (fabs(adod-d) > DP_TOL)
- {
- continue;
- }
- for (tl = 1; tl < tess-1; tl++)
- {
- divarc(xus[3*j], xus[1+3*j], xus[2+3*j],
- xus[3*i], xus[1+3*i], xus[2+3*i],
- tl, tess, &xji, &yji, &zji);
- divarc(xus[3*k], xus[1+3*k], xus[2+3*k],
- xus[3*i], xus[1+3*i], xus[2+3*i],
- tl, tess, &xki, &yki, &zki);
-
- for (tl2 = 1; tl2 < tess-tl; tl2++)
- {
- divarc(xus[3*i], xus[1+3*i], xus[2+3*i],
- xus[3*j], xus[1+3*j], xus[2+3*j],
- tl2, tess, &xij, &yij, &zij);
- divarc(xus[3*k], xus[1+3*k], xus[2+3*k],
- xus[3*j], xus[1+3*j], xus[2+3*j],
- tl2, tess, &xkj, &ykj, &zkj);
- divarc(xus[3*i], xus[1+3*i], xus[2+3*i],
- xus[3*k], xus[1+3*k], xus[2+3*k],
- tess-tl-tl2, tess, &xik, &yik, &zik);
- divarc(xus[3*j], xus[1+3*j], xus[2+3*j],
- xus[3*k], xus[1+3*k], xus[2+3*k],
- tess-tl-tl2, tess, &xjk, &yjk, &zjk);
- if (tn >= n_dot)
- {
- ERROR("ico_dot: tn exceeds dimension of xus");
- }
- divarc(xki, yki, zki, xji, yji, zji, tl2, tess-tl,
- &x, &y, &z);
- divarc(xkj, ykj, zkj, xij, yij, zij, tl, tess-tl2,
- &x2, &y2, &z2);
- divarc(xjk, yjk, zjk, xik, yik, zik, tl, tl+tl2,
- &x3, &y3, &z3);
- x = x+x2+x3; y = y+y2+y3; z = z+z2+z3;
- d = sqrt(x*x+y*y+z*z);
- xus[3*tn] = x/d;
- xus[1+3*tn] = y/d;
- xus[2+3*tn] = z/d;
- tn++;
- } /* cycle tl2 */
- } /* cycle tl */
- } /* cycle k */
- } /* cycle j */
- } /* cycle i */
- if (n_dot != tn)
- {
- ERROR("ico_dot: n_dot(%d) and tn(%d) differ", n_dot, tn);
- }
- } /* end of if (tess > 1) */
-
- return n_dot;
-} /* end of routine ico_dot_dod */
-
-int unsp_type(int densit)
-{
- int i1, i2;
- i1 = 1;
- while (10*i1*i1+2 < densit)
- {
- i1++;
- }
- i2 = 1;
- while (30*i2*i2+2 < densit)
- {
- i2++;
- }
- if (10*i1*i1-2 < 30*i2*i2-2)
- {
- return UNSP_ICO_ARC;
- }
- else
- {
- return UNSP_ICO_DOD;
- }
-}
-
-int make_unsp(int densit, int mode, int * num_dot, int cubus)
-{
- int *ico_wk, *ico_pt;
- int ndot, ico_cube_cb, i, j, k, l, ijk, tn, tl, tl2;
- real *xus;
- int *work;
- real x, y, z;
-
- if (xpunsp)
- {
- free(xpunsp);
- }
-
- k = 1; if (mode < 0)
- {
- k = 0; mode = -mode;
- }
- if (mode == UNSP_ICO_ARC)
- {
- ndot = ico_dot_arc(densit);
- }
- else if (mode == UNSP_ICO_DOD)
- {
- ndot = ico_dot_dod(densit);
- }
- else
- {
- WARNING("make_unsp: mode %c%d not allowed", (k) ? '+' : '-', mode);
- return 1;
- }
-
- last_n_dot = ndot; last_densit = densit; last_unsp = mode;
- *num_dot = ndot; if (k)
- {
- return 0;
- }
-
- /* in the following the dots of the unit sphere may be resorted */
- last_unsp = -last_unsp;
-
- /* determine distribution of points in elementary cubes */
- if (cubus)
- {
- ico_cube = cubus;
- }
- else
- {
- last_cubus = 0;
- i = 1;
- while (i*i*i*2 < ndot)
- {
- i++;
- }
- ico_cube = max(i-1, 0);
- }
- ico_cube_cb = ico_cube*ico_cube*ico_cube;
- del_cube = 2./((real)ico_cube);
- snew(work, ndot);
- xus = xpunsp;
- for (l = 0; l < ndot; l++)
- {
- i = max((int) floor((1.+xus[3*l])/del_cube), 0);
- if (i >= ico_cube)
- {
- i = ico_cube-1;
- }
- j = max((int) floor((1.+xus[1+3*l])/del_cube), 0);
- if (j >= ico_cube)
- {
- j = ico_cube-1;
- }
- k = max((int) floor((1.+xus[2+3*l])/del_cube), 0);
- if (k >= ico_cube)
- {
- k = ico_cube-1;
- }
- ijk = i+j*ico_cube+k*ico_cube*ico_cube;
- work[l] = ijk;
- }
-
- snew(ico_wk, 2*ico_cube_cb+1);
-
- ico_pt = ico_wk+ico_cube_cb;
- for (l = 0; l < ndot; l++)
- {
- ico_wk[work[l]]++; /* dots per elementary cube */
- }
-
- /* reordering of the coordinate array in accordance with box number */
- tn = 0;
- for (i = 0; i < ico_cube; i++)
- {
- for (j = 0; j < ico_cube; j++)
- {
- for (k = 0; k < ico_cube; k++)
- {
- tl = 0;
- tl2 = tn;
- ijk = i+ico_cube*j+ico_cube*ico_cube*k;
- *(ico_pt+ijk) = tn;
- for (l = tl2; l < ndot; l++)
- {
- if (ijk == work[l])
- {
- x = xus[3*l]; y = xus[1+3*l]; z = xus[2+3*l];
- xus[3*l] = xus[3*tn];
- xus[1+3*l] = xus[1+3*tn]; xus[2+3*l] = xus[2+3*tn];
- xus[3*tn] = x; xus[1+3*tn] = y; xus[2+3*tn] = z;
- ijk = work[l]; work[l] = work[tn]; work[tn] = ijk;
- tn++; tl++;
- }
- }
- *(ico_wk+ijk) = tl;
- } /* cycle k */
- } /* cycle j */
- } /* cycle i */
- sfree(ico_wk);
- sfree(work);
-
- return 0;
-}
-
-
-typedef struct _stwknb {
- real x;
- real y;
- real z;
- real dot;
-} Neighb;
-
-int nsc_dclm_pbc(const rvec *coords, real *radius, int nat,
- int densit, int mode,
- real *value_of_area, real **at_area,
- real *value_of_vol,
- real **lidots, int *nu_dots,
- atom_id index[], int ePBC, matrix box)
-{
- int iat, i, ii, iii, ix, iy, iz, ixe, ixs, iye, iys, ize, izs, i_ac;
- int jat, j, jj, jjj, jx, jy, jz;
- int distribution;
- int l;
- int maxnei, nnei, last, maxdots = 0;
- int *wkdot = NULL, *wkbox = NULL, *wkat1 = NULL, *wkatm = NULL;
- Neighb *wknb, *ctnb;
- int iii1, iii2, iiat, lfnr = 0, i_at, j_at;
- real dx, dy, dz, dd, ai, aisq, ajsq, aj, as, a;
- real xi, yi, zi, xs = 0., ys = 0., zs = 0.;
- real dotarea, area, vol = 0.;
- real *xus, *dots = NULL, *atom_area = NULL;
- int nxbox, nybox, nzbox, nxy, nxyz;
- real xmin = 0, ymin = 0, zmin = 0, xmax, ymax, zmax, ra2max, d;
- const real *pco;
- /* Added DvdS 2006-07-19 */
- t_pbc pbc;
- rvec ddx, *x = NULL;
- int iat_xx, jat_xx;
-
- distribution = unsp_type(densit);
- if (distribution != -last_unsp || last_cubus != 4 ||
- (densit != last_densit && densit != last_n_dot))
- {
- if (make_unsp(densit, (-distribution), &n_dot, 4))
- {
- return 1;
- }
- }
- xus = xpunsp;
-
- dotarea = FOURPI/(real) n_dot;
- area = 0.;
-
- if (debug)
- {
- fprintf(debug, "nsc_dclm: n_dot=%5d %9.3f\n", n_dot, dotarea);
- }
-
- /* start with neighbour list */
- /* calculate neighbour list with the box algorithm */
- if (nat == 0)
- {
- WARNING("nsc_dclm: no surface atoms selected");
- return 1;
- }
- if (mode & FLAG_VOLUME)
- {
- vol = 0.;
- }
- if (mode & FLAG_DOTS)
- {
- maxdots = (3*n_dot*nat)/10;
- /* should be set to NULL on first user call */
- if (dots == NULL)
- {
- snew(dots, maxdots);
- }
- else
- {
- srenew(dots, maxdots);
- }
-
- lfnr = 0;
- }
- if (mode & FLAG_ATOM_AREA)
- {
- /* should be set to NULL on first user call */
- if (atom_area == NULL)
- {
- snew(atom_area, nat);
- }
- else
- {
- srenew(atom_area, nat);
- }
- }
-
- /* Compute minimum size for grid cells */
- ra2max = radius[index[0]];
- for (iat_xx = 1; (iat_xx < nat); iat_xx++)
- {
- iat = index[iat_xx];
- ra2max = max(ra2max, radius[iat]);
- }
- ra2max = 2*ra2max;
-
- /* Added DvdS 2006-07-19 */
- /* Updated 2008-10-09 */
- if (box)
- {
- set_pbc(&pbc, ePBC, box);
- snew(x, nat);
- for (i = 0; (i < nat); i++)
- {
- iat = index[0];
- copy_rvec(coords[iat], x[i]);
- }
- put_atoms_in_triclinic_unitcell(ecenterTRIC, box, nat, x);
- nxbox = max(1, floor(norm(box[XX])/ra2max));
- nybox = max(1, floor(norm(box[YY])/ra2max));
- nzbox = max(1, floor(norm(box[ZZ])/ra2max));
- if (debug)
- {
- fprintf(debug, "nbox = %d, %d, %d\n", nxbox, nybox, nzbox);
- }
- }
- else
- {
- /* dimensions of atomic set, cell edge is 2*ra_max */
- iat = index[0];
- xmin = coords[iat][XX]; xmax = xmin; xs = xmin;
- ymin = coords[iat][YY]; ymax = ymin; ys = ymin;
- zmin = coords[iat][ZZ]; zmax = zmin; zs = zmin;
-
- for (iat_xx = 1; (iat_xx < nat); iat_xx++)
- {
- iat = index[iat_xx];
- pco = coords[iat];
- xmin = min(xmin, *pco); xmax = max(xmax, *pco);
- ymin = min(ymin, *(pco+1)); ymax = max(ymax, *(pco+1));
- zmin = min(zmin, *(pco+2)); zmax = max(zmax, *(pco+2));
- xs = xs+ *pco; ys = ys+ *(pco+1); zs = zs+ *(pco+2);
- }
- xs = xs/ (real) nat;
- ys = ys/ (real) nat;
- zs = zs/ (real) nat;
- if (debug)
- {
- fprintf(debug, "nsc_dclm: n_dot=%5d ra2max=%9.3f %9.3f\n", n_dot, ra2max, dotarea);
- }
-
- d = xmax-xmin; nxbox = (int) max(ceil(d/ra2max), 1.);
- d = (((real)nxbox)*ra2max-d)/2.;
- xmin = xmin-d; xmax = xmax+d;
- d = ymax-ymin; nybox = (int) max(ceil(d/ra2max), 1.);
- d = (((real)nybox)*ra2max-d)/2.;
- ymin = ymin-d; ymax = ymax+d;
- d = zmax-zmin; nzbox = (int) max(ceil(d/ra2max), 1.);
- d = (((real)nzbox)*ra2max-d)/2.;
- zmin = zmin-d; zmax = zmax+d;
- }
- /* Help variables */
- nxy = nxbox*nybox;
- nxyz = nxy*nzbox;
-
- /* box number of atoms */
- snew(wkatm, nat);
- snew(wkat1, nat);
- snew(wkdot, n_dot);
- snew(wkbox, nxyz+1);
-
- if (box)
- {
- matrix box_1;
- rvec x_1;
- int ix, iy, iz, m;
- m_inv(box, box_1);
- for (i = 0; (i < nat); i++)
- {
- mvmul(box_1, x[i], x_1);
- ix = ((int)floor(x_1[XX]*nxbox) + 2*nxbox) % nxbox;
- iy = ((int)floor(x_1[YY]*nybox) + 2*nybox) % nybox;
- iz = ((int)floor(x_1[ZZ]*nzbox) + 2*nzbox) % nzbox;
- j = ix + iy*nxbox + iz*nxbox*nybox;
- if (debug)
- {
- fprintf(debug, "Atom %d cell index %d. x = (%8.3f,%8.3f,%8.3f) fc = (%8.3f,%8.3f,%8.3f)\n",
- i, j, x[i][XX], x[i][YY], x[i][ZZ], x_1[XX], x_1[YY], x_1[ZZ]);
- }
- range_check(j, 0, nxyz);
- wkat1[i] = j;
- wkbox[j]++;
- }
- }
- else
- {
- /* Put the atoms in their boxes */
- for (iat_xx = 0; (iat_xx < nat); iat_xx++)
- {
- iat = index[iat_xx];
- pco = coords[iat];
- i = (int) max(floor((pco[XX]-xmin)/ra2max), 0);
- i = min(i, nxbox-1);
- j = (int) max(floor((pco[YY]-ymin)/ra2max), 0);
- j = min(j, nybox-1);
- l = (int) max(floor((pco[ZZ]-zmin)/ra2max), 0);
- l = min(l, nzbox-1);
- i = i+j*nxbox+l*nxy;
- wkat1[iat_xx] = i;
- wkbox[i]++;
- }
- }
-
- /* sorting of atoms in accordance with box numbers */
- j = wkbox[0];
- for (i = 1; i < nxyz; i++)
- {
- j = max(wkbox[i], j);
- }
- for (i = 1; i <= nxyz; i++)
- {
- wkbox[i] += wkbox[i-1];
- }
-
- /* maxnei = (int) floor(ra2max*ra2max*ra2max*0.5); */
- maxnei = min(nat, 27*j);
- snew(wknb, maxnei);
- for (iat_xx = 0; iat_xx < nat; iat_xx++)
- {
- iat = index[iat_xx];
- range_check(wkat1[iat_xx], 0, nxyz);
- wkatm[--wkbox[wkat1[iat_xx]]] = iat_xx;
- if (debug)
- {
- fprintf(debug, "atom %5d on place %5d\n", iat, wkbox[wkat1[iat_xx]]);
- }
- }
-
- if (debug)
- {
- fprintf(debug, "nsc_dclm: n_dot=%5d ra2max=%9.3f %9.3f\n",
- n_dot, ra2max, dotarea);
- fprintf(debug, "neighbour list calculated/box(xyz):%d %d %d\n",
- nxbox, nybox, nzbox);
-
- for (i = 0; i < nxyz; i++)
- {
- fprintf(debug, "box %6d : atoms %4d-%4d %5d\n",
- i, wkbox[i], wkbox[i+1]-1, wkbox[i+1]-wkbox[i]);
- }
- for (i = 0; i < nat; i++)
- {
- fprintf(debug, "list place %5d by atom %7d\n", i, index[wkatm[i]]);
- }
- }
-
- /* calculate surface for all atoms, step cube-wise */
- for (iz = 0; iz < nzbox; iz++)
- {
- iii = iz*nxy;
- if (box)
- {
- izs = iz-1;
- ize = min(iz+2, izs+nzbox);
- }
- else
- {
- izs = max(iz-1, 0);
- ize = min(iz+2, nzbox);
- }
- for (iy = 0; iy < nybox; iy++)
- {
- ii = iy*nxbox+iii;
- if (box)
- {
- iys = iy-1;
- iye = min(iy+2, iys+nybox);
- }
- else
- {
- iys = max(iy-1, 0);
- iye = min(iy+2, nybox);
- }
- for (ix = 0; ix < nxbox; ix++)
- {
- i = ii+ix;
- iii1 = wkbox[i];
- iii2 = wkbox[i+1];
- if (iii1 >= iii2)
- {
- continue;
- }
- if (box)
- {
- ixs = ix-1;
- ixe = min(ix+2, ixs+nxbox);
- }
- else
- {
- ixs = max(ix-1, 0);
- ixe = min(ix+2, nxbox);
- }
- iiat = 0;
- /* make intermediate atom list */
- for (jz = izs; jz < ize; jz++)
- {
- jjj = ((jz+nzbox) % nzbox)*nxy;
- for (jy = iys; jy < iye; jy++)
- {
- jj = ((jy+nybox) % nybox)*nxbox+jjj;
- for (jx = ixs; jx < ixe; jx++)
- {
- j = jj+((jx+nxbox) % nxbox);
- for (jat = wkbox[j]; jat < wkbox[j+1]; jat++)
- {
- range_check(wkatm[jat], 0, nat);
- range_check(iiat, 0, nat);
- wkat1[iiat] = wkatm[jat];
- iiat++;
- } /* end of cycle "jat" */
- } /* end of cycle "jx" */
- } /* end of cycle "jy" */
- } /* end of cycle "jz" */
- for (iat = iii1; iat < iii2; iat++)
- {
- i_at = index[wkatm[iat]];
- ai = radius[i_at];
- aisq = ai*ai;
- pco = coords[i_at];
- xi = pco[XX]; yi = pco[YY]; zi = pco[ZZ];
- for (i = 0; i < n_dot; i++)
- {
- wkdot[i] = 0;
- }
-
- ctnb = wknb; nnei = 0;
- for (j = 0; j < iiat; j++)
- {
- j_at = index[wkat1[j]];
- if (j_at == i_at)
- {
- continue;
- }
-
- aj = radius[j_at];
- ajsq = aj*aj;
- pco = coords[j_at];
-
- /* Added DvdS 2006-07-19 */
- if (box)
- {
- /*rvec xxi;
-
- xxi[XX] = xi;
- xxi[YY] = yi;
- xxi[ZZ] = zi;
- pbc_dx(&pbc,pco,xxi,ddx);*/
- pbc_dx(&pbc, coords[j_at], coords[i_at], ddx);
- dx = ddx[XX];
- dy = ddx[YY];
- dz = ddx[ZZ];
- }
- else
- {
- dx = pco[XX]-xi;
- dy = pco[YY]-yi;
- dz = pco[ZZ]-zi;
- }
- dd = dx*dx+dy*dy+dz*dz;
- as = ai+aj;
- if (dd > as*as)
- {
- continue;
- }
- nnei++;
- ctnb->x = dx;
- ctnb->y = dy;
- ctnb->z = dz;
- ctnb->dot = (dd+aisq-ajsq)/(2.*ai); /* reference dot product */
- ctnb++;
- }
-
- /* check points on accessibility */
- if (nnei)
- {
- last = 0; i_ac = 0;
- for (l = 0; l < n_dot; l++)
- {
- if (xus[3*l]*(wknb+last)->x+
- xus[1+3*l]*(wknb+last)->y+
- xus[2+3*l]*(wknb+last)->z <= (wknb+last)->dot)
- {
- for (j = 0; j < nnei; j++)
- {
- if (xus[3*l]*(wknb+j)->x+xus[1+3*l]*(wknb+j)->y+
- xus[2+3*l]*(wknb+j)->z > (wknb+j)->dot)
- {
- last = j;
- break;
- }
- }
- if (j >= nnei)
- {
- i_ac++;
- wkdot[l] = 1;
- }
- } /* end of cycle j */
- } /* end of cycle l */
- }
- else
- {
- i_ac = n_dot;
- for (l = 0; l < n_dot; l++)
- {
- wkdot[l] = 1;
- }
- }
-
- if (debug)
- {
- fprintf(debug, "i_ac=%d, dotarea=%8.3f, aisq=%8.3f\n",
- i_ac, dotarea, aisq);
- }
-
- a = aisq*dotarea* (real) i_ac;
- area = area + a;
- if (mode & FLAG_ATOM_AREA)
- {
- range_check(wkatm[iat], 0, nat);
- atom_area[wkatm[iat]] = a;
- }
- if (mode & FLAG_DOTS)
- {
- for (l = 0; l < n_dot; l++)
- {
- if (wkdot[l])
- {
- lfnr++;
- if (maxdots <= 3*lfnr+1)
- {
- maxdots = maxdots+n_dot*3;
- srenew(dots, maxdots);
- }
- dots[3*lfnr-3] = ai*xus[3*l]+xi;
- dots[3*lfnr-2] = ai*xus[1+3*l]+yi;
- dots[3*lfnr-1] = ai*xus[2+3*l]+zi;
- }
- }
- }
- if (mode & FLAG_VOLUME)
- {
- dx = 0.; dy = 0.; dz = 0.;
- for (l = 0; l < n_dot; l++)
- {
- if (wkdot[l])
- {
- dx = dx+xus[3*l];
- dy = dy+xus[1+3*l];
- dz = dz+xus[2+3*l];
- }
- }
- vol = vol+aisq*(dx*(xi-xs)+dy*(yi-ys)+dz*(zi-zs)+ai* (real) i_ac);
- }
-
- } /* end of cycle "iat" */
- } /* end of cycle "ix" */
- } /* end of cycle "iy" */
- } /* end of cycle "iz" */
-
- sfree(wkatm);
- sfree(wkat1);
- sfree(wkdot);
- sfree(wkbox);
- sfree(wknb);
- if (box)
- {
- sfree(x);
- }
- if (mode & FLAG_VOLUME)
- {
- vol = vol*FOURPI/(3.* (real) n_dot);
- *value_of_vol = vol;
- }
- if (mode & FLAG_DOTS)
- {
- *nu_dots = lfnr;
- *lidots = dots;
- }
- if (mode & FLAG_ATOM_AREA)
- {
- *at_area = atom_area;
- }
- *value_of_area = area;
-
- if (debug)
- {
- fprintf(debug, "area=%8.3f\n", area);
- }
-
- return 0;
-}
-
-
-#if TEST_NSC > 0
-#define NAT 2
-main () {
-
- int i, j, ndots;
- real co[3*NAT], ra[NAT], area, volume, a, b, c;
- real * dots;
- real * at_area;
- FILE *fp;
-
-
- a = 1.; c = 0.1;
- fp = fopen("nsc.txt", "w+");
- for (i = 1; i <= NAT; i++)
- {
- j = i-1;
- co[3*i-3] = j*1*c;
- co[3*i-2] = j*1*c;
- co[3*i-1] = j*1*c;
- /*
- co[3*i-3] = i*1.4;
- co[3*i-2] = 0.;
- co[3*i-1] = 0.;
- */
- /*
- co[3*i-2] = a*0.3;
- a = -a; b=0;
- if (i%3 == 0) b=0.5;
- co[3*i-1] = b;
- ra[i-1] = 2.0;
- */
- ra[i-1] = (1.+j*0.5)*c;
- }
- /*
- if (NSC(co, ra, NAT, 42, NULL, &area,
- */
- if (NSC(co, ra, NAT, 42, NULL, &area,
- NULL, NULL, NULL, NULL))
- {
- ERROR("error in NSC");
- }
- fprintf(fp, "\n");
- fprintf(fp, "area : %8.3f\n", area);
- fprintf(fp, "\n");
- fprintf(fp, "\n");
- fprintf(fp, "next call\n");
- fprintf(fp, "\n");
- fprintf(fp, "\n");
-
- if (NSC(co, ra, NAT, 42, FLAG_VOLUME | FLAG_ATOM_AREA | FLAG_DOTS, &area,
- &at_area, &volume,
- &dots, &ndots))
- {
- ERROR("error in NSC");
- }
-
- fprintf(fp, "\n");
- fprintf(fp, "area : %8.3f\n", area);
- printf("area : %8.3f\n", area);
- fprintf(fp, "volume : %8.3f\n", volume);
- printf("volume : %8.3f\n", volume);
- fprintf(fp, "ndots : %8d\n", ndots);
- printf("ndots : %8d\n", ndots);
- fprintf(fp, "\n");
- for (i = 1; i <= NAT; i++)
- {
- fprintf(fp, "%4d ATOM %7.2f %7.2f %7.2f ra=%4.1f area=%8.3f\n",
- i, co[3*i-3], co[3*i-2], co[3*i-1], ra[i-1], at_area[i-1]);
- }
- fprintf(fp, "\n");
- fprintf(fp, "DOTS : %8d\n", ndots);
- for (i = 1; i <= ndots; i++)
- {
- fprintf(fp, "%4d DOTS %8.2f %8.2f %8.2f\n",
- i, dots[3*i-3], dots[3*i-2], dots[3*i-1]);
- }
-}
-#endif
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "typedefs.h"
-
-#define FLAG_DOTS 01
-#define FLAG_VOLUME 02
-#define FLAG_ATOM_AREA 04
-
-#ifdef __cplusplus
-extern "C"
-{
-#endif
-
-int nsc_dclm_pbc(const rvec *coords, real *radius, int nat,
- int densit, int mode,
- real *value_of_area, real **at_area,
- real *value_of_vol,
- real **lidots, int *nu_dots,
- atom_id index[], int ePBC, matrix box);
-
-/*
- User notes :
- The input requirements :
- The arrays with atom coordinates and radii are thought to start
- with index 0, i.e., places 0, 1, and 2 are the x-, y-, and z-
- coordinates of the zero-th atom and place 0 in the other array
- is its radius.
-
- PLEASE TAKE INTO ACCOUNT THAT THE RADII GIVEN HERE ARE DIRECTLY
- USED FOR SURFACE CALCULATION. NSC does not increment with a probe
- radius.
-
- The user can define any number of dots. The program selects a
- dot density that is the lowest possible with at least the required
- number of dots. The points are distributed in accordance with the
- icosahedron-based or the dodecahedron-based method as described in
- ref. 1.
-
- The output requirements are :
- 1 and 3 : pointer to an existing real
- 2 and 4 : pointer to an existing pointer to real
- NSC allocates memory for an array
- 5 : pointer to an existing integer
-
- The subroutine NSC makes use of variant 2 described in reference 1.
- By selecting the necessary output via flags, the requirements for
- cpu-time and computer memory can be adapted to the actual needs.
-
- Example : flag = FLAG_VOLUME | FLAG_ATOM_AREA | FLAG_DOTS
- The routine calculates the area, volume and the dot surface. The
- program allocates arrays for the atomwise areas and for the surface
- dots. The addresses are returned in the pointers to pointers to
- real.
- This variant is not recommended because normally the dot surface
- is needed for low point density (e.g.42) at which area and volume
- are inaccurate. The sign "|" is used as binary AND !
-
- flag = FLAG_VOLUME | FLAG_ATOM_AREA
- In this case the large arrays for storing the surface dots
- are not allocated. A large point number of the fully accessible
- sphere can be selected. Good accuracy is already achieved with
- 600-700 points per sphere (accuracy of about 1.5 square Angstrem
- per atomic sphere).
- Output pointers 4 and 5 may be NULL.
-
- flag = FLAG_DOTS
- Only the dot surface is produced.
- Output pointers 2 and 3 may be NULL.
-
- The output pointer 1 cannot be set to NULL in any circumstances. The
- overall area value is returned in every mode.
-
- All files calling NSC should include nsc.h !!
-
-
- Example for calling NSC (contents of user file):
-
- ...
- #include "nsc.h"
-
- int routine_calling_NSC(int n_atom, real *coordinates, real *radii) {
- real area, volume, *atomwise_area, *surface_dots;
- int i, density = 300, n_dots;
-
- ...
-
- for (i=0; i<n_atom; i++) {
- radii[i] += 1.4 /# add the probe radius if necessary #/
-
- if (NSC(coordinates, radii, n_atom, density,
- FLAG_AREA | FLAG_VOLUME | FLAG_DOTS,
- &area, &atomwise_area, &volume, &surface_dots, &n_dots))
- printf("error occured\n");
- return 1;
- }
-
- ...
-
- /# do something with areas, volume and surface dots #/
-
- ...
-
- return 0;
- }
-
- */
-
-#ifdef __cplusplus
-}
-#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements gmx::analysismodules::PairDistance.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#include "gmxpre.h"
+
+#include "pairdist.h"
+
+#include <cmath>
+
+#include <algorithm>
+#include <limits>
+#include <string>
+#include <vector>
+
+#include "gromacs/analysisdata/analysisdata.h"
+#include "gromacs/analysisdata/modules/plot.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/options.h"
+#include "gromacs/selection/nbsearch.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectionoption.h"
+#include "gromacs/trajectoryanalysis/analysissettings.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/stringutil.h"
+
+namespace gmx
+{
+
+namespace analysismodules
+{
+
+namespace
+{
+
+//! \addtogroup module_trajectoryanalysis
+//! \{
+
+//! Enum value to store the selected value for `-type`.
+enum DistanceType
+{
+ eDistanceType_Min,
+ eDistanceType_Max
+};
+
+//! Enum value to store the selected value for `-refgrouping`/`-selgrouping`.
+enum GroupType
+{
+ eGroupType_All,
+ eGroupType_Residue,
+ eGroupType_Molecule,
+ eGroupType_None
+};
+
+//! Strings corresponding to DistanceType.
+const char *const c_distanceTypes[] = { "min", "max" };
+//! Strings corresponding to GroupType.
+const char *const c_groupTypes[] = { "all", "res", "mol", "none" };
+
+/*! \brief
+ * Implements `gmx pairdist` trajectory analysis module.
+ */
+class PairDistance : public TrajectoryAnalysisModule
+{
+ public:
+ PairDistance();
+
+ virtual void initOptions(Options *options,
+ TrajectoryAnalysisSettings *settings);
+ virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
+ const TopologyInformation &top);
+
+ virtual TrajectoryAnalysisModuleDataPointer startFrames(
+ const AnalysisDataParallelOptions &opt,
+ const SelectionCollection &selections);
+ virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
+ TrajectoryAnalysisModuleData *pdata);
+
+ virtual void finishAnalysis(int nframes);
+ virtual void writeOutput();
+
+ private:
+ /*! \brief
+ * Computed distances as a function of time.
+ *
+ * There is one data set for each selection in `sel_`.
+ * Within each data set, there is one column for each distance to be
+ * computed, as explained in the `-h` text.
+ */
+ AnalysisData distances_;
+
+ /*! \brief
+ * Reference selection to compute distances to.
+ *
+ * mappedId() identifies the group (of type `refGroupType_`) into which
+ * each position belogs.
+ */
+ Selection refSel_;
+ /*! \brief
+ * Selections to compute distances from.
+ *
+ * mappedId() identifies the group (of type `selGroupType_`) into which
+ * each position belogs.
+ */
+ SelectionList sel_;
+
+ std::string fnDist_;
+
+ double cutoff_;
+ int distanceType_;
+ int refGroupType_;
+ int selGroupType_;
+
+ //! Number of groups in `refSel_`.
+ int refGroupCount_;
+ //! Maximum number of pairs of groups for one selection.
+ int maxGroupCount_;
+ //! Initial squared distance for distance accumulation.
+ real initialDist2_;
+ //! Cutoff squared for use in the actual calculation.
+ real cutoff2_;
+
+ //! Neighborhood search object for the pair search.
+ AnalysisNeighborhood nb_;
+
+ // Copy and assign disallowed by base.
+};
+
+PairDistance::PairDistance()
+ : TrajectoryAnalysisModule(PairDistanceInfo::name, PairDistanceInfo::shortDescription),
+ cutoff_(0.0), distanceType_(eDistanceType_Min),
+ refGroupType_(eGroupType_All), selGroupType_(eGroupType_All),
+ refGroupCount_(0), maxGroupCount_(0), initialDist2_(0.0), cutoff2_(0.0)
+{
+ registerAnalysisDataset(&distances_, "dist");
+}
+
+
+void
+PairDistance::initOptions(Options *options, TrajectoryAnalysisSettings * /*settings*/)
+{
+ static const char *const desc[] = {
+ "[THISMODULE] calculates pairwise distances between one reference",
+ "selection (given with [TT]-ref[tt]) and one or more other selections",
+ "(given with [TT]-sel[tt]). It can calculate either the minimum",
+ "distance (the default), or the maximum distance (with",
+ "[TT]-type max[tt]). Distances to each selection provided with",
+ "[TT]-sel[tt] are computed independently.[PAR]",
+ "By default, the global minimum/maximum distance is computed.",
+ "To compute more distances (e.g., minimum distances to each residue",
+ "in [TT]-ref[tt]), use [TT]-refgrouping[tt] and/or [TT]-selgrouping[tt]",
+ "to specify how the positions within each selection should be",
+ "grouped.[PAR]",
+ "Computed distances are written to the file specified with [TT]-o[tt].",
+ "If there are N groups in [TT]-ref[tt] and M groups in the first",
+ "selection in [TT]-sel[tt], then the output contains N*M columns",
+ "for the first selection. The columns contain distances like this:",
+ "r1-s1, r2-s1, ..., r1-s2, r2-s2, ..., where rn is the n'th group",
+ "in [TT]-ref[tt] and sn is the n'th group in the other selection.",
+ "The distances for the second selection comes as separate columns",
+ "after the first selection, and so on. If some selections are",
+ "dynamic, only the selected positions are used in the computation",
+ "but the same number of columns is always written out. If there",
+ "are no positions contributing to some group pair, then the cutoff",
+ "value is written (see below).[PAR]",
+ "[TT]-cutoff[tt] sets a cutoff for the computed distances.",
+ "If the result would contain a distance over the cutoff, the cutoff",
+ "value is written to the output file instead. By default, no cutoff",
+ "is used, but if you are not interested in values beyond a cutoff,",
+ "or if you know that the minimum distance is smaller than a cutoff,",
+ "you should set this option to allow the tool to use grid-based",
+ "searching and be significantly faster.[PAR]",
+ "If you want to compute distances between fixed pairs,",
+ "[gmx-distance] may be a more suitable tool."
+ };
+
+ options->setDescription(desc);
+
+ options->addOption(FileNameOption("o").filetype(eftPlot).outputFile().required()
+ .store(&fnDist_).defaultBasename("dist")
+ .description("Distances as function of time"));
+
+ options->addOption(DoubleOption("cutoff").store(&cutoff_)
+ .description("Maximum distance to consider"));
+ options->addOption(StringOption("type").storeEnumIndex(&distanceType_)
+ .defaultEnumIndex(0).enumValue(c_distanceTypes)
+ .description("Type of distances to calculate"));
+ options->addOption(StringOption("refgrouping").storeEnumIndex(&refGroupType_)
+ .defaultEnumIndex(0).enumValue(c_groupTypes)
+ .description("Grouping of -ref positions to compute the min/max over"));
+ options->addOption(StringOption("selgrouping").storeEnumIndex(&selGroupType_)
+ .defaultEnumIndex(0).enumValue(c_groupTypes)
+ .description("Grouping of -sel positions to compute the min/max over"));
+
+ options->addOption(SelectionOption("ref").store(&refSel_).required()
+ .description("Reference positions to calculate distances from"));
+ options->addOption(SelectionOption("sel").storeVector(&sel_).required().multiValue()
+ .description("Positions to calculate distances for"));
+}
+
+//! Helper function to initialize the grouping for a selection.
+int initSelectionGroups(Selection *sel, t_topology *top, int type)
+{
+ e_index_t indexType = INDEX_UNKNOWN;
+ switch (type)
+ {
+ case eGroupType_All: indexType = INDEX_ALL; break;
+ case eGroupType_Residue: indexType = INDEX_RES; break;
+ case eGroupType_Molecule: indexType = INDEX_MOL; break;
+ case eGroupType_None: indexType = INDEX_ATOM; break;
+ }
+ return sel->initOriginalIdsToGroup(top, indexType);
+}
+
+
+void
+PairDistance::initAnalysis(const TrajectoryAnalysisSettings &settings,
+ const TopologyInformation &top)
+{
+ refGroupCount_ = initSelectionGroups(&refSel_, top.topology(), refGroupType_);
+
+ maxGroupCount_ = 0;
+ distances_.setDataSetCount(sel_.size());
+ for (size_t i = 0; i < sel_.size(); ++i)
+ {
+ const int selGroupCount
+ = initSelectionGroups(&sel_[i], top.topology(), selGroupType_);
+ const int columnCount = refGroupCount_ * selGroupCount;
+ maxGroupCount_ = std::max(maxGroupCount_, columnCount);
+ distances_.setColumnCount(i, columnCount);
+ }
+
+ if (!fnDist_.empty())
+ {
+ AnalysisDataPlotModulePointer plotm(
+ new AnalysisDataPlotModule(settings.plotSettings()));
+ plotm->setFileName(fnDist_);
+ if (distanceType_ == eDistanceType_Max)
+ {
+ plotm->setTitle("Maximum distance");
+ }
+ else
+ {
+ plotm->setTitle("Minimum distance");
+ }
+ // TODO: Figure out and add a descriptive subtitle and/or a longer
+ // title and/or better legends based on the grouping and the reference
+ // selection.
+ plotm->setXAxisIsTime();
+ plotm->setYLabel("Distance (nm)");
+ for (size_t g = 0; g < sel_.size(); ++g)
+ {
+ plotm->appendLegend(sel_[g].name());
+ }
+ distances_.addModule(plotm);
+ }
+
+ nb_.setCutoff(cutoff_);
+ if (cutoff_ <= 0.0)
+ {
+ cutoff_ = 0.0;
+ initialDist2_ = std::numeric_limits<real>::max();
+ }
+ else
+ {
+ initialDist2_ = cutoff_ * cutoff_;
+ }
+ if (distanceType_ == eDistanceType_Max)
+ {
+ initialDist2_ = 0.0;
+ }
+ cutoff2_ = cutoff_ * cutoff_;
+}
+
+/*! \brief
+ * Temporary memory for use within a single-frame calculation.
+ */
+class PairDistanceModuleData : public TrajectoryAnalysisModuleData
+{
+ public:
+ /*! \brief
+ * Reserves memory for the frame-local data.
+ */
+ PairDistanceModuleData(TrajectoryAnalysisModule *module,
+ const AnalysisDataParallelOptions &opt,
+ const SelectionCollection &selections,
+ int refGroupCount,
+ const Selection &refSel,
+ int maxGroupCount)
+ : TrajectoryAnalysisModuleData(module, opt, selections)
+ {
+ distArray_.resize(maxGroupCount);
+ countArray_.resize(maxGroupCount);
+ refCountArray_.resize(refGroupCount);
+ if (!refSel.isDynamic())
+ {
+ initRefCountArray(refSel);
+ }
+ }
+
+ virtual void finish() { finishDataHandles(); }
+
+ /*! \brief
+ * Computes the number of positions in each group in \p refSel
+ * and stores them into `refCountArray_`.
+ */
+ void initRefCountArray(const Selection &refSel)
+ {
+ std::fill(refCountArray_.begin(), refCountArray_.end(), 0);
+ int refPos = 0;
+ while (refPos < refSel.posCount())
+ {
+ const int refIndex = refSel.position(refPos).mappedId();
+ const int startPos = refPos;
+ ++refPos;
+ while (refPos < refSel.posCount()
+ && refSel.position(refPos).mappedId() == refIndex)
+ {
+ ++refPos;
+ }
+ refCountArray_[refIndex] = refPos - startPos;
+ }
+ }
+
+ /*! \brief
+ * Squared distance between each group
+ *
+ * One entry for each group pair for the current selection.
+ * Enough memory is allocated to fit the largest calculation selection.
+ * This is needed to support neighborhood searching, which may not
+ * return the pairs in order: for each group pair, we need to search
+ * through all the position pairs and update this array to find the
+ * minimum/maximum distance between them.
+ */
+ std::vector<real> distArray_;
+ /*! \brief
+ * Number of pairs within the cutoff that have contributed to the value
+ * in `distArray_`.
+ *
+ * This is needed to identify whether there were any pairs inside the
+ * cutoff and whether there were additional pairs outside the cutoff
+ * that were not covered by the neihborhood search.
+ */
+ std::vector<int> countArray_;
+ /*! \brief
+ * Number of positions within each reference group.
+ *
+ * This is used to more efficiently compute the total number of pairs
+ * (for comparison with `countArray_`), as otherwise these numbers
+ * would need to be recomputed for each selection.
+ */
+ std::vector<int> refCountArray_;
+};
+
+TrajectoryAnalysisModuleDataPointer PairDistance::startFrames(
+ const AnalysisDataParallelOptions &opt,
+ const SelectionCollection &selections)
+{
+ return TrajectoryAnalysisModuleDataPointer(
+ new PairDistanceModuleData(this, opt, selections, refGroupCount_,
+ refSel_, maxGroupCount_));
+}
+
+void
+PairDistance::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
+ TrajectoryAnalysisModuleData *pdata)
+{
+ AnalysisDataHandle dh = pdata->dataHandle(distances_);
+ const Selection &refSel = pdata->parallelSelection(refSel_);
+ const SelectionList &sel = pdata->parallelSelections(sel_);
+ PairDistanceModuleData &frameData = *static_cast<PairDistanceModuleData *>(pdata);
+ std::vector<real> &distArray = frameData.distArray_;
+ std::vector<int> &countArray = frameData.countArray_;
+
+ if (cutoff_ > 0.0 && refSel.isDynamic())
+ {
+ // Count the number of reference positions in each group, so that
+ // this does not need to be computed again for each selection.
+ // This is needed only if it is possible that the neighborhood search
+ // does not cover all the pairs, hence the cutoff > 0.0 check.
+ // If refSel is static, then the array contents are static as well,
+ // and it has been initialized in the constructor of the data object.
+ frameData.initRefCountArray(refSel);
+ }
+ const std::vector<int> &refCountArray = frameData.refCountArray_;
+
+ AnalysisNeighborhoodSearch nbsearch = nb_.initSearch(pbc, refSel);
+ dh.startFrame(frnr, fr.time);
+ for (size_t g = 0; g < sel.size(); ++g)
+ {
+ const int columnCount = distances_.columnCount(g);
+ std::fill(distArray.begin(), distArray.begin() + columnCount, initialDist2_);
+ std::fill(countArray.begin(), countArray.begin() + columnCount, 0);
+
+ // Accumulate the number of position pairs within the cutoff and the
+ // min/max distance for each group pair.
+ AnalysisNeighborhoodPairSearch pairSearch = nbsearch.startPairSearch(sel[g]);
+ AnalysisNeighborhoodPair pair;
+ while (pairSearch.findNextPair(&pair))
+ {
+ const SelectionPosition &refPos = refSel.position(pair.refIndex());
+ const SelectionPosition &selPos = sel[g].position(pair.testIndex());
+ const int refIndex = refPos.mappedId();
+ const int selIndex = selPos.mappedId();
+ const int index = selIndex * refGroupCount_ + refIndex;
+ const real r2 = pair.distance2();
+ if (distanceType_ == eDistanceType_Min)
+ {
+ if (distArray[index] > r2)
+ {
+ distArray[index] = r2;
+ }
+ }
+ else
+ {
+ if (distArray[index] < r2)
+ {
+ distArray[index] = r2;
+ }
+ }
+ ++countArray[index];
+ }
+
+ // If it is possible that positions outside the cutoff (or lack of
+ // them) affects the result, then we need to check whether there were
+ // any. This is necessary for two cases:
+ // - With max distances, if there are pairs outside the cutoff, then
+ // the computed distance should be equal to the cutoff instead of
+ // the largest distance that was found above.
+ // - With either distance type, if all pairs are outside the cutoff,
+ // then countArray must be updated so that the presence flag
+ // in the output data reflects the dynamic selection status, not
+ // whether something was inside the cutoff or not.
+ if (cutoff_ > 0.0)
+ {
+ int selPos = 0;
+ // Loop over groups in this selection (at start, selPos is always
+ // the first position in the next group).
+ while (selPos < sel[g].posCount())
+ {
+ // Count the number of positions in this group.
+ const int selIndex = sel[g].position(selPos).mappedId();
+ const int startPos = selPos;
+ ++selPos;
+ while (selPos < sel[g].posCount()
+ && sel[g].position(selPos).mappedId() == selIndex)
+ {
+ ++selPos;
+ }
+ const int count = selPos - startPos;
+ // Check all group pairs that contain this group.
+ for (int i = 0; i < refGroupCount_; ++i)
+ {
+ const int index = selIndex * refGroupCount_ + i;
+ const int totalCount = refCountArray[i] * count;
+ // If there were positions outside the cutoff,
+ // update the distance if necessary and the count.
+ if (countArray[index] < totalCount)
+ {
+ if (distanceType_ == eDistanceType_Max)
+ {
+ distArray[index] = cutoff2_;
+ }
+ countArray[index] = totalCount;
+ }
+ }
+ }
+ }
+
+ // Write the computed distances to the output data.
+ dh.selectDataSet(g);
+ for (int i = 0; i < columnCount; ++i)
+ {
+ if (countArray[i] > 0)
+ {
+ dh.setPoint(i, std::sqrt(distArray[i]));
+ }
+ else
+ {
+ // If there are no contributing positions, write out the cutoff
+ // value.
+ dh.setPoint(i, cutoff_, false);
+ }
+ }
+ }
+ dh.finishFrame();
+}
+
+void
+PairDistance::finishAnalysis(int /*nframes*/)
+{
+}
+
+void
+PairDistance::writeOutput()
+{
+}
+
+//! \}
+
+} // namespace
+
+const char PairDistanceInfo::name[] = "pairdist";
+const char PairDistanceInfo::shortDescription[] =
+ "Calculate pairwise distances between groups of positions";
+
+TrajectoryAnalysisModulePointer PairDistanceInfo::create()
+{
+ return TrajectoryAnalysisModulePointer(new PairDistance);
+}
+
+} // namespace analysismodules
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Declares trajectory analysis module for pairwise distance calculations.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#ifndef GMX_TRAJECTORYANALYSIS_MODULES_PAIRDIST_H
+#define GMX_TRAJECTORYANALYSIS_MODULES_PAIRDIST_H
+
+#include "gromacs/trajectoryanalysis/analysismodule.h"
+
+namespace gmx
+{
+
+namespace analysismodules
+{
+
+class PairDistanceInfo
+{
+ public:
+ static const char name[];
+ static const char shortDescription[];
+ static TrajectoryAnalysisModulePointer create();
+};
+
+} // namespace analysismodules
+
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements gmx::analysismodules::Rdf.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com> (C++ conversion)
+ * \ingroup module_trajectoryanalysis
+ */
+#include "gmxpre.h"
+
+#include "rdf.h"
+
+#include <cmath>
+
+#include <algorithm>
+#include <limits>
+#include <string>
+#include <vector>
+
+#include "gromacs/analysisdata/analysisdata.h"
+#include "gromacs/analysisdata/modules/average.h"
+#include "gromacs/analysisdata/modules/histogram.h"
+#include "gromacs/analysisdata/modules/plot.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/options.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/selection/nbsearch.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectionoption.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysissettings.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/stringutil.h"
+
+namespace gmx
+{
+
+namespace analysismodules
+{
+
+namespace
+{
+
+//! \addtogroup module_trajectoryanalysis
+//! \{
+
+/********************************************************************
+ * Actual analysis module
+ */
+
+/*! \brief
+ * Implements `gmx rdf` trajectory analysis module.
+ */
+class Rdf : public TrajectoryAnalysisModule
+{
+ public:
+ Rdf();
+
+ virtual void initOptions(Options *options,
+ TrajectoryAnalysisSettings *settings);
+ virtual void optionsFinished(Options *options,
+ TrajectoryAnalysisSettings *settings);
+ virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
+ const TopologyInformation &top);
+ virtual void initAfterFirstFrame(const TrajectoryAnalysisSettings &settings,
+ const t_trxframe &fr);
+
+ virtual TrajectoryAnalysisModuleDataPointer startFrames(
+ const AnalysisDataParallelOptions &opt,
+ const SelectionCollection &selections);
+ virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
+ TrajectoryAnalysisModuleData *pdata);
+
+ virtual void finishAnalysis(int nframes);
+ virtual void writeOutput();
+
+ private:
+ std::string fnRdf_;
+ std::string fnCumulative_;
+ std::string surface_;
+ AnalysisDataPlotSettings plotSettings_;
+
+ /*! \brief
+ * Reference selection to compute RDFs around.
+ *
+ * With -surf, Selection::originalIds() and Selection::mappedIds()
+ * store the index of the surface group to which that position belongs.
+ * The RDF is computed by finding the nearest position from each
+ * surface group for each position, and then binning those distances.
+ */
+ Selection refSel_;
+ /*! \brief
+ * Selections to compute RDFs for.
+ */
+ SelectionList sel_;
+
+ /*! \brief
+ * Raw pairwise distance data from which the RDF is computed.
+ *
+ * There is a data set for each selection in `sel_`, with a single
+ * column. Each point set will contain a single pairwise distance
+ * that contributes to the RDF.
+ */
+ AnalysisData pairDist_;
+ /*! \brief
+ * Normalization factors for each frame.
+ *
+ * The first column contains the number of positions in `refSel_` for
+ * that frame (with surface RDF, the number of groups). There are
+ * `sel_.size()` more columns, each containing the number density of
+ * positions for one selection.
+ */
+ AnalysisData normFactors_;
+ /*! \brief
+ * Histogram module that computes the actual RDF from `pairDist_`.
+ *
+ * The per-frame histograms are raw pair counts in each bin;
+ * the averager is normalized by the average number of reference
+ * positions (average of the first column of `normFactors_`).
+ */
+ AnalysisDataSimpleHistogramModulePointer pairCounts_;
+ /*! \brief
+ * Average normalization factors.
+ */
+ AnalysisDataAverageModulePointer normAve_;
+ //! Neighborhood search with `refSel_` as the reference positions.
+ AnalysisNeighborhood nb_;
+
+ // User input options.
+ double binwidth_;
+ double cutoff_;
+ double rmax_;
+ bool bNormalize_;
+ bool bXY_;
+ bool bExclusions_;
+
+ // Pre-computed values for faster access during analysis.
+ real cut2_;
+ real rmax2_;
+ int surfaceGroupCount_;
+
+ // Copy and assign disallowed by base.
+};
+
+Rdf::Rdf()
+ : TrajectoryAnalysisModule(RdfInfo::name, RdfInfo::shortDescription),
+ pairCounts_(new AnalysisDataSimpleHistogramModule()),
+ normAve_(new AnalysisDataAverageModule()),
+ binwidth_(0.002), cutoff_(0.0), rmax_(0.0),
+ bNormalize_(true), bXY_(false), bExclusions_(false),
+ cut2_(0.0), rmax2_(0.0), surfaceGroupCount_(0)
+{
+ pairDist_.setMultipoint(true);
+ pairDist_.addModule(pairCounts_);
+ registerAnalysisDataset(&pairDist_, "pairdist");
+ registerBasicDataset(pairCounts_.get(), "paircount");
+
+ normFactors_.addModule(normAve_);
+ registerAnalysisDataset(&normFactors_, "norm");
+}
+
+void
+Rdf::initOptions(Options *options, TrajectoryAnalysisSettings * /*settings*/)
+{
+ static const char *const desc[] = {
+ "[THISMODULE] calculates radial distribution functions from one",
+ "refernce set of position (set with [TT]-ref[tt]) to one or more",
+ "sets of positions (set with [TT]-sel[tt]). To compute the RDF with",
+ "respect to the closest position in a set in [TT]-ref[tt] instead, use",
+ "[TT]-surf[tt]: if set, then [TT]-ref[tt] is partitioned into sets",
+ "based on the value of [TT]-surf[tt], and the closest position in each",
+ "set is used. To compute the RDF around axes parallel to the",
+ "[IT]z[it]-axis, i.e., only in the [IT]x[it]-[IT]y[it] plane, use",
+ "[TT]-xy[tt].[PAR]",
+ "To set the bin width and maximum distance to use in the RDF, use",
+ "[TT]-bin[tt] and [TT]-rmax[tt], respectively. The latter can be",
+ "used to limit the computational cost if the RDF is not of interest",
+ "up to the default (half of the box size with PBC, three times the",
+ "box size without PBC).[PAR]",
+ "To use exclusions from the topology ([TT]-s[tt]), set [TT]-excl[tt]",
+ "and ensure that both [TT]-ref[tt] and [TT]-sel[tt] only select atoms.",
+ "A rougher alternative to exclude intra-molecular peaks is to set",
+ "[TT]-cut[tt] to a non-zero value to clear the RDF at small",
+ "distances.[PAR]",
+ "The RDFs are normalized by 1) average number of positions in",
+ "[TT]-ref[tt] (the number of groups with [TT]-surf[tt]), 2) volume",
+ "of the bin, and 3) average particle density of [TT]-sel[tt] positions",
+ "for that selection. To only use the first factor for normalization,",
+ "set [TT]-nonorm[tt]. In this case, the RDF is only scaled with the",
+ "bin width to make the integral of the curve represent the number of",
+ "pairs within a range. Note that exclusions do not affect the",
+ "normalization: even if [TT]-excl[tt] is set, or [TT]-ref[tt] and",
+ "[TT]-sel[tt] contain the same selection, the normalization factor",
+ "is still N*M, not N*(M-excluded).[PAR]",
+ "For [TT]-surf[tt], the selection provided to [TT]-ref[tt] must",
+ "select atoms, i.e., centers of mass are not supported. Further,",
+ "[TT]-nonorm[tt] is implied, as the bins have irregular shapes and",
+ "the volume of a bin is not easily computable.[PAR]",
+ "Option [TT]-cn[tt] produces the cumulative number RDF,",
+ "i.e. the average number of particles within a distance r.[PAR]"
+ };
+
+ options->setDescription(desc);
+
+ options->addOption(FileNameOption("o").filetype(eftPlot).outputFile().required()
+ .store(&fnRdf_).defaultBasename("rdf")
+ .description("Computed RDFs"));
+ options->addOption(FileNameOption("cn").filetype(eftPlot).outputFile()
+ .store(&fnCumulative_).defaultBasename("rdf_cn")
+ .description("Cumulative RDFs"));
+
+ options->addOption(DoubleOption("bin").store(&binwidth_)
+ .description("Bin width (nm)"));
+ options->addOption(BooleanOption("norm").store(&bNormalize_)
+ .description("Normalize for bin volume and density"));
+ options->addOption(BooleanOption("xy").store(&bXY_)
+ .description("Use only the x and y components of the distance"));
+ options->addOption(BooleanOption("excl").store(&bExclusions_)
+ .description("Use exclusions from topology"));
+ options->addOption(DoubleOption("cut").store(&cutoff_)
+ .description("Shortest distance (nm) to be considered"));
+ options->addOption(DoubleOption("rmax").store(&rmax_)
+ .description("Largest distance (nm) to calculate"));
+
+ const char *const cSurfaceEnum[] = { "no", "mol", "res" };
+ options->addOption(StringOption("surf").enumValue(cSurfaceEnum)
+ .defaultEnumIndex(0).store(&surface_)
+ .description("RDF with respect to the surface of the reference"));
+
+ options->addOption(SelectionOption("ref").store(&refSel_).required()
+ .description("Reference selection for RDF computation"));
+ options->addOption(SelectionOption("sel").storeVector(&sel_)
+ .required().multiValue()
+ .description("Selections to compute RDFs for from the reference"));
+}
+
+void
+Rdf::optionsFinished(Options *options, TrajectoryAnalysisSettings *settings)
+{
+ if (surface_ != "no")
+ {
+ settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
+
+ if (options->isSet("norm") && bNormalize_)
+ {
+ GMX_THROW(InconsistentInputError("-surf cannot be combined with -norm"));
+ }
+ bNormalize_ = false;
+ if (bExclusions_)
+ {
+ GMX_THROW(InconsistentInputError("-surf cannot be combined with -excl"));
+ }
+ }
+ if (bExclusions_)
+ {
+ settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
+ }
+ if (cutoff_ < 0.0)
+ {
+ cutoff_ = 0.0;
+ }
+}
+
+void
+Rdf::initAnalysis(const TrajectoryAnalysisSettings &settings,
+ const TopologyInformation &top)
+{
+ pairDist_.setDataSetCount(sel_.size());
+ for (size_t i = 0; i < sel_.size(); ++i)
+ {
+ pairDist_.setColumnCount(i, 1);
+ }
+ plotSettings_ = settings.plotSettings();
+ nb_.setXYMode(bXY_);
+
+ normFactors_.setColumnCount(0, sel_.size() + 1);
+
+ const bool bSurface = (surface_ != "no");
+ if (bSurface)
+ {
+ if (!refSel_.hasOnlyAtoms())
+ {
+ GMX_THROW(InconsistentInputError("-surf only works with -refsel that consists of atoms"));
+ }
+ const e_index_t type = (surface_ == "mol" ? INDEX_MOL : INDEX_RES);
+ surfaceGroupCount_ = refSel_.initOriginalIdsToGroup(top.topology(), type);
+ }
+
+ if (bExclusions_)
+ {
+ if (!refSel_.hasOnlyAtoms())
+ {
+ GMX_THROW(InconsistentInputError("-excl only works with selections that consist of atoms"));
+ }
+ for (size_t i = 0; i < sel_.size(); ++i)
+ {
+ if (!sel_[i].hasOnlyAtoms())
+ {
+ GMX_THROW(InconsistentInputError("-excl only works with selections that consist of atoms"));
+ }
+ }
+ const t_topology *topology = top.topology();
+ if (topology->excls.nr == 0)
+ {
+ GMX_THROW(InconsistentInputError("-excl is set, but the file provided to -s does not define exclusions"));
+ }
+ nb_.setTopologyExclusions(&topology->excls);
+ }
+}
+
+void
+Rdf::initAfterFirstFrame(const TrajectoryAnalysisSettings &settings,
+ const t_trxframe &fr)
+{
+ // If -rmax is not provided, determine one from the box for the first frame.
+ if (rmax_ <= 0.0)
+ {
+ matrix box;
+ copy_mat(fr.box, box);
+ if (settings.hasPBC())
+ {
+ if (bXY_)
+ {
+ box[ZZ][ZZ] = 2*std::max(box[XX][XX], box[YY][YY]);
+ }
+ rmax_ = std::sqrt(0.99*0.99*max_cutoff2(bXY_ ? epbcXY : epbcXYZ, box));
+ }
+ else
+ {
+ if (bXY_)
+ {
+ clear_rvec(box[ZZ]);
+ }
+ rmax_ = 3*std::max(box[XX][XX], std::max(box[YY][YY], box[ZZ][ZZ]));
+ }
+ }
+ cut2_ = sqr(cutoff_);
+ rmax2_ = sqr(rmax_);
+ nb_.setCutoff(rmax_);
+ // We use the double amount of bins, so we can correctly
+ // write the rdf and rdf_cn output at i*binwidth values.
+ pairCounts_->init(histogramFromRange(0.0, rmax_).binWidth(binwidth_ / 2.0));
+}
+
+/*! \brief
+ * Temporary memory for use within a single-frame calculation.
+ */
+class RdfModuleData : public TrajectoryAnalysisModuleData
+{
+ public:
+ /*! \brief
+ * Reserves memory for the frame-local data.
+ *
+ * `surfaceGroupCount` will be zero if -surf is not specified.
+ */
+ RdfModuleData(TrajectoryAnalysisModule *module,
+ const AnalysisDataParallelOptions &opt,
+ const SelectionCollection &selections,
+ int surfaceGroupCount)
+ : TrajectoryAnalysisModuleData(module, opt, selections)
+ {
+ surfaceDist2_.resize(surfaceGroupCount);
+ }
+
+ virtual void finish() { finishDataHandles(); }
+
+ /*! \brief
+ * Minimum distance to each surface group.
+ *
+ * One entry for each group (residue/molecule, per -surf) in the
+ * reference selection.
+ * This is needed to support neighborhood searching, which may not
+ * return the reference positions in order: for each position, we need
+ * to search through all the reference positions and update this array
+ * to find the minimum distance to each surface group, and then compute
+ * the RDF from these numbers.
+ */
+ std::vector<real> surfaceDist2_;
+};
+
+TrajectoryAnalysisModuleDataPointer Rdf::startFrames(
+ const AnalysisDataParallelOptions &opt,
+ const SelectionCollection &selections)
+{
+ return TrajectoryAnalysisModuleDataPointer(
+ new RdfModuleData(this, opt, selections, surfaceGroupCount_));
+}
+
+void
+Rdf::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
+ TrajectoryAnalysisModuleData *pdata)
+{
+ AnalysisDataHandle dh = pdata->dataHandle(pairDist_);
+ AnalysisDataHandle nh = pdata->dataHandle(normFactors_);
+ const Selection &refSel = pdata->parallelSelection(refSel_);
+ const SelectionList &sel = pdata->parallelSelections(sel_);
+ RdfModuleData &frameData = *static_cast<RdfModuleData *>(pdata);
+ const bool bSurface = !frameData.surfaceDist2_.empty();
+
+ matrix boxForVolume;
+ copy_mat(fr.box, boxForVolume);
+ if (bXY_)
+ {
+ // Set z-size to 1 so we get the surface are iso the volume
+ clear_rvec(boxForVolume[ZZ]);
+ boxForVolume[ZZ][ZZ] = 1;
+ }
+ const real inverseVolume = 1.0 / det(boxForVolume);
+
+ nh.startFrame(frnr, fr.time);
+ // Compute the normalization factor for the number of reference positions.
+ if (bSurface)
+ {
+ if (refSel.isDynamic())
+ {
+ // Count the number of distinct groups.
+ // This assumes that each group is continuous, which is currently
+ // the case.
+ int count = 0;
+ int prevId = -1;
+ for (int i = 0; i < refSel.posCount(); ++i)
+ {
+ const int id = refSel.position(i).mappedId();
+ if (id != prevId)
+ {
+ ++count;
+ prevId = id;
+ }
+ }
+ nh.setPoint(0, count);
+ }
+ else
+ {
+ nh.setPoint(0, surfaceGroupCount_);
+ }
+ }
+ else
+ {
+ nh.setPoint(0, refSel.posCount());
+ }
+
+ dh.startFrame(frnr, fr.time);
+ AnalysisNeighborhoodSearch nbsearch = nb_.initSearch(pbc, refSel);
+ for (size_t g = 0; g < sel.size(); ++g)
+ {
+ dh.selectDataSet(g);
+
+ if (bSurface)
+ {
+ // Special loop for surface calculation, where a separate neighbor
+ // search is done for each position in the selection, and the
+ // nearest position from each surface group is tracked.
+ std::vector<real> &surfaceDist2 = frameData.surfaceDist2_;
+ for (int i = 0; i < sel[g].posCount(); ++i)
+ {
+ std::fill(surfaceDist2.begin(), surfaceDist2.end(),
+ std::numeric_limits<real>::max());
+ AnalysisNeighborhoodPairSearch pairSearch =
+ nbsearch.startPairSearch(sel[g].position(i));
+ AnalysisNeighborhoodPair pair;
+ while (pairSearch.findNextPair(&pair))
+ {
+ const real r2 = pair.distance2();
+ const int refId = refSel.position(pair.refIndex()).mappedId();
+ if (r2 < surfaceDist2[refId])
+ {
+ surfaceDist2[refId] = r2;
+ }
+ }
+ // Accumulate the RDF from the distances to the surface.
+ for (size_t i = 0; i < surfaceDist2.size(); ++i)
+ {
+ const real r2 = surfaceDist2[i];
+ // Here, we need to check for rmax, since the value might
+ // be above the cutoff if no points were close to some
+ // surface positions.
+ if (r2 > cut2_ && r2 <= rmax2_)
+ {
+ dh.setPoint(0, std::sqrt(r2));
+ dh.finishPointSet();
+ }
+ }
+ }
+ }
+ else
+ {
+ // Standard neighborhood search over all pairs within the cutoff
+ // for the -surf no case.
+ AnalysisNeighborhoodPairSearch pairSearch = nbsearch.startPairSearch(sel[g]);
+ AnalysisNeighborhoodPair pair;
+ while (pairSearch.findNextPair(&pair))
+ {
+ const real r2 = pair.distance2();
+ if (r2 > cut2_)
+ {
+ // TODO: Consider whether the histogramming could be done with
+ // less overhead (after first measuring the overhead).
+ dh.setPoint(0, std::sqrt(r2));
+ dh.finishPointSet();
+ }
+ }
+ }
+ // Normalization factor for the number density (only used without
+ // -surf, but does not hurt to populate otherwise).
+ nh.setPoint(g + 1, sel[g].posCount() * inverseVolume);
+ }
+ dh.finishFrame();
+ nh.finishFrame();
+}
+
+void
+Rdf::finishAnalysis(int /*nframes*/)
+{
+ // Normalize the averager with the number of reference positions,
+ // from where the normalization propagates to all the output.
+ const real refPosCount = normAve_->average(0, 0);
+ pairCounts_->averager().scaleAll(1.0 / refPosCount);
+ pairCounts_->averager().done();
+
+ // TODO: Consider how these could be exposed to the testing framework
+ // through the dataset registration mechanism.
+ AverageHistogramPointer finalRdf
+ = pairCounts_->averager().resampleDoubleBinWidth(true);
+
+ if (bNormalize_)
+ {
+ // Normalize by the volume of the bins (volume of sphere segments or
+ // length of circle segments).
+ std::vector<real> invBinVolume;
+ const int nbin = finalRdf->settings().binCount();
+ invBinVolume.resize(nbin);
+ real prevSphereVolume = 0.0;
+ for (int i = 0; i < nbin; ++i)
+ {
+ const real r = (i + 0.5)*binwidth_;
+ real sphereVolume;
+ if (bXY_)
+ {
+ sphereVolume = M_PI*r*r;
+ }
+ else
+ {
+ sphereVolume = (4.0/3.0)*M_PI*r*r*r;
+ }
+ const real binVolume = sphereVolume - prevSphereVolume;
+ invBinVolume[i] = 1.0 / binVolume;
+ prevSphereVolume = sphereVolume;
+ }
+ finalRdf->scaleAllByVector(&invBinVolume[0]);
+
+ // Normalize by particle density.
+ for (size_t g = 0; g < sel_.size(); ++g)
+ {
+ finalRdf->scaleSingle(g, 1.0 / normAve_->average(0, g + 1));
+ }
+ }
+ else
+ {
+ // With -nonorm, just scale with bin width to make the integral of the
+ // curve (instead of raw bin sum) represent the pair count.
+ finalRdf->scaleAll(1.0 / binwidth_);
+ }
+ finalRdf->done();
+
+ // TODO: Consider if some of this should be done in writeOutput().
+ {
+ AnalysisDataPlotModulePointer plotm(
+ new AnalysisDataPlotModule(plotSettings_));
+ plotm->setFileName(fnRdf_);
+ plotm->setTitle("Radial distribution");
+ plotm->setSubtitle(formatString("reference %s", refSel_.name()));
+ plotm->setXLabel("r (nm)");
+ plotm->setYLabel("g(r)");
+ for (size_t i = 0; i < sel_.size(); ++i)
+ {
+ plotm->appendLegend(sel_[i].name());
+ }
+ finalRdf->addModule(plotm);
+ }
+
+ if (!fnCumulative_.empty())
+ {
+ AverageHistogramPointer cumulativeRdf
+ = pairCounts_->averager().resampleDoubleBinWidth(false);
+ cumulativeRdf->makeCumulative();
+ cumulativeRdf->done();
+
+ AnalysisDataPlotModulePointer plotm(
+ new AnalysisDataPlotModule(plotSettings_));
+ plotm->setFileName(fnCumulative_);
+ plotm->setTitle("Cumulative Number RDF");
+ plotm->setSubtitle(formatString("reference %s", refSel_.name()));
+ plotm->setXLabel("r (nm)");
+ plotm->setYLabel("number");
+ for (size_t i = 0; i < sel_.size(); ++i)
+ {
+ plotm->appendLegend(sel_[i].name());
+ }
+ cumulativeRdf->addModule(plotm);
+ }
+}
+
+void
+Rdf::writeOutput()
+{
+}
+
+//! \}
+
+} // namespace
+
+const char RdfInfo::name[] = "rdf";
+const char RdfInfo::shortDescription[] =
+ "Calculate radial distribution functions";
+
+TrajectoryAnalysisModulePointer RdfInfo::create()
+{
+ return TrajectoryAnalysisModulePointer(new Rdf);
+}
+
+} // namespace analysismodules
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Declares trajectory analysis module for RDF calculations.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#ifndef GMX_TRAJECTORYANALYSIS_MODULES_RDF_H
+#define GMX_TRAJECTORYANALYSIS_MODULES_RDF_H
+
+#include "gromacs/trajectoryanalysis/analysismodule.h"
+
+namespace gmx
+{
+
+namespace analysismodules
+{
+
+class RdfInfo
+{
+ public:
+ static const char name[];
+ static const char shortDescription[];
+ static TrajectoryAnalysisModulePointer create();
+};
+
+} // namespace analysismodules
+
+} // namespace gmx
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2006, The GROMACS development team.
- * Copyright (c) 2008,2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com> (C++ conversion)
* \ingroup module_trajectoryanalysis
*/
+#include "gmxpre.h"
+
#include "sasa.h"
#include <algorithm>
#include <string>
#include <vector>
-#include "gromacs/legacyheaders/atomprop.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/physics.h"
-#include "gromacs/legacyheaders/symtab.h"
-#include "gromacs/legacyheaders/vec.h"
-
#include "gromacs/analysisdata/analysisdata.h"
#include "gromacs/analysisdata/modules/average.h"
#include "gromacs/analysisdata/modules/plot.h"
#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/options/options.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/selection.h"
#include "gromacs/selection/selectionoption.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/trajectoryanalysis/analysismodule.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
#include "gromacs/utility/exceptions.h"
-#include "gromacs/utility/scoped_ptr_sfree.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/scoped_cptr.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
-#include "nsc.h"
+#include "surfacearea.h"
namespace gmx
{
* Empty if the free energy output has not been requested.
*/
std::vector<real> dgsFactor_;
+ //! Calculation algorithm.
+ SurfaceAreaCalculator calculator_;
// Copy and assign disallowed by base.
};
//"which can be used to restrain surface atoms.[PAR]",
"With the [TT]-tv[tt] option the total volume and density of the",
- "molecule can be computed.",
- "Please consider whether the normal probe radius is appropriate",
+ "molecule can be computed. With [TT]-pbc[tt] (the default), you",
+ "must ensure that your molecule/surface group is not split across PBC.",
+ "Otherwise, you will get non-sensical results.",
+ "Please also consider whether the normal probe radius is appropriate",
"in this case or whether you would rather use, e.g., 0. It is good",
"to keep in mind that the results for volume and density are very",
"approximate. For example, in ice Ih, one can easily fit water molecules in the",
dgsFactor_.reserve(surfaceSel_.posCount());
}
+ const int resCount = surfaceSel_.initOriginalIdsToGroup(top_, INDEX_RES);
+
// TODO: Not exception-safe, but nice solution would be to have a C++
// atom properties class...
gmx_atomprop_t aps = gmx_atomprop_init();
ConstArrayRef<int> atomIndices = surfaceSel_.atomIndices();
- int prevResind = atoms.atom[atomIndices[0]].resind;
- int resCount = 0;
int ndefault = 0;
for (int i = 0; i < surfaceSel_.posCount(); i++)
{
const int ii = atomIndices[i];
const int resind = atoms.atom[ii].resind;
- if (resind != prevResind)
- {
- ++resCount;
- prevResind = resind;
- }
- surfaceSel_.setOriginalId(i, resCount);
real radius;
if (!gmx_atomprop_query(aps, epropVDW,
*(atoms.resinfo[resind].name),
}
gmx_atomprop_destroy(aps);
- // The loop above doesn't count the last residue.
- ++resCount;
-
// Pre-compute mapping from the output groups to the calculation group,
// and store it in the selection ID map for easy lookup.
for (size_t g = 0; g < outputSel_.size(); ++g)
}
}
+ calculator_.setDotCount(ndots_);
+ calculator_.setRadii(radii_);
+
// Initialize all the output data objects and initialize the output plotters.
area_.setColumnCount(0, 1 + outputSel_.size());
real totarea, totvolume;
real *area = NULL, *surfacedots = NULL;
int nsurfacedots;
- int retval = nsc_dclm_pbc(surfaceSel.coordinates().data(), &radii_[0],
- frameData.index_.size(), ndots_, flag, &totarea,
- &area, &totvolume, &surfacedots, &nsurfacedots,
- &frameData.index_[0],
- pbc != NULL ? pbc->ePBC : epbcNONE,
- pbc != NULL ? pbc->box : NULL);
+ calculator_.calculate(surfaceSel.coordinates().data(), pbc,
+ frameData.index_.size(), &frameData.index_[0], flag,
+ &totarea, &totvolume, &area,
+ &surfacedots, &nsurfacedots);
// Unpack the atomwise areas into the frameData.atomAreas_ array for easier
// indexing in the case of dynamic surfaceSel.
if (area != NULL)
}
sfree(area);
}
- scoped_ptr_sfree dotsGuard(surfacedots);
- if (retval != 0)
- {
- GMX_THROW(InternalError("nsc_dclm_pbc failed"));
- }
+ scoped_guard_sfree dotsGuard(surfacedots);
if (bConnolly)
{
#ifndef GMX_TRAJECTORYANALYSIS_MODULES_SASA_H
#define GMX_TRAJECTORYANALYSIS_MODULES_SASA_H
-#include "../analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
namespace gmx
{
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
+#include "gmxpre.h"
+
#include "select.h"
#include <cstdio>
#include "gromacs/analysisdata/modules/lifetime.h"
#include "gromacs/analysisdata/modules/plot.h"
#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/trx.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/options/options.h"
#include "gromacs/selection/selection.h"
#include "gromacs/selection/selectionoption.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/scoped_ptr_sfree.h"
+#include "gromacs/utility/scoped_cptr.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
{
GMX_RELEASE_ASSERT(top_->hasTopology(),
"Topology should have been loaded or an error given earlier");
- t_atoms atoms;
+ t_atoms atoms;
atoms = top_->topology()->atoms;
- t_pdbinfo *pdbinfo;
+ t_pdbinfo *pdbinfo;
snew(pdbinfo, atoms.nr);
- scoped_ptr_sfree pdbinfoGuard(pdbinfo);
+ scoped_guard_sfree pdbinfoGuard(pdbinfo);
if (atoms.pdbinfo != NULL)
{
std::memcpy(pdbinfo, atoms.pdbinfo, atoms.nr*sizeof(*pdbinfo));
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TRAJECTORYANALYSIS_MODULES_SELECT_H
#define GMX_TRAJECTORYANALYSIS_MODULES_SELECT_H
-#include "../analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
namespace gmx
{
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2007, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "surfacearea.h"
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include <algorithm>
+#include <vector>
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/selection/nbsearch.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
+
+using namespace gmx;
+
+#define UNSP_ICO_DOD 9
+#define UNSP_ICO_ARC 10
+
+#define FOURPI (4.*M_PI)
+#define TORAD(A) ((A)*0.017453293)
+#define DP_TOL 0.001
+
+static real safe_asin(real f)
+{
+ if ( (fabs(f) < 1.00) )
+ {
+ return( asin(f) );
+ }
+ GMX_ASSERT(fabs(f) - 1.0 > DP_TOL, "Invalid argument");
+ return(M_PI_2);
+}
+
+/* routines for dot distributions on the surface of the unit sphere */
+static real icosaeder_vertices(real *xus)
+{
+ const real rh = sqrt(1.-2.*cos(TORAD(72.)))/(1.-cos(TORAD(72.)));
+ const real rg = cos(TORAD(72.))/(1.-cos(TORAD(72.)));
+ /* icosaeder vertices */
+ xus[ 0] = 0.; xus[ 1] = 0.; xus[ 2] = 1.;
+ xus[ 3] = rh*cos(TORAD(72.)); xus[ 4] = rh*sin(TORAD(72.)); xus[ 5] = rg;
+ xus[ 6] = rh*cos(TORAD(144.)); xus[ 7] = rh*sin(TORAD(144.)); xus[ 8] = rg;
+ xus[ 9] = rh*cos(TORAD(216.)); xus[10] = rh*sin(TORAD(216.)); xus[11] = rg;
+ xus[12] = rh*cos(TORAD(288.)); xus[13] = rh*sin(TORAD(288.)); xus[14] = rg;
+ xus[15] = rh; xus[16] = 0; xus[17] = rg;
+ xus[18] = rh*cos(TORAD(36.)); xus[19] = rh*sin(TORAD(36.)); xus[20] = -rg;
+ xus[21] = rh*cos(TORAD(108.)); xus[22] = rh*sin(TORAD(108.)); xus[23] = -rg;
+ xus[24] = -rh; xus[25] = 0; xus[26] = -rg;
+ xus[27] = rh*cos(TORAD(252.)); xus[28] = rh*sin(TORAD(252.)); xus[29] = -rg;
+ xus[30] = rh*cos(TORAD(324.)); xus[31] = rh*sin(TORAD(324.)); xus[32] = -rg;
+ xus[33] = 0.; xus[34] = 0.; xus[35] = -1.;
+ return rh;
+}
+
+
+static void divarc(real x1, real y1, real z1,
+ real x2, real y2, real z2,
+ int div1, int div2, real *xr, real *yr, real *zr)
+{
+
+ real xd, yd, zd, dd, d1, d2, s, x, y, z;
+ real phi, sphi, cphi;
+
+ xd = y1*z2-y2*z1;
+ yd = z1*x2-z2*x1;
+ zd = x1*y2-x2*y1;
+ dd = sqrt(xd*xd+yd*yd+zd*zd);
+ GMX_ASSERT(dd >= DP_TOL, "Rotation axis vector too short");
+
+ d1 = x1*x1+y1*y1+z1*z1;
+ d2 = x2*x2+y2*y2+z2*z2;
+ GMX_ASSERT(d1 >= 0.5, "Vector 1 too short");
+ GMX_ASSERT(d2 >= 0.5, "Vector 2 too short");
+
+ phi = safe_asin(dd/sqrt(d1*d2));
+ phi = phi*((real)div1)/((real)div2);
+ sphi = sin(phi); cphi = cos(phi);
+ s = (x1*xd+y1*yd+z1*zd)/dd;
+
+ x = xd*s*(1.-cphi)/dd + x1 * cphi + (yd*z1-y1*zd)*sphi/dd;
+ y = yd*s*(1.-cphi)/dd + y1 * cphi + (zd*x1-z1*xd)*sphi/dd;
+ z = zd*s*(1.-cphi)/dd + z1 * cphi + (xd*y1-x1*yd)*sphi/dd;
+ dd = sqrt(x*x+y*y+z*z);
+ *xr = x/dd; *yr = y/dd; *zr = z/dd;
+}
+
+/* densit...required dots per unit sphere */
+static std::vector<real> ico_dot_arc(int densit)
+{
+ /* dot distribution on a unit sphere based on an icosaeder *
+ * great circle average refining of icosahedral face */
+
+ int i, j, k, tl, tl2, tn;
+ real a, d, x, y, z, x2, y2, z2, x3, y3, z3;
+ real xij, yij, zij, xji, yji, zji, xik, yik, zik, xki, yki, zki,
+ xjk, yjk, zjk, xkj, ykj, zkj;
+
+ /* calculate tessalation level */
+ a = sqrt((((real) densit)-2.)/10.);
+ const int tess = (int) ceil(a);
+ const int ndot = 10*tess*tess+2;
+ GMX_RELEASE_ASSERT(ndot >= densit, "Inconsistent surface dot formula");
+
+ std::vector<real> xus(3*ndot);
+ const real rh = icosaeder_vertices(&xus[0]);
+
+ if (tess > 1)
+ {
+ tn = 12;
+ a = rh*rh*2.*(1.-cos(TORAD(72.)));
+ /* calculate tessalation of icosaeder edges */
+ for (i = 0; i < 11; i++)
+ {
+ for (j = i+1; j < 12; j++)
+ {
+ x = xus[3*i]-xus[3*j];
+ y = xus[1+3*i]-xus[1+3*j]; z = xus[2+3*i]-xus[2+3*j];
+ d = x*x+y*y+z*z;
+ if (fabs(a-d) > DP_TOL)
+ {
+ continue;
+ }
+ for (tl = 1; tl < tess; tl++)
+ {
+ GMX_ASSERT(tn < ndot, "Inconsistent precomputed surface dot count");
+ divarc(xus[3*i], xus[1+3*i], xus[2+3*i],
+ xus[3*j], xus[1+3*j], xus[2+3*j],
+ tl, tess, &xus[3*tn], &xus[1+3*tn], &xus[2+3*tn]);
+ tn++;
+ }
+ }
+ }
+ /* calculate tessalation of icosaeder faces */
+ for (i = 0; i < 10; i++)
+ {
+ for (j = i+1; j < 11; j++)
+ {
+ x = xus[3*i]-xus[3*j];
+ y = xus[1+3*i]-xus[1+3*j]; z = xus[2+3*i]-xus[2+3*j];
+ d = x*x+y*y+z*z;
+ if (fabs(a-d) > DP_TOL)
+ {
+ continue;
+ }
+
+ for (k = j+1; k < 12; k++)
+ {
+ x = xus[3*i]-xus[3*k];
+ y = xus[1+3*i]-xus[1+3*k]; z = xus[2+3*i]-xus[2+3*k];
+ d = x*x+y*y+z*z;
+ if (fabs(a-d) > DP_TOL)
+ {
+ continue;
+ }
+ x = xus[3*j]-xus[3*k];
+ y = xus[1+3*j]-xus[1+3*k]; z = xus[2+3*j]-xus[2+3*k];
+ d = x*x+y*y+z*z;
+ if (fabs(a-d) > DP_TOL)
+ {
+ continue;
+ }
+ for (tl = 1; tl < tess-1; tl++)
+ {
+ divarc(xus[3*j], xus[1+3*j], xus[2+3*j],
+ xus[3*i], xus[1+3*i], xus[2+3*i],
+ tl, tess, &xji, &yji, &zji);
+ divarc(xus[3*k], xus[1+3*k], xus[2+3*k],
+ xus[3*i], xus[1+3*i], xus[2+3*i],
+ tl, tess, &xki, &yki, &zki);
+
+ for (tl2 = 1; tl2 < tess-tl; tl2++)
+ {
+ divarc(xus[3*i], xus[1+3*i], xus[2+3*i],
+ xus[3*j], xus[1+3*j], xus[2+3*j],
+ tl2, tess, &xij, &yij, &zij);
+ divarc(xus[3*k], xus[1+3*k], xus[2+3*k],
+ xus[3*j], xus[1+3*j], xus[2+3*j],
+ tl2, tess, &xkj, &ykj, &zkj);
+ divarc(xus[3*i], xus[1+3*i], xus[2+3*i],
+ xus[3*k], xus[1+3*k], xus[2+3*k],
+ tess-tl-tl2, tess, &xik, &yik, &zik);
+ divarc(xus[3*j], xus[1+3*j], xus[2+3*j],
+ xus[3*k], xus[1+3*k], xus[2+3*k],
+ tess-tl-tl2, tess, &xjk, &yjk, &zjk);
+ divarc(xki, yki, zki, xji, yji, zji, tl2, tess-tl,
+ &x, &y, &z);
+ divarc(xkj, ykj, zkj, xij, yij, zij, tl, tess-tl2,
+ &x2, &y2, &z2);
+ divarc(xjk, yjk, zjk, xik, yik, zik, tl, tl+tl2,
+ &x3, &y3, &z3);
+ GMX_ASSERT(tn < ndot,
+ "Inconsistent precomputed surface dot count");
+ x = x+x2+x3; y = y+y2+y3; z = z+z2+z3;
+ d = sqrt(x*x+y*y+z*z);
+ xus[3*tn] = x/d;
+ xus[1+3*tn] = y/d;
+ xus[2+3*tn] = z/d;
+ tn++;
+ } /* cycle tl2 */
+ } /* cycle tl */
+ } /* cycle k */
+ } /* cycle j */
+ } /* cycle i */
+ GMX_ASSERT(tn == ndot, "Inconsistent precomputed surface dot count");
+ } /* end of if (tess > 1) */
+
+ return xus;
+} /* end of routine ico_dot_arc */
+
+/* densit...required dots per unit sphere */
+static std::vector<real> ico_dot_dod(int densit)
+{
+ /* dot distribution on a unit sphere based on an icosaeder *
+ * great circle average refining of icosahedral face */
+
+ int i, j, k, tl, tl2, tn, tess, j1, j2;
+ real a, d, x, y, z, x2, y2, z2, x3, y3, z3, ai_d, adod;
+ real xij, yij, zij, xji, yji, zji, xik, yik, zik, xki, yki, zki,
+ xjk, yjk, zjk, xkj, ykj, zkj;
+
+ /* calculate tesselation level */
+ a = sqrt((((real) densit)-2.)/30.);
+ tess = std::max((int) ceil(a), 1);
+ const int ndot = 30*tess*tess+2;
+ GMX_RELEASE_ASSERT(ndot >= densit, "Inconsistent surface dot formula");
+
+ std::vector<real> xus(3*ndot);
+ const real rh = icosaeder_vertices(&xus[0]);
+
+ tn = 12;
+ /* square of the edge of an icosaeder */
+ a = rh*rh*2.*(1.-cos(TORAD(72.)));
+ /* dodecaeder vertices */
+ for (i = 0; i < 10; i++)
+ {
+ for (j = i+1; j < 11; j++)
+ {
+ x = xus[3*i]-xus[3*j];
+ y = xus[1+3*i]-xus[1+3*j]; z = xus[2+3*i]-xus[2+3*j];
+ d = x*x+y*y+z*z;
+ if (fabs(a-d) > DP_TOL)
+ {
+ continue;
+ }
+ for (k = j+1; k < 12; k++)
+ {
+ x = xus[3*i]-xus[3*k];
+ y = xus[1+3*i]-xus[1+3*k]; z = xus[2+3*i]-xus[2+3*k];
+ d = x*x+y*y+z*z;
+ if (fabs(a-d) > DP_TOL)
+ {
+ continue;
+ }
+ x = xus[3*j]-xus[3*k];
+ y = xus[1+3*j]-xus[1+3*k]; z = xus[2+3*j]-xus[2+3*k];
+ d = x*x+y*y+z*z;
+ if (fabs(a-d) > DP_TOL)
+ {
+ continue;
+ }
+ x = xus[ 3*i]+xus[ 3*j]+xus[ 3*k];
+ y = xus[1+3*i]+xus[1+3*j]+xus[1+3*k];
+ z = xus[2+3*i]+xus[2+3*j]+xus[2+3*k];
+ d = sqrt(x*x+y*y+z*z);
+ xus[3*tn] = x/d; xus[1+3*tn] = y/d; xus[2+3*tn] = z/d;
+ tn++;
+ }
+ }
+ }
+
+ if (tess > 1)
+ {
+ tn = 32;
+ /* square of the edge of an dodecaeder */
+ adod = 4.*(cos(TORAD(108.))-cos(TORAD(120.)))/(1.-cos(TORAD(120.)));
+ /* square of the distance of two adjacent vertices of ico- and dodecaeder */
+ ai_d = 2.*(1.-sqrt(1.-a/3.));
+
+ /* calculate tessalation of mixed edges */
+ for (i = 0; i < 31; i++)
+ {
+ j1 = 12; j2 = 32; a = ai_d;
+ if (i >= 12)
+ {
+ j1 = i+1; a = adod;
+ }
+ for (j = j1; j < j2; j++)
+ {
+ x = xus[3*i]-xus[3*j];
+ y = xus[1+3*i]-xus[1+3*j]; z = xus[2+3*i]-xus[2+3*j];
+ d = x*x+y*y+z*z;
+ if (fabs(a-d) > DP_TOL)
+ {
+ continue;
+ }
+ for (tl = 1; tl < tess; tl++)
+ {
+ GMX_ASSERT(tn < ndot,
+ "Inconsistent precomputed surface dot count");
+ divarc(xus[3*i], xus[1+3*i], xus[2+3*i],
+ xus[3*j], xus[1+3*j], xus[2+3*j],
+ tl, tess, &xus[3*tn], &xus[1+3*tn], &xus[2+3*tn]);
+ tn++;
+ }
+ }
+ }
+ /* calculate tessalation of pentakisdodecahedron faces */
+ for (i = 0; i < 12; i++)
+ {
+ for (j = 12; j < 31; j++)
+ {
+ x = xus[3*i]-xus[3*j];
+ y = xus[1+3*i]-xus[1+3*j]; z = xus[2+3*i]-xus[2+3*j];
+ d = x*x+y*y+z*z;
+ if (fabs(ai_d-d) > DP_TOL)
+ {
+ continue;
+ }
+
+ for (k = j+1; k < 32; k++)
+ {
+ x = xus[3*i]-xus[3*k];
+ y = xus[1+3*i]-xus[1+3*k]; z = xus[2+3*i]-xus[2+3*k];
+ d = x*x+y*y+z*z;
+ if (fabs(ai_d-d) > DP_TOL)
+ {
+ continue;
+ }
+ x = xus[3*j]-xus[3*k];
+ y = xus[1+3*j]-xus[1+3*k]; z = xus[2+3*j]-xus[2+3*k];
+ d = x*x+y*y+z*z;
+ if (fabs(adod-d) > DP_TOL)
+ {
+ continue;
+ }
+ for (tl = 1; tl < tess-1; tl++)
+ {
+ divarc(xus[3*j], xus[1+3*j], xus[2+3*j],
+ xus[3*i], xus[1+3*i], xus[2+3*i],
+ tl, tess, &xji, &yji, &zji);
+ divarc(xus[3*k], xus[1+3*k], xus[2+3*k],
+ xus[3*i], xus[1+3*i], xus[2+3*i],
+ tl, tess, &xki, &yki, &zki);
+
+ for (tl2 = 1; tl2 < tess-tl; tl2++)
+ {
+ divarc(xus[3*i], xus[1+3*i], xus[2+3*i],
+ xus[3*j], xus[1+3*j], xus[2+3*j],
+ tl2, tess, &xij, &yij, &zij);
+ divarc(xus[3*k], xus[1+3*k], xus[2+3*k],
+ xus[3*j], xus[1+3*j], xus[2+3*j],
+ tl2, tess, &xkj, &ykj, &zkj);
+ divarc(xus[3*i], xus[1+3*i], xus[2+3*i],
+ xus[3*k], xus[1+3*k], xus[2+3*k],
+ tess-tl-tl2, tess, &xik, &yik, &zik);
+ divarc(xus[3*j], xus[1+3*j], xus[2+3*j],
+ xus[3*k], xus[1+3*k], xus[2+3*k],
+ tess-tl-tl2, tess, &xjk, &yjk, &zjk);
+ divarc(xki, yki, zki, xji, yji, zji, tl2, tess-tl,
+ &x, &y, &z);
+ divarc(xkj, ykj, zkj, xij, yij, zij, tl, tess-tl2,
+ &x2, &y2, &z2);
+ divarc(xjk, yjk, zjk, xik, yik, zik, tl, tl+tl2,
+ &x3, &y3, &z3);
+ GMX_ASSERT(tn < ndot,
+ "Inconsistent precomputed surface dot count");
+ x = x+x2+x3; y = y+y2+y3; z = z+z2+z3;
+ d = sqrt(x*x+y*y+z*z);
+ xus[3*tn] = x/d;
+ xus[1+3*tn] = y/d;
+ xus[2+3*tn] = z/d;
+ tn++;
+ } /* cycle tl2 */
+ } /* cycle tl */
+ } /* cycle k */
+ } /* cycle j */
+ } /* cycle i */
+ GMX_ASSERT(tn == ndot, "Inconsistent precomputed surface dot count");
+ } /* end of if (tess > 1) */
+
+ return xus;
+} /* end of routine ico_dot_dod */
+
+static int unsp_type(int densit)
+{
+ int i1, i2;
+ i1 = 1;
+ while (10*i1*i1+2 < densit)
+ {
+ i1++;
+ }
+ i2 = 1;
+ while (30*i2*i2+2 < densit)
+ {
+ i2++;
+ }
+ if (10*i1*i1-2 < 30*i2*i2-2)
+ {
+ return UNSP_ICO_ARC;
+ }
+ else
+ {
+ return UNSP_ICO_DOD;
+ }
+}
+
+static std::vector<real> make_unsp(int densit, int cubus)
+{
+ int *ico_wk, *ico_pt;
+ int ico_cube, ico_cube_cb, i, j, k, l, ijk, tn, tl, tl2;
+ int *work;
+ real x, y, z;
+
+ int mode = unsp_type(densit);
+ std::vector<real> xus;
+ if (mode == UNSP_ICO_ARC)
+ {
+ xus = ico_dot_arc(densit);
+ }
+ else if (mode == UNSP_ICO_DOD)
+ {
+ xus = ico_dot_dod(densit);
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(false, "Invalid unit sphere mode");
+ }
+
+ const int ndot = static_cast<int>(xus.size())/3;
+
+ /* determine distribution of points in elementary cubes */
+ if (cubus)
+ {
+ ico_cube = cubus;
+ }
+ else
+ {
+ i = 1;
+ while (i*i*i*2 < ndot)
+ {
+ i++;
+ }
+ ico_cube = std::max(i-1, 0);
+ }
+ ico_cube_cb = ico_cube*ico_cube*ico_cube;
+ const real del_cube = 2./((real)ico_cube);
+ snew(work, ndot);
+ for (l = 0; l < ndot; l++)
+ {
+ i = std::max((int) floor((1.+xus[3*l])/del_cube), 0);
+ if (i >= ico_cube)
+ {
+ i = ico_cube-1;
+ }
+ j = std::max((int) floor((1.+xus[1+3*l])/del_cube), 0);
+ if (j >= ico_cube)
+ {
+ j = ico_cube-1;
+ }
+ k = std::max((int) floor((1.+xus[2+3*l])/del_cube), 0);
+ if (k >= ico_cube)
+ {
+ k = ico_cube-1;
+ }
+ ijk = i+j*ico_cube+k*ico_cube*ico_cube;
+ work[l] = ijk;
+ }
+
+ snew(ico_wk, 2*ico_cube_cb+1);
+
+ ico_pt = ico_wk+ico_cube_cb;
+ for (l = 0; l < ndot; l++)
+ {
+ ico_wk[work[l]]++; /* dots per elementary cube */
+ }
+
+ /* reordering of the coordinate array in accordance with box number */
+ tn = 0;
+ for (i = 0; i < ico_cube; i++)
+ {
+ for (j = 0; j < ico_cube; j++)
+ {
+ for (k = 0; k < ico_cube; k++)
+ {
+ tl = 0;
+ tl2 = tn;
+ ijk = i+ico_cube*j+ico_cube*ico_cube*k;
+ *(ico_pt+ijk) = tn;
+ for (l = tl2; l < ndot; l++)
+ {
+ if (ijk == work[l])
+ {
+ x = xus[3*l]; y = xus[1+3*l]; z = xus[2+3*l];
+ xus[3*l] = xus[3*tn];
+ xus[1+3*l] = xus[1+3*tn]; xus[2+3*l] = xus[2+3*tn];
+ xus[3*tn] = x; xus[1+3*tn] = y; xus[2+3*tn] = z;
+ ijk = work[l]; work[l] = work[tn]; work[tn] = ijk;
+ tn++; tl++;
+ }
+ }
+ *(ico_wk+ijk) = tl;
+ } /* cycle k */
+ } /* cycle j */
+ } /* cycle i */
+ sfree(ico_wk);
+ sfree(work);
+
+ return xus;
+}
+
+static void
+nsc_dclm_pbc(const rvec *coords, const ConstArrayRef<real> &radius, int nat,
+ const real *xus, int n_dot, int mode,
+ real *value_of_area, real **at_area,
+ real *value_of_vol,
+ real **lidots, int *nu_dots,
+ atom_id index[], AnalysisNeighborhood *nb,
+ const t_pbc *pbc)
+{
+ const real dotarea = FOURPI/(real) n_dot;
+
+ if (debug)
+ {
+ fprintf(debug, "nsc_dclm: n_dot=%5d %9.3f\n", n_dot, dotarea);
+ }
+
+ /* start with neighbour list */
+ /* calculate neighbour list with the box algorithm */
+ if (nat == 0)
+ {
+ return;
+ }
+ real area = 0.0, vol = 0.0;
+ real *dots = NULL, *atom_area = NULL;
+ int lfnr = 0, maxdots = 0;
+ if (mode & FLAG_VOLUME)
+ {
+ vol = 0.;
+ }
+ if (mode & FLAG_DOTS)
+ {
+ maxdots = (3*n_dot*nat)/10;
+ snew(dots, maxdots);
+ lfnr = 0;
+ }
+ if (mode & FLAG_ATOM_AREA)
+ {
+ snew(atom_area, nat);
+ }
+
+ // Compute the center of the molecule for volume calculation.
+ // In principle, the center should not influence the results, but that is
+ // only true at the limit of infinite dot density, so this makes the
+ // results translation-invariant.
+ // With PBC, if the molecule is broken across the boundary, the computation
+ // is broken in other ways as well, so it does not need to be considered
+ // here.
+ real xs = 0.0, ys = 0.0, zs = 0.0;
+ for (int i = 0; i < nat; ++i)
+ {
+ const int iat = index[i];
+ xs += coords[iat][XX];
+ ys += coords[iat][YY];
+ zs += coords[iat][ZZ];
+ }
+ xs /= nat;
+ ys /= nat;
+ zs /= nat;
+
+ AnalysisNeighborhoodPositions pos(coords, radius.size());
+ pos.indexed(constArrayRefFromArray(index, nat));
+ AnalysisNeighborhoodSearch nbsearch(nb->initSearch(pbc, pos));
+
+ std::vector<int> wkdot(n_dot);
+
+ for (int i = 0; i < nat; ++i)
+ {
+ const int iat = index[i];
+ const real ai = radius[iat];
+ const real aisq = ai*ai;
+ AnalysisNeighborhoodPairSearch pairSearch(
+ nbsearch.startPairSearch(coords[iat]));
+ AnalysisNeighborhoodPair pair;
+ std::fill(wkdot.begin(), wkdot.end(), 1);
+ int currDotCount = n_dot;
+ while (currDotCount > 0 && pairSearch.findNextPair(&pair))
+ {
+ const int jat = index[pair.refIndex()];
+ const real aj = radius[jat];
+ const real d2 = pair.distance2();
+ if (iat == jat || d2 > sqr(ai+aj))
+ {
+ continue;
+ }
+ const rvec &dx = pair.dx();
+ const real refdot = (d2 + aisq - aj*aj)/(2*ai);
+ // TODO: Consider whether micro-optimizations from the old
+ // implementation would be useful, compared to the complexity that
+ // they bring: instead of this direct loop, the neighbors were
+ // stored into a temporary array, the loop order was
+ // reversed (first over dots, then over neighbors), and for each
+ // dot, it was first checked whether the same neighbor that
+ // resulted in marking the previous dot covered would also cover
+ // this dot. This presumably plays together with sorting of the
+ // surface dots (done in make_unsp) to avoid some of the looping.
+ // Alternatively, we could keep a skip list here to avoid
+ // repeatedly looping over dots that have already marked as
+ // covered.
+ for (int j = 0; j < n_dot; ++j)
+ {
+ if (wkdot[j] && iprod(&xus[3*j], dx) > refdot)
+ {
+ --currDotCount;
+ wkdot[j] = 0;
+ }
+ }
+ }
+
+ const real a = aisq * dotarea * currDotCount;
+ area = area + a;
+ if (mode & FLAG_ATOM_AREA)
+ {
+ atom_area[i] = a;
+ }
+ const real xi = coords[iat][XX];
+ const real yi = coords[iat][YY];
+ const real zi = coords[iat][ZZ];
+ if (mode & FLAG_DOTS)
+ {
+ for (int l = 0; l < n_dot; l++)
+ {
+ if (wkdot[l])
+ {
+ lfnr++;
+ if (maxdots <= 3*lfnr+1)
+ {
+ maxdots = maxdots+n_dot*3;
+ srenew(dots, maxdots);
+ }
+ dots[3*lfnr-3] = ai*xus[3*l]+xi;
+ dots[3*lfnr-2] = ai*xus[1+3*l]+yi;
+ dots[3*lfnr-1] = ai*xus[2+3*l]+zi;
+ }
+ }
+ }
+ if (mode & FLAG_VOLUME)
+ {
+ real dx = 0.0, dy = 0.0, dz = 0.0;
+ for (int l = 0; l < n_dot; l++)
+ {
+ if (wkdot[l])
+ {
+ dx = dx+xus[3*l];
+ dy = dy+xus[1+3*l];
+ dz = dz+xus[2+3*l];
+ }
+ }
+ vol = vol+aisq*(dx*(xi-xs)+dy*(yi-ys)+dz*(zi-zs) + ai*currDotCount);
+ }
+ }
+
+ if (mode & FLAG_VOLUME)
+ {
+ *value_of_vol = vol*FOURPI/(3.*n_dot);
+ }
+ if (mode & FLAG_DOTS)
+ {
+ *nu_dots = lfnr;
+ *lidots = dots;
+ }
+ if (mode & FLAG_ATOM_AREA)
+ {
+ *at_area = atom_area;
+ }
+ *value_of_area = area;
+
+ if (debug)
+ {
+ fprintf(debug, "area=%8.3f\n", area);
+ }
+}
+
+namespace gmx
+{
+
+class SurfaceAreaCalculator::Impl
+{
+ public:
+ Impl() : flags_(0)
+ {
+ }
+
+ std::vector<real> unitSphereDots_;
+ ConstArrayRef<real> radius_;
+ int flags_;
+ mutable AnalysisNeighborhood nb_;
+};
+
+SurfaceAreaCalculator::SurfaceAreaCalculator()
+ : impl_(new Impl())
+{
+}
+
+SurfaceAreaCalculator::~SurfaceAreaCalculator()
+{
+}
+
+void SurfaceAreaCalculator::setDotCount(int dotCount)
+{
+ impl_->unitSphereDots_ = make_unsp(dotCount, 4);
+}
+
+void SurfaceAreaCalculator::setRadii(const ConstArrayRef<real> &radius)
+{
+ impl_->radius_ = radius;
+ if (!radius.empty())
+ {
+ const real maxRadius = *std::max_element(radius.begin(), radius.end());
+ impl_->nb_.setCutoff(2*maxRadius);
+ }
+}
+
+void SurfaceAreaCalculator::setCalculateVolume(bool bVolume)
+{
+ if (bVolume)
+ {
+ impl_->flags_ |= FLAG_VOLUME;
+ }
+ else
+ {
+ impl_->flags_ &= ~FLAG_VOLUME;
+ }
+}
+
+void SurfaceAreaCalculator::setCalculateAtomArea(bool bAtomArea)
+{
+ if (bAtomArea)
+ {
+ impl_->flags_ |= FLAG_ATOM_AREA;
+ }
+ else
+ {
+ impl_->flags_ &= ~FLAG_ATOM_AREA;
+ }
+}
+
+void SurfaceAreaCalculator::setCalculateSurfaceDots(bool bDots)
+{
+ if (bDots)
+ {
+ impl_->flags_ |= FLAG_DOTS;
+ }
+ else
+ {
+ impl_->flags_ &= ~FLAG_DOTS;
+ }
+}
+
+void SurfaceAreaCalculator::calculate(
+ const rvec *x, const t_pbc *pbc,
+ int nat, atom_id index[], int flags, real *area, real *volume,
+ real **at_area, real **lidots, int *n_dots) const
+{
+ flags |= impl_->flags_;
+ *area = 0;
+ if (volume == NULL)
+ {
+ flags &= ~FLAG_VOLUME;
+ }
+ else
+ {
+ *volume = 0;
+ }
+ if (at_area == NULL)
+ {
+ flags &= ~FLAG_ATOM_AREA;
+ }
+ else
+ {
+ *at_area = NULL;
+ }
+ if (lidots == NULL)
+ {
+ flags &= ~FLAG_DOTS;
+ }
+ else
+ {
+ *lidots = NULL;
+ }
+ if (n_dots == NULL)
+ {
+ flags &= ~FLAG_DOTS;
+ }
+ else
+ {
+ *n_dots = 0;
+ }
+ nsc_dclm_pbc(x, impl_->radius_, nat,
+ &impl_->unitSphereDots_[0], impl_->unitSphereDots_.size()/3,
+ flags, area, at_area, volume, lidots, n_dots, index,
+ &impl_->nb_, pbc);
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_TRAJECTORYANALYSIS_SURFACEAREA_H
+#define GMX_TRAJECTORYANALYSIS_SURFACEAREA_H
+
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/classhelpers.h"
+
+struct t_pbc;
+
+#define FLAG_DOTS 01
+#define FLAG_VOLUME 02
+#define FLAG_ATOM_AREA 04
+
+namespace gmx
+{
+
+/*! \internal
+ * \brief
+ * Computes surface areas for a group of atoms/spheres.
+ *
+ * This class provides a surface area/volume calculator.
+ *
+ * The algorithm is based on representing each atom/sphere surface as a set of
+ * dots, and determining which dots are on the surface (not covered by any
+ * other atom/sphere). The dots are distributed evenly using an icosahedron- or
+ * a dodecahedron-based method (see the original reference cited in the code).
+ * The area is then estimated from the area represented by each dot.
+ * The volume is calculated by selecting a fixed point and integrating over the
+ * surface dots, summing up the cones whose tip is at the fixed point and base
+ * at the surface points.
+ *
+ * The default dot density per sphere is 32, which gives quite inaccurate
+ * areas and volumes, but a reasonable number of surface points. According to
+ * original documentation of the method, a density of 600-700 dots gives an
+ * accuracy of 1.5 A^2 per atom.
+ *
+ * \ingroup module_trajectoryanalysis
+ */
+class SurfaceAreaCalculator
+{
+ public:
+ /*! \brief
+ * Initializes a surface area calculator.
+ *
+ * \throws std::bad_alloc if out of memory.
+ */
+ SurfaceAreaCalculator();
+ ~SurfaceAreaCalculator();
+
+ /*! \brief
+ * Sets the number of surface dots per sphere to use.
+ *
+ * This function must be called before calculate() to set the desired
+ * accuracy/computational cost.
+ */
+ void setDotCount(int dotCount);
+ /*! \brief
+ * Sets the radii of spheres to use in the calculation.
+ *
+ * \param[in] radius Radius for each atom/sphere.
+ *
+ * This function must be called before calculate() to set the radii for
+ * the spheres. All calculations must use the same set of radii to
+ * share the same grid search.
+ * These radii are used as-is, without adding any probe radius.
+ * The passed array must remain valid for the lifetime of this object.
+ *
+ * Does not throw.
+ */
+ void setRadii(const ConstArrayRef<real> &radius);
+
+ /*! \brief
+ * Requests calculation of volume.
+ *
+ * If not called, and FLAG_VOLUME is not passed to calculate(), the
+ * volume output is not produced.
+ *
+ * Does not throw.
+ */
+ void setCalculateVolume(bool bVolume);
+ /*! \brief
+ * Requests output of per-atom areas.
+ *
+ * If not called, and FLAG_ATOM_AREA is not passed to calculate(), the
+ * atom area output is not produced.
+ *
+ * Does not throw.
+ */
+ void setCalculateAtomArea(bool bAtomArea);
+ /*! \brief
+ * Requests output of all surface dots.
+ *
+ * If not called, and FLAG_DOTS is not passed to calculate(), the
+ * surface dot output is not produced.
+ *
+ * Does not throw.
+ */
+ void setCalculateSurfaceDots(bool bDots);
+
+ /*! \brief
+ * Calculates the surface area for a set of positions.
+ *
+ * \param[in] x Atom positions (sphere centers).
+ * \param[in] pbc PBC information (if `NULL`, calculation is done
+ * without PBC).
+ * \param[in] nat Number of atoms to calculate.
+ * \param[in] index Atom indices to include in the calculation.
+ * \param[in] flags Additional flags for the calculation.
+ * \param[out] area Total surface area (must be non-`NULL`).
+ * \param[out] volume Total volume (can be `NULL`).
+ * \param[out] at_area Surface area for each atom in \p index
+ * (\p nat values) (can be `NULL`).
+ * \param[out] lidots Surface dots as x,y,z triplets (`3*lidots` values)
+ * (can be `NULL`).
+ * \param[out] n_dots Number of surface dots in \p lidots
+ * (can be `NULL`).
+ *
+ * Calculates the surface area of spheres centered at `x[index[0]]`,
+ * ..., `x[index[nat-1]]`, with radii `radii[index[0]]`, ..., where
+ * `radii` is the array passed to setRadii().
+ *
+ * If \p flags is 0, the calculation is done for the items specified
+ * with setCalculateVolume(), setCalculateAtomArea(), and
+ * setCalculateSurfaceDots(). Flags can specify FLAG_VOLUME,
+ * FLAG_ATOM_AREA, and/or FLAG_DOTS to request additional output for
+ * this particular calculation. If any output is `NULL`, that output
+ * is not calculated, irrespective of the calculation mode set.
+ *
+ * \todo
+ * Make the output options more C++-like, in particular for the array
+ * outputs.
+ */
+ void calculate(const rvec *x, const t_pbc *pbc,
+ int nat, atom_id index[], int flags, real *area,
+ real *volume, real **at_area,
+ real **lidots, int *n_dots) const;
+
+ private:
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
+};
+
+} // namespace gmx
+
+#endif
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
-#include "runnercommon.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include "config.h"
-#endif
+#include "runnercommon.h"
#include <string.h>
-#include "gromacs/legacyheaders/oenv.h"
-#include "gromacs/legacyheaders/rmpbc.h"
-#include "gromacs/legacyheaders/vec.h"
-
#include "gromacs/fileio/timecontrol.h"
#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trx.h"
#include "gromacs/fileio/trxio.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/math/vec.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/options/options.h"
+#include "gromacs/pbcutil/rmpbc.h"
#include "gromacs/selection/indexutil.h"
#include "gromacs/selection/selectioncollection.h"
#include "gromacs/selection/selectionfileoption.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
}
time_unit_t time_unit
= static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
- output_env_init(&impl_->oenv_, getProgramContext(), time_unit, FALSE, exvgNONE, 0, 0);
+ output_env_init(&impl_->oenv_, getProgramContext(), time_unit, FALSE, exvgNONE, 0);
int frflags = impl_->settings_.frflags();
frflags |= TRX_NEED_X;
"Trajectory (%d atoms) does not match topology (%d atoms)",
impl_->fr->natoms, top.topology()->atoms.nr)));
}
- // TODO: Check index groups if they have been initialized based on the topology.
- /*
- if (top)
- {
- for (int i = 0; i < impl_->sel->nr(); ++i)
- {
- gmx_ana_index_check(impl_->sel->sel(i)->indexGroup(),
- impl_->fr->natoms);
- }
- }
- */
}
else
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_TRAJECTORYANALYSIS_RUNNERCOMMON_H
#define GMX_TRAJECTORYANALYSIS_RUNNERCOMMON_H
-#include "../legacyheaders/types/simple.h"
-#include "gromacs/fileio/trx.h"
+#include "gromacs/utility/classhelpers.h"
-#include "../utility/common.h"
+struct t_trxframe;
namespace gmx
{
angle.cpp
distance.cpp
freevolume.cpp
+ pairdist.cpp
+ rdf.cpp
sasa.cpp
select.cpp
+ surfacearea.cpp
$<TARGET_OBJECTS:analysisdata-test-shared>)
add_executable(test_selection ${UNITTEST_TARGET_OPTIONS} test_selection.cpp)
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
-#include <gtest/gtest.h>
+#include "gmxpre.h"
#include "gromacs/trajectoryanalysis/modules/angle.h"
+#include <gtest/gtest.h>
+
#include "testutils/cmdlinetest.h"
#include "moduletest.h"
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
-#include <gtest/gtest.h>
+#include "gmxpre.h"
#include "gromacs/trajectoryanalysis/modules/distance.h"
+#include <gtest/gtest.h>
+
#include "testutils/cmdlinetest.h"
#include "moduletest.h"
* \author David van der Spoel <david.vanderspoel@icm.uu.se>
* \ingroup module_trajectoryanalysis
*/
-#include <gtest/gtest.h>
+#include "gmxpre.h"
#include "gromacs/trajectoryanalysis/modules/freevolume.h"
+#include <gtest/gtest.h>
+
#include "testutils/cmdlinetest.h"
#include "moduletest.h"
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
+#include "gmxpre.h"
+
#include "moduletest.h"
#include <map>
#include "gromacs/trajectoryanalysis/analysismodule.h"
#include "gromacs/trajectoryanalysis/cmdlinerunner.h"
-#include "gromacs/utility/file.h"
-#include "gromacs/utility/stringutil.h"
#include "gromacs/analysisdata/tests/datatest.h"
#include "testutils/cmdlinetest.h"
#include "testutils/refdata.h"
#include "testutils/testasserts.h"
-#include "testutils/testfilemanager.h"
namespace gmx
{
FloatingPointTolerance tolerance;
};
- struct OutputFileInfo
- {
- OutputFileInfo(const char *option, const std::string &path)
- : option(option), path(path)
- {
- }
-
- std::string option;
- std::string path;
- };
-
typedef std::map<std::string, DatasetInfo> DatasetList;
- typedef std::vector<OutputFileInfo> OutputFileList;
explicit Impl(AbstractTrajectoryAnalysisModuleTestFixture *parent);
AbstractTrajectoryAnalysisModuleTestFixture &parent_;
TrajectoryAnalysisModulePointer module_;
- TestReferenceData data_;
- CommandLine cmdline_;
- TestFileManager tempFiles_;
DatasetList datasets_;
- OutputFileList outputFiles_;
bool bDatasetsIncluded_;
};
AbstractTrajectoryAnalysisModuleTestFixture *parent)
: parent_(*parent), bDatasetsIncluded_(false)
{
- cmdline_.append("module");
}
TrajectoryAnalysisModule &
void
AbstractTrajectoryAnalysisModuleTestFixture::setTopology(const char *filename)
{
- impl_->cmdline_.append("-s");
- impl_->cmdline_.append(TestFileManager::getInputFilePath(filename));
+ setInputFile("-s", filename);
}
void
AbstractTrajectoryAnalysisModuleTestFixture::setTrajectory(const char *filename)
{
- impl_->cmdline_.append("-f");
- impl_->cmdline_.append(TestFileManager::getInputFilePath(filename));
-}
-
-void
-AbstractTrajectoryAnalysisModuleTestFixture::setOutputFile(const char *option,
- const char *filename)
-{
- std::string fullFilename = impl_->tempFiles_.getTemporaryFilePath(filename);
- impl_->cmdline_.append(option);
- impl_->cmdline_.append(fullFilename);
- impl_->outputFiles_.push_back(Impl::OutputFileInfo(option, fullFilename));
-}
-
-void
-AbstractTrajectoryAnalysisModuleTestFixture::setOutputFileNoTest(
- const char *option, const char *extension)
-{
- std::string fullFilename = impl_->tempFiles_.getTemporaryFilePath(
- formatString("%d.%s", impl_->cmdline_.argc(), extension));
- impl_->cmdline_.append(option);
- impl_->cmdline_.append(fullFilename);
+ setInputFile("-f", filename);
}
void
void
AbstractTrajectoryAnalysisModuleTestFixture::runTest(const CommandLine &args)
{
- TrajectoryAnalysisModule &module = impl_->module();
- // Skip first argument if it is the module name.
- int firstArg = (args.arg(0)[0] == '-' ? 0 : 1);
- for (int i = firstArg; i < args.argc(); ++i)
- {
- impl_->cmdline_.append(args.arg(i));
- }
-
- TestReferenceChecker rootChecker(impl_->data_.rootChecker());
+ TrajectoryAnalysisModule &module = impl_->module();
+ CommandLine &cmdline = commandLine();
+ cmdline.merge(args);
+ TestReferenceChecker rootChecker(this->rootChecker());
rootChecker.checkString(args.toString(), "CommandLine");
if (impl_->hasCheckedDatasets())
TrajectoryAnalysisCommandLineRunner runner(&module);
runner.setUseDefaultGroups(false);
int rc = 0;
- EXPECT_NO_THROW_GMX(rc = runner.run(impl_->cmdline_.argc(), impl_->cmdline_.argv()));
+ EXPECT_NO_THROW_GMX(rc = runner.run(cmdline.argc(), cmdline.argv()));
EXPECT_EQ(0, rc);
- if (!impl_->outputFiles_.empty())
- {
- TestReferenceChecker outputChecker(
- rootChecker.checkCompound("OutputFiles", "Files"));
- Impl::OutputFileList::const_iterator outfile;
- for (outfile = impl_->outputFiles_.begin();
- outfile != impl_->outputFiles_.end();
- ++outfile)
- {
- std::string output = File::readToString(outfile->path);
- outputChecker.checkStringBlock(output, outfile->option.c_str());
- }
- }
+ checkOutputFiles();
}
} // namespace test
#include <gtest/gtest.h>
#include "gromacs/trajectoryanalysis/analysismodule.h"
-#include "gromacs/utility/common.h"
+#include "gromacs/utility/classhelpers.h"
+
+#include "testutils/cmdlinetest.h"
namespace gmx
{
namespace test
{
-class CommandLine;
class FloatingPointTolerance;
/*! \internal
* methods in this class. runTest() then runs the specified module with the
* given options and performs all the requested tests against reference data.
*
+ * Tests should prefer to test the underlying data sets instead of string
+ * comparison on the output files using setOutputFile().
+ *
* The actual module to be tested is constructed in the pure virtual
* createModule() method, which should be implemented in a subclass.
* Typically, the TrajectoryAnalysisModuleTestFixture template can be used.
*
* Any method in this class may throw std::bad_alloc if out of memory.
*
+ * \todo
+ * Adding facilities to AnalysisData to check whether there are any
+ * output modules attached to the data object (directly or indirectly),
+ * marking the mocks as output modules, and using these checks in the
+ * tools instead of or in addition to the output file presence would be
+ * a superior.
+ * Also, the full file names should be deducible from the options.
+ *
* \ingroup module_trajectoryanalysis
*/
-class AbstractTrajectoryAnalysisModuleTestFixture : public ::testing::Test
+class AbstractTrajectoryAnalysisModuleTestFixture : public CommandLineTestBase
{
public:
AbstractTrajectoryAnalysisModuleTestFixture();
* must be called before runTest().
*/
void setTrajectory(const char *filename);
- /*! \brief
- * Sets an output file to use for the test.
- *
- * \param[in] option Option to set.
- * \param[in] filename Name of the output file.
- *
- * This method:
- * - Sets \p option in the tested module to a temporary file name
- * constructed from \p filename.
- * - Makes runTest() to check the contents of the file against
- * reference data after running the module.
- * - Marks the temporary file for removal at test teardown.
- *
- * \p filename is given to TestTemporaryFileManager to make a unique
- * filename for the temporary file, but is not otherwise used.
- *
- * Currently, this method should not be called for an XVG file, because
- * the comments in the beginning of the file contain timestamps and
- * other variable information, causing the test to fail. Best used
- * only for custom data formats. For numeric data, testing the
- * underlying dataset is typically sufficient.
- */
- void setOutputFile(const char *option, const char *filename);
- /*! \brief
- * Sets an output file parameter needed for the test.
- *
- * \param[in] option Option to set.
- * \param[in] extension Extension for the file to create.
- *
- * This method:
- * - Sets \p option in the tested module to a temporary file name.
- * - Marks the temporary file for removal at test teardown.
- *
- * This method provides the mechanism to set output files that are
- * required to trigger computation of values that are required for
- * the test. The contents of the output file are not tested.
- *
- * \todo
- * Adding facilities to AnalysisData to check whether there are any
- * output modules attached to the data object (directly or indirectly),
- * marking the mocks as output modules, and using these checks in the
- * tools instead of or in addition to the output file presence would be
- * a superior.
- * Also, the extension should be deducible from the option.
- */
- void setOutputFileNoTest(const char *option, const char *extension);
/*! \brief
* Includes only specified dataset for the test.
*
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for functionality of the "pairdist" trajectory analysis module.
+ *
+ * These tests test the basic functionality of the tool itself, but currently
+ * the following are missing:
+ * - Tests related to -odg output. This would require a full tpr file, and
+ * some investigation on what kind of tpr it should be to produce reasonable
+ * output.
+ * - Tests for the X axes in the area per atom/residue plots. These could be
+ * added once better X axes are implemented.
+ * - Tests for XVG labels. This is a limitation of the current testing
+ * framework.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#include "gmxpre.h"
+
+#include "gromacs/trajectoryanalysis/modules/pairdist.h"
+
+#include <gtest/gtest.h>
+
+#include "testutils/cmdlinetest.h"
+#include "testutils/testasserts.h"
+
+#include "moduletest.h"
+
+namespace
+{
+
+using gmx::test::CommandLine;
+
+/********************************************************************
+ * Tests for gmx::analysismodules::PairDistance.
+ */
+
+//! Test fixture for the select analysis module.
+typedef gmx::test::TrajectoryAnalysisModuleTestFixture<gmx::analysismodules::PairDistanceInfo>
+ PairDistanceModuleTest;
+
+TEST_F(PairDistanceModuleTest, ComputesAllDistances)
+{
+ const char *const cmdline[] = {
+ "pairdist",
+ "-ref", "resindex 1", "-refgrouping", "none",
+ "-sel", "resindex 3", "-selgrouping", "none"
+ };
+ setTopology("simple.gro");
+ setOutputFileNoTest("-o", "xvg");
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(PairDistanceModuleTest, ComputesAllDistancesWithCutoff)
+{
+ const char *const cmdline[] = {
+ "pairdist",
+ "-ref", "resindex 1", "-refgrouping", "none",
+ "-sel", "resindex 3", "-selgrouping", "none",
+ "-cutoff", "1.5"
+ };
+ setTopology("simple.gro");
+ setOutputFileNoTest("-o", "xvg");
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(PairDistanceModuleTest, ComputesMinDistanceWithCutoff)
+{
+ const char *const cmdline[] = {
+ "pairdist",
+ "-ref", "resindex 1",
+ "-sel", "resindex 3",
+ "-cutoff", "1.5"
+ };
+ setTopology("simple.gro");
+ setOutputFileNoTest("-o", "xvg");
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(PairDistanceModuleTest, ComputesMaxDistance)
+{
+ const char *const cmdline[] = {
+ "pairdist",
+ "-ref", "resindex 1",
+ "-sel", "resindex 3",
+ "-type", "max"
+ };
+ setTopology("simple.gro");
+ setOutputFileNoTest("-o", "xvg");
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(PairDistanceModuleTest, ComputesMaxDistanceWithCutoff)
+{
+ const char *const cmdline[] = {
+ "pairdist",
+ "-ref", "resindex 1",
+ "-sel", "resindex 3",
+ "-cutoff", "1.5", "-type", "max"
+ };
+ setTopology("simple.gro");
+ setOutputFileNoTest("-o", "xvg");
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(PairDistanceModuleTest, ComputesGroupedMinDistanceWithCutoff)
+{
+ const char *const cmdline[] = {
+ "pairdist",
+ "-ref", "resindex 1 to 2", "-refgrouping", "res",
+ "-sel", "resindex 3 to 5", "-selgrouping", "res",
+ "-cutoff", "2.5"
+ };
+ setTopology("simple.gro");
+ setOutputFileNoTest("-o", "xvg");
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(PairDistanceModuleTest, ComputesGroupedMaxDistanceWithCutoff)
+{
+ const char *const cmdline[] = {
+ "pairdist",
+ "-ref", "resindex 1 to 2", "-refgrouping", "res",
+ "-sel", "resindex 3 to 5", "-selgrouping", "res",
+ "-cutoff", "3.5", "-type", "max"
+ };
+ setTopology("simple.gro");
+ setOutputFileNoTest("-o", "xvg");
+ runTest(CommandLine(cmdline));
+}
+
+} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for functionality of the "rdf" trajectory analysis module.
+ *
+ * These tests are essentially regression tests for the actual RDF calculation
+ * from very small configurations. Exclusions are not tested (since the input
+ * does not contain any), nor is the effect of -cut of -rmax.
+ * At the moment, they do not test the final normalization, but only the pair
+ * counts calculated for each frame. Tests for the final normalization should
+ * be added once related TODOs in the implementation/framework have been
+ * resolved (currently, the test framework does not see the final output data).
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#include "gmxpre.h"
+
+#include "gromacs/trajectoryanalysis/modules/rdf.h"
+
+#include <gtest/gtest.h>
+
+#include "testutils/cmdlinetest.h"
+#include "testutils/testasserts.h"
+
+#include "moduletest.h"
+
+namespace
+{
+
+using gmx::test::CommandLine;
+
+/********************************************************************
+ * Tests for gmx::analysismodules::Rdf.
+ */
+
+//! Test fixture for the `rdf` analysis module.
+typedef gmx::test::TrajectoryAnalysisModuleTestFixture<gmx::analysismodules::RdfInfo>
+ RdfModuleTest;
+
+TEST_F(RdfModuleTest, BasicTest)
+{
+ const char *const cmdline[] = {
+ "rdf",
+ "-bin", "0.05",
+ "-ref", "name OW",
+ "-sel", "name OW", "not name OW"
+ };
+ setTopology("spc216.gro");
+ setOutputFileNoTest("-o", "xvg");
+ excludeDataset("pairdist");
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(RdfModuleTest, CalculatesSurf)
+{
+ const char *const cmdline[] = {
+ "rdf",
+ "-bin", "0.05", "-surf", "res",
+ "-ref", "within 0.5 of (resnr 1 and name OW)",
+ "-sel", "name OW", "not name OW"
+ };
+ setTopology("spc216.gro");
+ setOutputFileNoTest("-o", "xvg");
+ excludeDataset("pairdist");
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(RdfModuleTest, CalculatesXY)
+{
+ const char *const cmdline[] = {
+ "rdf",
+ "-bin", "0.05", "-xy",
+ "-ref", "name OW",
+ "-sel", "name OW", "not name OW"
+ };
+ setTopology("spc216.gro");
+ setOutputFileNoTest("-o", "xvg");
+ excludeDataset("pairdist");
+ // TODO: Consider if it is possible to get a more reproducible result
+ // and/or a stricter tolerance (e.g., by checking that the sum of
+ // neighboring values still stays constant).
+ setDatasetTolerance("paircount", gmx::test::absoluteTolerance(2.5));
+ runTest(CommandLine(cmdline));
+}
+
+} // namespace
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">pairdist -ref 'resindex 1' -refgrouping none -sel 'resindex 3' -selgrouping none</String>
+ <OutputData Name="Data">
+ <AnalysisData Name="dist">
+ <DataFrame Name="Frame0">
+ <Real Name="X">0</Real>
+ <DataValues>
+ <Int Name="Count">9</Int>
+ <DataValue>
+ <Real Name="Value">2.2360679774997898</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1.4142135623730951</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">3.1622776601683795</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2.2360679774997898</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1.4142135623730951</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2.2360679774997898</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2.8284271247461903</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ </AnalysisData>
+ </OutputData>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">pairdist -ref 'resindex 1' -refgrouping none -sel 'resindex 3' -selgrouping none -cutoff 1.5</String>
+ <OutputData Name="Data">
+ <AnalysisData Name="dist">
+ <DataFrame Name="Frame0">
+ <Real Name="X">0</Real>
+ <DataValues>
+ <Int Name="Count">9</Int>
+ <DataValue>
+ <Real Name="Value">1.5</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1.4142135623730951</Real>
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+</ReferenceData>
* - Tests for XVG labels. This is a limitation of the current testing
* framework.
*
- * The actual surface area algorithm should be tested separately with a more
- * extensive set of data, but those fit better as a separate set of unit tests.
+ * The actual surface area algorithm is tested separately in surfacearea.cpp.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
-#include <gtest/gtest.h>
+#include "gmxpre.h"
#include "gromacs/trajectoryanalysis/modules/sasa.h"
+#include <gtest/gtest.h>
+
#include "testutils/cmdlinetest.h"
#include "testutils/testasserts.h"
using gmx::test::CommandLine;
/********************************************************************
- * Tests for gmx::analysismodules::Sas.
+ * Tests for gmx::analysismodules::Sasa.
*/
-//! Test fixture for the select analysis module.
+//! Test fixture for the `sasa` analysis module.
typedef gmx::test::TrajectoryAnalysisModuleTestFixture<gmx::analysismodules::SasaInfo>
SasaModuleTest;
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
-#include <gtest/gtest.h>
+#include "gmxpre.h"
#include "gromacs/trajectoryanalysis/modules/select.h"
+#include <gtest/gtest.h>
+
#include "testutils/cmdlinetest.h"
#include "moduletest.h"
--- /dev/null
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--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for the surface area calculation used by the `sasa` analysis module.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#include "gmxpre.h"
+
+#include "gromacs/trajectoryanalysis/modules/surfacearea.h"
+
+#include <cstdlib>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/random/random.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+namespace
+{
+
+/********************************************************************
+ * SurfaceAreaTest
+ */
+
+class SurfaceAreaTest : public ::testing::Test
+{
+ public:
+ SurfaceAreaTest()
+ : rng_(NULL), area_(0.0), volume_(0.0),
+ atomArea_(NULL), dotCount_(0), dots_(NULL)
+ {
+ // TODO: Handle errors.
+ rng_ = gmx_rng_init(12345);
+ clear_mat(box_);
+ }
+ ~SurfaceAreaTest()
+ {
+ if (rng_ != NULL)
+ {
+ gmx_rng_destroy(rng_);
+ }
+ sfree(atomArea_);
+ sfree(dots_);
+ }
+
+ void addSphere(real x, real y, real z, real radius,
+ bool bAddToIndex = true)
+ {
+ if (bAddToIndex)
+ {
+ index_.push_back(x_.size());
+ }
+ x_.push_back(gmx::RVec(x, y, z));
+ radius_.push_back(radius);
+ }
+
+ void generateRandomPosition(rvec x, real *radius)
+ {
+ rvec fx;
+ fx[XX] = gmx_rng_uniform_real(rng_);
+ fx[YY] = gmx_rng_uniform_real(rng_);
+ fx[ZZ] = gmx_rng_uniform_real(rng_);
+ mvmul(box_, fx, x);
+ *radius = 1.5*gmx_rng_uniform_real(rng_) + 0.5;
+ }
+
+ void addDummySpheres(int count)
+ {
+ for (int i = 0; i < count; ++i)
+ {
+ rvec x;
+ real radius;
+ generateRandomPosition(x, &radius);
+ addSphere(x[XX], x[YY], x[ZZ], radius, false);
+ }
+ }
+
+ void generateRandomPositions(int count)
+ {
+ x_.reserve(count);
+ radius_.reserve(count);
+ index_.reserve(count);
+ for (int i = 0; i < count; ++i)
+ {
+ rvec x;
+ real radius;
+ generateRandomPosition(x, &radius);
+ addSphere(x[XX], x[YY], x[ZZ], radius);
+ }
+ }
+ void translatePoints(real x, real y, real z)
+ {
+ for (size_t i = 0; i < x_.size(); ++i)
+ {
+ x_[i][XX] += x;
+ x_[i][YY] += y;
+ x_[i][ZZ] += z;
+ }
+ }
+
+ void calculate(int ndots, int flags, bool bPBC)
+ {
+ volume_ = 0.0;
+ sfree(atomArea_);
+ atomArea_ = NULL;
+ dotCount_ = 0;
+ sfree(dots_);
+ dots_ = NULL;
+ t_pbc pbc;
+ if (bPBC)
+ {
+ set_pbc(&pbc, epbcXYZ, box_);
+ }
+ ASSERT_NO_THROW_GMX(
+ {
+ gmx::SurfaceAreaCalculator calculator;
+ calculator.setDotCount(ndots);
+ calculator.setRadii(radius_);
+ calculator.calculate(as_rvec_array(&x_[0]), bPBC ? &pbc : NULL,
+ index_.size(), &index_[0], flags,
+ &area_, &volume_, &atomArea_,
+ &dots_, &dotCount_);
+ });
+ }
+ real resultArea() const { return area_; }
+ real resultVolume() const { return volume_; }
+ real atomArea(int index) const { return atomArea_[index]; }
+
+ void checkReference(gmx::test::TestReferenceChecker *checker, const char *id,
+ bool checkDotCoordinates)
+ {
+ gmx::test::TestReferenceChecker compound(
+ checker->checkCompound("SASA", id));
+ compound.checkReal(area_, "Area");
+ if (volume_ > 0.0)
+ {
+ compound.checkReal(volume_, "Volume");
+ }
+ if (atomArea_ != NULL)
+ {
+ compound.checkSequenceArray(index_.size(), atomArea_, "AtomArea");
+ }
+ if (dots_ != NULL)
+ {
+ if (checkDotCoordinates)
+ {
+ // The algorithm may produce the dots in different order in
+ // single and double precision due to some internal
+ // sorting...
+ std::qsort(dots_, dotCount_, sizeof(rvec), &dotComparer);
+ compound.checkSequenceArray(3*dotCount_, dots_, "Dots");
+ }
+ else
+ {
+ compound.checkInteger(dotCount_, "DotCount");
+ }
+ }
+ }
+
+ gmx::test::TestReferenceData data_;
+ matrix box_;
+
+ private:
+ static int dotComparer(const void *a, const void *b)
+ {
+ for (int d = DIM - 1; d >= 0; --d)
+ {
+ const real ad = reinterpret_cast<const real *>(a)[d];
+ const real bd = reinterpret_cast<const real *>(b)[d];
+ // A fudge factor is needed to get an ordering that is the same
+ // in single and double precision, since the points are not
+ // exactly on the same Z plane even though in exact arithmetic
+ // they probably would be.
+ if (ad < bd - 0.001)
+ {
+ return -1;
+ }
+ else if (ad > bd + 0.001)
+ {
+ return 1;
+ }
+ }
+ return 0;
+ }
+
+ gmx_rng_t rng_;
+ std::vector<gmx::RVec> x_;
+ std::vector<real> radius_;
+ std::vector<int> index_;
+
+ real area_;
+ real volume_;
+ real *atomArea_;
+ int dotCount_;
+ real *dots_;
+};
+
+TEST_F(SurfaceAreaTest, ComputesSinglePoint)
+{
+ gmx::test::FloatingPointTolerance tolerance(
+ gmx::test::defaultRealTolerance());
+ addSphere(1, 1, 1, 1);
+ ASSERT_NO_FATAL_FAILURE(calculate(24, FLAG_VOLUME | FLAG_ATOM_AREA, false));
+ EXPECT_REAL_EQ_TOL(4*M_PI, resultArea(), tolerance);
+ EXPECT_REAL_EQ_TOL(4*M_PI, atomArea(0), tolerance);
+ EXPECT_REAL_EQ_TOL(4*M_PI/3, resultVolume(), tolerance);
+}
+
+TEST_F(SurfaceAreaTest, ComputesTwoPoints)
+{
+ gmx::test::FloatingPointTolerance tolerance(
+ gmx::test::relativeToleranceAsFloatingPoint(1.0, 0.005));
+ addSphere(1, 1, 1, 1);
+ addSphere(2, 1, 1, 1);
+ ASSERT_NO_FATAL_FAILURE(calculate(1000, FLAG_ATOM_AREA, false));
+ EXPECT_REAL_EQ_TOL(2*2*M_PI*1.5, resultArea(), tolerance);
+ EXPECT_REAL_EQ_TOL(2*M_PI*1.5, atomArea(0), tolerance);
+ EXPECT_REAL_EQ_TOL(2*M_PI*1.5, atomArea(1), tolerance);
+}
+
+TEST_F(SurfaceAreaTest, ComputesTwoPointsOfUnequalRadius)
+{
+ gmx::test::FloatingPointTolerance tolerance(
+ gmx::test::relativeToleranceAsFloatingPoint(1.0, 0.005));
+ // Spheres of radius 1 and 2 with intersection at 1.5
+ const real dist = 0.5 + sqrt(3.25);
+ addSphere(1.0, 1.0, 1.0, 1);
+ addSphere(1.0 + dist, 1.0, 1.0, 2);
+ ASSERT_NO_FATAL_FAILURE(calculate(1000, FLAG_ATOM_AREA, false));
+ EXPECT_REAL_EQ_TOL(2*M_PI*(1.5 + (dist - 0.5 + 2)*2), resultArea(), tolerance);
+ EXPECT_REAL_EQ_TOL(2*M_PI*1.5, atomArea(0), tolerance);
+ EXPECT_REAL_EQ_TOL(2*M_PI*(dist - 0.5 + 2)*2, atomArea(1), tolerance);
+}
+
+TEST_F(SurfaceAreaTest, SurfacePoints12)
+{
+ gmx::test::TestReferenceChecker checker(data_.rootChecker());
+ addSphere(0, 0, 0, 1);
+ ASSERT_NO_FATAL_FAILURE(calculate(12, FLAG_DOTS, false));
+ checkReference(&checker, "Surface", true);
+}
+
+TEST_F(SurfaceAreaTest, SurfacePoints32)
+{
+ gmx::test::TestReferenceChecker checker(data_.rootChecker());
+ addSphere(0, 0, 0, 1);
+ ASSERT_NO_FATAL_FAILURE(calculate(32, FLAG_DOTS, false));
+ checkReference(&checker, "Surface", true);
+}
+
+TEST_F(SurfaceAreaTest, SurfacePoints42)
+{
+ gmx::test::TestReferenceChecker checker(data_.rootChecker());
+ addSphere(0, 0, 0, 1);
+ ASSERT_NO_FATAL_FAILURE(calculate(42, FLAG_DOTS, false));
+ checkReference(&checker, "Surface", true);
+}
+
+TEST_F(SurfaceAreaTest, SurfacePoints122)
+{
+ gmx::test::TestReferenceChecker checker(data_.rootChecker());
+ addSphere(0, 0, 0, 1);
+ ASSERT_NO_FATAL_FAILURE(calculate(122, FLAG_DOTS, false));
+ checkReference(&checker, "Surface", true);
+}
+
+TEST_F(SurfaceAreaTest, Computes100Points)
+{
+ gmx::test::TestReferenceChecker checker(data_.rootChecker());
+ checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
+ box_[XX][XX] = 10.0;
+ box_[YY][YY] = 10.0;
+ box_[ZZ][ZZ] = 10.0;
+ generateRandomPositions(100);
+ ASSERT_NO_FATAL_FAILURE(calculate(24, FLAG_VOLUME | FLAG_ATOM_AREA | FLAG_DOTS, false));
+ checkReference(&checker, "100Points", false);
+}
+
+TEST_F(SurfaceAreaTest, Computes100PointsWithRectangularPBC)
+{
+ // TODO: It would be nice to check that this produces the same result as
+ // without PBC, without duplicating the reference files.
+ gmx::test::TestReferenceChecker checker(data_.rootChecker());
+ checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
+ box_[XX][XX] = 10.0;
+ box_[YY][YY] = 10.0;
+ box_[ZZ][ZZ] = 10.0;
+ generateRandomPositions(100);
+ box_[XX][XX] = 20.0;
+ box_[YY][YY] = 20.0;
+ box_[ZZ][ZZ] = 20.0;
+ const int flags = FLAG_ATOM_AREA | FLAG_VOLUME | FLAG_DOTS;
+ ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
+ checkReference(&checker, "100Points", false);
+
+ translatePoints(15.0, 0, 0);
+ ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
+ checkReference(&checker, "100Points", false);
+
+ translatePoints(-15.0, 15.0, 0);
+ ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
+ checkReference(&checker, "100Points", false);
+
+ translatePoints(0, -15.0, 15.0);
+ ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
+ checkReference(&checker, "100Points", false);
+}
+
+TEST_F(SurfaceAreaTest, Computes100PointsWithTriclinicPBC)
+{
+ // TODO: It would be nice to check that this produces the same result as
+ // without PBC, without duplicating the reference files.
+ gmx::test::TestReferenceChecker checker(data_.rootChecker());
+ checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
+ box_[XX][XX] = 10.0;
+ box_[YY][YY] = 10.0;
+ box_[ZZ][ZZ] = 10.0;
+ generateRandomPositions(100);
+ box_[XX][XX] = 20.0;
+ box_[YY][XX] = 10.0;
+ box_[YY][YY] = 10.0*sqrt(3.0);
+ box_[ZZ][XX] = 10.0;
+ box_[ZZ][YY] = 10.0*sqrt(1.0/3.0);
+ box_[ZZ][ZZ] = 20.0*sqrt(2.0/3.0);
+
+ const int flags = FLAG_ATOM_AREA | FLAG_VOLUME | FLAG_DOTS;
+ ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
+ checkReference(&checker, "100Points", false);
+
+ translatePoints(15.0, 0, 0);
+ ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
+ checkReference(&checker, "100Points", false);
+
+ translatePoints(-15.0, box_[YY][YY] - 5.0, 0);
+ ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
+ checkReference(&checker, "100Points", false);
+
+ translatePoints(0, -(box_[YY][YY] - 5.0), 15.0);
+ ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
+ checkReference(&checker, "100Points", false);
+}
+
+} // namespace
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
+#include "gmxpre.h"
+
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
#include "gromacs/selection/selection.h"
* The header file.h declares a gmx::File class for basic I/O support.
*
* The header path.h declares helpers for manipulating paths and for managing
- * directories (this has been moved to src/gromacs/fileio/ to wait for
- * resolution of #950).
+ * directories.
*
* The fate of these headers depends on what is decided in Redmine issue #950.
*
*
* <H3>Implementation Helpers</H3>
*
- * The header common.h implements a gmx::PrivateImplPointer template for easily
+ * The header basedefinitions.h contains common definitions and macros used
+ * throughout \Gromacs. It includes fixed-width integer types (`gmx_int64_t`
+ * and friends), `gmx_bool` for C code, some macros for compiler-specific
+ * attributes, and ::GMX_UNUSED_VALUE and ::GMX_IGNORE_RETURN_VALUE for
+ * handling warnings about unused values.
+ *
+ * The header classhelpers.h implements a gmx::PrivateImplPointer template for easily
* writing classes that use the private implementation idiom. This header also
* declares ::GMX_DISALLOW_COPY_AND_ASSIGN and ::GMX_DISALLOW_ASSIGN macros for
- * class declarations, and ::GMX_IGNORE_RETURN_VALUE for cleanly ignoring a
- * return value from a function.
+ * class declarations.
*
* The header flags.h implements a gmx::FlagsTemplate template for better type
* safety when using bit flag fields.
*
- * The header uniqueptr.h declares gmx::gmx_unique_ptr, which is intended for
- * declaring smart pointer types with unique ownership.
- *
*
* <H3>Other Functionality</H3>
*
* The header init.h declares gmx::init() and gmx::finalize() for initializing
- * and deinitializing the Gromacs library.
+ * and deinitializing the \Gromacs library.
*
* The header arrayref.h implements a gmx::ConstArrayRef class for exposing a
* C array or part of a std::vector (basically, any continuous stretch of
* The header messagestringcollector.h declares a gmx::MessageStringCollector
* class for composing messages with context information.
*
+ * The header sysinfo.h declares gmx_getpid() for getting the current process
+ * id.
+ *
* The header programcontext.h declares a gmx::ProgramContextInterface that is
* used to
* initialize and access information about the running program, such as the
* The header qsort_threadsafe.h provides a guaranteed threadsafe
* implementation for qsort().
*
+ * The header uniqueptr.h declares gmx::gmx_unique_ptr, which is intended for
+ * declaring smart pointer types with unique ownership.
+ *
* \endif
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
#ifndef GMX_UTILITY_H
#define GMX_UTILITY_H
-#include "utility/errorcodes.h"
-#include "utility/exceptions.h"
-#include "utility/gmxassert.h"
-#include "utility/init.h"
-#include "utility/programcontext.h"
+#include "gromacs/utility/errorcodes.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/init.h"
+#include "gromacs/utility/programcontext.h"
#endif
baseversion-gen.c
-gmx_header_config_gen.h
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
file(GLOB UTILITY_SOURCES *.c *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${UTILITY_SOURCES} PARENT_SCOPE)
-set(GENERATED_HEADER_CONFIG ${CMAKE_CURRENT_BINARY_DIR}/gmx_header_config_gen.h)
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/gmx_header_config_gen.h.cmakein
- ${GENERATED_HEADER_CONFIG})
-
-set(UTILITY_PUBLIC_HEADERS
+gmx_install_headers(
arrayref.h
+ basedefinitions.h
+ classhelpers.h
cstringutil.h
- common.h
+ datafilefinder.h
errorcodes.h
exceptions.h
+ fatalerror.h
file.h
flags.h
- gmx_header_config.h
+ futil.h
gmxassert.h
init.h
programcontext.h
+ real.h
smalloc.h
stringutil.h
- uniqueptr.h)
-gmx_install_headers(utility ${UTILITY_PUBLIC_HEADERS})
-gmx_install_headers(utility ${GENERATED_HEADER_CONFIG})
+ )
if (BUILD_TESTING)
add_subdirectory(tests)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <utility>
#include <vector>
-#include "gmxassert.h"
+#include "gromacs/utility/gmxassert.h"
namespace gmx
{
{
GMX_ASSERT(end >= begin, "Invalid range");
}
+ /*! \brief
+ * Constructs a reference to a whole vector.
+ *
+ * \param[in] v Vector to reference.
+ *
+ * Passed vector must remain valid and not be reallocated for the
+ * lifetime of this object.
+ *
+ * This constructor is not explicit to allow directly passing
+ * std::vector to a method that takes ArrayRef.
+ */
+ ArrayRef(std::vector<T> &v)
+ : begin_((!v.empty()) ? &v[0] : NULL),
+ end_((!v.empty()) ? &v[0] + v.size() : NULL)
+ {
+ }
//! \cond
// Doxygen 1.8.5 doesn't parse the declaration correctly...
/*! \brief
{
GMX_ASSERT(end >= begin, "Invalid range");
}
+ /*! \brief
+ * Constructs a reference to a whole vector.
+ *
+ * \param[in] v Vector to reference.
+ *
+ * Passed vector must remain valid and not be reallocated for the
+ * lifetime of this object.
+ *
+ * This constructor is not explicit to allow directly passing
+ * std::vector to a method that takes ConstArrayRef.
+ */
+ ConstArrayRef(const std::vector<T> &v)
+ : begin_((!v.empty()) ? &v[0] : NULL),
+ end_((!v.empty()) ? &v[0] + v.size() : NULL)
+ {
+ }
//! \cond
// Doxygen 1.8.5 doesn't parse the declaration correctly...
/*! \brief
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Basic types and macros used throughout \Gromacs.
+ *
+ * \inpublicapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_BASEDEFINITIONS_H
+#define GMX_UTILITY_BASEDEFINITIONS_H
+
+#include <stdint.h>
+#ifndef _MSC_VER
+#include <inttypes.h>
+#endif
+
+/*! \brief
+ * Boolean type for use in \Gromacs C code.
+ *
+ * There is no standard size for 'bool' in C++, so when
+ * we previously defined it to int for C code the data types
+ * (and structs) would have different size depending on your compiler,
+ * both at \Gromacs build time and when you use the library.
+ * The only way around this is to NOT assume anything about the C++ type,
+ * so we cannot use the name 'bool' in our C code anymore.
+ */
+typedef int gmx_bool;
+
+#ifndef FALSE
+/** False value for ::gmx_bool. */
+# define FALSE 0
+#endif
+#ifndef TRUE
+/** True value for ::gmx_bool. */
+# define TRUE 1
+#endif
+/** Number of gmx_bool values. */
+#define BOOL_NR 2
+
+/*! \name Fixed-width integer types
+ *
+ * These types and macros provide the equivalent of 32- and 64-bit integer
+ * types from C99 headers `stdint.h` and `inttypes.h`. These headers are also
+ * there in C++11. The types and macros from here should be used instead of
+ * `int32_t` etc.
+ * MSVC doesn't support these before Visual Studio 2013.
+ */
+/*! \{ */
+#ifdef _MSC_VER
+typedef __int32 gmx_int32_t;
+#define GMX_PRId32 "I32d"
+#define GMX_SCNd32 "I32d"
+
+typedef __int64 gmx_int64_t;
+#define GMX_PRId64 "I64d"
+#define GMX_SCNd64 "I64d"
+
+typedef unsigned __int32 gmx_uint32_t;
+#define GMX_PRIu32 "I32u"
+#define GMX_SCNu32 "I32u"
+
+typedef unsigned __int64 gmx_uint64_t;
+#define GMX_PRIu64 "I64u"
+#define GMX_SCNu64 "I64u"
+#else
+typedef int32_t gmx_int32_t;
+#define GMX_PRId32 PRId32
+#define GMX_SCNd32 SCNd32
+
+typedef int64_t gmx_int64_t;
+#define GMX_PRId64 PRId64
+#define GMX_SCNd64 SCNd64
+
+typedef uint32_t gmx_uint32_t;
+#define GMX_PRIu32 PRIu32
+#define GMX_SCNu32 SCNu32
+
+typedef uint64_t gmx_uint64_t;
+#define GMX_PRIu64 PRIu64
+#define GMX_SCNu64 SCNu64
+#endif
+
+#define GMX_INT32_MAX INT32_MAX
+#define GMX_INT32_MIN INT32_MIN
+
+#define GMX_INT64_MAX INT64_MAX
+#define GMX_INT64_MIN INT64_MIN
+
+#define GMX_UINT32_MAX UINT32_MAX
+#define GMX_UINT32_MIN UINT32_MIN
+
+#define GMX_UINT64_MAX UINT64_MAX
+#define GMX_UINT64_MIN UINT64_MIN
+/*! \} */
+
+/*! \def gmx_inline
+ * \brief
+ * Keyword to use in C code instead of C99 `inline`.
+ *
+ * Some of the C compilers we support do not recognize the C99 keyword
+ * `inline`. This macro should be used in C code and in shared C/C++ headers
+ * to indicate a function is inlined.
+ * C++ code should use plain `inline`, as that is already in C++98.
+ */
+#if !defined __cplusplus && _MSC_VER
+#define gmx_inline __inline
+#else
+/* C++ or C99 */
+#define gmx_inline inline
+#endif
+
+/* ICC, GCC, MSVC, Pathscale, PGI, XLC support __restrict.
+ * Any other compiler can be added here. */
+/*! \brief
+ * Keyword to use in instead of C99 `restrict`.
+ *
+ * We cannot use `restrict` because it is only in C99, but not in C++.
+ * This macro should instead be used to allow easily supporting different
+ * compilers.
+ */
+#define gmx_restrict __restrict
+
+/*! \def gmx_cxx_const
+ * \brief
+ * Keyword to work around C/C++ differences in possible const keyword usage.
+ *
+ * Some functions that do not modify their input parameters cannot declare
+ * those parameters as `const` and compile warning/error-free on both C and C++
+ * compilers because of differences in `const` semantics. This macro can be
+ * used in cases where C++ allows `const`, but C does not like it, to make the
+ * same declaration work for both.
+ */
+#ifdef __cplusplus
+#define gmx_cxx_const const
+#else
+#define gmx_cxx_const
+#endif
+
+/*! \def gmx_unused
+ * \brief
+ * Attribute to suppress compiler warnings about unused function parameters.
+ *
+ * This attribute suppresses compiler warnings about unused function arguments
+ * by marking them as possibly unused. Some arguments are unused but
+ * have to be retained to preserve a function signature
+ * that must match that of another function.
+ * Some arguments are only used in *some* conditional compilation code paths
+ * (e.g. MPI).
+ */
+#ifndef gmx_unused
+#ifdef __GNUC__
+/* GCC, clang, and some ICC pretending to be GCC */
+# define gmx_unused __attribute__ ((unused))
+#elif (defined(__INTEL_COMPILER) || defined(__ECC)) && !defined(_MSC_VER)
+/* ICC on *nix */
+# define gmx_unused __attribute__ ((unused))
+#elif defined(__PGI)
+/* Portland group compilers */
+# define gmx_unused __attribute__ ((unused))
+#elif defined _MSC_VER
+/* MSVC */
+# define gmx_unused /*@unused@*/
+#elif defined(__xlC__)
+/* IBM */
+# define gmx_unused __attribute__ ((unused))
+#else
+# define gmx_unused
+#endif
+#endif
+
+#ifndef __has_feature
+/** For compatibility with non-clang compilers. */
+#define __has_feature(x) 0
+#endif
+
+/*! \def gmx_noreturn
+ * \brief
+ * Indicate that a function is not expected to return.
+ */
+#ifndef gmx_noreturn
+#if defined(__GNUC__) || __has_feature(attribute_analyzer_noreturn)
+#define gmx_noreturn __attribute__((noreturn))
+#elif defined (_MSC_VER)
+#define gmx_noreturn __declspec(noreturn)
+#else
+#define gmx_noreturn
+#endif
+#endif
+
+/*! \brief
+ * Macro to explicitly ignore an unused value.
+ *
+ * \ingroup module_utility
+ */
+#define GMX_UNUSED_VALUE(value) (void)value
+
+#ifdef __cplusplus
+namespace gmx
+{
+namespace internal
+{
+/*! \cond internal */
+/*! \internal \brief
+ * Helper for ignoring values in macros.
+ *
+ * \ingroup module_utility
+ */
+template <typename T>
+static inline void ignoreValueHelper(const T &)
+{
+}
+//! \endcond
+} // namespace internal
+} // namespace gmx
+
+/*! \brief
+ * Macro to explicitly ignore a return value of a call.
+ *
+ * Mainly meant for ignoring values of functions declared with
+ * `__attribute__((warn_unused_return))`. Makes it easy to find those places if
+ * they need to be fixed, and document the intent in cases where the return
+ * value really can be ignored. It also makes it easy to adapt the approach so
+ * that they don't produce warnings. A cast to void doesn't remove the warning
+ * in gcc, while adding a dummy variable can cause warnings about an unused
+ * variable.
+ *
+ * \ingroup module_utility
+ */
+#define GMX_IGNORE_RETURN_VALUE(call) \
+ ::gmx::internal::ignoreValueHelper(call)
+#endif
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "basenetwork.h"
+
+#include "config.h"
+
+#include <climits>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+
+#include <exception>
+
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/programcontext.h"
+
+gmx_bool gmx_mpi_initialized(void)
+{
+#ifndef GMX_MPI
+ return 0;
+#else
+ int n;
+ MPI_Initialized(&n);
+
+ return n;
+#endif
+}
+
+int gmx_node_num(void)
+{
+#ifndef GMX_MPI
+ return 1;
+#else
+#ifdef GMX_THREAD_MPI
+ if (!gmx_mpi_initialized())
+ {
+ return 1;
+ }
+#endif
+ int i;
+ (void) MPI_Comm_size(MPI_COMM_WORLD, &i);
+ return i;
+#endif
+}
+
+int gmx_node_rank(void)
+{
+#ifndef GMX_MPI
+ return 0;
+#else
+#ifdef GMX_THREAD_MPI
+ if (!gmx_mpi_initialized())
+ {
+ return 0;
+ }
+#endif
+ int i;
+ (void) MPI_Comm_rank(MPI_COMM_WORLD, &i);
+ return i;
+#endif
+}
+
+static int mpi_hostname_hash(void)
+{
+ int hash_int;
+
+#ifndef GMX_LIB_MPI
+ /* We have a single physical node */
+ hash_int = 0;
+#else
+ int resultlen;
+ char mpi_hostname[MPI_MAX_PROCESSOR_NAME];
+
+ /* This procedure can only differentiate nodes with different names.
+ * Architectures where different physical nodes have identical names,
+ * such as IBM Blue Gene, should use an architecture specific solution.
+ */
+ MPI_Get_processor_name(mpi_hostname, &resultlen);
+
+ /* The string hash function returns an unsigned int. We cast to an int.
+ * Negative numbers are converted to positive by setting the sign bit to 0.
+ * This makes the hash one bit smaller.
+ * A 63-bit hash (with 64-bit int) should be enough for unique node hashes,
+ * even on a million node machine. 31 bits might not be enough though!
+ */
+ hash_int =
+ (int)gmx_string_fullhash_func(mpi_hostname, gmx_string_hash_init);
+ if (hash_int < 0)
+ {
+ hash_int -= INT_MIN;
+ }
+#endif
+
+ return hash_int;
+}
+
+#if defined GMX_LIB_MPI && defined GMX_TARGET_BGQ
+#ifdef __clang__
+/* IBM's declaration of this function in
+ * /bgsys/drivers/V1R2M2/ppc64/spi/include/kernel/process.h
+ * erroneously fails to specify __INLINE__, despite
+ * /bgsys/drivers/V1R2M2/ppc64/spi/include/kernel/cnk/process_impl.h
+ * specifiying __INLINE__, so bgclang thinks they are different enough
+ * to complain about. */
+static uint64_t Kernel_GetJobID();
+#endif
+#include <spi/include/kernel/location.h>
+
+static int bgq_nodenum(void)
+{
+ int hostnum;
+ Personality_t personality;
+ Kernel_GetPersonality(&personality, sizeof(personality));
+ /* Each MPI rank has a unique coordinate in a 6-dimensional space
+ (A,B,C,D,E,T), with dimensions A-E corresponding to different
+ physical nodes, and T within each node. Each node has sixteen
+ physical cores, each of which can have up to four hardware
+ threads, so 0 <= T <= 63 (but the maximum value of T depends on
+ the confituration of ranks and OpenMP threads per
+ node). However, T is irrelevant for computing a suitable return
+ value for gmx_hostname_num().
+ */
+ hostnum = personality.Network_Config.Acoord;
+ hostnum *= personality.Network_Config.Bnodes;
+ hostnum += personality.Network_Config.Bcoord;
+ hostnum *= personality.Network_Config.Cnodes;
+ hostnum += personality.Network_Config.Ccoord;
+ hostnum *= personality.Network_Config.Dnodes;
+ hostnum += personality.Network_Config.Dcoord;
+ hostnum *= personality.Network_Config.Enodes;
+ hostnum += personality.Network_Config.Ecoord;
+
+ if (debug)
+ {
+ std::fprintf(debug,
+ "Torus ID A: %d / %d B: %d / %d C: %d / %d D: %d / %d E: %d / %d\n"
+ "Node ID T: %d / %d core: %d / %d hardware thread: %d / %d\n",
+ personality.Network_Config.Acoord,
+ personality.Network_Config.Anodes,
+ personality.Network_Config.Bcoord,
+ personality.Network_Config.Bnodes,
+ personality.Network_Config.Ccoord,
+ personality.Network_Config.Cnodes,
+ personality.Network_Config.Dcoord,
+ personality.Network_Config.Dnodes,
+ personality.Network_Config.Ecoord,
+ personality.Network_Config.Enodes,
+ Kernel_ProcessorCoreID(),
+ 16,
+ Kernel_ProcessorID(),
+ 64,
+ Kernel_ProcessorThreadID(),
+ 4);
+ }
+ return hostnum;
+}
+#endif
+
+int gmx_physicalnode_id_hash(void)
+{
+ int hash;
+
+#ifndef GMX_MPI
+ hash = 0;
+#else
+#ifdef GMX_THREAD_MPI
+ /* thread-MPI currently puts the thread number in the process name,
+ * we might want to change this, as this is inconsistent with what
+ * most MPI implementations would do when running on a single node.
+ */
+ hash = 0;
+#else
+#ifdef GMX_TARGET_BGQ
+ hash = bgq_nodenum();
+#else
+ hash = mpi_hostname_hash();
+#endif
+#endif
+#endif
+
+ if (debug)
+ {
+ fprintf(debug, "In gmx_physicalnode_id_hash: hash %d\n", hash);
+ }
+
+ return hash;
+}
+
+#ifdef GMX_LIB_MPI
+void gmx_abort(int errorno)
+{
+ const char *programName = "GROMACS";
+ try
+ {
+ programName = gmx::getProgramContext().displayName();
+ }
+ catch (const std::exception &)
+ {
+ }
+ const int nnodes = gmx_node_num();
+ const int noderank = gmx_node_rank();
+ if (nnodes > 1)
+ {
+ std::fprintf(stderr, "Halting parallel program %s on rank %d out of %d\n",
+ programName, noderank, nnodes);
+ }
+ else
+ {
+ std::fprintf(stderr, "Halting program %s\n", programName);
+ }
+
+ MPI_Abort(MPI_COMM_WORLD, errorno);
+ std::exit(errorno);
+}
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Utility functions for basic MPI and network functionality.
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_BASENETWORK_H
+#define GMX_UTILITY_BASENETWORK_H
+
+#include <stddef.h>
+
+#include "gromacs/utility/basedefinitions.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*! \brief
+ * Returns whether MPI has been initialized.
+ *
+ * The return value is `FALSE` if MPI_Init() has not been called, or if
+ * \Gromacs has been compiled without MPI support.
+ * For thread-MPI, returns `TRUE` when the threads have been started.
+ *
+ * Note that there is a lot of code in between MPI_Init() and the thread-MPI
+ * thread start where the return value is different depending on compilation
+ * options.
+ */
+gmx_bool gmx_mpi_initialized(void);
+
+/*! \brief
+ * Returns the number of nodes.
+ *
+ * For thread-MPI, returns one before the threads have been started.
+ * This allows code between the real MPI_Init() and the thread-MPI "init" to
+ * still use this function to check for serial/parallel status and work as
+ * expected: for thread-MPI, at that point they should behave as if the run was
+ * serial.
+ */
+int gmx_node_num(void);
+
+/*! \brief
+ * Returns the rank of the node.
+ *
+ * For thread-MPI, returns zero before the threads have been started.
+ * This allows code between the real MPI_Init() and the thread-MPI "init" to
+ * still use this function to check for master node work as expected:
+ * for thread-MPI, at that point the only thread of execution should behave as
+ * if it the master node.
+ */
+int gmx_node_rank(void);
+
+/*! \brief
+ * Return a non-negative hash that is, hopefully, unique for each physical
+ * node.
+ *
+ * This hash is useful for determining hardware locality.
+ */
+int gmx_physicalnode_id_hash(void);
+
+/*! \brief
+ * Returns an integer characteristic of and, hopefully, unique to each
+ * physical node in the MPI system.
+ *
+ * If the first part of the MPI hostname (up to the first dot) ends with a
+ * number, returns this number. If the first part of the MPI hostname does not
+ * ends in a number (0-9 characters), returns 0.
+ *
+ * \todo
+ * This function should be fully replaced by gmx_physicalnode_id_hash().
+ */
+int gmx_hostname_num(void);
+
+/** Abort the parallel run */
+void gmx_abort(int errorno);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
*/
#include "gromacs/utility/baseversion-gen.h"
-const char _gmx_ver_string[] = "VERSION @GMX_PROJECT_VERSION_STR@";
-const char _gmx_full_git_hash[] = "@GMX_GIT_HEAD_HASH@";
-const char _gmx_central_base_hash[] = "@GMX_GIT_REMOTE_HASH@";
+const char _gmx_ver_string[] = "VERSION @GMX_VERSION_STRING_FULL@";
+const char _gmx_full_git_hash[] = "@GMX_VERSION_FULL_HASH@";
+const char _gmx_central_base_hash[] = "@GMX_VERSION_CENTRAL_BASE_HASH@";
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
#include "baseversion.h"
+
#include "baseversion-gen.h"
const char *gmx_version()
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares gmx_bitmask_t and associated functions
+ *
+ * \author Roland Schulz <roland@utk.edu>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+
+#ifndef GMX_MDLIB_BITMASK_H
+#define GMX_MDLIB_BITMASK_H
+
+#include "config.h" /* for GMX_MAX_OPENMP_THREADS */
+
+#include <string.h>
+
+#include "gromacs/utility/basedefinitions.h"
+
+/*! \brief Size of bitmask. Has to be 32 or multiple of 64. */
+#ifndef BITMASK_SIZE
+#define BITMASK_SIZE GMX_OPENMP_MAX_THREADS
+#endif
+
+#if BITMASK_SIZE != 32 && BITMASK_SIZE%64 != 0
+#error BITMASK_SIZE has to be 32 or a multiple of 64.
+#endif
+
+#if BITMASK_SIZE <= 64 || defined DOXYGEN
+#if BITMASK_SIZE == 32
+typedef gmx_uint32_t gmx_bitmask_t;
+#else
+typedef gmx_uint64_t gmx_bitmask_t; /**< bitmask type */
+#endif
+
+/*! \brief Initialize all bits to 0 */
+gmx_inline static void bitmask_clear(gmx_bitmask_t* m)
+{
+ *m = 0;
+}
+
+/*! \brief Set bit at position b to 1. */
+gmx_inline static void bitmask_set_bit(gmx_bitmask_t* m, int b)
+{
+ *m |= ((gmx_bitmask_t)1 << b);
+}
+
+/*! \brief Initialize all bits: bit b to 1, others to 0 */
+gmx_inline static void bitmask_init_bit(gmx_bitmask_t* m, int b)
+{
+ *m = ((gmx_bitmask_t)1 << b);
+}
+
+/*! \brief Initialize all bits: all bits below b to 1, others to 0 */
+gmx_inline static void bitmask_init_low_bits(gmx_bitmask_t* m, int b)
+{
+ *m = ((gmx_bitmask_t)1 << b) - 1;
+}
+
+/*! \brief Test if bit b is set */
+gmx_inline static gmx_bool bitmask_is_set(gmx_bitmask_t m, int b)
+{
+ return (m & ((gmx_bitmask_t)1 << b)) != 0;
+}
+
+/*! \brief Test if both bitmasks have no common bits enabled */
+gmx_inline static gmx_bool bitmask_is_disjoint(gmx_bitmask_t a, gmx_bitmask_t b)
+{
+ return !(a & b);
+}
+
+/*! \brief Test if both bitmasks are equal */
+gmx_inline static gmx_bool bitmask_is_equal(gmx_bitmask_t a, gmx_bitmask_t b)
+{
+ return a == b;
+}
+
+/*! \brief Test if bitmask has no enabled bits */
+gmx_inline static gmx_bool bitmask_is_zero(gmx_bitmask_t m)
+{
+ return !m;
+}
+
+/*! \brief Set all bits enabled in either mask and write into a */
+gmx_inline static void bitmask_union(gmx_bitmask_t* a, gmx_bitmask_t b)
+{
+ *a |= b;
+}
+#else
+#define BITMASK_ALEN (BITMASK_SIZE/64)
+typedef gmx_uint64_t gmx_bitmask_t[BITMASK_ALEN];
+
+gmx_inline static void bitmask_clear(gmx_bitmask_t* m)
+{
+ memset(*m, 0, BITMASK_SIZE/8);
+}
+
+gmx_inline static void bitmask_set_bit(gmx_bitmask_t* m, int b)
+{
+ (*m)[b/64] |= ((gmx_uint64_t)1 << (b%64));
+}
+
+gmx_inline static void bitmask_init_bit(gmx_bitmask_t* m, int b)
+{
+ bitmask_clear(m);
+ (*m)[b/64] = ((gmx_uint64_t)1 << (b%64));
+}
+
+gmx_inline static void bitmask_init_low_bits(gmx_bitmask_t* m, int b)
+{
+ memset(*m, 255, b/64*8);
+ (*m)[b/64] = ((gmx_uint64_t)1 << (b%64)) - 1;
+ memset(&(*m)[b/64+1], 0, (BITMASK_ALEN-b/64-1)*8);
+}
+
+gmx_inline static gmx_bool bitmask_is_set(gmx_bitmask_t m, int b)
+{
+ return (m[b/64] & ((gmx_uint64_t)1 << (b%64))) != 0;
+}
+
+gmx_inline static gmx_bool bitmask_is_disjoint(gmx_bitmask_t a, gmx_bitmask_t b)
+{
+ int i;
+ gmx_bool r = 1;
+ for (i = 0; i < BITMASK_ALEN; i++)
+ {
+ r = r && !(a[i] & b[i]);
+ }
+ return r;
+}
+
+gmx_inline static gmx_bool bitmask_is_equal(gmx_bitmask_t a, gmx_bitmask_t b)
+{
+ int i;
+ gmx_bool r = 1;
+ for (i = 0; i < BITMASK_ALEN; i++)
+ {
+ r = r && (a[i] == b[i]);
+ }
+ return r;
+}
+
+gmx_inline static gmx_bool bitmask_is_zero(gmx_bitmask_t m)
+{
+ int i;
+ gmx_bool r = 1;
+ for (i = 0; i < BITMASK_ALEN; i++)
+ {
+ r = r && !m[i];
+ }
+ return r;
+}
+
+gmx_inline static void bitmask_union(gmx_bitmask_t* a, gmx_bitmask_t b)
+{
+ int i;
+ for (i = 0; i < BITMASK_ALEN; i++)
+ {
+ (*a)[i] |= b[i];
+ }
+}
+#endif
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \inlibraryapi
* \ingroup module_utility
*/
-#ifndef GMX_UTILITY_COMMON_H
-#define GMX_UTILITY_COMMON_H
+#ifndef GMX_UTILITY_CLASSHELPERS_H
+#define GMX_UTILITY_CLASSHELPERS_H
#include <boost/scoped_ptr.hpp>
namespace gmx
{
-namespace internal
-{
-/*! \cond internal */
-/*! \internal \brief
- * Helper for ignoring values in macros.
- *
- * \ingroup module_utility
- */
-template <typename T>
-void inline ignoreValueHelper(const T &)
-{
-}
-//! \endcond
-} // namespace internal
/*! \brief
* Macro to declare a class non-copyable and non-assignable.
#define GMX_DISALLOW_ASSIGN(ClassName) \
private: \
ClassName &operator=(const ClassName &)
-/*! \brief
- * Macro to explicitly ignore a return value of a call.
- *
- * Mainly meant for ignoring values of functions declared with
- * `__attribute__((warn_unused_return))`. Makes it easy to find those places if
- * they need to be fixed, and document the intent in cases where the return
- * value really can be ignored. It also makes it easy to adapt the approach so
- * that they don't produce warnings. A cast to void doesn't remove the warning
- * in gcc, while adding a dummy variable can cause warnings about an unused
- * variable.
- *
- * \ingroup module_utility
- */
-#define GMX_IGNORE_RETURN_VALUE(call) \
- ::gmx::internal::ignoreValueHelper(call)
-/*! \brief
- * Macro to explicitly ignore an unused value.
- *
- * \ingroup module_utility
- */
-#define GMX_UNUSED_VALUE(value) (void)value
/*! \brief
* Helper class to manage a pointer to a private implementation class.
* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#include "cstringutil.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "cstringutil.h"
#include <assert.h>
#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include <time.h>
-
-#include <sys/types.h>
-#ifdef HAVE_SYS_TIME_H
-#include <sys/time.h>
-#endif
-#ifdef HAVE_PWD_H
-#include <pwd.h>
-#endif
-#ifdef HAVE_UNISTD_H
-#include <unistd.h>
-#endif
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/legacyheaders/main.h"
-
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/sysinfo.h"
int continuing(char *s)
{
rtrim (str);
}
-char *
-gmx_ctime_r(const time_t *clock, char *buf, int n)
+void nice_header(FILE *out, const char *fn)
{
-#ifdef _MSC_VER
- /* Windows */
- ctime_s( buf, n, clock );
-#elif defined(GMX_NATIVE_WINDOWS)
- char *tmpbuf = ctime( clock );
- strncpy(buf, tmpbuf, n-1);
- buf[n-1] = '\0';
-#elif (defined(__sun))
- /*Solaris*/
- ctime_r(clock, buf, n);
-#else
- char tmpbuf[STRLEN];
- ctime_r(clock, tmpbuf);
- strncpy(buf, tmpbuf, n-1);
- buf[n-1] = '\0';
-#endif
- return buf;
-}
-
-void nice_header (FILE *out, const char *fn)
-{
- const char *unk = "onbekend";
- time_t clock;
- const char *user = unk;
- int gh;
-#ifdef HAVE_PWD_H
- uid_t uid;
-#else
int uid;
-#endif
- char buf[256] = "";
+ char userbuf[256];
+ char hostbuf[256];
char timebuf[STRLEN];
-#ifdef HAVE_PWD_H
- struct passwd *pw;
-#endif
/* Print a nice header above the file */
- time(&clock);
- fprintf (out, "%c\n", COMMENTSIGN);
- fprintf (out, "%c\tFile '%s' was generated\n", COMMENTSIGN, fn ? fn : unk);
-
-#ifdef HAVE_PWD_H
- uid = getuid();
- pw = getpwuid(uid);
- gh = gmx_gethostname(buf, 255);
- /* pw returns null on error (e.g. compute nodes lack /etc/passwd) */
- user = pw ? pw->pw_name : unk;
-#else
- uid = 0;
- gh = -1;
-#endif
-
- gmx_ctime_r(&clock, timebuf, STRLEN);
- fprintf (out, "%c\tBy user: %s (%d)\n", COMMENTSIGN,
- user ? user : unk, (int) uid);
- fprintf(out, "%c\tOn host: %s\n", COMMENTSIGN, (gh == 0) ? buf : unk);
-
- fprintf (out, "%c\tAt date: %s", COMMENTSIGN, timebuf);
- fprintf (out, "%c\n", COMMENTSIGN);
+ fprintf(out, "%c\n", COMMENTSIGN);
+ fprintf(out, "%c\tFile '%s' was generated\n", COMMENTSIGN, fn ? fn : "unknown");
+
+ uid = gmx_getuid();
+ gmx_getusername(userbuf, 256);
+ gmx_gethostname(hostbuf, 256);
+ gmx_format_current_time(timebuf, STRLEN);
+
+ fprintf(out, "%c\tBy user: %s (%d)\n", COMMENTSIGN, userbuf, uid);
+ fprintf(out, "%c\tOn host: %s\n", COMMENTSIGN, hostbuf);
+ fprintf(out, "%c\tAt date: %s\n", COMMENTSIGN, timebuf);
+ fprintf(out, "%c\n", COMMENTSIGN);
}
-
int gmx_strcasecmp_min(const char *str1, const char *str2)
{
char ch1, ch2;
#endif
}
+char *gmx_step_str(gmx_int64_t i, char *buf)
+{
+ sprintf(buf, "%"GMX_PRId64, i);
+ return buf;
+}
+
void parse_digits_from_plain_string(const char *digitstring, int *ndigits, int **digitlist)
{
int i;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_UTILITY_CSTRINGUTIL_H
#include <stdio.h>
-#include <time.h>
-#include "../legacyheaders/types/simple.h"
-
-#include "gmx_header_config.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
#define CONTINUE '\\'
/** Comment sign to use. */
#define COMMENTSIGN ';'
+/** Standard size for char* string buffers. */
+#define STRLEN 4096
/*! \brief
* Strip trailing spaces and if s ends with a ::CONTINUE remove that too.
/** Remove leading and trailing whitespace from a string. */
void trim(char *str);
-/** Portable version of ctime_r. */
-char *gmx_ctime_r(const time_t *clock, char *buf, int n);
-
/** Prints creation time stamp and user information into a file as comments. */
void nice_header(FILE *out, const char *fn);
*/
gmx_int64_t str_to_int64_t(const char *str, char **endptr);
-#ifdef GMX_NATIVE_WINDOWS
-#define snprintf _snprintf
-#endif
+/** Minimum size of buffer to pass to gmx_step_str(). */
+#define STEPSTRSIZE 22
+
+/*! \brief
+ * Prints a gmx_int64_t value in buf and returns the pointer to buf.
+ *
+ * buf should be large enough to contain i: STEPSTRSIZE (22) chars.
+ * When multiple gmx_int64_t values are printed in the same printf call,
+ * be sure to call gmx_step_str with different buffers.
+ */
+char *gmx_step_str(gmx_int64_t i, char *buf);
/*! \brief Construct an array of digits found in the input string
*
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements gmx::DataFileFinder.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_utility
+ */
+#include "gmxpre.h"
+
+#include "datafilefinder.h"
+
+#include "config.h"
+
+#include <cstdlib>
+
+#include <string>
+#include <vector>
+
+#include "gromacs/utility/directoryenumerator.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/file.h"
+#include "gromacs/utility/path.h"
+#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/stringutil.h"
+
+namespace gmx
+{
+
+/********************************************************************
+ * DataFileFinder::Impl
+ */
+
+class DataFileFinder::Impl
+{
+ public:
+ static std::string getDefaultPath();
+
+ Impl() : envName_(NULL), bEnvIsSet_(false) {}
+
+ const char *envName_;
+ bool bEnvIsSet_;
+ std::vector<std::string> searchPath_;
+};
+
+std::string DataFileFinder::Impl::getDefaultPath()
+{
+ const InstallationPrefixInfo installPrefix
+ = getProgramContext().installationPrefix();
+ if (!isNullOrEmpty(installPrefix.path))
+ {
+ const char *const dataPath
+ = installPrefix.bSourceLayout ? "share" : DATA_INSTALL_DIR;
+ return Path::join(installPrefix.path, dataPath, "top");
+ }
+ return std::string();
+}
+
+/********************************************************************
+ * DataFileFinder
+ */
+
+DataFileFinder::DataFileFinder()
+ : impl_(NULL)
+{
+}
+
+DataFileFinder::~DataFileFinder()
+{
+}
+
+void DataFileFinder::setSearchPathFromEnv(const char *envVarName)
+{
+ if (!impl_.get())
+ {
+ impl_.reset(new Impl());
+ }
+ impl_->envName_ = envVarName;
+ const char *const lib = getenv(envVarName);
+ if (lib != NULL)
+ {
+ impl_->bEnvIsSet_ = true;
+ Path::splitPathEnvironment(lib, &impl_->searchPath_);
+ }
+}
+
+FILE *DataFileFinder::openFile(const DataFileOptions &options) const
+{
+ // TODO: There is a small race here, since there is some time between
+ // the exists() calls and actually opening the file. It would be better
+ // to leave the file open after a successful exists() if the desire is to
+ // actually open the file.
+ std::string filename = findFile(options);
+ if (filename.empty())
+ {
+ return NULL;
+ }
+#if 0
+ if (debug)
+ {
+ fprintf(debug, "Opening library file %s\n", fn);
+ }
+#endif
+ return File::openRawHandle(filename, "r");
+}
+
+std::string DataFileFinder::findFile(const DataFileOptions &options) const
+{
+ if (options.bCurrentDir_ && Path::exists(options.filename_))
+ {
+ return options.filename_;
+ }
+ if (impl_.get())
+ {
+ std::vector<std::string>::const_iterator i;
+ for (i = impl_->searchPath_.begin(); i != impl_->searchPath_.end(); ++i)
+ {
+ // TODO: Deal with an empty search path entry more reasonably.
+ std::string testPath = Path::join(*i, options.filename_);
+ // TODO: Consider skipping directories.
+ if (Path::exists(testPath))
+ {
+ return testPath;
+ }
+ }
+ }
+ const std::string &defaultPath = Impl::getDefaultPath();
+ if (!defaultPath.empty())
+ {
+ std::string testPath = Path::join(defaultPath, options.filename_);
+ if (Path::exists(testPath))
+ {
+ return testPath;
+ }
+ }
+ if (options.bThrow_)
+ {
+ const char *const envName = (impl_.get() ? impl_->envName_ : NULL);
+ const bool bEnvIsSet = (impl_.get() ? impl_->bEnvIsSet_ : false);
+ std::string message(
+ formatString("Library file '%s' not found", options.filename_));
+ if (options.bCurrentDir_)
+ {
+ message.append(" in current dir nor");
+ }
+ if (bEnvIsSet)
+ {
+ message.append(formatString(" in your %s path nor", envName));
+ }
+ message.append(" in the default directories.\nThe following paths were searched:");
+ if (options.bCurrentDir_)
+ {
+ message.append("\n ");
+ message.append(Path::getWorkingDirectory());
+ message.append(" (current dir)");
+ }
+ if (impl_.get())
+ {
+ std::vector<std::string>::const_iterator i;
+ for (i = impl_->searchPath_.begin(); i != impl_->searchPath_.end(); ++i)
+ {
+ message.append("\n ");
+ message.append(*i);
+ }
+ }
+ if (!defaultPath.empty())
+ {
+ message.append("\n ");
+ message.append(defaultPath);
+ message.append(" (default)");
+ }
+ if (!bEnvIsSet && envName != NULL)
+ {
+ message.append(
+ formatString("\nYou can set additional directories to search "
+ "with the %s path variable.", envName));
+ }
+ GMX_THROW(FileIOError(message));
+ }
+ return std::string();
+}
+
+std::vector<DataFileInfo>
+DataFileFinder::enumerateFiles(const DataFileOptions &options) const
+{
+ // TODO: Consider if not being able to list one of the directories should
+ // really be a fatal error. Or alternatively, check somewhere else that
+ // paths in GMXLIB are valid.
+ std::vector<DataFileInfo> result;
+ std::vector<std::string>::const_iterator i;
+ if (options.bCurrentDir_)
+ {
+ std::vector<std::string> files
+ = DirectoryEnumerator::enumerateFilesWithExtension(
+ ".", options.filename_, false);
+ for (i = files.begin(); i != files.end(); ++i)
+ {
+ result.push_back(DataFileInfo(".", *i, false));
+ }
+ }
+ if (impl_.get())
+ {
+ std::vector<std::string>::const_iterator j;
+ for (j = impl_->searchPath_.begin(); j != impl_->searchPath_.end(); ++j)
+ {
+ std::vector<std::string> files
+ = DirectoryEnumerator::enumerateFilesWithExtension(
+ j->c_str(), options.filename_, false);
+ for (i = files.begin(); i != files.end(); ++i)
+ {
+ result.push_back(DataFileInfo(*j, *i, false));
+ }
+ }
+ }
+ const std::string &defaultPath = Impl::getDefaultPath();
+ if (!defaultPath.empty())
+ {
+ std::vector<std::string> files
+ = DirectoryEnumerator::enumerateFilesWithExtension(
+ defaultPath.c_str(), options.filename_, false);
+ for (i = files.begin(); i != files.end(); ++i)
+ {
+ result.push_back(DataFileInfo(defaultPath, *i, true));
+ }
+ }
+ if (result.empty() && options.bThrow_)
+ {
+ // TODO: Print the search path as is done in findFile().
+ std::string message(
+ formatString("Could not find any files ending on '%s' in the "
+ "current directory or the GROMACS library search path",
+ options.filename_));
+ GMX_THROW(FileIOError(message));
+ }
+ return result;
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Declares gmx::DataFileFinder and related classes.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inpublicapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_LIBFILEFINDER_H
+#define GMX_UTILITY_LIBFILEFINDER_H
+
+#include <cstdio>
+
+#include <string>
+#include <vector>
+
+#include "gromacs/utility/classhelpers.h"
+
+namespace gmx
+{
+
+class DataFileFinder;
+
+/*! \brief
+ * Search parameters for DataFileFinder.
+ *
+ * This class implements a named parameter idiom for DataFileFinder::findFile()
+ * and DataFileFinder::openFile() to support an easily readable and
+ * customizable way of searching data files.
+ *
+ * By default, the search first considers the current directory, followed by
+ * specified and default data directories, and an exception is thrown if the
+ * file could not be found.
+ * To skip searching in the current directory, use includeCurrentDir().
+ *
+ * Methods in this class do not throw.
+ *
+ * \inpublicapi
+ * \ingroup module_utility
+ */
+class DataFileOptions
+{
+ public:
+ /*! \brief
+ * Constructs default options for searching for a file with the
+ * specified name.
+ *
+ * \param[in] filename File name to search for.
+ *
+ * This constructor is not explicit to allow passing a simple string to
+ * DataFileFinder methods to search for the string with the default
+ * parameters.
+ */
+ DataFileOptions(const char *filename)
+ : filename_(filename), bCurrentDir_(true), bThrow_(true)
+ {
+ }
+ //! \copydoc DataFileOptions(const char *)
+ DataFileOptions(const std::string &filename)
+ : filename_(filename.c_str()), bCurrentDir_(true), bThrow_(true)
+ {
+ }
+
+ //! Sets whether to search in the current (working) directory.
+ DataFileOptions &includeCurrentDir(bool bInclude)
+ {
+ bCurrentDir_ = bInclude;
+ return *this;
+ }
+ //! Sets whether an exception is thrown if the file could not be found.
+ DataFileOptions &throwIfNotFound(bool bThrow)
+ {
+ bThrow_ = bThrow;
+ return *this;
+ }
+
+ private:
+ const char *filename_;
+ bool bCurrentDir_;
+ bool bThrow_;
+
+ /*! \brief
+ * Needed to access the members without otherwise unnecessary accessors.
+ */
+ friend class DataFileFinder;
+};
+
+/*! \brief
+ * Information about a data file found by DataFileFinder::enumerateFiles().
+ *
+ * \inpublicapi
+ * \ingroup module_utility
+ */
+struct DataFileInfo
+{
+ //! Initializes the structure with given values.
+ DataFileInfo(const std::string &dir, const std::string &name, bool bDefault)
+ : dir(dir), name(name), bFromDefaultDir(bDefault)
+ {
+ }
+
+ /*! \brief
+ * Directory from which the file was found.
+ *
+ * If the file was found from the current directory, this will be `"."`.
+ * In other cases, this will be a full path (except if the user-provided
+ * search path contains relative paths).
+ */
+ std::string dir;
+ /*! \brief
+ * Name of the file without any directory name.
+ */
+ std::string name;
+ /*! \brief
+ * Whether the file was found from the default directory.
+ *
+ * If `true`, the file was found from the default installation data
+ * directory, not from the current directory or any user-provided (through
+ * DataFileFinder::setSearchPathFromEnv()) location.
+ * \todo
+ * Consider replacing with an enum that identifies the source (current dir,
+ * GMXLIB, default).
+ */
+ bool bFromDefaultDir;
+};
+
+/*! \brief
+ * Searches data files from a set of paths.
+ *
+ * \inpublicapi
+ * \ingroup module_utility
+ */
+class DataFileFinder
+{
+ public:
+ /*! \brief
+ * Constructs a default data file finder.
+ *
+ * The constructed finder searches only in the directory specified by
+ * the global program context (see ProgramContextInterface), and
+ * optionally in the current directory.
+ *
+ * Does not throw.
+ */
+ DataFileFinder();
+ ~DataFileFinder();
+
+ /*! \brief
+ * Adds search path from an environment variable.
+ *
+ * \param[in] envVarName Name of the environment variable to use.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * If the specified environment variable is set, it is interpreted like
+ * a `PATH` environment variable on the platform (split at appropriate
+ * separators), and each path found is added to the search path this
+ * finder searches. The added paths take precedence over the default
+ * directory specified by the global program context, but the current
+ * directory is searched first.
+ */
+ void setSearchPathFromEnv(const char *envVarName);
+
+ /*! \brief
+ * Opens a data file if found.
+ *
+ * \param[in] options Identifies the file to be searched for.
+ * \returns The opened file handle, or `NULL` if the file could not be
+ * found and exceptions were turned off.
+ * \throws std::bad_alloc if out of memory.
+ * \throws FileIOError if
+ * - no such file can be found, and \p options specifies that an
+ * exception should be thrown, or
+ * - there is an error opening the file (note that a file is skipped
+ * during the search if the user does not have rights to open the
+ * file at all).
+ *
+ * See findFile() for more details.
+ */
+ FILE *openFile(const DataFileOptions &options) const;
+ /*! \brief
+ * Finds a full path to a data file if found.
+ *
+ * \param[in] options Identifies the file to be searched for.
+ * \returns Full path to the data file, or an empty string if the file
+ * could not be found and exceptions were turned off.
+ * \throws std::bad_alloc if out of memory.
+ * \throws FileIOError if no such file can be found, and \p options
+ * specifies that an exception should be thrown.
+ *
+ * Searches for a data file in the search paths configured for the
+ * finder, as well as in the current directory if so required.
+ * Returns the full path to the first file found.
+ */
+ std::string findFile(const DataFileOptions &options) const;
+ /*! \brief
+ * Enumerates files in the data directories.
+ *
+ * \param[in] options Idenfies files to be searched for.
+ * \returns Information about each found file.
+ * \throws std::bad_alloc if out of memory.
+ * \throws FileIOError if no such file can be found, and \p options
+ * specifies that an exception should be thrown.
+ *
+ * Enumerates all files in the data directories that have the
+ * extension/suffix specified by the file name in \p options.
+ * Unlike findFile() and openFile(), this only works on files that are
+ * in the actual data directories, not for any entry within
+ * subdirectories of those.
+ * See DataFileInfo for details on what is returned for each found
+ * file.
+ * Files from the same directory will be returned as a continuous block
+ * in the returned vector.
+ */
+ std::vector<DataFileInfo> enumerateFiles(const DataFileOptions &options) const;
+
+ private:
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
+};
+
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Provides OS-specific directory-name separator
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_DIR_SEPARATOR_H
+#define GMX_UTILITY_DIR_SEPARATOR_H
+
+#include "config.h"
+
+/*! \def DIR_SEPARATOR
+ * \brief
+ * Directory separator on this OS.
+ *
+ * Native Windows uses backslash path separators (but accepts also slashes).
+ * Cygwin and most other systems use slash.
+ *
+ * \todo Get rid of this (Redmine #950). It is not necessary for
+ * constructing paths on the systems that it currently supports, and
+ * is not reliable in parsing input paths either, since Windows needs
+ * to accept both instead of only DIR_SEPARATOR. At the very least, we
+ * should refactor the clients of this header so that they operate
+ * upon path objects rather than raw path strings.
+ */
+#ifdef GMX_NATIVE_WINDOWS
+#define DIR_SEPARATOR '\\'
+#else
+#define DIR_SEPARATOR '/'
+#endif
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2010,2011,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements gmx::DirectoryEnumerator.
+ *
+ * \author Erik Lindahl (original C implementation)
+ * \author Teemu Murtola <teemu.murtola@gmail.com> (C++ wrapper + errno handling)
+ * \ingroup module_utility
+ */
+#include "gmxpre.h"
+
+#include "directoryenumerator.h"
+
+#include "config.h"
+
+#include <cerrno>
+#include <cstdio>
+
+#include <algorithm>
+#include <string>
+#include <vector>
+
+#ifdef HAVE_DIRENT_H
+#include <dirent.h>
+#endif
+#ifdef GMX_NATIVE_WINDOWS
+#include <io.h>
+#endif
+
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
+
+namespace gmx
+{
+
+/********************************************************************
+ * DirectoryEnumerator::Impl
+ */
+
+// TODO: Consider whether checking the return value of closing would be useful,
+// and what could we do if it fails?
+#if defined GMX_NATIVE_WINDOWS
+// TODO: Consider if Windows provides more error details through other APIs.
+class DirectoryEnumerator::Impl
+{
+ public:
+ static Impl *init(const char *dirname, bool bThrow)
+ {
+ std::string tmpname(dirname);
+ // Remove possible trailing directory separator.
+ // TODO: Use a method in gmx::Path instead.
+ if (tmpname.back() == '/' || tmpname.back() == '\\')
+ {
+ tmpname.pop_back();
+ }
+
+ // Add wildcard.
+ tmpname.append("/*");
+
+ errno = 0;
+ _finddata_t finddata;
+ intptr_t handle = _findfirst(tmpname.c_str(), &finddata);
+ if (handle < 0L)
+ {
+ if (errno != ENOENT && bThrow)
+ {
+ const int code = errno;
+ const std::string message =
+ formatString("Failed to list files in directory '%s'",
+ dirname);
+ GMX_THROW_WITH_ERRNO(FileIOError(message), "_findfirst", code);
+ }
+ return NULL;
+ }
+ return new Impl(handle, finddata);
+ }
+ Impl(intptr_t handle, _finddata_t finddata)
+ : windows_handle(handle), finddata(finddata), bFirst_(true)
+ {
+ }
+ ~Impl()
+ {
+ _findclose(windows_handle);
+ }
+
+ bool nextFile(std::string *filename)
+ {
+ if (bFirst_)
+ {
+ *filename = finddata.name;
+ bFirst_ = false;
+ return true;
+ }
+ else
+ {
+ errno = 0;
+ if (_findnext(windows_handle, &finddata) != 0)
+ {
+ if (errno == 0 || errno == ENOENT)
+ {
+ filename->clear();
+ return false;
+ }
+ else
+ {
+ GMX_THROW_WITH_ERRNO(
+ FileIOError("Failed to list files in a directory"),
+ "_findnext", errno);
+ }
+ }
+ *filename = finddata.name;
+ return true;
+ }
+ }
+
+ private:
+ intptr_t windows_handle;
+ _finddata_t finddata;
+ bool bFirst_;
+};
+#elif defined HAVE_DIRENT_H
+class DirectoryEnumerator::Impl
+{
+ public:
+ static Impl *init(const char *dirname, bool bThrow)
+ {
+ errno = 0;
+ DIR *handle = opendir(dirname);
+ if (handle == NULL)
+ {
+ if (bThrow)
+ {
+ const int code = errno;
+ const std::string message =
+ formatString("Failed to list files in directory '%s'",
+ dirname);
+ GMX_THROW_WITH_ERRNO(FileIOError(message), "opendir", code);
+ }
+ return NULL;
+ }
+ return new Impl(handle);
+ }
+ explicit Impl(DIR *handle) : dirent_handle(handle)
+ {
+ // TODO: Use memory allocation that throws, and handle
+ // exception safety (close handle) in such a case.
+ /* On some platforms no space is present for d_name in dirent.
+ * Since d_name is guaranteed to be the last entry, allocating
+ * extra space for dirent will allow more size for d_name.
+ * GMX_MAX_PATH should always be >= the max possible d_name.
+ */
+ smalloc(direntp_large, sizeof(*direntp_large) + GMX_PATH_MAX);
+ }
+ ~Impl()
+ {
+ sfree(direntp_large);
+ closedir(dirent_handle);
+ }
+
+ bool nextFile(std::string *filename)
+ {
+ errno = 0;
+ dirent *p;
+ int rc = readdir_r(dirent_handle, direntp_large, &p);
+ if (p == NULL && rc == 0)
+ {
+ filename->clear();
+ return false;
+ }
+ else if (rc != 0)
+ {
+ GMX_THROW_WITH_ERRNO(
+ FileIOError("Failed to list files in a directory"),
+ "readdir_r", errno);
+ }
+ *filename = direntp_large->d_name;
+ return true;
+ }
+
+ private:
+ DIR *dirent_handle;
+ dirent *direntp_large;
+};
+#else
+class DirectoryEnumerator::Impl
+{
+ public:
+ static Impl *init(const char * /*dirname*/, bool /*bThrow*/)
+ {
+ std::string message(
+ "Source compiled without POSIX dirent or Windows support "
+ "- cannot scan directories. In the very unlikely event "
+ "this is not a compile-time mistake you could consider "
+ "implementing support for your platform in "
+ "directoryenumerator.cpp, but contact the developers "
+ "to make sure it's really necessary!");
+ GMX_THROW(NotImplementedError(message));
+ }
+
+ bool nextFile(std::string * /*filename*/)
+ {
+ return false;
+ }
+};
+#endif
+
+/********************************************************************
+ * DirectoryEnumerator
+ */
+
+// static
+std::vector<std::string>
+DirectoryEnumerator::enumerateFilesWithExtension(
+ const char *dirname, const char *extension, bool bThrow)
+{
+ std::vector<std::string> result;
+ DirectoryEnumerator dir(dirname, bThrow);
+ std::string nextName;
+ while (dir.nextFile(&nextName))
+ {
+ if (debug)
+ {
+ std::fprintf(debug, "dir '%s' file '%s'\n",
+ dirname, nextName.c_str());
+ }
+ // TODO: What about case sensitivity?
+ if (endsWith(nextName, extension))
+ {
+ result.push_back(nextName);
+ }
+ }
+
+ std::sort(result.begin(), result.end());
+ return result;
+}
+
+
+DirectoryEnumerator::DirectoryEnumerator(const char *dirname, bool bThrow)
+ : impl_(NULL)
+{
+ GMX_RELEASE_ASSERT(dirname != NULL && dirname[0] != '\0',
+ "Attempted to open empty/null directory path");
+ impl_.reset(Impl::init(dirname, bThrow));
+}
+
+DirectoryEnumerator::DirectoryEnumerator(const std::string &dirname, bool bThrow)
+ : impl_(NULL)
+{
+ GMX_RELEASE_ASSERT(!dirname.empty(),
+ "Attempted to open empty/null directory path");
+ impl_.reset(Impl::init(dirname.c_str(), bThrow));
+}
+
+DirectoryEnumerator::~DirectoryEnumerator()
+{
+}
+
+bool DirectoryEnumerator::nextFile(std::string *filename)
+{
+ if (!impl_.get())
+ {
+ filename->clear();
+ return false;
+ }
+ return impl_->nextFile(filename);
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares gmx::DirectoryEnumerator.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_DIRECTORYENUMERATOR_H
+#define GMX_UTILITY_DIRECTORYENUMERATOR_H
+
+#include <string>
+#include <vector>
+
+#include "gromacs/utility/classhelpers.h"
+
+namespace gmx
+{
+
+/*! \libinternal \brief
+ * Lists files in a directory.
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+class DirectoryEnumerator
+{
+ public:
+ /*! \brief
+ * Convenience function to list files with certain extension from a
+ * directory.
+ *
+ * \param[in] dirname Path to the directory to list.
+ * \param[in] extension List files with the given extension
+ * (or suffix in file name).
+ * \param[in] bThrow Whether failure to open the directory should throw.
+ * \returns List of files with the given extension in \p dirname.
+ * \throws std::bad_alloc if out of memory.
+ * \throws FileIOError if opening the directory fails and `bThrow == true`.
+ * \throws FileIOError if some other I/O error occurs.
+ */
+ static std::vector<std::string> enumerateFilesWithExtension(
+ const char *dirname, const char *extension, bool bThrow);
+
+ /*! \brief
+ * Opens a directory for listing.
+ *
+ * \param[in] dirname Path to the directory to list.
+ * \param[in] bThrow Whether failure to open the directory should throw.
+ * \throws std::bad_alloc if out of memory.
+ * \throws FileIOError if opening the directory fails and `bThrow == true`
+ */
+ explicit DirectoryEnumerator(const char *dirname, bool bThrow = true);
+ //! \copydoc DirectoryEnumerator(const char *, bool)
+ explicit DirectoryEnumerator(const std::string &dirname, bool bThrow = true);
+ ~DirectoryEnumerator();
+
+ /*! \brief
+ * Gets next file in a directory.
+ *
+ * \param[out] filename Name of the next file.
+ * \returns `false` if there were no more files.
+ * \throws std::bad_alloc if out of memory.
+ * \throws FileIOError if listing the next file fails.
+ *
+ * If all files from the directory have been returned (or there are no
+ * files in the directory and this is the first call), the method
+ * returns `false` and \p filename is cleared.
+ * Otherwise, the return value is `true` and the first/next file name
+ * is returned in \p filename.
+ * \p filename will not contain any path information, only the name of
+ * the file.
+ *
+ * If `bThrow` passed to the constructor was `false` and the directory
+ * was not successfully opened, the first call to this function will
+ * return `false`.
+ */
+ bool nextFile(std::string *filename);
+
+ private:
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
+};
+
+} // namespace gmx
+
+#endif
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_utility
*/
-#include "gromacs/utility/errorcodes.h"
+#include "gmxpre.h"
+
+#include "errorcodes.h"
#include <cstdlib>
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_utility
*/
-#ifdef HAVE_CONFIG_H
-#include "config.h"
-#endif
+#include "gmxpre.h"
#include "errorformat.h"
+#include "config.h"
+
#include <cctype>
#include <cstdio>
#include <cstring>
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_utility
*/
+#include "gmxpre.h"
+
#include "exceptions.h"
-#ifdef HAVE_CONFIG_H
#include "config.h"
-#endif
#include <cstring>
#include <stdexcept>
#include <typeinfo>
-#include <boost/exception/get_error_info.hpp>
#include <boost/shared_ptr.hpp>
+#include <boost/exception/get_error_info.hpp>
#include "thread_mpi/system_error.h"
-#include "gromacs/legacyheaders/network.h"
-
+#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/errorcodes.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/stringutil.h"
const char *GromacsException::what() const throw()
{
const ErrorMessage *msg = boost::get_error_info<errinfo_message>(*this);
- while (msg != NULL && msg->isContext())
+ if (msg == NULL)
+ {
+ return "No reason provided";
+ }
+ while (msg->isContext())
{
msg = &msg->child();
}
- return msg != NULL ? msg->text().c_str() : "No reason provided";
+ return msg->text().c_str();
}
void GromacsException::prependContext(const std::string &context)
// funcPtr != NULL ? *funcPtr : "");
// }
+ bool bAnythingWritten = false;
// TODO: Remove duplicate context if present in multiple nested exceptions.
const ErrorMessage *msg = boost::get_error_info<errinfo_message>(*boostEx);
if (msg != NULL)
if (msg != NULL && !msg->text().empty())
{
writer->writeLine(msg->text().c_str(), indent*2);
+ bAnythingWritten = true;
}
}
else
{
writer->writeLine(ex.what(), indent*2);
+ bAnythingWritten = true;
}
const int *errorNumber
writer->writeErrNoInfo(*errorNumber,
funcName != NULL ? *funcName : NULL,
(indent+1)*2);
+ bAnythingWritten = true;
}
// TODO: Treat also boost::nested_exception (not currently used, though)
}
catch (const std::exception &nestedEx)
{
- formatExceptionMessageInternal(writer, nestedEx, indent + 1);
+ const int newIndent = indent + (bAnythingWritten ? 1 : 0);
+ formatExceptionMessageInternal(writer, nestedEx, newIndent);
}
}
}
#ifdef GMX_LIB_MPI
// TODO: Consider moving the output done in gmx_abort() into the message
// printing routine above, so that this could become a simple MPI_Abort().
- gmx_abort(gmx_node_rank(), gmx_node_num(), returnCode);
+ gmx_abort(returnCode);
#endif
return returnCode;
}
#include <vector>
#include <boost/exception_ptr.hpp>
+#include <boost/throw_exception.hpp>
#include <boost/exception/errinfo_api_function.hpp>
#include <boost/exception/errinfo_errno.hpp>
#include <boost/exception/exception.hpp>
#include <boost/exception/info.hpp>
-#include <boost/throw_exception.hpp>
namespace gmx
{
GMX_THROW((e) << boost::errinfo_errno(stored_errno_) \
<< boost::errinfo_api_function(syscall)); \
} while (0)
+//TODO: Add an equivalent macro for Windows GetLastError
/*! \brief
* Formats a standard fatal error message for reporting an exception.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "gmx_fatal.h"
-#include "gmx_fatal_collective.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "fatalerror.h"
-#include <ctype.h>
-#include <errno.h>
-#include <stdarg.h>
-#include <string.h>
+#include "config.h"
-#include "thread_mpi/threads.h"
+#include <cerrno>
+#include <cstddef>
+#include <cstdlib>
+#include <cstring>
+
+#include <exception>
-#include "main.h"
-#include "types/commrec.h"
-#include "network.h"
-#include "copyrite.h"
-#include "macros.h"
+#include "thread_mpi/threads.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/baseversion.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/programcontext.h"
+
+#ifdef GMX_MPI
+#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/gmxmpi.h"
-#include "gromacs/utility/smalloc.h"
+#endif
-static gmx_bool bDebug = FALSE;
-static FILE *log_file = NULL;
+static bool bDebug = false;
+static tMPI_Thread_mutex_t where_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
-static tMPI_Thread_mutex_t debug_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
-static tMPI_Thread_mutex_t where_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+FILE *debug = NULL;
+gmx_bool gmx_debug_at = FALSE;
-gmx_bool bDebugMode(void)
+static FILE *log_file = NULL;
+static tMPI_Thread_mutex_t error_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+static const char *const gmxuser
+ = "Please report this to the mailing list (gmx-users@gromacs.org)";
+
+void gmx_init_debug(const int dbglevel, const char *dbgfile)
{
- gmx_bool ret;
-#if 0
- tMPI_Thread_mutex_lock(&debug_mutex);
-#endif
- ret = bDebug;
-#if 0
- tMPI_Thread_mutex_unlock(&debug_mutex);
-#endif
- return bDebug;
+ if (!bDebug)
+ {
+ gmx_disable_file_buffering();
+ debug = gmx_ffopen(dbgfile, "w+");
+ bDebug = true;
+ if (dbglevel >= 2)
+ {
+ gmx_debug_at = TRUE;
+ }
+ }
}
-void gmx_fatal_set_log_file(FILE *fp)
+gmx_bool bDebugMode(void)
{
- log_file = fp;
+ return bDebug;
}
void _where(const char *file, int line)
}
}
+void gmx_fatal_set_log_file(FILE *fp)
+{
+ log_file = fp;
+}
+
static int fatal_errno = 0;
-static void quit_gmx(const char *msg)
+static void default_error_handler(const char *msg)
{
- tMPI_Thread_mutex_lock(&debug_mutex);
+ tMPI_Thread_mutex_lock(&error_mutex);
if (fatal_errno == 0)
{
if (log_file)
}
perror(msg);
}
+ tMPI_Thread_mutex_unlock(&error_mutex);
+}
-#ifdef GMX_LIB_MPI
- if (gmx_mpi_initialized())
- {
- int nnodes;
- int noderank;
-
- nnodes = gmx_node_num();
- noderank = gmx_node_rank();
-
- if (nnodes > 1)
- {
- fprintf(stderr, "Error on rank %d, will try to stop all ranks\n",
- noderank);
- }
- gmx_abort(noderank, nnodes, -1);
- }
-#endif
-
- if (debug)
- {
- fflush(debug);
- }
- if (bDebugMode())
- {
- fprintf(stderr, "dump core (y/n):");
- fflush(stderr);
- if (toupper(getc(stdin)) != 'N')
- {
- (void) abort();
- }
- }
+static void (*gmx_error_handler)(const char *msg) = default_error_handler;
- exit(fatal_errno);
- tMPI_Thread_mutex_unlock(&debug_mutex);
+void set_gmx_error_handler(void (*func)(const char *msg))
+{
+ // TODO: Either this is unnecessary, or also reads to the handler should be
+ // protected by a mutex.
+ tMPI_Thread_mutex_lock(&error_mutex);
+ gmx_error_handler = func;
+ tMPI_Thread_mutex_unlock(&error_mutex);
}
-/* The function below should be identical to quit_gmx,
- * except that is does not actually quit and call gmx_abort.
- */
-static void quit_gmx_noquit(const char *msg)
+static void call_error_handler(const char *key, const char *file, int line, const char *msg)
{
- tMPI_Thread_mutex_lock(&debug_mutex);
- if (!fatal_errno)
- {
- if (log_file)
- {
- fprintf(log_file, "%s\n", msg);
- }
- fprintf(stderr, "%s\n", msg);
- /* we set it to no-zero because if this function is called, something
- has gone wrong */
- fatal_errno = 255;
- }
- else
+ char buf[10240], errerrbuf[1024];
+ const char *llines = "-------------------------------------------------------";
+ char *strerr;
+
+ if (msg == NULL)
{
- if (fatal_errno != -1)
- {
- errno = fatal_errno;
- }
- perror(msg);
+ sprintf(errerrbuf, "Empty fatal_error message. %s", gmxuser);
}
-
-#ifndef GMX_LIB_MPI
- if (debug)
+ // In case ProgramInfo is not initialized and there is an issue with the
+ // initialization, fall back to "GROMACS".
+ const char *programName = "GROMACS";
+ try
{
- fflush(debug);
+ programName = gmx::getProgramContext().displayName();
}
- if (bDebugMode())
+ catch (const std::exception &)
{
- fprintf(stderr, "dump core (y/n):");
- fflush(stderr);
- if (toupper(getc(stdin)) != 'N')
- {
- (void) abort();
- }
}
-#endif
- tMPI_Thread_mutex_unlock(&debug_mutex);
-}
-
-void gmx_fatal(int f_errno, const char *file, int line, const char *fmt, ...)
-{
- va_list ap;
- char msg[STRLEN];
-
- va_start(ap, fmt);
- vsprintf(msg, fmt, ap);
- va_end(ap);
-
- tMPI_Thread_mutex_lock(&debug_mutex);
- fatal_errno = f_errno;
- tMPI_Thread_mutex_unlock(&debug_mutex);
+ strerr = gmx_strerror(key);
+ sprintf(buf, "\n%s\nProgram %s, %s\n"
+ "Source code file: %s, line: %d\n\n"
+ "%s:\n%s\nFor more information and tips for troubleshooting, please check the GROMACS\n"
+ "website at http://www.gromacs.org/Documentation/Errors\n%s\n",
+ llines, programName, gmx_version(), file, line,
+ strerr, msg ? msg : errerrbuf, llines);
+ free(strerr);
- _gmx_error("fatal", msg, file, line);
+ gmx_error_handler(buf);
}
-void gmx_fatal_collective(int f_errno, const char *file, int line,
- const t_commrec *cr, gmx_domdec_t *dd,
- const char *fmt, ...)
+gmx_noreturn static void do_exit(bool bMaster, bool bFinalize)
{
- gmx_bool bFinalize;
- va_list ap;
- char msg[STRLEN];
-#ifdef GMX_MPI
- int result;
-#endif
-
- bFinalize = TRUE;
-
-#ifdef GMX_MPI
- /* Check if we are calling on all processes in MPI_COMM_WORLD */
- if (cr != NULL)
- {
- MPI_Comm_compare(cr->mpi_comm_mysim, MPI_COMM_WORLD, &result);
- }
- else
+ if (debug)
{
- MPI_Comm_compare(dd->mpi_comm_all, MPI_COMM_WORLD, &result);
+ fflush(debug);
}
- /* Any result except MPI_UNEQUAL allows us to call MPI_Finalize */
- bFinalize = (result != MPI_UNEQUAL);
-#endif
- if ((cr != NULL && MASTER(cr) ) ||
- (dd != NULL && DDMASTER(dd)))
+#ifdef GMX_MPI
+ if (gmx_mpi_initialized())
{
- va_start(ap, fmt);
- vsprintf(msg, fmt, ap);
- va_end(ap);
-
- tMPI_Thread_mutex_lock(&debug_mutex);
- fatal_errno = f_errno;
- tMPI_Thread_mutex_unlock(&debug_mutex);
-
if (bFinalize)
{
- /* Use an error handler that does not quit */
- set_gmx_error_handler(quit_gmx_noquit);
+ /* Broadcast the fatal error number possibly modified
+ * on the master process, in case the user would like
+ * to use the return status on a non-master process.
+ * The master process in cr and dd always has global rank 0.
+ */
+ MPI_Bcast(&fatal_errno, sizeof(fatal_errno), MPI_BYTE,
+ 0, MPI_COMM_WORLD);
+
+ /* Finalize nicely instead of aborting */
+ MPI_Finalize();
+ }
+ else if (bMaster)
+ {
+#ifdef GMX_LIB_MPI
+ gmx_abort(1);
+#endif
+ }
+ else
+ {
+ /* Let all other processes wait till the master has printed
+ * the error message and issued MPI_Abort.
+ */
+ MPI_Barrier(MPI_COMM_WORLD);
}
-
- _gmx_error("fatal", msg, file, line);
}
+#else
+ GMX_UNUSED_VALUE(bMaster);
+ GMX_UNUSED_VALUE(bFinalize);
+#endif
-#ifdef GMX_MPI
- if (bFinalize)
- {
- /* Broadcast the fatal error number possibly modified
- * on the master process, in case the user would like
- * to use the return status on a non-master process.
- * The master process in cr and dd always has global rank 0.
- */
- MPI_Bcast(&fatal_errno, sizeof(fatal_errno), MPI_BYTE,
- 0, MPI_COMM_WORLD);
-
- /* Finalize nicely instead of aborting */
- MPI_Finalize();
- }
- else
+ if (bDebugMode())
{
- /* Let all other processes wait till the master has printed
- * the error message and issued MPI_Abort.
- */
- MPI_Barrier(MPI_COMM_WORLD);
+ std::abort();
}
-#endif
-
- exit(fatal_errno);
+ std::exit(1);
}
-/*
- * These files are global variables in the gromacs preprocessor
- * Every routine in a file that includes gmx_fatal.h can write to these
- * debug channels. Depending on the debuglevel used
- * 0 to 3 of these filed are redirected to /dev/null
- *
- */
-FILE *debug = NULL;
-gmx_bool gmx_debug_at = FALSE;
-
-void init_debug(const int dbglevel, const char *dbgfile)
+void gmx_fatal_mpi_va(int f_errno, const char *file, int line,
+ gmx_bool bMaster, gmx_bool bFinalize,
+ const char *fmt, va_list ap)
{
- tMPI_Thread_mutex_lock(&debug_mutex);
- if (!bDebug) /* another thread hasn't already run this*/
+ if (bMaster)
{
- no_buffers();
- debug = gmx_fio_fopen(dbgfile, "w+");
- bDebug = TRUE;
- if (dbglevel >= 2)
- {
- gmx_debug_at = TRUE;
- }
- }
- tMPI_Thread_mutex_unlock(&debug_mutex);
-}
+ char msg[STRLEN];
+ vsprintf(msg, fmt, ap);
+
+ tMPI_Thread_mutex_lock(&error_mutex);
+ fatal_errno = f_errno;
+ tMPI_Thread_mutex_unlock(&error_mutex);
-static const char *gmxuser = "Please report this to the mailing list (gmx-users@gromacs.org)";
+ call_error_handler("fatal", file, line, msg);
+ }
-static void (*gmx_error_handler)(const char *msg) = quit_gmx;
+ do_exit(bMaster, bFinalize);
+}
-void set_gmx_error_handler(void (*func)(const char *msg))
+void gmx_fatal(int f_errno, const char *file, int line, const char *fmt, ...)
{
- tMPI_Thread_mutex_lock(&debug_mutex);
- gmx_error_handler = func;
- tMPI_Thread_mutex_unlock(&debug_mutex);
+ va_list ap;
+ va_start(ap, fmt);
+ gmx_fatal_mpi_va(f_errno, file, line, TRUE, FALSE, fmt, ap);
+ va_end(ap);
}
char *gmx_strerror(const char *key)
{ "input", "Input error or input inconsistency" },
{ "mem", "Memory allocation/freeing error" },
{ "open", "Can not open file" },
- { "range", "Range checking error" }
+ { "range", "Range checking error" },
+ { NULL, NULL}
};
-#define NMSG asize(msg)
- char buf[1024];
- size_t i;
if (key == NULL)
{
}
else
{
- for (i = 0; (i < NMSG); i++)
+ for (size_t i = 0; msg[i].key != NULL; ++i)
{
if (strcmp(key, msg[i].key) == 0)
{
- break;
+ return strdup(msg[i].msg);
}
}
- if (i == NMSG)
- {
- sprintf(buf, "No error message associated with key %s\n%s", key, gmxuser);
- return strdup(buf);
- }
- else
- {
- return strdup(msg[i].msg);
- }
+ char buf[1024];
+ sprintf(buf, "No error message associated with key %s\n%s", key, gmxuser);
+ return strdup(buf);
}
}
void _gmx_error(const char *key, const char *msg, const char *file, int line)
{
- char buf[10240], errerrbuf[1024];
- const char *llines = "-------------------------------------------------------";
- char *strerr;
-
- /* protect the audience from suggestive discussions */
-
- if (msg == NULL)
- {
- sprintf(errerrbuf, "Empty fatal_error message. %s", gmxuser);
- }
-
- strerr = gmx_strerror(key);
- sprintf(buf, "\n%s\nProgram %s, %s\n"
- "Source code file: %s, line: %d\n\n"
- "%s:\n%s\nFor more information and tips for troubleshooting, please check the GROMACS\n"
- "website at http://www.gromacs.org/Documentation/Errors\n%s\n",
- llines, ShortProgram(), GromacsVersion(), file, line,
- strerr, msg ? msg : errerrbuf, llines);
- free(strerr);
-
- gmx_error_handler(buf);
+ call_error_handler(key, file, line, msg);
+ do_exit(true, false);
}
void _range_check(int n, int n_min, int n_max, const char *warn_str,
* Declares fatal error handling and debugging routines for C code.
*
* \inpublicapi
+ * \ingroup module_utility
*/
-#ifndef _fatal_h
-#define _fatal_h
+#ifndef GMX_UTILITY_FATALERROR_H
+#define GMX_UTILITY_FATALERROR_H
+#include <stdarg.h>
#include <stdio.h>
-#include "types/simple.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
#endif
-#ifndef __has_feature
-/** For compatibility with non-clang compilers. */
-#define __has_feature(x) 0
-#endif
+/*! \brief
+ * Debug log file.
+ *
+ * Functions can write to this file for debug info.
+ * Before writing to it, it should be checked whether the file is not NULL:
+ * \code
+ if (debug)
+ {
+ fprintf(debug, "%s", "Debug text");
+ }
+ \endcode
+ */
+extern FILE *debug;
+/** Whether extra debugging is enabled. */
+extern gmx_bool gmx_debug_at;
-/*! \def GMX_ATTRIBUTE_NORETURN
- * \brief
- * Indicate that a function is not expected to return.
+/*! \brief
+ * Initializes debugging variables.
*
- * \todo
- * There are functions outside this header that need the same attribute.
- * This could be moved to a generic header and made it affect also compiler
- * code generation.
+ * This function is not threadsafe. It should be called as part of
+ * initializing \Gromacs, before any other thread accesses the library.
+ * For command line programs, gmx::CommandLineModuleManager takes care
+ * of this if the user requests debugging.
*/
-#ifndef GMX_ATTRIBUTE_NORETURN
-#if __has_feature(attribute_analyzer_noreturn)
-#define GMX_ATTRIBUTE_NORETURN __attribute__((analyzer_noreturn))
-#else
-#define GMX_ATTRIBUTE_NORETURN
-#endif
-#endif
+void gmx_init_debug(const int dbglevel, const char *dbgfile);
+
+/** Returns TRUE when the program was started in debug mode */
+gmx_bool bDebugMode(void);
/** Implementation for where(). */
void
/** Prints filename and line to stdlog. */
#define where() _where(__FILE__, __LINE__)
+/** Sets the log file for printing error messages. */
+void
+gmx_fatal_set_log_file(FILE *fp);
+
+/*! \brief
+ * Sets an error handler for gmx_fatal() and other fatal error routines.
+ *
+ * The default handler prints the message.
+ * \Gromacs will terminate the program after the error handler returns.
+ * To make gmx_fatal_collective() work, the error handler should not terminate
+ * the program, as it cannot know what is the desired way of termination.
+ * The string passed to the handler may be a multi-line string.
+ *
+ * \see gmx_fatal()
+ */
+void
+set_gmx_error_handler(void (*func)(const char *msg));
+
+/*! \brief
+ * Low-level fatal error reporting routine for collective MPI errors.
+ *
+ * This function works as gmx_fatal(), but provides additional control for
+ * cases where it is known that the same error occurs on multiple MPI ranks.
+ * The error handler is called only if \p bMaster is `TRUE`, and MPI_Finalize()
+ * is called instead of MPI_Abort() in MPI-enabled \Gromacs if \p bFinalize is
+ * `TRUE`.
+ *
+ * This is used to implement gmx_fatal_collective() (which cannot be declared
+ * here, since it would bring with it mdrun-specific dependencies).
+ */
+gmx_noreturn void
+gmx_fatal_mpi_va(int fatal_errno, const char *file, int line, gmx_bool bMaster,
+ gmx_bool bFinalize, const char *fmt, va_list ap);
+
/*! \brief
* Fatal error reporting routine for \Gromacs.
*
* The format of \p fmt uses printf()-like formatting.
*
* In case all MPI processes want to stop with the same fatal error,
- * use gmx_fatal_collective(), declared in gmx_fatal_collective.h,
+ * use gmx_fatal_collective(), declared in network.h,
* to avoid having as many error messages as processes.
*
* The first three parameters can be provided through ::FARGS:
gmx_fatal(FARGS, fmt, ...);
\endcode
*/
-void
-gmx_fatal(int fatal_errno, const char *file, int line, const char *fmt, ...) GMX_ATTRIBUTE_NORETURN;
+gmx_noreturn void
+gmx_fatal(int fatal_errno, const char *file, int line, const char *fmt, ...);
/** Helper macro to pass first three parameters to gmx_fatal(). */
#define FARGS 0, __FILE__, __LINE__
-/** Sets the log file for printing error messages. */
-void
-gmx_fatal_set_log_file(FILE *fp);
-
-/*! \brief
- * Debug log file.
- *
- * Functions can write to this file for debug info.
- * Before writing to it, it should be checked whether the file is not NULL:
- * \code
- if (debug)
- {
- fprintf(debug, "%s", "Debug text");
- }
- \endcode
- */
-extern FILE *debug;
-/** Whether extra debugging is enabled. */
-extern gmx_bool gmx_debug_at;
-
-/** Initializes debugging variables */
-void init_debug(const int dbglevel, const char *dbgfile);
-
-/** Returns TRUE when the program was started in debug mode */
-gmx_bool bDebugMode(void);
-
-/*! \brief
- * Implementation for range_check() and range_check_mesg().
- *
- * \p warn_str can be NULL.
- */
-void _range_check(int n, int n_min, int n_max, const char *warn_str,
- const char *var,
- const char *file, int line);
-
-/*! \brief
- * Checks that a variable is within a range.
- *
- * If \p n is not in range [n_min, n_max), a fatal error is raised.
- * \p n_min is inclusive, but \p n_max is not.
- */
-#define range_check_mesg(n, n_min, n_max, str) _range_check(n, n_min, n_max, str,#n, __FILE__, __LINE__)
-
-/*! \brief
- * Checks that a variable is within a range.
- *
- * This works as range_check_mesg(), but with a default error message.
- */
-#define range_check(n, n_min, n_max) _range_check(n, n_min, n_max, NULL,#n, __FILE__, __LINE__)
-
/*! \brief
* Returns error message corresponding to a string key.
*
char *gmx_strerror(const char *key);
/** Implementation for gmx_error(). */
-void _gmx_error(const char *key, const char *msg, const char *file, int line) GMX_ATTRIBUTE_NORETURN;
+gmx_noreturn void _gmx_error(const char *key, const char *msg, const char *file, int line);
/*! \brief
* Alternative fatal error routine with canned messages.
*
/*! \} */
/*! \brief
- * Sets an error handler for gmx_fatal() and other fatal error routines.
+ * Implementation for range_check() and range_check_mesg().
*
- * The default handler prints the message and aborts the program.
- * If you set a custom handler, it must also abort the program, otherwise
- * \Gromacs will behave unpredictably (most likely, it crashes shortly after
- * the fatal error).
- * The string passed to the handler may be a multi-line string.
+ * \p warn_str can be NULL.
+ */
+void _range_check(int n, int n_min, int n_max, const char *warn_str,
+ const char *var,
+ const char *file, int line);
+
+/*! \brief
+ * Checks that a variable is within a range.
*
- * \see gmx_fatal()
+ * If \p n is not in range [n_min, n_max), a fatal error is raised.
+ * \p n_min is inclusive, but \p n_max is not.
*/
-void
-set_gmx_error_handler(void (*func)(const char *msg));
+#define range_check_mesg(n, n_min, n_max, str) _range_check(n, n_min, n_max, str,#n, __FILE__, __LINE__)
+
+/*! \brief
+ * Checks that a variable is within a range.
+ *
+ * This works as range_check_mesg(), but with a default error message.
+ */
+#define range_check(n, n_min, n_max) _range_check(n, n_min, n_max, NULL,#n, __FILE__, __LINE__)
/*! \brief
* Prints a warning message to stderr.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_utility
*/
+#include "gmxpre.h"
+
#include "file.h"
+#include "config.h"
+
#include <cerrno>
#include <cstdio>
#include <cstring>
#include <string>
#include <vector>
-#include "config.h"
-
#include <sys/stat.h>
+
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
}
}
+// static
+FILE *File::openRawHandle(const char *filename, const char *mode)
+{
+ FILE *fp = fopen(filename, mode);
+ if (fp == NULL)
+ {
+ GMX_THROW_WITH_ERRNO(
+ FileIOError(formatString("Could not open file '%s'", filename)),
+ "fopen", errno);
+ }
+ return fp;
+}
+
+// static
+FILE *File::openRawHandle(const std::string &filename, const char *mode)
+{
+ return openRawHandle(filename.c_str(), mode);
+}
+
File::File(const char *filename, const char *mode)
: impl_(new Impl(NULL, true))
{
GMX_RELEASE_ASSERT(impl_->fp_ == NULL,
"Attempted to open the same file object twice");
// TODO: Port all necessary functionality from gmx_ffopen() here.
- impl_->fp_ = fopen(filename, mode);
- if (impl_->fp_ == NULL)
- {
- GMX_THROW_WITH_ERRNO(
- FileIOError(formatString("Could not open file '%s'", filename)),
- "fopen", errno);
- }
+ impl_->fp_ = openRawHandle(filename, mode);
}
void File::open(const std::string &filename, const char *mode)
{
File file(filename, "w");
file.writeString(text);
+ file.close();
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
-#include "common.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
class File
{
public:
+ /*! \brief
+ * Opens a file and returns a `FILE` handle.
+ *
+ * \param[in] filename Path of the file to open.
+ * \param[in] mode Mode to open the file in (for fopen()).
+ * \throws FileIOError on any I/O error.
+ *
+ * Instead of returning `NULL` on errors, throws an exception with
+ * additional details (including the file name and `errno`).
+ */
+ static FILE *openRawHandle(const char *filename, const char *mode);
+ //! \copydoc openRawHandle(const char *, const char *)
+ static FILE *openRawHandle(const std::string &filename, const char *mode);
/*! \brief
* Creates a file object and opens a file.
*
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
+#include "gmxpre.h"
+
+#include "futil.h"
+
#include "config.h"
-#endif
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include <sys/types.h>
-#include <sys/stat.h>
#include <fcntl.h>
-
-#ifdef HAVE_DIRENT_H
-/* POSIX */
-#include <dirent.h>
-#endif
+#include <sys/stat.h>
+#include <sys/types.h>
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
-
#ifdef GMX_NATIVE_WINDOWS
-#include <windows.h>
-#include <direct.h>
+#include <direct.h> // For _chdir() and _getcwd()
#include <io.h>
-#endif
-
-/* Windows file stuff, only necessary for visual studio */
-#ifdef _MSC_VER
#include <windows.h>
#endif
#include "thread_mpi/threads.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/network.h"
-
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/path.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/datafilefinder.h"
+#include "gromacs/utility/dir_separator.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/path.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
struct t_pstack *prev;
} t_pstack;
-static t_pstack *pstack = NULL;
-static gmx_bool bUnbuffered = FALSE;
+static t_pstack *pstack = NULL;
+static bool bUnbuffered = false;
+static int s_maxBackupCount = 0;
/* this linked list is an intrinsically globally shared object, so we have
to protect it with mutexes */
static tMPI_Thread_mutex_t pstack_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
-void no_buffers(void)
+namespace gmx
{
- bUnbuffered = TRUE;
+namespace
+{
+//! Global library file finder; stores the object set with setLibraryFileFinder().
+const DataFileFinder *g_libFileFinder;
+//! Default library file finder if nothing is set.
+const DataFileFinder g_defaultLibFileFinder;
+} // namespace
+
+const DataFileFinder &getLibraryFileFinder()
+{
+ if (g_libFileFinder != NULL)
+ {
+ return *g_libFileFinder;
+ }
+ return g_defaultLibFileFinder;
+}
+
+void setLibraryFileFinder(const DataFileFinder *finder)
+{
+ g_libFileFinder = finder;
+}
+
+} // namespace gmx
+
+void gmx_disable_file_buffering(void)
+{
+ bUnbuffered = true;
+}
+
+void gmx_set_max_backup_count(int count)
+{
+ if (count < 0)
+ {
+ const char *env = getenv("GMX_MAXBACKUP");
+ if (env != NULL)
+ {
+ // TODO: Check that the value is converted properly.
+ count = strtol(env, NULL, 10);
+ if (count < 0)
+ {
+ count = 0;
+ }
+ }
+ else
+ {
+ // Use a reasonably low value for countmax; we might
+ // generate 4-5 files in each round, and we don't
+ // want to hit directory limits of 1024 or 2048 files.
+ count = 99;
+ }
+ }
+ s_maxBackupCount = count;
}
void push_ps(FILE *fp)
}
-#ifdef rewind
-#undef rewind
-#endif
-
void frewind(FILE *fp)
{
tMPI_Thread_mutex_lock(&pstack_mutex);
#endif
}
-
-gmx_bool is_pipe(FILE *fp)
+int gmx_truncate(const char *filename, gmx_off_t length)
{
- tMPI_Thread_mutex_lock(&pstack_mutex);
-
- t_pstack *ps = pstack;
- while (ps != NULL)
+#ifdef GMX_NATIVE_WINDOWS
+ FILE *fp = fopen(filename, "rb+");
+ if (fp == NULL)
{
- if (ps->fp == fp)
- {
- tMPI_Thread_mutex_unlock(&pstack_mutex);
- return TRUE;
- }
- ps = ps->prev;
+ return -1;
}
- tMPI_Thread_mutex_unlock(&pstack_mutex);
- return FALSE;
+#ifdef _MSC_VER
+ int rc = _chsize_s(fileno(fp), length);
+#else
+ int rc = _chsize(fileno(fp), length);
+#endif
+ fclose(fp);
+ return rc;
+#else
+ return truncate(filename, length);
+#endif
}
-
static FILE *uncompress(const char *fn, const char *mode)
{
FILE *fp;
}
}
-
-gmx_bool gmx_fexist_master(const char *fname, t_commrec *cr)
-{
- gmx_bool bExist;
-
- if (SIMMASTER(cr))
- {
- bExist = gmx_fexist(fname);
- }
- if (PAR(cr))
- {
- gmx_bcast(sizeof(bExist), &bExist, cr);
- }
- return bExist;
-}
-
-gmx_bool gmx_eof(FILE *fp)
-{
- char data[4];
- gmx_bool beof;
-
- if (is_pipe(fp))
- {
- return feof(fp);
- }
- else
- {
- if ((beof = fread(data, 1, 1, fp)) == 1)
- {
- gmx_fseek(fp, -1, SEEK_CUR);
- }
- return !beof;
- }
-}
-
-static char *backup_fn(const char *file, int count_max)
+static char *backup_fn(const char *file)
{
- /* Use a reasonably low value for countmax; we might
- * generate 4-5 files in each round, and we dont
- * want to hit directory limits of 1024 or 2048 files.
- */
-#define COUNTMAX 99
int i, count = 1;
char *directory, *fn;
char *buf;
- if (count_max == -1)
- {
- count_max = COUNTMAX;
- }
-
smalloc(buf, GMX_PATH_MAX);
for (i = strlen(file)-1; ((i > 0) && (file[i] != DIR_SEPARATOR)); i--)
sprintf(buf, "%s/#%s.%d#", directory, fn, count);
count++;
}
- while ((count <= count_max) && gmx_fexist(buf));
+ while ((count <= s_maxBackupCount) && gmx_fexist(buf));
/* Arbitrarily bail out */
- if (count > count_max)
+ if (count > s_maxBackupCount)
{
+ /* TODO: The error message is only accurate for code that starts with
+ * Gromacs command-line interface. */
gmx_fatal(FARGS, "Won't make more than %d backups of %s for you.\n"
"The env.var. GMX_MAXBACKUP controls this maximum, -1 disables backups.",
- count_max, fn);
+ s_maxBackupCount, fn);
}
sfree(directory);
return buf;
}
-gmx_bool make_backup(const char * name)
+void make_backup(const char *name)
{
- char * env;
- int count_max;
- char * backup;
-
-#ifdef GMX_FAHCORE
- return FALSE; /* skip making backups */
-#else
-
+ if (s_maxBackupCount <= 0)
+ {
+ return;
+ }
if (gmx_fexist(name))
{
- env = getenv("GMX_MAXBACKUP");
- if (env != NULL)
- {
- count_max = strtol(env, NULL, 10);
- if (count_max == -1)
- {
- /* Do not make backups and possibly overwrite old files */
- return TRUE;
- }
- }
- else
- {
- /* Use the default maximum */
- count_max = -1;
- }
- backup = backup_fn(name, count_max);
+ char *backup = backup_fn(name);
if (rename(name, backup) == 0)
{
fprintf(stderr, "\nBack Off! I just backed up %s to %s\n",
}
else
{
- fprintf(stderr, "Sorry couldn't backup %s to %s\n", name, backup);
- return FALSE;
+ fprintf(stderr, "\nSorry couldn't backup %s to %s\n", name, backup);
}
sfree(backup);
}
- return TRUE;
-#endif
}
FILE *gmx_ffopen(const char *file, const char *mode)
#endif
}
-/* Our own implementation of dirent-like functionality to scan directories. */
-struct gmx_directory
-{
-#if defined(GMX_NATIVE_WINDOWS)
- intptr_t windows_handle;
- struct _finddata_t finddata;
- int first;
-#elif defined(HAVE_DIRENT_H)
- DIR * dirent_handle;
-#else
- int dummy;
-#endif
-};
-
-
-int
-gmx_directory_open(gmx_directory_t *p_gmxdir, const char *dirname)
-{
- struct gmx_directory * gmxdir;
- int rc;
-
- snew(gmxdir, 1);
-
- *p_gmxdir = gmxdir;
-
-#if defined(GMX_NATIVE_WINDOWS)
- if (dirname != NULL && strlen(dirname) > 0)
- {
- char * tmpname;
- int len;
-
- len = strlen(dirname);
- snew(tmpname, len+3);
-
- strncpy(tmpname, dirname, len+1);
-
- /* Remove possible trailing directory separator */
- if (tmpname[len] == '/' || tmpname[len] == '\\')
- {
- tmpname[len] = '\0';
- }
-
- /* Add wildcard */
- strcat(tmpname, "/*");
-
- gmxdir->first = 1;
- if ( (gmxdir->windows_handle = _findfirst(tmpname, &gmxdir->finddata)) > 0L)
- {
- rc = 0;
- }
- else
- {
- if (errno == EINVAL)
- {
- sfree(gmxdir);
- *p_gmxdir = NULL;
- rc = EINVAL;
- }
- else
- {
- rc = 0;
- }
- }
- }
- else
- {
- rc = EINVAL;
- }
-#elif defined(HAVE_DIRENT_H)
- if ( (gmxdir->dirent_handle = opendir(dirname)) != NULL)
- {
- rc = 0;
- }
- else
- {
- sfree(gmxdir);
- *p_gmxdir = NULL;
- rc = EINVAL;
- }
-#else
- gmx_fatal(FARGS,
- "Source compiled without POSIX dirent or windows support - cannot scan directories.\n"
- "In the very unlikely event this is not a compile-time mistake you could consider\n"
- "implementing support for your platform in futil.c, but contact the developers\n"
- "to make sure it's really necessary!\n");
- rc = -1;
-#endif
- return rc;
-}
-
-
-int
-gmx_directory_nextfile(gmx_directory_t gmxdir, char *name, int maxlength_name)
-{
- int rc;
-
-#if defined(GMX_NATIVE_WINDOWS)
- if (gmxdir != NULL)
- {
- if (gmxdir->windows_handle <= 0)
- {
-
- name[0] = '\0';
- rc = ENOENT;
- }
- else if (gmxdir->first == 1)
- {
- strncpy(name, gmxdir->finddata.name, maxlength_name);
- rc = 0;
- gmxdir->first = 0;
- }
- else
- {
- if (_findnext(gmxdir->windows_handle, &gmxdir->finddata) == 0)
- {
- strncpy(name, gmxdir->finddata.name, maxlength_name);
- rc = 0;
- }
- else
- {
- name[0] = '\0';
- rc = ENOENT;
- }
- }
- }
- else
- {
- name[0] = '\0';
- rc = EINVAL;
- }
-#elif defined(HAVE_DIRENT_H)
- struct dirent * direntp_large;
- struct dirent * p;
-
-
- if (gmxdir != NULL && gmxdir->dirent_handle != NULL)
- {
- /* On some platforms no space is present for d_name in dirent.
- * Since d_name is guaranteed to be the last entry, allocating
- * extra space for dirent will allow more size for d_name.
- * GMX_MAX_PATH should always be >= the max possible d_name.
- */
- smalloc(direntp_large, sizeof(*direntp_large) + GMX_PATH_MAX);
- rc = readdir_r(gmxdir->dirent_handle, direntp_large, &p);
-
- if (p != NULL && rc == 0)
- {
- strncpy(name, direntp_large->d_name, maxlength_name);
- }
- else
- {
- name[0] = '\0';
- rc = ENOENT;
- }
- sfree(direntp_large);
- }
- else
- {
- name[0] = '\0';
- rc = EINVAL;
- }
-#else
- gmx_fatal(FARGS,
- "Source compiled without POSIX dirent or windows support - cannot scan directories.\n");
- rc = -1;
-#endif
- return rc;
-}
-
-
-int
-gmx_directory_close(gmx_directory_t gmxdir)
-{
- int rc;
-#if defined(GMX_NATIVE_WINDOWS)
- rc = (gmxdir != NULL) ? _findclose(gmxdir->windows_handle) : EINVAL;
-#elif defined(HAVE_DIRENT_H)
- rc = (gmxdir != NULL) ? closedir(gmxdir->dirent_handle) : EINVAL;
-#else
- gmx_fatal(FARGS,
- "Source compiled without POSIX dirent or windows support - cannot scan directories.\n");
- rc = -1;
-#endif
-
- sfree(gmxdir);
- return rc;
-}
-
char *low_gmxlibfn(const char *file, gmx_bool bAddCWD, gmx_bool bFatal)
{
- bool bEnvIsSet = false;
try
{
- if (bAddCWD && gmx_fexist(file))
+ const gmx::DataFileFinder &finder = gmx::getLibraryFileFinder();
+ std::string result =
+ finder.findFile(gmx::DataFileOptions(file)
+ .includeCurrentDir(bAddCWD)
+ .throwIfNotFound(bFatal));
+ if (!result.empty())
{
- return gmx_strdup(file);
- }
- else
- {
- std::string libpath;
- // GMXLIB can be a path.
- const char *lib = getenv("GMXLIB");
- if (lib != NULL)
- {
- bEnvIsSet = true;
- libpath = lib;
- }
- else
- {
- libpath = gmx::getProgramContext().defaultLibraryDataPath();
- }
-
- std::vector<std::string> pathEntries;
- gmx::Path::splitPathEnvironment(libpath, &pathEntries);
- std::vector<std::string>::const_iterator i;
- for (i = pathEntries.begin(); i != pathEntries.end(); ++i)
- {
- std::string testPath = gmx::Path::join(*i, file);
- if (gmx::Path::exists(testPath))
- {
- return gmx_strdup(testPath.c_str());
- }
- }
+ return gmx_strdup(result.c_str());
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
- if (bFatal)
- {
- if (bEnvIsSet)
- {
- gmx_fatal(FARGS,
- "Library file %s not found %sin your GMXLIB path.",
- file, bAddCWD ? "in current dir nor " : "");
- }
- else
- {
- gmx_fatal(FARGS,
- "Library file %s not found %sin default directories.\n"
- "(You can set the directories to search with the GMXLIB path variable)",
- file, bAddCWD ? "in current dir nor " : "");
- }
- }
return NULL;
}
FILE *low_libopen(const char *file, gmx_bool bFatal)
{
- FILE *ff;
- char *fn;
-
- fn = low_gmxlibfn(file, TRUE, bFatal);
-
- if (fn == NULL)
- {
- ff = NULL;
- }
- else
+ try
{
- if (debug)
- {
- fprintf(debug, "Opening library file %s\n", fn);
- }
- ff = fopen(fn, "r");
+ const gmx::DataFileFinder &finder = gmx::getLibraryFileFinder();
+ FILE *fp =
+ finder.openFile(gmx::DataFileOptions(file)
+ .includeCurrentDir(true)
+ .throwIfNotFound(bFatal));
+ return fp;
}
- sfree(fn);
-
- return ff;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ return NULL;
}
char *gmxlibfn(const char *file)
/* name in Buf should now be OK */
}
-int gmx_truncatefile(char *path, gmx_off_t length)
-{
-#ifdef GMX_NATIVE_WINDOWS
- /* Microsoft visual studio does not have "truncate" */
- HANDLE fh;
- LARGE_INTEGER win_length;
-
- win_length.QuadPart = length;
-
- fh = CreateFile(path, GENERIC_READ | GENERIC_WRITE, 0, NULL,
- OPEN_EXISTING, 0, NULL);
- SetFilePointerEx(fh, win_length, NULL, FILE_BEGIN);
- SetEndOfFile(fh);
- CloseHandle(fh);
-
- return 0;
-#else
- return truncate(path, length);
-#endif
-}
-
-
int gmx_file_rename(const char *oldname, const char *newname)
{
#ifndef GMX_NATIVE_WINDOWS
rc = fah_fsync(fp);
#else /* GMX_FAHCORE */
{
- int fn = -1;
+ int fn;
/* get the file number */
#if defined(HAVE_FILENO)
fn = fileno(fp);
#elif defined(HAVE__FILENO)
fn = _fileno(fp);
+#else
+ fn = -1;
#endif
/* do the actual fsync */
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Low-level wrappers for OS-specific file handling with some \Gromacs
+ * customizations.
+ *
+ * \inpublicapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_FUTIL_H
+#define GMX_UTILITY_FUTIL_H
+
+#include <limits.h>
+#include <stdio.h>
+
+#include "gromacs/utility/basedefinitions.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+#if 0
+}
+#endif
+
+/*! \def GMX_PATH_MAX
+ * \brief
+ * Maximum path length, if the OS provides one, otherwise a fixed constant.
+ */
+#ifdef PATH_MAX
+# define GMX_PATH_MAX PATH_MAX
+#elif defined MAX_PATH
+# define GMX_PATH_MAX MAX_PATH
+#else
+# define GMX_PATH_MAX 4096
+#endif
+
+/** \Gromacs definition to use instead of `off_t`. */
+typedef gmx_int64_t gmx_off_t;
+
+/*! \brief
+ * Turn off buffering for output files (which is default) for debugging
+ * purposes.
+ *
+ * This only has effect on files opened with gmx_ffopen().
+ */
+void gmx_disable_file_buffering(void);
+
+/*! \brief
+ * Enables backups with the specified number of maximum backups.
+ *
+ * If \p count == 0, disables backups. If not called, this is the default.
+ * If \p count == -1, reads the count from an environment variable.
+ *
+ * This is not currently thread-safe, as it is only called during
+ * initialization code.
+ */
+void gmx_set_max_backup_count(int count);
+
+/*! \brief
+ * Check whether a path exists.
+ *
+ * \returns `TRUE` when \p fname exists.
+ *
+ * Note that this returns `TRUE` even if \p fname is a directory instead of a
+ * file.
+ */
+gmx_bool gmx_fexist(const char *fname);
+
+/*! \brief
+ * Makes a backup of file if the file exists.
+ */
+void make_backup(const char *file);
+
+/*! \brief
+ * Opens a file, with \Gromacs-specific additions.
+ *
+ * If the file is in compressed format, opens a pipe which uncompresses the
+ * file on the fly. For this to work, gmx_ffclose() and frewind() should
+ * always be used for files opened with gmx_ffopen() instead of fclose() and
+ * rewind(). For compressed files, the \p file parameter should be passed
+ * without the compressed extension; if that file is not found, then a few
+ * compression extensions are tried.
+ * Creates a backup if a file opened for writing already exists before
+ * overwriting it.
+ * A fatal error results if the file cannot be opened, for whatever reason.
+ */
+FILE *gmx_ffopen(const char *file, const char *mode);
+
+/** Closes a file opened with gmx_ffopen(). */
+int gmx_ffclose(FILE *fp);
+
+/*! \brief
+ * Wraps rewind() for files opened with gmx_ffopen().
+ *
+ * A fatal error results if this function is called for a pipe (a compressed
+ * input file).
+ */
+void frewind(FILE *fp);
+
+/** OS-independent 64-bit fseek(). */
+int gmx_fseek(FILE *stream, gmx_off_t offset, int whence);
+
+/** OS-independent 64-bit ftell(). */
+gmx_off_t gmx_ftell(FILE *stream);
+
+/** OS-independent truncate(). */
+int gmx_truncate(const char *filename, gmx_off_t length);
+
+/*! \brief
+ * Finds full path for a library file.
+ *
+ * Searches first in the current directory, and then in the configured library
+ * directories.
+ * Fatal error results if the file is not found in any location.
+ * The caller is responsible of freeing the returned string.
+ */
+char *gmxlibfn(const char *file);
+
+/*! \brief
+ * Opens a library file for reading.
+ *
+ * Works as gmxlibfn(), except that it opens the file and returns a file
+ * handle.
+ */
+FILE *libopen(const char *file);
+
+/*! \brief
+ * More flexible gmxlibfn().
+ *
+ * Works as gmxlibfn(), but provides control whether the current working
+ * directory is searched or not, and whether a missing file is a fatal error or
+ * not.
+ */
+char *low_gmxlibfn(const char *file, gmx_bool bAddCWD, gmx_bool bFatal);
+
+/*! \brief
+ * Alternative for libopen() that optionally does not exit.
+ *
+ * Works as libopen(), but provides control whether a missing file is a fatal
+ * error or not.
+ */
+FILE *low_libopen(const char *file, gmx_bool bFatal);
+
+
+/*! \brief
+ * Creates unique name for temp file (wrapper around mkstemp).
+ *
+ * \p buf should be at least 7 bytes long
+ */
+void gmx_tmpnam(char *buf);
+
+/*! \brief
+ * OS-independent rename().
+ *
+ * Renames/moves a file atomically, if the OS makes that available.
+ */
+int gmx_file_rename(const char *oldname, const char *newname);
+
+/*! \brief
+ * Copies a file (data only) oldname to newname.
+ *
+ * If \p copy_if_empty is `FALSE`, the file won't be copied if it's empty.
+ */
+int gmx_file_copy(const char *oldname, const char *newname, gmx_bool copy_if_empty);
+
+/*! \brief
+ * OS-independent fsync().
+ *
+ * Only use this during checkpointing!
+ */
+int gmx_fsync(FILE *fp);
+
+/*! \brief
+ * OS-independent chdir().
+ *
+ * Exits with a fatal error if changing the directory fails.
+ */
+void gmx_chdir(const char *directory);
+/*! \brief
+ * OS-independent getcwd().
+ *
+ * Exits with a fatal error if the call fails.
+ */
+void gmx_getcwd(char *buffer, size_t size);
+
+#ifdef __cplusplus
+}
+
+namespace gmx
+{
+
+class DataFileFinder;
+
+/*! \brief
+ * Gets a finder for locating data files from share/top/.
+ *
+ * \returns Finder set with setLibraryFileFinder(), or a default finder.
+ *
+ * If setLibraryFileFinder() has not been called (or a `NULL` finder has been
+ * set), a default finder is returned.
+ * The default finder searches data files from the directory identified by the
+ * global program context; it does not respect GMXLIB environment variable.
+ * Calling initForCommandLine() sets a finder that respects GMXLIB.
+ *
+ * Does not throw.
+ *
+ * See setLibraryFileFinder() for thread safety.
+ *
+ * \ingroup module_utility
+ */
+const DataFileFinder &getLibraryFileFinder();
+/*! \brief
+ * Sets a finder for location data files from share/top/.
+ *
+ * \param[in] finder finder to set
+ * (can be NULL to restore the default finder).
+ *
+ * The library does not take ownership of \p finder.
+ * The provided object must remain valid until the global instance is changed
+ * by another call to setLibraryFileFinder().
+ *
+ * The global instance is used by gmxlibfn() and libopen().
+ *
+ * This method is not thread-safe. See setProgramContext(); the same
+ * constraints apply here as well.
+ *
+ * Does not throw.
+ */
+void setLibraryFileFinder(const DataFileFinder *finder);
+
+} // namespace gmx
+#endif
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_utility
*/
+#include "gmxpre.h"
+
#include "gmxassert.h"
#include <cstdio>
#include <boost/current_function.hpp>
+#include "gromacs/utility/basedefinitions.h"
+
//! \addtogroup module_utility
//! \{
*
* \ingroup module_utility
*/
-#if defined(_MSC_VER)
-__declspec(noreturn)
-#elif defined(__GNUC__)
-__attribute__((__noreturn__))
-#endif
+gmx_noreturn
void assertHandler(const char *condition, const char *msg,
const char *func, const char *file, int line);
#ifndef GMX_UTILITY_GMXMPI_H
#define GMX_UTILITY_GMXMPI_H
-#ifdef HAVE_CONFIG_H
#include "config.h"
-#endif
/*! \cond */
#ifdef GMX_LIB_MPI
#endif /*MPI_INT64_T*/
#else
#ifdef GMX_THREAD_MPI
-#include "thread_mpi/tmpi.h"
-#include "thread_mpi/mpi_bindings.h"
+#include "thread_mpi/mpi_bindings.h" /* IWYU pragma: export */
+#include "thread_mpi/tmpi.h" /* IWYU pragma: export */
#else
typedef void* MPI_Comm;
typedef void* MPI_Request;
*
* \ingroup module_utility
*/
-#include "gromacs/utility/gmxomp.h"
+#include "gmxpre.h"
+
+#include "gmxomp.h"
#include "config.h"
#include <stdio.h>
+#include <stdlib.h>
#ifdef GMX_OPENMP
#include <omp.h>
#endif
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/legacyheaders/md_logging.h"
-
-#include "gromacs/utility/common.h"
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/stringutil.h"
int gmx_omp_get_max_threads(void)
{
#endif
}
-/*!
- * Thread affinity set by the OpenMP library can conflict with the GROMACS
- * internal affinity setting.
- *
- * While GNU OpenMP does not set affinity by default, the Intel OpenMP library
- * does. This conflicts with the internal affinity (especially thread-MPI)
- * setting, results in incorrectly locked threads, and causes dreadful performance.
- *
- * The KMP_AFFINITY environment variable is used by Intel, GOMP_CPU_AFFINITY
- * by the GNU compilers (Intel also honors it well). If any of the variables
- * is set, we honor it, disable the internal pinning, and warn the user.
- * When using Intel OpenMP, we will disable affinity if the user did not set it
- * anually through one of the aforementioned environment variables.
- *
- * Note that the Intel OpenMP affinity disabling iwll only take effect if this
- * function is called before the OpenMP library gets initialized which happens
- * when the first call is made into a compilation unit that contains OpenMP
- * pragmas.
- */
-void gmx_omp_check_thread_affinity(FILE *fplog,
- const t_commrec *cr,
- gmx_hw_opt_t *hw_opt)
+gmx_bool gmx_omp_check_thread_affinity(char **message)
{
- /* no need to worry if internal thread pinning is turned off */
- if (hw_opt->thread_affinity == threadaffOFF)
- {
- return;
- }
+ bool shouldSetAffinity = true;
-#ifndef GMX_OPENMP
- GMX_UNUSED_VALUE(fplog);
- GMX_UNUSED_VALUE(cr);
-#else
+ *message = NULL;
+#ifdef GMX_OPENMP
/* We assume that the affinity setting is available on all platforms
* gcc supports. Even if this is not the case (e.g. Mac OS) the user
* will only get a warning. */
#if defined(__GNUC__) || defined(__INTEL_COMPILER)
+ const char *programName;
+ try
+ {
+ programName = gmx::getProgramContext().displayName();
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+
const char *const gomp_env = getenv("GOMP_CPU_AFFINITY");
const bool bGompCpuAffinitySet = (gomp_env != NULL);
/* turn off internal pinning if GOMP_CPU_AFFINITY is set & non-empty */
if (bGompCpuAffinitySet && *gomp_env != '\0')
{
- /* TODO: with -pin auto we should only warn when using all cores */
- md_print_warn(cr, fplog,
- "NOTE: GOMP_CPU_AFFINITY set, will turn off %s internal affinity\n"
- " setting as the two can conflict and cause performance degradation.\n"
- " To keep using the %s internal affinity setting, unset the\n"
- " GOMP_CPU_AFFINITY environment variable.",
- ShortProgram(), ShortProgram());
-
- hw_opt->thread_affinity = threadaffOFF;
+ try
+ {
+ std::string buf = gmx::formatString(
+ "NOTE: GOMP_CPU_AFFINITY set, will turn off %s internal affinity\n"
+ " setting as the two can conflict and cause performance degradation.\n"
+ " To keep using the %s internal affinity setting, unset the\n"
+ " GOMP_CPU_AFFINITY environment variable.",
+ programName, programName);
+ *message = gmx_strdup(buf.c_str());
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ shouldSetAffinity = false;
}
#endif /* __GNUC__ || __INTEL_COMPILER */
/* turn off internal pinning KMP_AFFINITY != "disabled" */
if (bKmpAffinitySet && (gmx_strncasecmp(kmp_env, "disabled", 8) != 0))
{
- /* TODO: with -pin auto we should only warn when using all cores */
- md_print_warn(cr, fplog,
- "NOTE: KMP_AFFINITY set, will turn off %s internal affinity\n"
- " setting as the two can conflict and cause performance degradation.\n"
- " To keep using the %s internal affinity setting, set the\n"
- " KMP_AFFINITY=disabled environment variable.",
- ShortProgram(), ShortProgram());
-
- hw_opt->thread_affinity = threadaffOFF;
+ try
+ {
+ std::string buf = gmx::formatString(
+ "NOTE: KMP_AFFINITY set, will turn off %s internal affinity\n"
+ " setting as the two can conflict and cause performance degradation.\n"
+ " To keep using the %s internal affinity setting, set the\n"
+ " KMP_AFFINITY=disabled environment variable.",
+ programName, programName);
+ *message = gmx_strdup(buf.c_str());
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ shouldSetAffinity = false;
}
#endif /* __INTEL_COMPILER */
#endif /* GMX_OPENMP */
+ return shouldSetAffinity;
}
#ifndef GMX_UTILITY_OMP_H
#define GMX_UTILITY_OMP_H
-#ifdef HAVE_CONFIG_H
#include "config.h"
-#endif
+
+#include <stdio.h>
#ifndef GMX_NATIVE_WINDOWS
/* Ugly hack because the openmp implementation below hacks into the SIMD
#include <windows.h>
#endif
-#include "types/commrec.h"
-#include "mdrun.h"
+#include "gromacs/utility/basedefinitions.h"
#ifdef __cplusplus
extern "C"
/*! \brief
* Check for externally set thread affinity to avoid conflicts with \Gromacs
* internal setting.
+ *
+ * \param[out] message Receives the message to be shown to the user.
+ * \returns `true` if we can set thread affinity ourselves.
+ *
+ * While GNU OpenMP does not set affinity by default, the Intel OpenMP library
+ * does. This conflicts with the internal affinity (especially thread-MPI)
+ * setting, results in incorrectly locked threads, and causes dreadful performance.
+ *
+ * The KMP_AFFINITY environment variable is used by Intel, GOMP_CPU_AFFINITY
+ * by the GNU compilers (Intel also honors it well). If any of the variables
+ * is set, we should honor it and disable the internal pinning.
+ * When using Intel OpenMP, we will disable affinity if the user did not set it
+ * manually through one of the aforementioned environment variables.
+ *
+ * Note that the Intel OpenMP affinity disabling will only take effect if this
+ * function is called before the OpenMP library gets initialized, which happens
+ * when the first call is made into a compilation unit that contains OpenMP
+ * pragmas.
+ *
+ * If this function returns `false`, the caller is responsible to disable the
+ * pinning, show the message from \p *message to the user, and free the memory
+ * allocated for \p *message.
+ * If the return value is `true`, \p *message is NULL.
*/
-void gmx_omp_check_thread_affinity(FILE *fplog, const t_commrec *cr,
- gmx_hw_opt_t *hw_opt);
+gmx_bool gmx_omp_check_thread_affinity(char **message);
/*! \brief
* Pause for use in a spin-wait loop.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_utility
*/
+#include "gmxpre.h"
+
#include "gmxregex.h"
-#ifdef HAVE_CONFIG_H
#include "config.h"
-#endif
#if defined(HAVE_POSIX_REGEX)
-// old Mac needs sys/types.h before regex.h
#include <sys/types.h>
+// old Mac needs sys/types.h before regex.h
#include <regex.h>
#define USE_POSIX_REGEX
#elif defined(HAVE_CXX11_REGEX)
#define USE_CXX11_REGEX
#endif
-#include "exceptions.h"
-#include "stringutil.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/stringutil.h"
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
-#include "common.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_utility
*/
-#include "gromacs/utility/init.h"
+#include "gmxpre.h"
+
+#include "init.h"
-#ifdef HAVE_CONFIG_H
#include "config.h"
-#endif
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/gmxassert.h"
#ifdef GMX_LIB_MPI
#include "gromacs/utility/gmxmpi.h"
#endif
-#include "gromacs/utility/common.h"
-#include "gromacs/utility/gmxassert.h"
-
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_utility
*/
-#include "gromacs/utility/messagestringcollector.h"
+#include "gmxpre.h"
+
+#include "messagestringcollector.h"
#include <vector>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
-#include "../utility/common.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* Implements functions in path.h.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
- * \ingroup module_fileio
+ * \ingroup module_utility
*/
+#include "gmxpre.h"
+
#include "path.h"
+#include "config.h"
+
#include <cctype>
#include <cerrno>
#include <cstdlib>
#include <algorithm>
-#include "config.h"
-
#include <sys/stat.h>
+
#ifdef GMX_NATIVE_WINDOWS
+#include <Windows.h>
#include <direct.h>
#else
#ifdef HAVE_UNISTD_H
#endif
#endif
-#include "gromacs/fileio/futil.h"
+#include "gromacs/utility/dir_separator.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/stringutil.h"
namespace
return isAbsolute(path.c_str());
}
-bool Path::startsWith(const std::string &path, const std::string &prefix)
+#ifdef GMX_NATIVE_WINDOWS
+namespace
+{
+struct handle_wrapper
{
- return gmx::startsWith(normalize(path), normalize(prefix));
+ HANDLE handle;
+ handle_wrapper(HANDLE h)
+ : handle(h){}
+ ~handle_wrapper()
+ {
+ if (handle != INVALID_HANDLE_VALUE)
+ {
+ ::CloseHandle(handle);
+ }
+ }
+};
+}
+#endif
+
+bool Path::isEquivalent(const std::string &path1, const std::string &path2)
+{
+ //based on boost_1_56_0/libs/filesystem/src/operations.cpp under BSL
+#ifdef GMX_NATIVE_WINDOWS
+ // Note well: Physical location on external media is part of the
+ // equivalence criteria. If there are no open handles, physical location
+ // can change due to defragmentation or other relocations. Thus handles
+ // must be held open until location information for both paths has
+ // been retrieved.
+
+ // p2 is done first, so any error reported is for p1
+ // FixME: #1635
+ handle_wrapper h2(
+ CreateFile(
+ path2.c_str(),
+ 0,
+ FILE_SHARE_DELETE | FILE_SHARE_READ | FILE_SHARE_WRITE,
+ 0,
+ OPEN_EXISTING,
+ FILE_FLAG_BACKUP_SEMANTICS,
+ 0));
+
+ handle_wrapper h1(
+ CreateFile(
+ path1.c_str(),
+ 0,
+ FILE_SHARE_DELETE | FILE_SHARE_READ | FILE_SHARE_WRITE,
+ 0,
+ OPEN_EXISTING,
+ FILE_FLAG_BACKUP_SEMANTICS,
+ 0));
+
+ if (h1.handle == INVALID_HANDLE_VALUE
+ || h2.handle == INVALID_HANDLE_VALUE)
+ {
+ // if one is invalid and the other isn't, then they aren't equivalent,
+ // but if both are invalid then it is an error
+ if (h1.handle == INVALID_HANDLE_VALUE
+ && h2.handle == INVALID_HANDLE_VALUE)
+ {
+ GMX_THROW(FileIOError("Path::isEquivalent called with two invalid files"));
+ }
+
+ return false;
+ }
+
+ // at this point, both handles are known to be valid
+
+ BY_HANDLE_FILE_INFORMATION info1, info2;
+
+ if (!GetFileInformationByHandle(h1.handle, &info1))
+ {
+ GMX_THROW(FileIOError("Path::isEquivalent: GetFileInformationByHandle failed"));
+ }
+
+ if (!GetFileInformationByHandle(h2.handle, &info2))
+ {
+ GMX_THROW(FileIOError("Path::isEquivalent: GetFileInformationByHandle failed"));
+ }
+
+ // In theory, volume serial numbers are sufficient to distinguish between
+ // devices, but in practice VSN's are sometimes duplicated, so last write
+ // time and file size are also checked.
+ return
+ info1.dwVolumeSerialNumber == info2.dwVolumeSerialNumber
+ && info1.nFileIndexHigh == info2.nFileIndexHigh
+ && info1.nFileIndexLow == info2.nFileIndexLow
+ && info1.nFileSizeHigh == info2.nFileSizeHigh
+ && info1.nFileSizeLow == info2.nFileSizeLow
+ && info1.ftLastWriteTime.dwLowDateTime
+ == info2.ftLastWriteTime.dwLowDateTime
+ && info1.ftLastWriteTime.dwHighDateTime
+ == info2.ftLastWriteTime.dwHighDateTime;
+#else
+ struct stat s1, s2;
+ int e2 = stat(path2.c_str(), &s2);
+ int e1 = stat(path1.c_str(), &s1);
+
+ if (e1 != 0 || e2 != 0)
+ {
+ // if one is invalid and the other isn't then they aren't equivalent,
+ // but if both are invalid then it is an error.
+ if (e1 != 0 && e2 != 0)
+ {
+ GMX_THROW_WITH_ERRNO(
+ FileIOError("Path::isEquivalent called with two invalid files"),
+ "stat", errno);
+ }
+ return false;
+ }
+
+ // both stats now known to be valid
+ return s1.st_dev == s2.st_dev && s1.st_ino == s2.st_ino
+ // According to the POSIX stat specs, "The st_ino and st_dev fields
+ // taken together uniquely identify the file within the system."
+ // Just to be sure, size and mod time are also checked.
+ && s1.st_size == s2.st_size && s1.st_mtime == s2.st_mtime;
+#endif
}
std::string Path::join(const std::string &path1,
std::string Path::getParentPath(const std::string &path)
{
+ /* Expects that the path doesn't contain "." or "..". If used on a path for
+ * which this isn't guaranteed realpath needs to be called first. */
size_t pos = path.find_last_of(cDirSeparators);
if (pos == std::string::npos)
{
return path.substr(pos+1);
}
+bool Path::hasExtension(const std::string &path)
+{
+ return getFilename(path).find('.') != std::string::npos;
+}
+
+std::string Path::stripExtension(const std::string &path)
+{
+ size_t dirSeparatorPos = path.find_last_of(cDirSeparators);
+ size_t extPos = path.find_last_of('.');
+ if (extPos == std::string::npos
+ || (dirSeparatorPos != std::string::npos && extPos < dirSeparatorPos))
+ {
+ return path;
+ }
+ return path.substr(0, extPos);
+}
+
std::string Path::normalize(const std::string &path)
{
std::string result(path);
- // TODO: Remove . and .. entries.
if (DIR_SEPARATOR != '/')
{
std::replace(result.begin(), result.end(), '/', DIR_SEPARATOR);
}
-#ifdef GMX_NATIVE_WINDOWS
- if (std::isalpha(result[0]) && result[1] == ':')
- {
- result[0] = std::toupper(result[0]);
- }
-#endif
return result;
}
std::string Path::resolveSymlinks(const std::string &path)
{
+ /* Does not fully resolve the path like realpath/boost::canonical would.
+ * It doesn't resolve path elements (including "." or ".."), but only
+ * resolves the entire path (it does that recursively). */
std::string result(path);
#ifndef GMX_NATIVE_WINDOWS
char buf[GMX_PATH_MAX];
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \inlibraryapi
- * \ingroup module_fileio
+ * \ingroup module_utility
*/
-#ifndef GMX_FILEIO_PATH_H
-#define GMX_FILEIO_PATH_H
+#ifndef GMX_UTILITY_PATH_H
+#define GMX_UTILITY_PATH_H
#include <string>
#include <utility>
static bool containsDirectory(const std::string &path);
static bool isAbsolute(const char *path);
static bool isAbsolute(const std::string &path);
- static bool startsWith(const std::string &path,
- const std::string &prefix);
+ static bool isEquivalent(const std::string &path1,
+ const std::string &path2);
static std::string join(const std::string &path1,
const std::string &path2);
static std::string normalize(const std::string &path);
static std::string getParentPath(const std::string &path);
static std::string getFilename(const std::string &path);
+ static bool hasExtension(const std::string &path);
+ static std::string stripExtension(const std::string &path);
static bool exists(const char *path);
static bool exists(const std::string &path);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_utility
*/
-#include "gromacs/utility/programcontext.h"
+#include "gmxpre.h"
+
+#include "programcontext.h"
#include <cstddef>
virtual const char *programName() const { return "GROMACS"; }
virtual const char *displayName() const { return "GROMACS"; }
virtual const char *fullBinaryPath() const { return ""; }
- virtual const char *defaultLibraryDataPath() const { return ""; }
+ virtual InstallationPrefixInfo installationPrefix() const
+ {
+ return InstallationPrefixInfo("", false);
+ }
virtual const char *commandLine() const { return ""; }
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! \addtogroup module_utility
//! \{
+/*! \brief
+ * Provides information about installation prefix (see
+ * ProgramContextInterface::installationPrefix()).
+ *
+ * \inpublicapi
+ */
+struct InstallationPrefixInfo
+{
+ //! Initializes the structure with given values.
+ InstallationPrefixInfo(const char *path, bool bSource)
+ : path(path), bSourceLayout(bSource)
+ {
+ }
+
+ /*! \brief
+ * Path to the installation prefix of the current \Gromacs instance.
+ *
+ * If this is `NULL` or empty, data files cannot be looked up from the
+ * install tree and \Gromacs functions that access such files may fail.
+ * This can also contain a path to the source tree (see \a bSourceLayout).
+ */
+ const char *const path;
+ /*! \brief
+ * Whether \a path points to a source tree -like layout.
+ *
+ * For testing, it is useful to read data files from the source tree.
+ * For such cases, the program context can return the source tree root path
+ * in \a path, and set this to `true` to indicate that the data files
+ * should be searched using the layout of the source tree instead of the
+ * installation.
+ */
+ const bool bSourceLayout;
+};
+
+
/*! \brief
* Provides context information about the program that is calling the library.
*
*/
virtual const char *fullBinaryPath() const = 0;
/*! \brief
- * Returns the default path for \Gromacs data files.
+ * Returns the installation prefix for \Gromacs.
*
* This path is used to locate the data files that are in `share/top/`
* in the source directory.
* The implementation can provide an empty string if the path is not
* available; in such a case, functions that require data files may
* fail.
+ *
+ * The returned structure also contains a flag to indicate whether the
+ * prefix actually points to the source tree. This is used for tests
+ * and to support running binaries directly from the build tree.
*/
- virtual const char *defaultLibraryDataPath() const = 0;
+ virtual InstallationPrefixInfo installationPrefix() const = 0;
/*! \brief
* Returns the full command line used to invoke the binary.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
#include "qsort_threadsafe.h"
#include <stdlib.h>
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Declares `real` and related constants.
+ *
+ * \inpublicapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_REAL_H
+#define GMX_UTILITY_REAL_H
+
+/*! \brief Double precision accuracy */
+#define GMX_DOUBLE_EPS 2.2204460492503131e-16
+
+/*! \brief Maximum double precision value - reduced 1 unit in last digit for MSVC */
+#define GMX_DOUBLE_MAX 1.7976931348623157e+308
+
+/*! \brief Minimum double precision value */
+#define GMX_DOUBLE_MIN 2.2250738585072014e-308
+
+/*! \brief Single precision accuracy */
+#define GMX_FLOAT_EPS 1.19209290e-07F
+
+/*! \brief Maximum single precision value - reduced 1 unit in last digit for MSVC */
+#define GMX_FLOAT_MAX 3.40282346E+38F
+
+/*! \brief Minimum single precision value */
+#define GMX_FLOAT_MIN 1.175494351E-38F
+
+#ifdef __PGI
+/* The portland group x86 C/C++ compilers do not treat negative zero initializers
+ * correctly, but "optimizes" them to positive zero, so we implement it explicitly.
+ * These constructs are optimized to simple loads at compile time. If you want to
+ * use them on other compilers those have to support gcc preprocessor extensions.
+ * Note: These initializers might be sensitive to the endianness (which can
+ * be different for byte and word order), so check that it works for your platform
+ * and add a separate section if necessary before adding to the ifdef above.
+ */
+# define GMX_DOUBLE_NEGZERO ({ const union { int di[2]; double d; } _gmx_dzero = {0, -2147483648}; _gmx_dzero.d; })
+# define GMX_FLOAT_NEGZERO ({ const union { int fi; float f; } _gmx_fzero = {-2147483648}; _gmx_fzero.f; })
+#else
+/*! \brief Negative zero in double */
+# define GMX_DOUBLE_NEGZERO (-0.0)
+
+/*! \brief Negative zero in float */
+# define GMX_FLOAT_NEGZERO (-0.0f)
+#endif
+
+/*! \typedef real
+ * \brief Precision-dependent \Gromacs floating-point type.
+ */
+/*! \def HAVE_REAL
+ * \brief Used to check whether `real` is already defined.
+ */
+/*! \def GMX_MPI_REAL
+ * \brief MPI data type for `real`.
+ */
+/*! \def GMX_REAL_EPS
+ * \brief Accuracy for `real`.
+ */
+/*! \def GMX_REAL_MIN
+ * \brief Smallest non-zero value for `real`.
+ */
+/*! \def GMX_REAL_MAX
+ * \brief Largest finite value for `real`.
+ */
+/*! \def GMX_REAL_NEGZERO
+ * \brief Negative zero for `real`.
+ */
+/*! \def gmx_real_fullprecision_pfmt
+ * \brief Format string for full `real` precision.
+ */
+#ifdef GMX_DOUBLE
+
+#ifndef HAVE_REAL
+typedef double real;
+#define HAVE_REAL
+#endif
+
+#define GMX_MPI_REAL MPI_DOUBLE
+#define GMX_REAL_EPS GMX_DOUBLE_EPS
+#define GMX_REAL_MIN GMX_DOUBLE_MIN
+#define GMX_REAL_MAX GMX_DOUBLE_MAX
+#define GMX_REAL_NEGZERO GMX_DOUBLE_NEGZERO
+#define gmx_real_fullprecision_pfmt "%21.14e"
+
+#else /* GMX_DOUBLE */
+
+#ifndef HAVE_REAL
+typedef float real;
+#define HAVE_REAL
+#endif
+
+#define GMX_MPI_REAL MPI_FLOAT
+#define GMX_REAL_EPS GMX_FLOAT_EPS
+#define GMX_REAL_MIN GMX_FLOAT_MIN
+#define GMX_REAL_MAX GMX_FLOAT_MAX
+#define GMX_REAL_NEGZERO GMX_FLOAT_NEGZERO
+#define gmx_real_fullprecision_pfmt "%14.7e"
+
+#endif /* GMX_DOUBLE */
+
+#endif
*/
/*! \libinternal \file
* \brief
- * Declares gmx::scoped_ptr_sfree.
+ * Declares gmx::scoped_cptr and gmx::scoped_guard_sfree.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \inlibraryapi
#ifndef GMX_UTILITY_SCOPED_PTR_SFREE_H
#define GMX_UTILITY_SCOPED_PTR_SFREE_H
-#include "common.h"
+#include "config.h"
+
+#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/smalloc.h"
namespace gmx
{
+//! sfree wrapper to be used as scoped_cptr deleter
+template <class T>
+inline void sfree_wrapper(T *p)
+{
+ sfree(p);
+}
+
/*! \libinternal \brief
- * Stripped-down version of scoped_ptr that uses sfree().
+ * Stripped-down version of scoped_ptr that uses sfree() or custom deleter.
*
- * Currently only implements constructor from a pointer value and destructor;
- * other operations can be added if they become necessary.
+ * Currently only implements some operations; other operations can be added
+ * if they become necessary.
+ * The presence of a release() method is not strictly according to `scoped_ptr`
+ * design, but makes it easier to make existing C code exception-safe, and does
+ * not really warrant a separate class for such a purpose.
*
- * This class provides a very basic guard/smart pointer for C pointers.
- * Currently, boost::shared_ptr is used in a few locations that require more
- * flexibility, but is not suitable for all cases either. A scoped_ptr with
- * deleter support would be a general enough implementation for all uses.
- * C++11 unique_ptr has this, but for non-C++11 support we need something else.
+ * This class provides a basic guard/smart pointer for C pointers.
*
* Methods in this class do not throw.
*
* \inlibraryapi
* \ingroup module_utility
*/
-class scoped_ptr_sfree
+template <class T, void D(T *) = sfree_wrapper>
+class scoped_cptr
{
public:
/*! \brief
*
* \param[in] ptr Pointer to use for initialization.
*/
- explicit scoped_ptr_sfree(void *ptr) : ptr_(ptr) {}
+ explicit scoped_cptr(T *ptr = NULL) : ptr_(ptr) {}
//! Frees the pointer passed to the constructor.
- ~scoped_ptr_sfree() { sfree(ptr_); }
+ ~scoped_cptr() { D(ptr_); }
+ //! Returns the stored pointer.
+ T *get() const { return ptr_; }
+ //! Check for non-null pointer in boolean context.
+#ifdef GMX_CXX11
+ explicit
+#endif
+ operator bool () const { return ptr_ != 0; }
+ //! Sets the pointer and frees previous pointer if necessary.
+ void reset(T *ptr) { D(ptr_); ptr_ = ptr; }
+ //! Clears the pointer without freeing the memory, and returns the old value.
+ T *release() { T *ptr = ptr_; ptr_ = NULL; return ptr; }
private:
- void *ptr_;
+ T *ptr_;
- GMX_DISALLOW_COPY_AND_ASSIGN(scoped_ptr_sfree);
+ GMX_DISALLOW_COPY_AND_ASSIGN(scoped_cptr);
};
+//! Simple guard which calls sfree. See scoped_cptr for details.
+typedef scoped_cptr<void> scoped_guard_sfree;
+
} // namespace gmx
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "gromacs/utility/smalloc.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "smalloc.h"
+
+#include "config.h"
#include <errno.h>
#include <stdio.h>
#include <malloc.h>
#endif
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "thread_mpi/threads.h"
+#include "gromacs/utility/dir_separator.h"
+#include "gromacs/utility/fatalerror.h"
#ifdef PRINT_ALLOC_KB
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/gmxmpi.h"
#endif
-#ifdef DEBUG
-#include "thread_mpi/threads.h"
+static gmx_bool g_bOverAllocDD = FALSE;
+static tMPI_Thread_mutex_t g_over_alloc_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+#ifdef DEBUG
static void log_action(int bMal, const char *what, const char *file, int line,
int nelem, int size, void *ptr)
{
}
#endif
- allocate_fail = FALSE; /* stop compiler warnings */
#ifdef HAVE_POSIX_MEMALIGN
allocate_fail = (0 != posix_memalign(&malloced, alignment, nelem*elsize));
#elif defined HAVE_MEMALIGN
#endif
}
}
+
+void set_over_alloc_dd(gmx_bool set)
+{
+ tMPI_Thread_mutex_lock(&g_over_alloc_mutex);
+ /* we just make sure that we don't set this at the same time.
+ We don't worry too much about reading this rarely-set variable */
+ g_bOverAllocDD = set;
+ tMPI_Thread_mutex_unlock(&g_over_alloc_mutex);
+}
+
+int over_alloc_dd(int n)
+{
+ if (g_bOverAllocDD)
+ {
+ return OVER_ALLOC_FAC*n + 100;
+ }
+ else
+ {
+ return n;
+ }
+}
#include <stddef.h>
+#include "gromacs/utility/basedefinitions.h"
+
#ifdef __cplusplus
extern "C" {
#endif
#endif
+#ifdef __cplusplus
+extern "C" {
+#endif
+
/*! \brief
* Frees memory referenced by \p ptr.
*
*/
#define sfree_aligned(ptr) save_free_aligned(#ptr, __FILE__, __LINE__, (ptr))
+/*! \brief
+ * Over allocation factor for memory allocations.
+ *
+ * Memory (re)allocation can be VERY slow, especially with some
+ * MPI libraries that replace the standard malloc and realloc calls.
+ * To avoid slow memory allocation we use over_alloc to set the memory
+ * allocation size for large data blocks. Since this scales the size
+ * with a factor, we use log(n) realloc calls instead of n.
+ * This can reduce allocation times from minutes to seconds.
+ *
+ * This factor leads to 4 realloc calls to double the array size.
+ */
+#define OVER_ALLOC_FAC 1.19
+
+/*! \brief
+ * Turns over allocation for variable size atoms/cg/top arrays on or off,
+ * default is off.
+ *
+ * \todo
+ * This is mdrun-specific, so it might be better to put this and
+ * over_alloc_dd() much higher up.
+ */
+void set_over_alloc_dd(gmx_bool set);
+
+/*! \brief
+ * Returns new allocation count for domain decomposition allocations.
+ *
+ * Returns n when domain decomposition over allocation is off.
+ * Returns OVER_ALLOC_FAC*n + 100 when over allocation in on.
+ * This is to avoid frequent reallocation during domain decomposition in mdrun.
+ */
+int over_alloc_dd(int n);
+
+/** Over allocation for small data types: int, real etc. */
+#define over_alloc_small(n) (int)(OVER_ALLOC_FAC*(n) + 8000)
+
+/** Over allocation for large data types: complex structs */
+#define over_alloc_large(n) (int)(OVER_ALLOC_FAC*(n) + 1000)
+
+#ifdef __cplusplus
+}
+#endif
+
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \libinternal \file
+ * \brief Provide snprintf symbol on all OS (for internal Gromacs use)
+ *
+ * \todo When all callers of snprintf compile as C++, perhaps use
+ * gmx::formatString() everywhere instead of snprintf.
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_SNPRINTF_H
+#define GMX_UTILITY_SNPRINTF_H
-#ifndef _shift_h
-#define _shift_h
+#include "config.h"
-#include "typedefs.h"
+#include <stdio.h>
-#ifdef __cplusplus
-extern "C" {
+#ifdef GMX_NATIVE_WINDOWS
+#define snprintf _snprintf
#endif
-real *mk_shift_tab(int n, real r1, real rc, real dr, real *sfac);
-/* Return a table of length n, containing the parabolic
- * shift function from HJC Berendsen
- */
-
-#ifdef __cplusplus
-}
#endif
-
-#endif /* _shift_h */
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_utility
*/
+#include "gmxpre.h"
+
#include "stringutil.h"
#include <cctype>
-#include <cstdio>
#include <cstdarg>
+#include <cstdio>
#include <cstring>
#include <algorithm>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! \addtogroup module_utility
//! \{
+/*! \brief
+ * Tests whether a string is null or empty.
+ *
+ * Does not throw.
+ */
+bool inline isNullOrEmpty(const char *str)
+{
+ return str == NULL || str[0] == '\0';
+}
+
/*! \brief
* Tests whether a string starts with another string.
*
*/
std::string formatString(const char *fmt, ...);
-/*! \brief
- * Splits a string to whitespace separated tokens.
+/*! \brief Function object that wraps a call to formatString() that
+ * expects a single conversion argument, for use with algorithms. */
+class StringFormatter
+{
+ public:
+ /*! \brief Constructor
+ *
+ * \param[in] format The printf-style format string that will
+ * be applied to convert values of type T to
+ * string. Exactly one argument to the conversion
+ * specification(s) in `format` is supported. */
+ explicit StringFormatter(const char *format) : format_(format)
+ {
+ }
+
+ //! Implements the formatting functionality
+ template <typename T>
+ std::string operator()(const T &value) const
+ {
+ return formatString(format_, value);
+ }
+
+ private:
+ //! Format string to use
+ const char *format_;
+};
+
+/*! \brief Function object to implement the same interface as
+ * `StringFormatter` to use with strings that should not be formatted
+ * further. */
+class IdentityFormatter
+{
+ public:
+ //! Implements the formatting non-functionality
+ std::string operator()(const std::string &value) const
+ {
+ return value;
+ }
+};
+
+/*! \brief Formats all the range as strings, and then joins them with
+ * a separator in between.
*
- * \param[in] str String to process.
- * \returns \p str split into tokens at each whitespace sequence.
+ * \param[in] begin Iterator the beginning of the range to join.
+ * \param[in] end Iterator the end of the range to join.
+ * \param[in] separator String to put in between the joined strings.
+ * \param[in] formatter Function object to format the objects in
+ * `container` as strings
+ * \returns All objects in the range from `begin` to `end` formatted
+ * as strings and concatenated with `separator` between each pair.
* \throws std::bad_alloc if out of memory.
+ */
+template <typename InputIterator, typename FormatterType>
+std::string formatAndJoin(InputIterator begin, InputIterator end, const char *separator, const FormatterType &formatter)
+{
+ std::string result;
+ const char *currentSeparator = "";
+ for (InputIterator i = begin; i != end; ++i)
+ {
+ result.append(currentSeparator);
+ result.append(formatter(*i));
+ currentSeparator = separator;
+ }
+ return result;
+}
+
+/*! \brief Formats all elements of the container as strings, and then
+ * joins them with a separator in between.
*
- * This function works like `split` in Python, i.e., leading and trailing
- * whitespace is ignored, and consecutive whitespaces are treated as a single
- * separator.
+ * \param[in] container Objects to join.
+ * \param[in] separator String to put in between the joined strings.
+ * \param[in] formatter Function object to format the objects in
+ * `container` as strings
+ * \returns All objects from `container` formatted as strings and
+ * concatenated with `separator` between each pair.
+ * \throws std::bad_alloc if out of memory.
*/
-std::vector<std::string> splitString(const std::string &str);
+template <typename ContainerType, typename FormatterType>
+std::string formatAndJoin(const ContainerType &container, const char *separator, const FormatterType &formatter)
+{
+ return formatAndJoin(container.begin(), container.end(), separator, formatter);
+}
/*! \brief
* Joins strings from a range with a separator in between.
std::string joinStrings(InputIterator begin, InputIterator end,
const char *separator)
{
- std::string result;
- const char *currentSeparator = "";
- for (InputIterator i = begin; i != end; ++i)
- {
- result.append(currentSeparator);
- result.append(*i);
- currentSeparator = separator;
- }
- return result;
+ return formatAndJoin(begin, end, separator, IdentityFormatter());
}
+
/*! \brief
* Joins strings from a container with a separator in between.
*
return concatenateStrings(sarray, count);
}
+/*! \brief
+ * Splits a string to whitespace separated tokens.
+ *
+ * \param[in] str String to process.
+ * \returns \p str split into tokens at each whitespace sequence.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * This function works like `split` in Python, i.e., leading and trailing
+ * whitespace is ignored, and consecutive whitespaces are treated as a single
+ * separator.
+ */
+std::vector<std::string> splitString(const std::string &str);
+
/*! \brief
* Replace all occurrences of a string with another string.
*
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements functions from sysinfo.h.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_utility
+ */
+#include "gmxpre.h"
+
+#include "sysinfo.h"
+
+#include "config.h"
+
+#include <string.h>
+#include <time.h>
+
+#include <sys/types.h>
+#ifdef HAVE_SYS_TIME_H
+#include <sys/time.h>
+#endif
+#ifdef GMX_NATIVE_WINDOWS
+#include <Windows.h>
+#include <process.h>
+#endif
+#ifdef HAVE_PWD_H
+#include <pwd.h>
+#endif
+#ifdef HAVE_UNISTD_H
+#include <unistd.h>
+#endif
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/gmxassert.h"
+
+namespace
+{
+//! Static return value for cases when a string value is not available.
+const char c_unknown[] = "unknown";
+} // namespace
+
+int gmx_gethostname(char *buf, size_t len)
+{
+ GMX_RELEASE_ASSERT(len >= 8, "Input buffer is too short");
+#ifdef GMX_NATIVE_WINDOWS
+ DWORD dlen = len;
+ if (GetComputerName(buf, &dlen))
+ {
+ return 0;
+ }
+#elif defined(HAVE_UNISTD_H) && !defined(__native_client__)
+ if (gethostname(buf, len-1) == 0)
+ {
+ buf[len-1] = '\0';
+ return 0;
+ }
+#endif
+ strcpy(buf, c_unknown);
+ return -1;
+}
+
+int gmx_getpid()
+{
+#ifdef GMX_NATIVE_WINDOWS
+ return _getpid();
+#else
+ return getpid();
+#endif
+}
+
+int gmx_getuid()
+{
+#if defined(HAVE_UNISTD_H) && !defined(__MINGW32__)
+ return getuid();
+#else
+ return -1;
+#endif
+}
+
+int gmx_getusername(char *buf, size_t len)
+{
+ GMX_RELEASE_ASSERT(len >= 8, "Input buffer is too short");
+ // TODO: nice_header() used getpwuid() instead; consider using getpwuid_r()
+ // here. If not, get rid of HAVE_PWD_H completely.
+#ifdef GMX_NATIVE_WINDOWS
+ DWORD dlen = len;
+ if (GetUserName(buf, &dlen))
+ {
+ return 0;
+ }
+#elif defined(HAVE_UNISTD_H) && !__has_feature(memory_sanitizer) //MSAN Issue 83
+ if (!getlogin_r(buf, len))
+ {
+ buf[len-1] = '\0';
+ return 0;
+ }
+#endif
+ strcpy(buf, c_unknown);
+ return -1;
+}
+
+char *
+gmx_ctime_r(const time_t *clock, char *buf, size_t len)
+{
+#ifdef _MSC_VER
+ /* Windows */
+ ctime_s(buf, len, clock);
+#elif defined(GMX_NATIVE_WINDOWS)
+ char *tmpbuf = ctime(clock);
+ strncpy(buf, tmpbuf, len-1);
+ buf[len-1] = '\0';
+#elif (defined(__sun))
+ /*Solaris*/
+ ctime_r(clock, buf, len);
+#else
+ char tmpbuf[30];
+ ctime_r(clock, tmpbuf);
+ strncpy(buf, tmpbuf, len-1);
+ buf[len-1] = '\0';
+#endif
+ return buf;
+}
+
+void gmx_format_current_time(char *buf, size_t len)
+{
+ time_t clock = time(NULL);
+ gmx_ctime_r(&clock, buf, len);
+}
+
+int gmx_set_nice(int level)
+{
+#ifdef GMX_USE_NICE
+ // TODO: This may not be reliable, but currently the return value is not
+ // used.
+ if (nice(level) != -1)
+ {
+ return 0;
+ }
+#else
+ GMX_UNUSED_VALUE(level);
+#endif
+ return -1;
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares functions for obtaining information about the operating environment
+ * and the current process.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_SYSINFO_H
+#define GMX_UTILITY_SYSINFO_H
+
+#include <stddef.h>
+#include <time.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*! \addtogroup module_utility
+ * \{
+ */
+
+/*! \brief
+ * Gets the hostname as given by gethostname(), if available.
+ *
+ * \param[out] buf Buffer to receive the hostname.
+ * \param[in] len Length of buffer \p buf (must be >= 8).
+ * \returns 0 on success, -1 on error.
+ *
+ * If the value is not available, "unknown" is returned.
+ * \p name should have at least size \p len.
+ *
+ * Does not throw.
+ */
+int gmx_gethostname(char *buf, size_t len);
+
+/*! \brief
+ * Returns the process ID of the current process.
+ *
+ * Does not throw.
+ */
+int gmx_getpid(void);
+/*! \brief
+ * Returns the current user ID, or -1 if not available.
+ *
+ * Does not throw.
+ */
+int gmx_getuid(void);
+/*! \brief
+ * Gets the current user name, if available.
+ *
+ * \param[out] buf Buffer to receive the username.
+ * \param[in] len Length of buffer \p buf (must be >= 8).
+ * \returns 0 on success, -1 on error.
+ *
+ * Does not throw.
+ */
+int gmx_getusername(char *buf, size_t len);
+
+/*! \brief
+ * Portable version of ctime_r.
+ *
+ * Does not throw.
+ */
+char *gmx_ctime_r(const time_t *clock, char *buf, size_t len);
+/*! \brief
+ * Gets the current time as a string.
+ *
+ * \param[out] buf Buffer to receive the string.
+ * \param[in] len Length of buffer \p buf (26 characters should be sufficient).
+ *
+ * Does not throw.
+ */
+void gmx_format_current_time(char *buf, size_t len);
+
+/*! \brief
+ * Wrapper for nice().
+ *
+ * Does not throw.
+ */
+int gmx_set_nice(int level);
+
+/*! \} */
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
# the research papers on the package. Check out http://www.gromacs.org.
gmx_add_unit_test(UtilityUnitTests utility-test
+ bitmask32.cpp bitmask64.cpp bitmask128.cpp
stringutil.cpp)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for bitmask functionality.
+ *
+ * These tests check the functionality of bitmask.h
+
+ * \author Roland Schulz <roland@rschulz.eu>
+ * \ingroup module_utility
+ */
+#include <gtest/gtest.h>
+
+#include "gromacs/utility/bitmask.h"
+
+//! Implemenation of BITMASK_CLASSNAME
+#define BITMASK_CLASSNAME_(S) BitmaskTest ## S
+//! Returns name of Bitmask test fixture class
+#define BITMASK_CLASSNAME(S) BITMASK_CLASSNAME_(S)
+//! Implementation of BITMASK_TEST_P
+#define BITMASK_TEST_P_(C, T) TEST_P(C, T)
+//! Defines a parameterized bitmask test
+#define BITMASK_TEST_P(T) BITMASK_TEST_P_(BITMASK_CLASSNAME(BITMASK_SIZE), T)
+
+class BITMASK_CLASSNAME(BITMASK_SIZE) : public ::testing::TestWithParam<int>
+{
+};
+
+BITMASK_TEST_P(SetAndClear)
+{
+ gmx_bitmask_t m;
+ int i = GetParam();
+ bitmask_clear(&m);
+ EXPECT_TRUE(bitmask_is_zero(m));
+ EXPECT_FALSE(bitmask_is_set(m, i));
+ bitmask_set_bit(&m, i);
+ for (int j = 0; j < BITMASK_SIZE; j++)
+ {
+ EXPECT_EQ(bitmask_is_set(m, j), j == i);
+ }
+ bitmask_clear(&m);
+ EXPECT_TRUE(bitmask_is_zero(m));
+}
+
+BITMASK_TEST_P(InitBit)
+{
+ gmx_bitmask_t m1, m2;
+ int i = GetParam();
+ bitmask_init_bit(&m1, i);
+ bitmask_clear(&m2);
+ EXPECT_FALSE(bitmask_is_equal(m1, m2));
+ bitmask_set_bit(&m2, i);
+ EXPECT_TRUE(bitmask_is_equal(m1, m2));
+}
+
+BITMASK_TEST_P(InitLowBits)
+{
+ gmx_bitmask_t m;
+ int i = GetParam();
+ bitmask_init_low_bits(&m, i);
+ for (int j = 0; j < BITMASK_SIZE; j++)
+ {
+ EXPECT_EQ(bitmask_is_set(m, j), j < i);
+ }
+}
+
+BITMASK_TEST_P(Disjoint)
+{
+ gmx_bitmask_t m1, m2;
+ int i = GetParam();
+ bitmask_init_bit(&m1, i);
+ bitmask_init_bit(&m2, i);
+ EXPECT_FALSE(bitmask_is_disjoint(m1, m2));
+ bitmask_init_low_bits(&m2, i);
+ EXPECT_TRUE(bitmask_is_disjoint(m1, m2));
+}
+
+BITMASK_TEST_P(Union)
+{
+ gmx_bitmask_t m1, m2;
+ int i = GetParam();
+ int j = (i + BITMASK_SIZE/2)%BITMASK_SIZE;
+ bitmask_init_bit(&m1, i);
+ bitmask_init_bit(&m2, j);
+ bitmask_union(&m1, m2);
+ for (int k = 0; k < BITMASK_SIZE; k++)
+ {
+ EXPECT_EQ(bitmask_is_set(m1, k), k == i || k == j);
+ }
+
+ bitmask_init_bit(&m1, i);
+ bitmask_clear(&m2);
+ bitmask_union(&m1, m2);
+ bitmask_init_bit(&m2, i);
+ EXPECT_TRUE(bitmask_is_equal(m1, m2));
+
+ bitmask_clear(&m1);
+ bitmask_init_bit(&m2, i);
+ bitmask_union(&m1, m2);
+ EXPECT_TRUE(bitmask_is_equal(m1, m2));
+}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include <stdio.h>
-#include "physics.h"
+#include "gmxpre.h"
-int main(int argc, char *argv[])
-{
- int i;
- double x, y, z;
+#define BITMASK_SIZE 128
+#include "bitmask.h"
- x = 3.25;
- for (i = 0; (i < eg2cNR); i++)
- {
- y = gmx2convert(x, i);
- z = convert2gmx(y, i);
- printf("Converted %g [type %d] to %g and back to %g. Diff %g\n",
- x, i, y, z, x-z);
- }
-}
+INSTANTIATE_TEST_CASE_P(BitmaskTest128_9_78, BitmaskTest128, ::testing::Values(9, 78));
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _types_symtab_h
-#define _types_symtab_h
+#include "gmxpre.h"
+#define BITMASK_SIZE 32
+#include "bitmask.h"
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-typedef struct symbuf {
- int bufsize;
- char **buf;
- struct symbuf *next;
-} t_symbuf;
-
-typedef struct
-{
- int nr;
- t_symbuf *symbuf;
-} t_symtab;
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
+INSTANTIATE_TEST_CASE_P(BitmaskTest32_11, BitmaskTest32, ::testing::Values(11));
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#define BITMASK_SIZE 64
+#include "bitmask.h"
+
+INSTANTIATE_TEST_CASE_P(BitmaskTest64_10_42, BitmaskTest64, ::testing::Values(10, 42));
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_utility
*/
+#include "gmxpre.h"
+
+#include "gromacs/utility/stringutil.h"
+
#include <string>
#include <vector>
#include <gmock/gmock.h>
#include <gtest/gtest.h>
-#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/arrayref.h"
#include "testutils/refdata.h"
#include "testutils/stringtest.h"
EXPECT_EQ("x10", longString.substr(1999));
}
+/********************************************************************
+ * Tests for StringFormatter
+ */
+
+TEST(StringFormatterTest, HandlesBasicFormatting)
+{
+ int value = 103;
+ EXPECT_EQ("103", gmx::StringFormatter("%d") (value));
+ EXPECT_EQ("null", gmx::StringFormatter("null") (value));
+}
+
+/********************************************************************
+ * Tests for formatAndJoin
+ */
+
+TEST(formatAndJoinTest, Works)
+{
+ const char * const words[] = { "The", "quick", "brown", "fox" };
+ EXPECT_EQ("The .quick .brown .fox ",
+ gmx::formatAndJoin(gmx::ConstArrayRef<const char *>(words), ".",
+ gmx::StringFormatter("%-10s")));
+
+ const int values[] = { 0, 1, 4 };
+ EXPECT_EQ("0,1,4", gmx::formatAndJoin(gmx::ConstArrayRef<int>(values), ",",
+ gmx::StringFormatter("%d")));
+}
+
+/********************************************************************
+ * Tests for joinStrings
+ */
+
+TEST(JoinStringsTest, Works)
+{
+ const char * const words[] = { "The", "quick", "brown", "fox" };
+ gmx::ConstArrayRef<const char *> refToWords(words);
+ EXPECT_EQ("The; quick; brown; fox", gmx::joinStrings(refToWords.begin(), refToWords.end(), "; "));
+ EXPECT_EQ("The-quick-brown-fox", gmx::joinStrings(refToWords, "-"));
+}
+
/********************************************************************
* Tests for concatenateStrings()
*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/*! \file
+/*! \libinternal \file
* \brief
* Declares gmx::gmx_unique_ptr and supporting functionality.
*
#ifndef GMX_UTILITY_UNIQUEPTR_H
#define GMX_UTILITY_UNIQUEPTR_H
-#include "gmx_header_config.h"
+#include "config.h"
-#ifdef GMX_CXX11 // C++11 Compiler
-#include <memory>
-#include <utility>
-#else // C++03 Compiler
+#ifdef GMX_CXX11 // C++11 Compiler
+#include <memory> // IWYU pragma: export
+#include <utility> // IWYU pragma: export
+#else // C++03 Compiler
#include <boost/shared_ptr.hpp>
#endif
namespace gmx
{
-/*! \class gmx_unique_ptr
+//! \cond libapi
+/*! \libinternal \class gmx_unique_ptr
* \brief
* Smart pointer for unique ownership.
*
* \ingroup module_utility
* \inlibraryapi
*/
-/*! \typedef gmx_unique_ptr::type
+/*! \libinternal \typedef gmx_unique_ptr::type
* \brief The smart pointer type.
* Work-around for the non-existence of template typedefs in C++03.
*/
typedef boost::shared_ptr<T> type;
};
#endif
+//! \endcond
} // namespace gmx
* For 4.6 and 5.0 (and likely for some time in the future as well), this
* tracks the exact \Gromacs version.
*/
-#define GMX_API_VERSION @API_VERSION@
+#define GMX_API_VERSION @GMX_API_VERSION@
/*! \brief
* Exact \Gromacs version of this set of headers.
* This specifies the version number of the actual \Gromacs library that
* installed these headers.
*/
-#define GMX_VERSION @NUM_VERSION@
+#define GMX_VERSION @GMX_VERSION_NUMERIC@
#endif
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+if (NOT DEFINED GMX_EXECUTABLE)
+ message(FATAL_ERROR "Required input parameter not set")
+endif()
+
+file(MAKE_DIRECTORY completion)
+execute_process(
+ COMMAND ${GMX_EXECUTABLE} -quiet help -export completion
+ WORKING_DIRECTORY completion
+ RESULT_VARIABLE exitcode)
+if (exitcode)
+ # Ensure that no partial output is left behind.
+ file(REMOVE_RECURSE completion)
+ if (ERRORS_ARE_FATAL)
+ message(FATAL_ERROR
+ "Failed to generate shell completions. "
+ "Set GMX_BUILD_HELP=OFF if you want to skip the completions.\n"
+ "Error/exit code: ${exitcode}")
+ else()
+ message(
+ "Failed to generate shell completions, will build GROMACS without. "
+ "Set GMX_BUILD_HELP=OFF if you want to skip this notification and "
+ "warnings during installation.")
+ endif()
+endif()
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
########################
# Completion generation
+ include(gmxCustomCommandUtilities)
+
set(COMPLETION_DIR ${CMAKE_CURRENT_SOURCE_DIR}/completion)
- if(SOURCE_IS_SOURCE_DISTRIBUTION)
- # Make sure source package contains the completions.
- if(NOT EXISTS "${COMPLETION_DIR}/gmx-completion.bash")
- message(FATAL_ERROR "Shell completions are missing from source package.")
- endif()
- endif()
- file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/completion)
- add_custom_target(completion
- gmx -quiet help -export completion
- COMMENT "Generating command-line completions for programs"
- WORKING_DIRECTORY completion
- VERBATIM)
# Using GMX_BUILD_HELP here is somewhat confusing, but the conditions when
# this can be done are exactly the same (ability to run the compiled
# binaries).
if (GMX_BUILD_HELP)
+ gmx_add_custom_output_target(completion OUTPUT STAMP
+ COMMAND ${CMAKE_COMMAND}
+ -D GMX_EXECUTABLE=$<TARGET_FILE:gmx>
+ -D ERRORS_ARE_FATAL=${GMX_BUILD_HELP_FORCE}
+ -P ${CMAKE_CURRENT_SOURCE_DIR}/BuildCompletions.cmake
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ DEPENDS gmx ${CMAKE_CURRENT_SOURCE_DIR}/BuildCompletions.cmake
+ COMMENT "Generating command-line completions for programs")
set_target_properties(completion PROPERTIES EXCLUDE_FROM_ALL OFF)
set_directory_properties(PROPERTIES
ADDITIONAL_MAKE_CLEAN_FILES "completion")
endif()
if (SOURCE_IS_SOURCE_DISTRIBUTION OR GMX_BUILD_HELP)
install(DIRECTORY ${COMPLETION_DIR}/
- DESTINATION ${BIN_INSTALL_DIR} COMPONENT runtime)
+ DESTINATION ${BIN_INSTALL_DIR} COMPONENT runtime OPTIONAL)
file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/gmx-completion-${BINARY_NAME}.bash
"complete -o nospace -F _gmx_compl ${BINARY_NAME}")
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/gmx-completion-${BINARY_NAME}.bash
DESTINATION ${BIN_INSTALL_DIR} COMPONENT runtime)
endif()
-
- if (GMX_SYMLINK_OLD_BINARY_NAMES)
- configure_file(CreateLinks.cmake.cmakein CreateLinks.cmake @ONLY)
- set(CREATE_LINKS_SCRIPT ${CMAKE_CURRENT_BINARY_DIR}/CreateLinks.cmake)
- install(SCRIPT ${CREATE_LINKS_SCRIPT} COMPONENT links)
- endif()
+ gmx_cpack_add_generated_source_directory(completion)
if(BUILD_TESTING)
add_subdirectory(mdrun/tests)
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public License
-# as published by the Free Software Foundation; either version 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-# TODO: It would be nicer to have the list generated from the binary,
-# but this has some complications. As the same list is also needed for
-# man page generation, this can wait for now.
-set(SYMLINK_NAMES
- mdrun
- gmxcheck
- gmxdump
- grompp
- pdb2gmx
- tpbconv
- g_protonate
- g_x2top
- do_dssp
- editconf
- eneconv
- genbox
- genconf
- genion
- genrestr
- make_edi
- make_ndx
- mk_angndx
- trjcat
- trjconv
- trjorder
- xpm2ps
- g_anadock
- g_anaeig
- g_analyze
- g_angle
- g_bar
- g_bond
- g_bundle
- g_chi
- g_cluster
- g_clustsize
- g_confrms
- g_covar
- g_current
- g_density
- g_densmap
- g_densorder
- g_dielectric
- g_dipoles
- g_disre
- g_dist
- g_dos
- g_dyecoupl
- g_dyndom
- g_enemat
- g_energy
- g_filter
- g_gyrate
- g_h2order
- g_hbond
- g_helix
- g_helixorient
- g_hydorder
- g_lie
- g_mdmat
- g_mindist
- g_morph
- g_msd
- g_nmeig
- g_nmens
- g_nmtraj
- g_options
- g_order
- g_pme_error
- g_polystat
- g_potential
- g_principal
- g_rama
- g_rdf
- g_rms
- g_rmsdist
- g_rmsf
- g_rotacf
- g_rotmat
- g_saltbr
- g_sans
- g_sas
- g_saxs
- g_select
- g_sgangle
- g_sham
- g_sigeps
- g_sorient
- g_spatial
- g_spol
- g_tcaf
- g_traj
- g_tune_pme
- g_vanhove
- g_velacc
- g_wham
- g_wheel
- )
-
-if (NOT DEFINED BINARY_DIRECTORY)
- set(BINARY_DIRECTORY "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/@BIN_INSTALL_DIR@")
-endif ()
-set(BINARY_SUFFIX "@GMX_BINARY_SUFFIX@@CMAKE_EXECUTABLE_SUFFIX@")
-set(GMX_NATIVE_WINDOWS "@GMX_NATIVE_WINDOWS@")
-
-foreach (linkname ${SYMLINK_NAMES})
- set(linkpath ${BINARY_DIRECTORY}/${linkname}${BINARY_SUFFIX})
- # Based on documentation, CMake only supports symbolic links on Unix,
- # although NTFS also has those (since Windows Vista; they require admin
- # permissions to create).
- if (GMX_NATIVE_WINDOWS)
- if (NOT QUIETLY)
- message(STATUS "Installing: Creating alias binary ${linkpath}")
- endif ()
- execute_process(
- COMMAND ${CMAKE_COMMAND} -E copy_if_different
- ${BINARY_DIRECTORY}/gmx${BINARY_SUFFIX} ${linkpath})
- else()
- if (NOT QUIETLY)
- message(STATUS "Installing: Creating symbolic link ${linkpath}")
- endif ()
- if (EXISTS ${linkpath})
- FILE(REMOVE ${linkpath})
- endif ()
- execute_process(
- COMMAND ${CMAKE_COMMAND} -E create_symlink
- gmx${BINARY_SUFFIX} ${linkpath})
- endif()
-endforeach ()
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
*/
-#include "gromacs/commandline/cmdlinemodulemanager.h"
+#include "gmxpre.h"
+
#include "gromacs/commandline/cmdlineinit.h"
-#include "gromacs/selection/selectioncollection.h"
+#include "gromacs/commandline/cmdlinemodulemanager.h"
+#include "gromacs/selection/selhelp.h"
#include "gromacs/trajectoryanalysis/modules.h"
#include "gromacs/utility/exceptions.h"
gmx::CommandLineModuleManager manager("gmx", &context);
registerTrajectoryAnalysisModules(&manager);
registerLegacyModules(&manager);
- manager.addHelpTopic(gmx::SelectionCollection::createDefaultHelpTopic());
+ manager.addHelpTopic(gmx::createSelectionHelpTopic());
int rc = manager.run(argc, argv);
gmx::finalizeForCommandLine();
return rc;
catch (const std::exception &ex)
{
gmx::printFatalErrorMessage(stderr, ex);
- return gmx::processExceptionAtExit(ex);
+ return gmx::processExceptionAtExitForCommandLine(ex);
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
*/
+#include "gmxpre.h"
+
#include "legacymodules.h"
#include <cstdio>
#include "gromacs/commandline/cmdlinemodule.h"
#include "gromacs/commandline/cmdlinemodulemanager.h"
-
+#include "gromacs/commandline/cmdlineoptionsmodule.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxpreprocess/genconf.h"
#include "gromacs/gmxpreprocess/grompp.h"
return NULL;
}
+ virtual void init(gmx::CommandLineModuleSettings * /*settings*/)
+ {
+ }
virtual int run(int /*argc*/, char * /*argv*/[])
{
printMessage();
}
const char *name_;
+};
+
+// TODO: Consider removing duplication with CMainCommandLineModule from
+// cmdlinemodulemanager.cpp.
+class NoNiceModule : public gmx::CommandLineModuleInterface
+{
+ public:
+ //! \copydoc gmx::CommandLineModuleManager::CMainFunction
+ typedef gmx::CommandLineModuleManager::CMainFunction CMainFunction;
+
+ /*! \brief
+ * Creates a wrapper module for the given main function.
+ *
+ * \param[in] name Name for the module.
+ * \param[in] shortDescription One-line description for the module.
+ * \param[in] mainFunction Main function to wrap.
+ *
+ * Does not throw.
+ */
+ NoNiceModule(const char *name, const char *shortDescription,
+ CMainFunction mainFunction)
+ : name_(name), shortDescription_(shortDescription),
+ mainFunction_(mainFunction)
+ {
+ }
+
+ virtual const char *name() const
+ {
+ return name_;
+ }
+ virtual const char *shortDescription() const
+ {
+ return shortDescription_;
+ }
+
+ virtual void init(gmx::CommandLineModuleSettings *settings)
+ {
+ settings->setDefaultNiceLevel(0);
+ }
+ virtual int run(int argc, char *argv[])
+ {
+ return mainFunction_(argc, argv);
+ }
+ virtual void writeHelp(const gmx::CommandLineHelpContext &context) const
+ {
+ writeCommandLineHelpCMain(context, name_, mainFunction_);
+ }
+ private:
+ const char *name_;
+ const char *shortDescription_;
+ CMainFunction mainFunction_;
};
/*! \brief
manager->addModuleCMain(name, shortDescription, mainFunction);
}
+/*! \brief
+ * Convenience function for creating and registering a module that defaults to
+ * -nice 0.
+ *
+ * \param[in] manager Module manager to which to register the module.
+ * \param[in] mainFunction Main function to wrap.
+ * \param[in] name Name for the new module.
+ * \param[in] shortDescription One-line description for the new module.
+ */
+void registerModuleNoNice(gmx::CommandLineModuleManager *manager,
+ gmx::CommandLineModuleManager::CMainFunction mainFunction,
+ const char *name, const char *shortDescription)
+{
+ gmx::CommandLineModulePointer module(
+ new NoNiceModule(name, shortDescription, mainFunction));
+ manager->addModule(move(module));
+}
+
/*! \brief
* Convenience function for registering a module for an obsolete tool.
*
registerModule(manager, &gmx_x2top, "x2top",
"Generate a primitive topology from coordinates");
- registerModule(manager, &gmx_mdrun, "mdrun",
- "Perform a simulation, do a normal mode analysis or an energy minimization");
+ registerModuleNoNice(manager, &gmx_mdrun, "mdrun",
+ "Perform a simulation, do a normal mode analysis or an energy minimization");
+
+ gmx::CommandLineOptionsModuleInterface::registerModule(
+ manager, gmx::InsertMoleculesInfo::name,
+ gmx::InsertMoleculesInfo::shortDescription,
+ &gmx::InsertMoleculesInfo::create);
// Modules from gmx_ana.h.
registerModule(manager, &gmx_do_dssp, "do_dssp",
"Convert energy files");
registerModule(manager, &gmx_solvate, "solvate",
"Solvate a system");
- registerModule(manager, &gmx_insert_molecules, "insert-molecules",
- "Insert molecules into existing vacancies");
registerObsoleteTool(manager, "genbox");
registerModule(manager, &gmx_genconf, "genconf",
"Multiply a conformation in 'random' orientations");
"Generate an ensemble of structures from the normal modes");
registerModule(manager, &gmx_nmtraj, "nmtraj",
"Generate a virtual oscillating trajectory from an eigenvector");
- registerModule(manager, &gmx_options, "options", NULL);
registerModule(manager, &gmx_order, "order",
"Compute the order parameter per atom for carbon tails");
registerModule(manager, &gmx_pme_error, "pme_error",
"Calculate principal axes of inertia for a group of atoms");
registerModule(manager, &gmx_rama, "rama",
"Compute Ramachandran plots");
- registerModule(manager, &gmx_rdf, "rdf",
- "Calculate radial distribution functions");
registerModule(manager, &gmx_rms, "rms",
"Calculate RMSDs with a reference structure and RMSD matrices");
registerModule(manager, &gmx_rmsdist, "rmsdist",
"Perform weighted histogram analysis after umbrella sampling");
registerModule(manager, &gmx_wheel, "wheel",
"Plot helical wheels");
- registerModule(manager, &gmx_view, "view",
- "View a trajectory on an X-Windows terminal");
+ registerModuleNoNice(manager, &gmx_view, "view",
+ "View a trajectory on an X-Windows terminal");
{
gmx::CommandLineModuleGroup group =
#include "thread_mpi/threads.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+
#ifdef __cplusplus
extern "C" {
#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "vec.h"
-#include "vcm.h"
-#include "mdebin.h"
-#include "nrnb.h"
-#include "calcmu.h"
-#include "index.h"
-#include "vsite.h"
-#include "update.h"
-#include "ns.h"
-#include "mdrun.h"
-#include "md_support.h"
-#include "md_logging.h"
-#include "network.h"
-#include "xvgr.h"
-#include "physics.h"
-#include "names.h"
-#include "force.h"
-#include "disre.h"
-#include "orires.h"
-#include "pme.h"
-#include "mdatoms.h"
-#include "repl_ex.h"
-#include "deform.h"
-#include "qmmm.h"
-#include "domdec.h"
-#include "domdec_network.h"
-#include "gromacs/gmxlib/topsort.h"
-#include "coulomb.h"
-#include "constr.h"
-#include "shellfc.h"
-#include "gromacs/gmxpreprocess/compute_io.h"
-#include "checkpoint.h"
-#include "mtop_util.h"
-#include "sighandler.h"
-#include "txtdump.h"
-#include "gromacs/utility/cstringutil.h"
-#include "pme_loadbal.h"
-#include "bondf.h"
-#include "membed.h"
-#include "types/nlistheuristics.h"
-#include "types/iteratedconstraints.h"
-#include "nbnxn_cuda_data_mgmt.h"
+#include "config.h"
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "thread_mpi/threads.h"
-#include "gromacs/utility/gmxmpi.h"
-#include "gromacs/fileio/confio.h"
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/domdec_network.h"
+#include "gromacs/ewald/pme-load-balancing.h"
+#include "gromacs/ewald/pme.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/mdoutf.h"
#include "gromacs/fileio/trajectory_writing.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trx.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/xtcio.h"
-#include "gromacs/timing/wallcycle.h"
-#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/gmxpreprocess/compute_io.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/ebin.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/shellfc.h"
+#include "gromacs/legacyheaders/sighandler.h"
+#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/vcm.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/constr.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/fcdata.h"
+#include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/legacyheaders/types/globsig.h"
+#include "gromacs/legacyheaders/types/group.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/interaction_const.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
+#include "gromacs/legacyheaders/types/membedt.h"
+#include "gromacs/legacyheaders/types/nrnb.h"
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/legacyheaders/types/shellfc.h"
+#include "gromacs/legacyheaders/types/state.h"
+#include "gromacs/listed-forces/manage-threading.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/swap/swapcoords.h"
-#include "gromacs/imd/imd.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/real.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "deform.h"
+#include "membed.h"
+#include "repl_ex.h"
#ifdef GMX_FAHCORE
#include "corewrap.h"
gmx_int64_t *step_rel, t_inputrec *ir,
gmx_wallcycle_t wcycle, t_nrnb *nrnb,
gmx_walltime_accounting_t walltime_accounting,
- nbnxn_cuda_ptr_t cu_nbv)
+ struct nonbonded_verlet_t *nbv)
{
char sbuf[STEPSTRSIZE];
md_print_warn(cr, fplog, "step %s: resetting all time and cycle counters\n",
gmx_step_str(step, sbuf));
- if (cu_nbv)
- {
- nbnxn_cuda_reset_timings(cu_nbv);
- }
+ nbnxn_cuda_reset_timings(nbv);
wallcycle_stop(wcycle, ewcRUN);
wallcycle_reset_all(wcycle);
t_trxstatus *status;
rvec mu_tot;
t_vcm *vcm;
- t_state *bufstate = NULL;
- matrix *scale_tot, pcoupl_mu, M, ebox;
- gmx_nlheur_t nlh;
+ matrix pcoupl_mu, M;
t_trxframe rerun_fr;
gmx_repl_ex_t repl_ex = NULL;
int nchkpt = 1;
gmx_ekindata_t *ekind, *ekind_save;
gmx_shellfc_t shellfc;
int count, nconverged = 0;
- real timestep = 0;
- double tcount = 0;
- gmx_bool bConverged = TRUE, bOK, bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
- gmx_bool bAppend;
+ double tcount = 0;
+ gmx_bool bConverged = TRUE, bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
gmx_bool bResetCountersHalfMaxH = FALSE;
- gmx_bool bVV, bIterativeCase, bFirstIterate, bTemp, bPres, bTrotter;
+ gmx_bool bVV, bTemp, bPres, bTrotter;
gmx_bool bUpdateDoLR;
real dvdl_constr;
rvec *cbuf = NULL;
int cbuf_nalloc = 0;
matrix lastbox;
- real veta_save, scalevir, tracevir;
- real vetanew = 0;
int lamnew = 0;
/* for FEP */
int nstfep;
double cycles;
real saved_conserved_quantity = 0;
real last_ekin = 0;
- int iter_i;
t_extmass MassQ;
int **trotter_seq;
char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
int handled_stop_condition = gmx_stop_cond_none; /* compare to get_stop_condition*/
- gmx_iterate_t iterate;
- gmx_int64_t multisim_nsteps = -1; /* number of steps to do before first multisim
+ gmx_int64_t multisim_nsteps = -1; /* number of steps to do before first multisim
simulation stops. If equal to zero, don't
communicate any more between multisims.*/
/* PME load balancing data for GPU kernels */
/* Check for special mdrun options */
bRerunMD = (Flags & MD_RERUN);
- bAppend = (Flags & MD_APPENDFILES);
if (Flags & MD_RESETCOUNTERSHALFWAY)
{
if (ir->nsteps > 0)
/* md-vv uses averaged full step velocities for T-control
md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
- bVV = EI_VV(ir->eI);
- /* all the iteratative cases - only if there are constraints */
- bIterativeCase = ((IR_NPH_TROTTER(ir) || IR_NPT_TROTTER(ir)) && (constr) && (!bRerunMD));
- gmx_iterate_init(&iterate, FALSE); /* The default value of iterate->bIterationActive is set to
- false in this step. The correct value, true or false,
- is set at each step, as it depends on the frequency of temperature
- and pressure control.*/
+ bVV = EI_VV(ir->eI);
bTrotter = (bVV && (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir) || IR_NVT_TROTTER(ir)));
if (bRerunMD)
gmx_fatal(FARGS, "Normal Mode analysis is not supported with virtual sites.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
}
- if (bRerunMD && fr->cutoff_scheme == ecutsVERLET && ir->opts.ngener > 1 && fr->nbv && fr->nbv->bUseGPU)
+ if (bRerunMD && fr->cutoff_scheme == ecutsVERLET && ir->opts.ngener > 1 && usingGpu(fr->nbv))
{
gmx_fatal(FARGS, "The Verlet scheme on GPUs does not support energy groups, so your rerun should probably use a .tpr file without energy groups, or mdrun -nb auto");
}
*/
if ((Flags & MD_TUNEPME) &&
EEL_PME(fr->eeltype) &&
- ( (fr->cutoff_scheme == ecutsVERLET && fr->nbv->bUseGPU) || !(cr->duty & DUTY_PME)) &&
+ ( use_GPU(fr->nbv) || !(cr->duty & DUTY_PME)) &&
!bRerunMD)
{
pme_loadbal_init(&pme_loadbal, ir, state->box, fr->ic, fr->pmedata);
and there is no previous step */
}
- /* if using an iterative algorithm, we need to create a working directory for the state. */
- if (bIterativeCase)
- {
- bufstate = init_bufstate(state);
- }
-
/* need to make an initiation call to get the Trotter variables set, as well as other constants for non-trotter
temperature control */
trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
bStateFromTPX = !bStateFromCP;
bInitStep = bFirstStep && (bStateFromTPX || bVV);
bStartingFromCpt = (Flags & MD_STARTFROMCPT) && bInitStep;
- bLastStep = FALSE;
bSumEkinhOld = FALSE;
- bDoReplEx = FALSE;
bExchanged = FALSE;
bNeedRepartition = FALSE;
step = ir->init_step;
step_rel = 0;
- if (ir->nstlist == -1)
- {
- init_nlistheuristics(&nlh, bGStatEveryStep, step);
- }
-
if (MULTISIM(cr) && (repl_ex_nst <= 0 ))
{
/* check how many steps are left in other sims */
/* Determine whether or not to do Neighbour Searching and LR */
bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
- bNS = (bFirstStep || bExchanged || bNeedRepartition || bNStList || bDoFEP ||
- (ir->nstlist == -1 && nlh.nabnsb > 0));
-
- if (bNS && ir->nstlist == -1)
- {
- set_nlistheuristics(&nlh, bFirstStep || bExchanged || bNeedRepartition || bDoFEP, step);
- }
+ bNS = (bFirstStep || bExchanged || bNeedRepartition || bNStList || bDoFEP);
}
/* check whether we should stop because another simulation has
/* Do we need global communication ? */
bGStat = (bCalcVir || bCalcEner || bStopCM ||
- do_per_step(step, nstglobalcomm) || (bVV && IR_NVT_TROTTER(ir) && do_per_step(step-1, nstglobalcomm)) ||
- (ir->nstlist == -1 && !bRerunMD && step >= nlh.step_nscheck));
+ do_per_step(step, nstglobalcomm) ||
+ (bVV && IR_NVT_TROTTER(ir) && do_per_step(step-1, nstglobalcomm)));
do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
ekind, M, upd, bInitStep, etrtVELOCITY1,
cr, nrnb, constr, &top->idef);
- if (bIterativeCase && do_per_step(step-1, ir->nstpcouple) && !bInitStep)
- {
- gmx_iterate_init(&iterate, TRUE);
- }
- /* for iterations, we save these vectors, as we will be self-consistently iterating
- the calculations */
-
- /*#### UPDATE EXTENDED VARIABLES IN TROTTER FORMULATION */
-
- /* save the state */
- if (iterate.bIterationActive)
- {
- copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
- }
-
- bFirstIterate = TRUE;
- while (bFirstIterate || iterate.bIterationActive)
+ /* TODO remove the brace below, once iteration is removed */
{
- if (iterate.bIterationActive)
- {
- copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
- if (bFirstIterate && bTrotter)
- {
- /* The first time through, we need a decent first estimate
- of veta(t+dt) to compute the constraints. Do
- this by computing the box volume part of the
- trotter integration at this time. Nothing else
- should be changed by this routine here. If
- !(first time), we start with the previous value
- of veta. */
-
- veta_save = state->veta;
- trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ0);
- vetanew = state->veta;
- state->veta = veta_save;
- }
- }
-
- bOK = TRUE;
if (!bRerunMD || rerun_fr.bV || bForceUpdate) /* Why is rerun_fr.bV here? Unclear. */
{
wallcycle_stop(wcycle, ewcUPDATE);
- update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+ update_constraints(fplog, step, NULL, ir, mdatoms,
state, fr->bMolPBC, graph, f,
&top->idef, shake_vir,
cr, nrnb, wcycle, upd, constr,
- TRUE, bCalcVir, vetanew);
+ TRUE, bCalcVir);
wallcycle_start(wcycle, ewcUPDATE);
-
if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
{
/* Correct the virial for multiple time stepping */
m_sub(shake_vir, fr->vir_twin_constr, shake_vir);
}
-
- if (!bOK)
- {
- gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
- }
-
}
else if (graph)
{
called in the previous step */
unshift_self(graph, state->box, state->x);
}
-
/* if VV, compute the pressure and constraints */
/* For VV2, we strictly only need this if using pressure
* control, but we really would like to have accurate pressures
/*bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK && IR_NPT_TROTTER(ir)));*/
bPres = TRUE;
bTemp = ((ir->eI == eiVV && (!bInitStep)) || (ir->eI == eiVVAK));
- if (bCalcEner && ir->eI == eiVVAK) /*MRS: 7/9/2010 -- this still doesn't fix it?*/
+ if (bCalcEner && ir->eI == eiVVAK)
{
bSumEkinhOld = TRUE;
}
| (bTemp ? CGLO_TEMPERATURE : 0)
| (bPres ? CGLO_PRESSURE : 0)
| (bPres ? CGLO_CONSTRAINT : 0)
- | ((iterate.bIterationActive) ? CGLO_ITERATE : 0)
- | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
| CGLO_SCALEEKIN
);
/* explanation of above:
}
}
}
-
- if (iterate.bIterationActive &&
- done_iterating(cr, fplog, step, &iterate, bFirstIterate,
- state->veta, &vetanew))
- {
- break;
- }
- bFirstIterate = FALSE;
}
-
+ /* TODO remove the brace above, once iteration is removed */
if (bTrotter && !bInitStep)
{
copy_mat(shake_vir, state->svir_prev);
wallcycle_stop(wcycle, ewcUPDATE);
}
- /* MRS -- now done iterating -- compute the conserved quantity */
+ /* compute the conserved quantity */
if (bVV)
{
saved_conserved_quantity = compute_conserved_from_auxiliary(ir, state, &MassQ);
gs.sig[eglsRESETCOUNTERS] = 1;
}
- if (ir->nstlist == -1 && !bRerunMD)
- {
- /* When bGStatEveryStep=FALSE, global_stat is only called
- * when we check the atom displacements, not at NS steps.
- * This means that also the bonded interaction count check is not
- * performed immediately after NS. Therefore a few MD steps could
- * be performed with missing interactions.
- * But wrong energies are never written to file,
- * since energies are only written after global_stat
- * has been called.
- */
- if (step >= nlh.step_nscheck)
- {
- nlh.nabnsb = natoms_beyond_ns_buffer(ir, fr, &top->cgs,
- nlh.scale_tot, state->x);
- }
- else
- {
- /* This is not necessarily true,
- * but step_nscheck is determined quite conservatively.
- */
- nlh.nabnsb = 0;
- }
- }
-
/* In parallel we only have to check for checkpointing in steps
* where we do global communication,
* otherwise the other nodes don't know.
/* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
if (constr && bIfRandomize)
{
- update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+ update_constraints(fplog, step, NULL, ir, mdatoms,
state, fr->bMolPBC, graph, f,
&top->idef, tmp_vir,
cr, nrnb, wcycle, upd, constr,
- TRUE, bCalcVir, vetanew);
+ TRUE, bCalcVir);
}
}
}
-
- if (bIterativeCase && do_per_step(step, ir->nstpcouple))
- {
- gmx_iterate_init(&iterate, TRUE);
- /* for iterations, we save these vectors, as we will be redoing the calculations */
- copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
- }
-
- bFirstIterate = TRUE;
- while (bFirstIterate || iterate.bIterationActive)
+ /* TODO remove the brace below, once iteration is removed */
{
- /* We now restore these vectors to redo the calculation with improved extended variables */
- if (iterate.bIterationActive)
- {
- copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
- }
-
- /* We make the decision to break or not -after- the calculation of Ekin and Pressure,
- so scroll down for that logic */
-
/* ######### START SECOND UPDATE STEP ################# */
/* Box is changed in update() when we do pressure coupling,
* but we should still use the old box for energy corrections and when
*/
copy_mat(state->box, lastbox);
- bOK = TRUE;
dvdl_constr = 0;
- if (!(bRerunMD && !rerun_fr.bV && !bForceUpdate))
+ if (!bRerunMD || rerun_fr.bV || bForceUpdate)
{
wallcycle_start(wcycle, ewcUPDATE);
/* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
if (bTrotter)
{
- if (iterate.bIterationActive)
- {
- if (bFirstIterate)
- {
- scalevir = 1;
- }
- else
- {
- /* we use a new value of scalevir to converge the iterations faster */
- scalevir = tracevir/trace(shake_vir);
- }
- msmul(shake_vir, scalevir, shake_vir);
- m_add(force_vir, shake_vir, total_vir);
- clear_mat(shake_vir);
- }
trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
/* We can only do Berendsen coupling after we have summed
* the kinetic energy or virial. Since the happens
ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
wallcycle_stop(wcycle, ewcUPDATE);
- update_constraints(fplog, step, &dvdl_constr, ir, ekind, mdatoms, state,
+ update_constraints(fplog, step, &dvdl_constr, ir, mdatoms, state,
fr->bMolPBC, graph, f,
&top->idef, shake_vir,
cr, nrnb, wcycle, upd, constr,
- FALSE, bCalcVir, state->veta);
+ FALSE, bCalcVir);
if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
{
* to numerical errors, or are they important
* physically? I'm thinking they are just errors, but not completely sure.
* For now, will call without actually constraining, constr=NULL*/
- update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+ update_constraints(fplog, step, NULL, ir, mdatoms,
state, fr->bMolPBC, graph, f,
&top->idef, tmp_vir,
cr, nrnb, wcycle, upd, NULL,
- FALSE, bCalcVir,
- state->veta);
- }
- if (!bOK)
- {
- gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
- }
-
- if (fr->bSepDVDL && fplog && do_log)
- {
- gmx_print_sepdvdl(fplog, "Constraint dV/dl", 0.0, dvdl_constr);
+ FALSE, bCalcVir);
}
if (bVV)
{
*/
if (bGStat || (!EI_VV(ir->eI) && do_per_step(step+1, nstglobalcomm)))
{
- if (ir->nstlist == -1 && bFirstIterate)
- {
- gs.sig[eglsNABNSB] = nlh.nabnsb;
- }
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
- constr,
- bFirstIterate ? &gs : NULL,
+ constr, &gs,
(step_rel % gs.nstms == 0) &&
(multisim_nsteps < 0 || (step_rel < multisim_nsteps)),
lastbox,
| (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
| (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
| (!EI_VV(ir->eI) || bRerunMD ? CGLO_PRESSURE : 0)
- | (iterate.bIterationActive ? CGLO_ITERATE : 0)
- | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
| CGLO_CONSTRAINT
);
- if (ir->nstlist == -1 && bFirstIterate)
- {
- nlh.nabnsb = gs.set[eglsNABNSB];
- gs.set[eglsNABNSB] = 0;
- }
}
- /* bIterate is set to keep it from eliminating the old ekin kinetic energy terms */
+
/* ############# END CALC EKIN AND PRESSURE ################# */
/* Note: this is OK, but there are some numerical precision issues with using the convergence of
the virial that should probably be addressed eventually. state->veta has better properies,
but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
-
- if (iterate.bIterationActive &&
- done_iterating(cr, fplog, step, &iterate, bFirstIterate,
- trace(shake_vir), &tracevir))
- {
- break;
- }
- bFirstIterate = FALSE;
}
+ /* TODO remove the brace above, once iteration is removed */
if (!bVV || bRerunMD)
{
- /* sum up the foreign energy and dhdl terms for md and sd. currently done every step so that dhdl is correct in the .edr */
+ /* Sum up the foreign energy and dhdl terms for md and sd.
+ Currently done every step so that dhdl is correct in the .edr */
sum_dhdl(enerd, state->lambda, ir->fepvals);
}
update_box(fplog, step, ir, mdatoms, state, f,
- ir->nstlist == -1 ? &nlh.scale_tot : NULL, pcoupl_mu, nrnb, upd);
+ pcoupl_mu, nrnb, upd);
/* ################# END UPDATE STEP 2 ################# */
/* #### We now have r(t+dt) and v(t+dt/2) ############# */
dd_bcast(cr->dd, sizeof(gmx_bool), &bPMETuneRunning);
if (bPMETuneRunning &&
- fr->nbv->bUseGPU && DOMAINDECOMP(cr) &&
+ use_GPU(fr->nbv) && DOMAINDECOMP(cr) &&
!(cr->duty & DUTY_PME))
{
/* Lock DLB=auto to off (does nothing when DLB=yes/no).
{
/* Reset all the counters related to performance over the run */
reset_all_counters(fplog, cr, step, &step_rel, ir, wcycle, nrnb, walltime_accounting,
- fr->nbv != NULL && fr->nbv->bUseGPU ? fr->nbv->cu_nbv : NULL);
+ use_GPU(fr->nbv) ? fr->nbv : NULL);
wcycle_set_reset_counters(wcycle, -1);
if (!(cr->duty & DUTY_PME))
{
done_mdoutf(outf);
debug_gmx();
- if (ir->nstlist == -1 && nlh.nns > 0 && fplog)
- {
- fprintf(fplog, "Average neighborlist lifetime: %.1f steps, std.dev.: %.1f steps\n", nlh.s1/nlh.nns, sqrt(nlh.s2/nlh.nns - sqr(nlh.s1/nlh.nns)));
- fprintf(fplog, "Average number of atoms that crossed the half buffer length: %.1f\n\n", nlh.ab/nlh.nns);
- }
-
if (pme_loadbal != NULL)
{
pme_loadbal_done(pme_loadbal, cr, fplog,
- fr->nbv != NULL && fr->nbv->bUseGPU);
+ use_GPU(fr->nbv));
}
if (shellfc && fplog)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "mdrun_main.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
#include "config.h"
-#endif
#include <stdio.h>
+#include <string.h>
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/filenm.h"
#include "gromacs/legacyheaders/checkpoint.h"
#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/main.h"
#include "gromacs/legacyheaders/mdrun.h"
#include "gromacs/legacyheaders/readinp.h"
#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/utility/fatalerror.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/filenm.h"
+#include "mdrun_main.h"
+
+static bool is_multisim_option_set(int argc, const char *const argv[])
+{
+ for (int i = 0; i < argc; ++i)
+ {
+ if (strcmp(argv[i], "-multi") == 0 || strcmp(argv[i], "-multidir") == 0)
+ {
+ return true;
+ }
+ }
+ return false;
+}
int gmx_mdrun(int argc, char *argv[])
{
"The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
"and distributes the topology over ranks if needed.",
"[TT]mdrun[tt] produces at least four output files.",
- "A single log file ([TT]-g[tt]) is written, unless the option",
- "[TT]-seppot[tt] is used, in which case each rank writes a log file.",
+ "A single log file ([TT]-g[tt]) is written.",
"The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
"optionally forces.",
"The structure file ([TT]-c[tt]) contains the coordinates and",
"([TT]-x[tt]).[PAR]",
"The option [TT]-dhdl[tt] is only used when free energy calculation is",
"turned on.[PAR]",
- "A simulation can be run in parallel using two different parallelization",
- "schemes: MPI parallelization and/or OpenMP thread parallelization.",
- "The MPI parallelization uses multiple processes when [TT]mdrun[tt] is",
- "compiled with a normal MPI library or threads when [TT]mdrun[tt] is",
- "compiled with the GROMACS built-in thread-MPI library. OpenMP threads",
- "are supported when [TT]mdrun[tt] is compiled with OpenMP. Full OpenMP support",
- "is only available with the Verlet cut-off scheme, with the (older)",
- "group scheme only PME-only ranks can use OpenMP parallelization.",
- "In all cases [TT]mdrun[tt] will by default try to use all the available",
- "hardware resources. With a normal MPI library only the options",
- "[TT]-ntomp[tt] (with the Verlet cut-off scheme) and [TT]-ntomp_pme[tt],",
- "for PME-only ranks, can be used to control the number of threads.",
- "With thread-MPI there are additional options [TT]-nt[tt], which sets",
- "the total number of threads, and [TT]-ntmpi[tt], which sets the number",
- "of thread-MPI threads.",
- "The number of OpenMP threads used by [TT]mdrun[tt] can also be set with",
- "the standard environment variable, [TT]OMP_NUM_THREADS[tt].",
- "The [TT]GMX_PME_NUM_THREADS[tt] environment variable can be used to specify",
- "the number of threads used by the PME-only ranks.[PAR]",
- "Note that combined MPI+OpenMP parallelization is in many cases",
- "slower than either on its own. However, at high parallelization, using the",
- "combination is often beneficial as it reduces the number of domains and/or",
- "the number of MPI ranks. (Less and larger domains can improve scaling,",
- "with separate PME ranks, using fewer MPI ranks reduces communication costs.)",
- "OpenMP-only parallelization is typically faster than MPI-only parallelization",
- "on a single CPU(-die). Since we currently don't have proper hardware",
- "topology detection, [TT]mdrun[tt] compiled with thread-MPI will only",
- "automatically use OpenMP-only parallelization when you use up to 4",
- "threads, up to 12 threads with Intel Nehalem/Westmere, or up to 16",
- "threads with Intel Sandy Bridge or newer CPUs. Otherwise MPI-only",
- "parallelization is used (except with GPUs, see below).",
- "[PAR]",
- "To quickly test the performance of the new Verlet cut-off scheme",
- "with old [TT].tpr[tt] files, either on CPUs or CPUs+GPUs, you can use",
- "the [TT]-testverlet[tt] option. This should not be used for production,",
- "since it can slightly modify potentials and it will remove charge groups",
- "making analysis difficult, as the [TT].tpr[tt] file will still contain",
- "charge groups. For production simulations it is highly recommended",
- "to specify [TT]cutoff-scheme = Verlet[tt] in the [TT].mdp[tt] file.",
- "[PAR]",
- "With GPUs (only supported with the Verlet cut-off scheme), the number",
- "of GPUs should match the number of particle-particle ranks, i.e.",
- "excluding PME-only ranks. With thread-MPI, unless set on the command line, the number",
- "of MPI threads will automatically be set to the number of GPUs detected.",
- "To use a subset of the available GPUs, or to manually provide a mapping of",
- "GPUs to PP ranks, you can use the [TT]-gpu_id[tt] option. The argument of [TT]-gpu_id[tt] is",
- "a string of digits (without delimiter) representing device id-s of the GPUs to be used.",
- "For example, \"[TT]02[tt]\" specifies using GPUs 0 and 2 in the first and second PP ranks per compute node",
- "respectively. To select different sets of GPU-s",
- "on different nodes of a compute cluster, use the [TT]GMX_GPU_ID[tt] environment",
- "variable instead. The format for [TT]GMX_GPU_ID[tt] is identical to ",
- "[TT]-gpu_id[tt], with the difference that an environment variable can have",
- "different values on different compute nodes. Multiple MPI ranks on each node",
- "can share GPUs. This is accomplished by specifying the id(s) of the GPU(s)",
- "multiple times, e.g. \"[TT]0011[tt]\" for four ranks sharing two GPUs in this node.",
- "This works within a single simulation, or a multi-simulation, with any form of MPI.",
- "[PAR]",
- "With the Verlet cut-off scheme and verlet-buffer-tolerance set,",
- "the pair-list update interval nstlist can be chosen freely with",
- "the option [TT]-nstlist[tt]. [TT]mdrun[tt] will then adjust",
- "the pair-list cut-off to maintain accuracy, and not adjust nstlist.",
- "Otherwise, by default, [TT]mdrun[tt] will try to increase the",
- "value of nstlist set in the [TT].mdp[tt] file to improve the",
- "performance. For CPU-only runs, nstlist might increase to 20, for",
- "GPU runs up to 40. For medium to high parallelization or with",
- "fast GPUs, a (user-supplied) larger nstlist value can give much",
- "better performance.",
- "[PAR]",
- "When using PME with separate PME ranks or with a GPU, the two major",
- "compute tasks, the non-bonded force calculation and the PME calculation",
- "run on different compute resources. If this load is not balanced,",
- "some of the resources will be idle part of time. With the Verlet",
- "cut-off scheme this load is automatically balanced when the PME load",
- "is too high (but not when it is too low). This is done by scaling",
- "the Coulomb cut-off and PME grid spacing by the same amount. In the first",
- "few hundred steps different settings are tried and the fastest is chosen",
- "for the rest of the simulation. This does not affect the accuracy of",
- "the results, but it does affect the decomposition of the Coulomb energy",
- "into particle and mesh contributions. The auto-tuning can be turned off",
- "with the option [TT]-notunepme[tt].",
- "[PAR]",
- "[TT]mdrun[tt] pins (sets affinity of) threads to specific cores,",
- "when all (logical) cores on a compute node are used by [TT]mdrun[tt],",
- "even when no multi-threading is used,",
- "as this usually results in significantly better performance.",
- "If the queuing systems or the OpenMP library pinned threads, we honor",
- "this and don't pin again, even though the layout may be sub-optimal.",
- "If you want to have [TT]mdrun[tt] override an already set thread affinity",
- "or pin threads when using less cores, use [TT]-pin on[tt].",
- "With SMT (simultaneous multithreading), e.g. Intel Hyper-Threading,",
- "there are multiple logical cores per physical core.",
- "The option [TT]-pinstride[tt] sets the stride in logical cores for",
- "pinning consecutive threads. Without SMT, 1 is usually the best choice.",
- "With Intel Hyper-Threading 2 is best when using half or less of the",
- "logical cores, 1 otherwise. The default value of 0 do exactly that:",
- "it minimizes the threads per logical core, to optimize performance.",
- "If you want to run multiple [TT]mdrun[tt] jobs on the same physical node,"
- "you should set [TT]-pinstride[tt] to 1 when using all logical cores.",
- "When running multiple [TT]mdrun[tt] (or other) simulations on the same physical",
- "node, some simulations need to start pinning from a non-zero core",
- "to avoid overloading cores; with [TT]-pinoffset[tt] you can specify",
- "the offset in logical cores for pinning.",
- "[PAR]",
- "When [TT]mdrun[tt] is started with more than 1 rank,",
- "parallelization with domain decomposition is used.",
- "[PAR]",
- "With domain decomposition, the spatial decomposition can be set",
- "with option [TT]-dd[tt]. By default [TT]mdrun[tt] selects a good decomposition.",
- "The user only needs to change this when the system is very inhomogeneous.",
- "Dynamic load balancing is set with the option [TT]-dlb[tt],",
- "which can give a significant performance improvement,",
- "especially for inhomogeneous systems. The only disadvantage of",
- "dynamic load balancing is that runs are no longer binary reproducible,",
- "but in most cases this is not important.",
- "By default the dynamic load balancing is automatically turned on",
- "when the measured performance loss due to load imbalance is 5% or more.",
- "At low parallelization these are the only important options",
- "for domain decomposition.",
- "At high parallelization the options in the next two sections",
- "could be important for increasing the performace.",
- "[PAR]",
- "When PME is used with domain decomposition, separate ranks can",
- "be assigned to do only the PME mesh calculation;",
- "this is computationally more efficient starting at about 12 ranks,",
- "or even fewer when OpenMP parallelization is used.",
- "The number of PME ranks is set with option [TT]-npme[tt],",
- "but this cannot be more than half of the ranks.",
- "By default [TT]mdrun[tt] makes a guess for the number of PME",
- "ranks when the number of ranks is larger than 16. With GPUs,",
- "using separate PME ranks is not selected automatically,",
- "since the optimal setup depends very much on the details",
- "of the hardware. In all cases, you might gain performance",
- "by optimizing [TT]-npme[tt]. Performance statistics on this issue",
- "are written at the end of the log file.",
- "For good load balancing at high parallelization, the PME grid x and y",
- "dimensions should be divisible by the number of PME ranks",
- "(the simulation will run correctly also when this is not the case).",
- "[PAR]",
- "This section lists all options that affect the domain decomposition.",
- "[PAR]",
- "Option [TT]-rdd[tt] can be used to set the required maximum distance",
- "for inter charge-group bonded interactions.",
- "Communication for two-body bonded interactions below the non-bonded",
- "cut-off distance always comes for free with the non-bonded communication.",
- "Atoms beyond the non-bonded cut-off are only communicated when they have",
- "missing bonded interactions; this means that the extra cost is minor",
- "and nearly indepedent of the value of [TT]-rdd[tt].",
- "With dynamic load balancing option [TT]-rdd[tt] also sets",
- "the lower limit for the domain decomposition cell sizes.",
- "By default [TT]-rdd[tt] is determined by [TT]mdrun[tt] based on",
- "the initial coordinates. The chosen value will be a balance",
- "between interaction range and communication cost.",
- "[PAR]",
- "When inter charge-group bonded interactions are beyond",
- "the bonded cut-off distance, [TT]mdrun[tt] terminates with an error message.",
- "For pair interactions and tabulated bonds",
- "that do not generate exclusions, this check can be turned off",
- "with the option [TT]-noddcheck[tt].",
- "[PAR]",
- "When constraints are present, option [TT]-rcon[tt] influences",
- "the cell size limit as well.",
- "Atoms connected by NC constraints, where NC is the LINCS order plus 1,",
- "should not be beyond the smallest cell size. A error message is",
- "generated when this happens and the user should change the decomposition",
- "or decrease the LINCS order and increase the number of LINCS iterations.",
- "By default [TT]mdrun[tt] estimates the minimum cell size required for P-LINCS",
- "in a conservative fashion. For high parallelization it can be useful",
- "to set the distance required for P-LINCS with the option [TT]-rcon[tt].",
- "[PAR]",
- "The [TT]-dds[tt] option sets the minimum allowed x, y and/or z scaling",
- "of the cells with dynamic load balancing. [TT]mdrun[tt] will ensure that",
- "the cells can scale down by at least this factor. This option is used",
- "for the automated spatial decomposition (when not using [TT]-dd[tt])",
- "as well as for determining the number of grid pulses, which in turn",
- "sets the minimum allowed cell size. Under certain circumstances",
- "the value of [TT]-dds[tt] might need to be adjusted to account for",
- "high or low spatial inhomogeneity of the system.",
- "[PAR]",
- "The option [TT]-gcom[tt] can be used to only do global communication",
- "every n steps.",
- "This can improve performance for highly parallel simulations",
- "where this global communication step becomes the bottleneck.",
- "For a global thermostat and/or barostat the temperature",
- "and/or pressure will also only be updated every [TT]-gcom[tt] steps.",
- "By default it is set to the minimum of nstcalcenergy and nstlist.[PAR]",
- "With [TT]-rerun[tt] an input trajectory can be given for which ",
- "forces and energies will be (re)calculated. Neighbor searching will be",
- "performed for every frame, unless [TT]nstlist[tt] is zero",
- "(see the [TT].mdp[tt] file).[PAR]",
+ "Running mdrun efficiently in parallel is a complex topic topic,",
+ "many aspects of which are covered in the online User Guide. You",
+ "should look there for practical advice on using many of the options",
+ "available in mdrun.[PAR]",
"ED (essential dynamics) sampling and/or additional flooding potentials",
"are switched on by using the [TT]-ei[tt] flag followed by an [TT].edi[tt]",
"file. The [TT].edi[tt] file can be produced with the [TT]make_edi[tt] tool",
"The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
"coordinates and forces when pulling is selected",
"in the [TT].mdp[tt] file.[PAR]",
- "With [TT]-multi[tt] or [TT]-multidir[tt], multiple systems can be ",
- "simulated in parallel.",
- "As many input files/directories are required as the number of systems. ",
- "The [TT]-multidir[tt] option takes a list of directories (one for each ",
- "system) and runs in each of them, using the input/output file names, ",
- "such as specified by e.g. the [TT]-s[tt] option, relative to these ",
- "directories.",
- "With [TT]-multi[tt], the system number is appended to the run input ",
- "and each output filename, for instance [TT]topol.tpr[tt] becomes",
- "[TT]topol0.tpr[tt], [TT]topol1.tpr[tt] etc.",
- "The number of ranks per system is the total number of ranks",
- "divided by the number of systems.",
- "One use of this option is for NMR refinement: when distance",
- "or orientation restraints are present these can be ensemble averaged",
- "over all the systems.[PAR]",
- "With [TT]-replex[tt] replica exchange is attempted every given number",
- "of steps. The number of replicas is set with the [TT]-multi[tt] or ",
- "[TT]-multidir[tt] option, described above.",
- "All run input files should use a different coupling temperature,",
- "the order of the files is not important. The random seed is set with",
- "[TT]-reseed[tt]. The velocities are scaled and neighbor searching",
- "is performed after every exchange.[PAR]",
"Finally some experimental algorithms can be tested when the",
"appropriate options have been given. Currently under",
"investigation are: polarizability.",
"[PAR]",
"With option [TT]-maxh[tt] a simulation is terminated and a checkpoint",
"file is written at the first neighbor search step where the run time",
- "exceeds [TT]-maxh[tt]*0.99 hours.",
+ "exceeds [TT]-maxh[tt]*0.99 hours. This option is particularly useful in",
+ "combination with setting [TT]nsteps[tt] to -1 either in the mdp or using the",
+ "similarly named command line option. This results in an infinite run,",
+ "terminated only when the time limit set by [TT]-maxh[tt] is reached (if any)"
+ "or upon receiving a signal."
"[PAR]",
"When [TT]mdrun[tt] receives a TERM signal, it will set nsteps to the current",
"step plus one. When [TT]mdrun[tt] receives an INT signal (e.g. when ctrl+C is",
};
t_commrec *cr;
t_filenm fnm[] = {
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efTRN, "-o", NULL, ffWRITE },
{ efCOMPRESSED, "-x", NULL, ffOPTWR },
- { efCPT, "-cpi", NULL, ffOPTRD },
+ { efCPT, "-cpi", NULL, ffOPTRD | ffALLOW_MISSING },
{ efCPT, "-cpo", NULL, ffOPTWR },
{ efSTO, "-c", "confout", ffWRITE },
{ efEDR, "-e", "ener", ffWRITE },
gmx_bool bDDBondCheck = TRUE;
gmx_bool bDDBondComm = TRUE;
gmx_bool bTunePME = TRUE;
- gmx_bool bTestVerlet = FALSE;
gmx_bool bVerbose = FALSE;
gmx_bool bCompact = TRUE;
- gmx_bool bSepPot = FALSE;
gmx_bool bRerunVSite = FALSE;
gmx_bool bConfout = TRUE;
gmx_bool bReproducible = FALSE;
{ "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
"Number of OpenMP threads per MPI rank to start (0 is -ntomp)" },
{ "-pin", FALSE, etENUM, {thread_aff_opt},
- "Set thread affinities" },
+ "Whether mdrun should try to set thread affinities" },
{ "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
- "The starting logical core number for pinning to cores; used to avoid pinning threads from different mdrun instances to the same core" },
+ "The lowest logical core number to which mdrun should pin the first thread" },
{ "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
"Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
{ "-gpu_id", FALSE, etSTR, {&hw_opt.gpu_opt.gpu_id},
"Set nstlist when using a Verlet buffer tolerance (0 is guess)" },
{ "-tunepme", FALSE, etBOOL, {&bTunePME},
"Optimize PME load between PP/PME ranks or GPU/CPU" },
- { "-testverlet", FALSE, etBOOL, {&bTestVerlet},
- "Test the Verlet non-bonded scheme" },
{ "-v", FALSE, etBOOL, {&bVerbose},
"Be loud and noisy" },
{ "-compact", FALSE, etBOOL, {&bCompact},
"Write a compact log file" },
- { "-seppot", FALSE, etBOOL, {&bSepPot},
- "Write separate V and dVdl terms for each interaction type and rank to the log file(s)" },
{ "-pforce", FALSE, etREAL, {&pforce},
"Print all forces larger than this (kJ/mol nm)" },
{ "-reprod", FALSE, etBOOL, {&bReproducible},
{ "-append", FALSE, etBOOL, {&bAppendFiles},
"Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
{ "-nsteps", FALSE, etINT64, {&nsteps},
- "Run this number of steps, overrides .mdp file option" },
+ "Run this number of steps, overrides .mdp file option (-1 means infinite, -2 means use mdp option, smaller is invalid)" },
{ "-maxh", FALSE, etREAL, {&max_hours},
"Terminate after 0.99 times this time (hours)" },
{ "-multi", FALSE, etINT, {&nmultisim},
{ "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
"HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
};
- unsigned long Flags, PCA_Flags;
+ unsigned long Flags;
ivec ddxyz;
int dd_node_order;
gmx_bool bAddPart;
int rc;
char **multidir = NULL;
-
cr = init_commrec();
- PCA_Flags = (PCA_CAN_SET_DEFFNM | (MASTER(cr) ? 0 : PCA_QUIET));
+ unsigned long PCA_Flags = PCA_CAN_SET_DEFFNM;
+ // With -multi or -multidir, the file names are going to get processed
+ // further (or the working directory changed), so we can't check for their
+ // existence during parsing. It isn't useful to do any completion based on
+ // file system contents, either.
+ if (is_multisim_option_set(argc, argv))
+ {
+ PCA_Flags |= PCA_DISABLE_INPUT_FILE_CHECKING;
+ }
/* Comment this in to do fexist calls only on master
* works not with rerun or tables at the moment
sim_part_fn = sim_part;
if (opt2bSet("-cpi", NFILE, fnm))
{
- if (bSepPot && bAppendFiles)
- {
- gmx_fatal(FARGS, "Output file appending is not supported with -seppot");
- }
-
bAppendFiles =
read_checkpoint_simulation_part(opt2fn_master("-cpi", NFILE,
fnm, cr),
}
Flags = opt2bSet("-rerun", NFILE, fnm) ? MD_RERUN : 0;
- Flags = Flags | (bSepPot ? MD_SEPPOT : 0);
Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
Flags = Flags | (bDDBondComm ? MD_DDBONDCOMM : 0);
Flags = Flags | (bTunePME ? MD_TUNEPME : 0);
- Flags = Flags | (bTestVerlet ? MD_TESTVERLET : 0);
Flags = Flags | (bConfout ? MD_CONFOUT : 0);
Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
/* We postpone opening the log file if we are appending, so we can
first truncate the old log file and append to the correct position
there instead. */
- if ((MASTER(cr) || bSepPot) && !bAppendFiles)
+ if (MASTER(cr) && !bAppendFiles)
{
gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr,
- !bSepPot, Flags & MD_APPENDFILES, &fplog);
+ Flags & MD_APPENDFILES, &fplog);
please_cite(fplog, "Hess2008b");
please_cite(fplog, "Spoel2005a");
please_cite(fplog, "Lindahl2001a");
please_cite(fplog, "Berendsen95a");
}
- else if (!MASTER(cr) && bSepPot)
- {
- gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr, !bSepPot, Flags, &fplog);
- }
else
{
fplog = NULL;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "membed.h"
#include <signal.h>
#include <stdlib.h>
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "vec.h"
-#include "macros.h"
-#include "main.h"
-#include "gromacs/fileio/futil.h"
+
#include "gromacs/essentialdynamics/edsam.h"
-#include "index.h"
-#include "physics.h"
-#include "names.h"
-#include "mtop_util.h"
#include "gromacs/fileio/tpxio.h"
-#include "gromacs/utility/cstringutil.h"
-#include "membed.h"
-#include "pbc.h"
-#include "readinp.h"
#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
/* information about scaling center */
typedef struct {
get_input(membed_input, &xy_fac, &xy_max, &z_fac, &z_max, &it_xy, &it_z, &probe_rad, &low_up_rm,
&maxwarn, &pieces, &bALLOW_ASYMMETRY);
- tpr_version = get_tpr_version(ftp2fn(efTPX, nfile, fnm));
+ tpr_version = get_tpr_version(ftp2fn(efTPR, nfile, fnm));
if (tpr_version < membed_version)
{
gmx_fatal(FARGS, "Version of *.tpr file to old (%d). "
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _gmx_membed_h
#define _gmx_membed_h
-#include "typedefs.h"
-#include "types/membedt.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/membedt.h"
#ifdef __cplusplus
extern "C" {
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <math.h>
+#include "gmxpre.h"
+
#include "repl_ex.h"
-#include "network.h"
+
+#include "config.h"
+
+#include <math.h>
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
#include "gromacs/utility/smalloc.h"
-#include "physics.h"
-#include "copyrite.h"
-#include "macros.h"
-#include "vec.h"
-#include "names.h"
-#include "domdec.h"
-#include "gromacs/random/random.h"
#define PROBABILITYCUTOFF 100
/* we don't bother evaluating if events are more rare than exp(-100) = 3.7x10^-44 */
{
real *qall;
gmx_bool bDiff;
- int i, s;
+ int s;
snew(qall, ms->nsim);
qall[re->repl] = q;
const t_inputrec *ir,
int nst, int nex, int init_seed)
{
- real temp, pres;
+ real pres;
int i, j, k;
struct gmx_repl_ex *re;
gmx_bool bTemp;
real time)
{
int m, i, j, a, b, ap, bp, i0, i1, tmp;
- real ediff = 0, delta = 0, dpV = 0;
+ real delta = 0;
gmx_bool bPrint, bMultiEx;
gmx_bool *bEx = re->bEx;
real *prob = re->prob;
gmx_bool bEpot = FALSE;
gmx_bool bDLambda = FALSE;
gmx_bool bVol = FALSE;
- gmx_rng_t rng;
bMultiEx = (re->nex > 1); /* multiple exchanges at each state */
- fprintf(fplog, "Replica exchange at step " "%"GMX_PRId64 " time %.5f\n", step, time);
+ fprintf(fplog, "Replica exchange at step %" GMX_PRId64 " time %.5f\n", step, time);
if (re->bNPT)
{
t_state *state, gmx_enerdata_t *enerd,
t_state *state_local, gmx_int64_t step, real time)
{
- int i, j;
+ int j;
int replica_id = 0;
int exchange_partner;
int maxswap = 0;
#ifndef _repl_ex_h
#define _repl_ex_h
-#include "typedefs.h"
-#include "types/commrec.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
/* Abstract type for replica exchange */
typedef struct gmx_repl_ex *gmx_repl_ex_t;
extern void print_replica_exchange_statistics(FILE *fplog, gmx_repl_ex_t re);
/* Should only be called on the master nodes */
+#ifdef __cplusplus
+}
+#endif
+
#endif /* _repl_ex_h */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include <assert.h>
#include <signal.h>
#include <stdlib.h>
-#ifdef HAVE_UNISTD_H
-#include <unistd.h>
-#endif
#include <string.h>
-#include <assert.h>
-#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "copyrite.h"
-#include "force.h"
-#include "mdrun.h"
-#include "md_logging.h"
-#include "md_support.h"
-#include "network.h"
-#include "names.h"
-#include "disre.h"
-#include "orires.h"
-#include "pme.h"
-#include "mdatoms.h"
-#include "repl_ex.h"
-#include "deform.h"
-#include "qmmm.h"
-#include "domdec.h"
-#include "coulomb.h"
-#include "constr.h"
-#include "mvdata.h"
-#include "checkpoint.h"
-#include "mtop_util.h"
-#include "sighandler.h"
-#include "txtdump.h"
-#include "gmx_detect_hardware.h"
-#include "gmx_omp_nthreads.h"
-#include "gromacs/gmxpreprocess/calc_verletbuf.h"
-#include "gmx_fatal_collective.h"
-#include "membed.h"
-#include "macros.h"
-#include "gmx_thread_affinity.h"
-#include "inputrec.h"
+#include <algorithm>
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/ewald/pme.h"
#include "gromacs/fileio/tpxio.h"
-#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/gmxpreprocess/calc_verletbuf.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/gmx_detect_hardware.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/gmx_thread_affinity.h"
+#include "gromacs/legacyheaders/inputrec.h"
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/sighandler.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/calculate-ewald-splitting-coefficient.h"
+#include "gromacs/math/vec.h"
#include "gromacs/mdlib/nbnxn_consts.h"
-#include "gromacs/timing/wallcycle.h"
-#include "gromacs/utility/gmxmpi.h"
-#include "gromacs/utility/gmxomp.h"
-#include "gromacs/swap/swapcoords.h"
-#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/pulling/pull_rotation.h"
+#include "gromacs/swap/swapcoords.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "deform.h"
+#include "membed.h"
+#include "repl_ex.h"
#ifdef GMX_FAHCORE
#include "corewrap.h"
#endif
-#include "gpu_utils.h"
-#include "nbnxn_cuda_data_mgmt.h"
+#include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
typedef struct {
gmx_integrator_t *func;
else if (hw_opt->nthreads_omp > 0)
{
/* Here we could oversubscribe, when we do, we issue a warning later */
- nthreads_tmpi = max(1, nthreads_tot/hw_opt->nthreads_omp);
+ nthreads_tmpi = std::max(1, nthreads_tot/hw_opt->nthreads_omp);
}
else
{
const int nthreads_omp_always_faster = 4;
const int nthreads_omp_always_faster_Nehalem = 12;
const int nthreads_omp_always_faster_SandyBridge = 16;
- const int first_model_Nehalem = 0x1A;
- const int first_model_SandyBridge = 0x2A;
gmx_bool bIntel_Family6;
bIntel_Family6 =
{
int nthreads_hw, nthreads_tot_max, nthreads_tmpi, nthreads_new, ngpu;
int min_atoms_per_mpi_thread;
- char *env;
- char sbuf[STRLEN];
gmx_bool bCanUseGPU;
if (hw_opt->nthreads_tmpi > 0)
{
/* the thread number was chosen automatically, but there are too many
threads (too few atoms per thread) */
- nthreads_new = max(1, mtop->natoms/min_atoms_per_mpi_thread);
+ nthreads_new = std::max(1, mtop->natoms/min_atoms_per_mpi_thread);
/* Avoid partial use of Hyper-Threading */
if (gmx_cpuid_x86_smt(hwinfo->cpuid_info) == GMX_CPUID_X86_SMT_ENABLED &&
/* We determine the extra cost of the non-bonded kernels compared to
* a reference nstlist value of 10 (which is the default in grompp).
*/
-static const int nbnxn_reference_nstlist = 10;
+static const int nbnxnReferenceNstlist = 10;
/* The values to try when switching */
const int nstlist_try[] = { 20, 25, 40 };
#define NNSTL sizeof(nstlist_try)/sizeof(nstlist_try[0])
float listfac_ok, listfac_max;
int nstlist_orig, nstlist_prev;
verletbuf_list_setup_t ls;
- real rlist_nstlist10, rlist_inc, rlist_ok, rlist_max;
+ real rlistWithReferenceNstlist, rlist_inc, rlist_ok, rlist_max;
real rlist_new, rlist_prev;
- int nstlist_ind = 0;
+ size_t nstlist_ind = 0;
t_state state_tmp;
gmx_bool bBox, bDD, bCont;
const char *nstl_gpu = "\nFor optimal performance with a GPU nstlist (now %d) should be larger.\nThe optimum depends on your CPU and GPU resources.\nYou might want to try several nstlist values.\n";
const char *box_err = "Can not increase nstlist because the box is too small";
const char *dd_err = "Can not increase nstlist because of domain decomposition limitations";
char buf[STRLEN];
+ const float oneThird = 1.0f / 3.0f;
if (nstlist_cmdline <= 0)
{
verletbuf_get_list_setup(bGPU, &ls);
/* Allow rlist to make the list a given factor larger than the list
- * would be with nstlist=10.
+ * would be with the reference value for nstlist (10).
*/
nstlist_prev = ir->nstlist;
- ir->nstlist = 10;
+ ir->nstlist = nbnxnReferenceNstlist;
calc_verlet_buffer_size(mtop, det(box), ir, -1, &ls, NULL,
- &rlist_nstlist10);
+ &rlistWithReferenceNstlist);
ir->nstlist = nstlist_prev;
/* Determine the pair list size increase due to zero interactions */
rlist_inc = nbnxn_get_rlist_effective_inc(ls.cluster_size_j,
mtop->natoms/det(box));
- rlist_ok = (rlist_nstlist10 + rlist_inc)*pow(listfac_ok, 1.0/3.0) - rlist_inc;
- rlist_max = (rlist_nstlist10 + rlist_inc)*pow(listfac_max, 1.0/3.0) - rlist_inc;
+ rlist_ok = (rlistWithReferenceNstlist + rlist_inc)*pow(listfac_ok, oneThird) - rlist_inc;
+ rlist_max = (rlistWithReferenceNstlist + rlist_inc)*pow(listfac_max, oneThird) - rlist_inc;
if (debug)
{
fprintf(debug, "nstlist tuning: rlist_inc %.3f rlist_ok %.3f rlist_max %.3f\n",
}
}
-static void convert_to_verlet_scheme(FILE *fplog,
- t_inputrec *ir,
- gmx_mtop_t *mtop, real box_vol)
-{
- char *conv_mesg = "Converting input file with group cut-off scheme to the Verlet cut-off scheme";
-
- md_print_warn(NULL, fplog, "%s\n", conv_mesg);
-
- ir->cutoff_scheme = ecutsVERLET;
- ir->verletbuf_tol = 0.005;
-
- if (ir->rcoulomb != ir->rvdw)
- {
- gmx_fatal(FARGS, "The VdW and Coulomb cut-offs are different, whereas the Verlet scheme only supports equal cut-offs");
- }
-
- if (ir->vdwtype == evdwUSER || EEL_USER(ir->coulombtype))
- {
- gmx_fatal(FARGS, "User non-bonded potentials are not (yet) supported with the Verlet scheme");
- }
- else if (ir_vdw_switched(ir) || ir_coulomb_switched(ir))
- {
- if (ir_vdw_switched(ir) && ir->vdw_modifier == eintmodNONE)
- {
- ir->vdwtype = evdwCUT;
-
- switch (ir->vdwtype)
- {
- case evdwSHIFT: ir->vdw_modifier = eintmodFORCESWITCH; break;
- case evdwSWITCH: ir->vdw_modifier = eintmodPOTSWITCH; break;
- default: gmx_fatal(FARGS, "The Verlet scheme does not support Van der Waals interactions of type '%s'", evdw_names[ir->vdwtype]);
- }
- }
- if (ir_coulomb_switched(ir) && ir->coulomb_modifier == eintmodNONE)
- {
- if (EEL_FULL(ir->coulombtype))
- {
- /* With full electrostatic only PME can be switched */
- ir->coulombtype = eelPME;
- ir->coulomb_modifier = eintmodPOTSHIFT;
- }
- else
- {
- md_print_warn(NULL, fplog, "NOTE: Replacing %s electrostatics with reaction-field with epsilon-rf=inf\n", eel_names[ir->coulombtype]);
- ir->coulombtype = eelRF;
- ir->epsilon_rf = 0.0;
- ir->coulomb_modifier = eintmodPOTSHIFT;
- }
- }
-
- /* We set the pair energy error tolerance to a small number.
- * Note that this is only for testing. For production the user
- * should think about this and set the mdp options.
- */
- ir->verletbuf_tol = 1e-4;
- }
-
- if (inputrec2nboundeddim(ir) != 3)
- {
- gmx_fatal(FARGS, "Can only convert old tpr files to the Verlet cut-off scheme with 3D pbc");
- }
-
- if (ir->efep != efepNO || ir->implicit_solvent != eisNO)
- {
- gmx_fatal(FARGS, "Will not convert old tpr files to the Verlet cut-off scheme with free-energy calculations or implicit solvent");
- }
-
- if (EI_DYNAMICS(ir->eI) && !(EI_MD(ir->eI) && ir->etc == etcNO))
- {
- verletbuf_list_setup_t ls;
-
- verletbuf_get_list_setup(FALSE, &ls);
- calc_verlet_buffer_size(mtop, box_vol, ir, -1, &ls, NULL, &ir->rlist);
- }
- else
- {
- real rlist_fac;
-
- if (EI_MD(ir->eI))
- {
- rlist_fac = 1 + verlet_buffer_ratio_NVE_T0;
- }
- else
- {
- rlist_fac = 1 + verlet_buffer_ratio_nodynamics;
- }
- ir->verletbuf_tol = -1;
- ir->rlist = rlist_fac*max(ir->rvdw, ir->rcoulomb);
- }
-
- gmx_mtop_remove_chargegroups(mtop);
-}
-
static void print_hw_opt(FILE *fp, const gmx_hw_opt_t *hw_opt)
{
fprintf(fp, "hw_opt: nt %d ntmpi %d ntomp %d ntomp_pme %d gpu_id '%s'\n",
t_inputrec *ir,
const t_commrec *cr)
{
- char sbuf[STEPSTRSIZE];
-
assert(ir);
assert(cr);
/* override with anything else than the default -2 */
if (nsteps_cmdline > -2)
{
- char stmp[STRLEN];
+ char sbuf_steps[STEPSTRSIZE];
+ char sbuf_msg[STRLEN];
ir->nsteps = nsteps_cmdline;
if (EI_DYNAMICS(ir->eI) && nsteps_cmdline != -1)
{
- sprintf(stmp, "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
- gmx_step_str(nsteps_cmdline, sbuf),
+ sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
+ gmx_step_str(nsteps_cmdline, sbuf_steps),
fabs(nsteps_cmdline*ir->delta_t));
}
else
{
- sprintf(stmp, "Overriding nsteps with value passed on the command line: %s steps",
- gmx_step_str(nsteps_cmdline, sbuf));
+ sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps",
+ gmx_step_str(nsteps_cmdline, sbuf_steps));
}
- md_print_warn(cr, fplog, "%s\n", stmp);
+ md_print_warn(cr, fplog, "%s\n", sbuf_msg);
}
-}
-
-/* Frees GPU memory and destroys the CUDA context.
- *
- * Note that this function needs to be called even if GPUs are not used
- * in this run because the PME ranks have no knowledge of whether GPUs
- * are used or not, but all ranks need to enter the barrier below.
- */
-static void free_gpu_resources(const t_forcerec *fr,
- const t_commrec *cr)
-{
- gmx_bool bIsPPrankUsingGPU;
- char gpu_err_str[STRLEN];
-
- bIsPPrankUsingGPU = (cr->duty & DUTY_PP) && fr->nbv != NULL && fr->nbv->bUseGPU;
-
- if (bIsPPrankUsingGPU)
+ else if (nsteps_cmdline < -2)
{
- /* free nbnxn data in GPU memory */
- nbnxn_cuda_free(fr->nbv->cu_nbv);
-
- /* With tMPI we need to wait for all ranks to finish deallocation before
- * destroying the context in free_gpu() as some ranks may be sharing
- * GPU and context.
- * Note: as only PP ranks need to free GPU resources, so it is safe to
- * not call the barrier on PME ranks.
- */
-#ifdef GMX_THREAD_MPI
- if (PAR(cr))
- {
- gmx_barrier(cr);
- }
-#endif /* GMX_THREAD_MPI */
-
- /* uninitialize GPU (by destroying the context) */
- if (!free_gpu(gpu_err_str))
- {
- gmx_warning("On rank %d failed to free GPU #%d: %s",
- cr->nodeid, get_current_gpu_device_id(), gpu_err_str);
- }
+ gmx_fatal(FARGS, "Invalid nsteps value passed on the command line: %d",
+ nsteps_cmdline);
}
+ /* Do nothing if nsteps_cmdline == -2 */
}
int mdrunner(gmx_hw_opt_t *hw_opt,
const char *deviceOptions, int imdport, unsigned long Flags)
{
gmx_bool bForceUseGPU, bTryUseGPU, bRerunMD, bCantUseGPU;
- double nodetime = 0, realtime;
t_inputrec *inputrec;
t_state *state = NULL;
matrix box;
gmx_ddbox_t ddbox = {0};
int npme_major, npme_minor;
- real tmpr1, tmpr2;
t_nrnb *nrnb;
gmx_mtop_t *mtop = NULL;
t_mdatoms *mdatoms = NULL;
gmx_pme_t *pmedata = NULL;
gmx_vsite_t *vsite = NULL;
gmx_constr_t constr;
- int i, m, nChargePerturbed = -1, nTypePerturbed = 0, status, nalloc;
- char *gro;
+ int nChargePerturbed = -1, nTypePerturbed = 0, status;
gmx_wallcycle_t wcycle;
gmx_bool bReadEkin;
- int list;
gmx_walltime_accounting_t walltime_accounting = NULL;
int rc;
gmx_int64_t reset_counters;
gmx_edsam_t ed = NULL;
- t_commrec *cr_old = cr;
int nthreads_pme = 1;
int nthreads_pp = 1;
gmx_membed_t membed = NULL;
if (SIMMASTER(cr))
{
/* Read (nearly) all data required for the simulation */
- read_tpx_state(ftp2fn(efTPX, nfile, fnm), inputrec, state, NULL, mtop);
-
- if (inputrec->cutoff_scheme != ecutsVERLET &&
- ((Flags & MD_TESTVERLET) || getenv("GMX_VERLET_SCHEME") != NULL))
- {
- convert_to_verlet_scheme(fplog, inputrec, mtop, det(state->box));
- }
+ read_tpx_state(ftp2fn(efTPR, nfile, fnm), inputrec, state, NULL, mtop);
if (inputrec->cutoff_scheme == ecutsVERLET)
{
{
md_print_warn(cr, fplog,
"NOTE: GPU(s) found, but the current simulation can not use GPUs\n"
- " To use a GPU, set the mdp option: cutoff-scheme = Verlet\n"
- " (for quick performance testing you can use the -testverlet option)\n");
+ " To use a GPU, set the mdp option: cutoff-scheme = Verlet\n");
}
if (bForceUseGPU)
}
}
- /* Check for externally set OpenMP affinity and turn off internal
- * pinning if any is found. We need to do this check early to tell
- * thread-MPI whether it should do pinning when spawning threads.
- * TODO: the above no longer holds, we should move these checks down
- */
- gmx_omp_check_thread_affinity(fplog, cr, hw_opt);
-
/* Check and update the hardware options for internal consistency */
check_and_update_hw_opt_1(hw_opt, SIMMASTER(cr));
+ /* Early check for externally set process affinity. */
+ gmx_check_thread_affinity_set(fplog, cr,
+ hw_opt, hwinfo->nthreads_hw_avail, FALSE);
if (SIMMASTER(cr))
{
-#ifdef GMX_THREAD_MPI
- /* Early check for externally set process affinity.
- * With thread-MPI this is needed as pinning might get turned off,
- * which needs to be known before starting thread-MPI.
- * With thread-MPI hw_opt is processed here on the master rank
- * and passed to the other ranks later, so we only do this on master.
- */
- gmx_check_thread_affinity_set(fplog,
- NULL,
- hw_opt, hwinfo->nthreads_hw_avail, FALSE);
-#endif
#ifdef GMX_THREAD_MPI
if (cr->npmenodes > 0 && hw_opt->nthreads_tmpi <= 0)
if (hw_opt->nthreads_tmpi > 1)
{
+ t_commrec *cr_old = cr;
/* now start the threads. */
cr = mdrunner_start_threads(hw_opt, fplog, cr_old, nfile, fnm,
oenv, bVerbose, bCompact, nstglobalcomm,
"but %s was not started through mpirun/mpiexec or only one rank was requested through mpirun/mpiexec"
#endif
#endif
- , ShortProgram()
+ , output_env_get_program_display_name(oenv)
);
}
}
}
- if (((MASTER(cr) || (Flags & MD_SEPPOT)) && (Flags & MD_APPENDFILES))
-#ifdef GMX_THREAD_MPI
- /* With thread MPI only the master node/thread exists in mdrun.c,
- * therefore non-master nodes need to open the "seppot" log file here.
- */
- || (!MASTER(cr) && (Flags & MD_SEPPOT))
-#endif
- )
+ if (MASTER(cr) && (Flags & MD_APPENDFILES))
{
- gmx_log_open(ftp2fn(efLOG, nfile, fnm), cr, !(Flags & MD_SEPPOT),
+ gmx_log_open(ftp2fn(efLOG, nfile, fnm), cr,
Flags, &fplog);
}
(cr->duty & DUTY_PP) == 0,
inputrec->cutoff_scheme == ecutsVERLET);
+#ifndef NDEBUG
+ if (integrator[inputrec->eI].func != do_tpi &&
+ inputrec->cutoff_scheme == ecutsVERLET)
+ {
+ gmx_feenableexcept();
+ }
+#endif
if (PAR(cr))
{
/* The master rank decided on the use of GPUs,
/*init_forcerec(fplog,fr,fcd,inputrec,mtop,cr,box,FALSE,
"nofile","nofile","nofile","nofile",FALSE,pforce);
*/
- fr->bSepDVDL = ((Flags & MD_SEPPOT) == MD_SEPPOT);
/* Initialize QM-MM */
if (fr->bQMMM)
if (DOMAINDECOMP(cr))
{
+ GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
dd_init_bondeds(fplog, cr->dd, mtop, vsite, inputrec,
Flags & MD_DDBONDCHECK, fr->cginfo_mb);
}
else
{
+ GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
/* do PME only */
walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
gmx_pmeonly(*pmedata, cr, nrnb, wcycle, walltime_accounting, ewaldcoeff_q, ewaldcoeff_lj, inputrec);
*/
finish_run(fplog, cr,
inputrec, nrnb, wcycle, walltime_accounting,
- fr != NULL && fr->nbv != NULL && fr->nbv->bUseGPU ?
- nbnxn_cuda_get_timings(fr->nbv->cu_nbv) : NULL,
+ fr ? fr->nbv : NULL,
EI_DYNAMICS(inputrec->eI) && !MULTISIM(cr));
/* Free GPU memory and context */
- free_gpu_resources(fr, cr);
+ free_gpu_resources(fr, cr, &hwinfo->gpu_info, fr ? fr->gpu_opt : NULL);
if (opt2bSet("-membed", nfile, fnm))
{
rc = (int)gmx_get_stop_condition();
+ done_ed(&ed);
+
#ifdef GMX_THREAD_MPI
/* we need to join all threads. The sub-threads join when they
exit this function, but the master thread needs to be told to
* \author Mark Abraham <mark.j.abraham@gmail.com>
* \ingroup module_mdrun
*/
-#include "moduletest.h"
-#include <gtest/gtest.h>
+#include "gmxpre.h"
+
#include <string>
+
+#include <gtest/gtest.h>
+
#include "gromacs/options/filenameoption.h"
#include "gromacs/tools/check.h"
+
#include "testutils/cmdlinetest.h"
+#include "moduletest.h"
+
namespace
{
"nsteps = 1\n"
"nstxout-compressed = 1\n");
mdpFile += GetParam();
- useStringAsMdpFile(mdpFile.c_str());
- useTopGroAndNdxFromDatabase("spc2");
- ASSERT_EQ(0, callGrompp());
+ runner_.useStringAsMdpFile(mdpFile.c_str());
+ runner_.useTopGroAndNdxFromDatabase("spc2");
+ ASSERT_EQ(0, runner_.callGrompp());
- reducedPrecisionTrajectoryFileName = fileManager_.getTemporaryFilePath(".xtc");
- ASSERT_EQ(0, callMdrun());
+ runner_.reducedPrecisionTrajectoryFileName_ = fileManager_.getTemporaryFilePath(".xtc");
+ ASSERT_EQ(0, runner_.callMdrun());
::gmx::test::CommandLine checkCaller;
checkCaller.append("check");
- checkCaller.addOption("-f", reducedPrecisionTrajectoryFileName);
+ checkCaller.addOption("-f", runner_.reducedPrecisionTrajectoryFileName_);
ASSERT_EQ(0, gmx_check(checkCaller.argc(), checkCaller.argv()));
}
* \author Carsten Kutzner <ckutzne@gwdg.de>
* \ingroup module_mdrun
*/
+#include "gmxpre.h"
+
#include "moduletest.h"
namespace gmx
TEST_F(ImdTest, ImdCanRun)
{
std::string name = "spc2";
- useTopGroAndNdxFromDatabase(name.c_str());
- mdpInputFileName = fileManager_.getInputFilePath((name + "-IMD.mdp").c_str());
+ runner_.useTopGroAndNdxFromDatabase(name.c_str());
+ runner_.mdpInputFileName_ = fileManager_.getInputFilePath((name + "-IMD.mdp").c_str());
- EXPECT_EQ(0, callGrompp());
+ EXPECT_EQ(0, runner_.callGrompp());
::gmx::test::CommandLine imdCaller;
imdCaller.append("mdrun");
imdCaller.append("-noimdterm");
// Do an mdrun with IMD enabled
- ASSERT_EQ(0, callMdrun(imdCaller));
+ ASSERT_EQ(0, runner_.callMdrun(imdCaller));
}
* \author Mark Abraham <mark.j.abraham@gmail.com>
* \ingroup module_mdrun
*/
+#include "gmxpre.h"
+
#include "moduletest.h"
-#ifdef HAVE_CONFIG_H
-# include <config.h>
-#endif
+#include "config.h"
-#include "testutils/integrationtests.h"
-#include "testutils/testoptions.h"
-#include "testutils/cmdlinetest.h"
-#include "gromacs/options/options.h"
+#include "gromacs/gmxpreprocess/grompp.h"
#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/options.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/file.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/gmxpreprocess/grompp.h"
#include "programs/mdrun/mdrun_main.h"
+#include "testutils/cmdlinetest.h"
+#include "testutils/integrationtests.h"
+#include "testutils/testoptions.h"
+
namespace gmx
{
namespace test
GMX_UNUSED_VALUE(options);
#ifdef GMX_THREAD_MPI
options->addOption(IntegerOption("nt").store(&g_numThreads)
- .description("Number of thread-MPI threads/ranks for child mdrun call"));
+ .description("Number of thread-MPI threads/ranks for child mdrun calls"));
#endif
#ifdef GMX_OPENMP
options->addOption(IntegerOption("nt_omp").store(&g_numOpenMPThreads)
- .description("Number of OpenMP threads for child mdrun call"));
+ .description("Number of OpenMP threads for child mdrun calls"));
#endif
}
//! \endcond
}
-MdrunTestFixture::MdrunTestFixture() :
- topFileName(),
- groFileName(),
- fullPrecisionTrajectoryFileName(),
- ndxFileName(),
- mdpInputFileName(fileManager_.getTemporaryFilePath("input.mdp")),
- mdpOutputFileName(fileManager_.getTemporaryFilePath("output.mdp")),
- tprFileName(fileManager_.getTemporaryFilePath(".tpr")),
- logFileName(fileManager_.getTemporaryFilePath(".log")),
- edrFileName(fileManager_.getTemporaryFilePath(".edr")),
- nsteps(-2)
+SimulationRunner::SimulationRunner(IntegrationTestFixture *fixture) :
+ fixture_(fixture),
+ topFileName_(),
+ groFileName_(),
+ fullPrecisionTrajectoryFileName_(),
+ ndxFileName_(),
+ mdpInputFileName_(fixture_->fileManager_.getTemporaryFilePath("input.mdp")),
+ mdpOutputFileName_(fixture_->fileManager_.getTemporaryFilePath("output.mdp")),
+ tprFileName_(fixture_->fileManager_.getTemporaryFilePath(".tpr")),
+ logFileName_(fixture_->fileManager_.getTemporaryFilePath(".log")),
+ edrFileName_(fixture_->fileManager_.getTemporaryFilePath(".edr")),
+ nsteps_(-2)
{
#ifdef GMX_LIB_MPI
GMX_RELEASE_ASSERT(gmx_mpi_initialized(), "MPI system not initialized for mdrun tests");
#endif
}
-MdrunTestFixture::~MdrunTestFixture()
-{
-}
-
// TODO The combination of defaulting to Verlet cut-off scheme, NVE,
// and verlet-buffer-tolerance = -1 gives a grompp error. If we keep
// things that way, this function should be renamed. For now,
// force the use of the group scheme.
void
-MdrunTestFixture::useEmptyMdpFile()
+SimulationRunner::useEmptyMdpFile()
{
useStringAsMdpFile("cutoff-scheme = Group\n");
}
void
-MdrunTestFixture::useStringAsMdpFile(const char *mdpString)
+SimulationRunner::useStringAsMdpFile(const char *mdpString)
{
useStringAsMdpFile(std::string(mdpString));
}
void
-MdrunTestFixture::useStringAsMdpFile(const std::string &mdpString)
+SimulationRunner::useStringAsMdpFile(const std::string &mdpString)
{
- gmx::File::writeFileFromString(mdpInputFileName, mdpString);
+ gmx::File::writeFileFromString(mdpInputFileName_, mdpString);
}
void
-MdrunTestFixture::useStringAsNdxFile(const char *ndxString)
+SimulationRunner::useStringAsNdxFile(const char *ndxString)
{
- gmx::File::writeFileFromString(ndxFileName, ndxString);
+ gmx::File::writeFileFromString(ndxFileName_, ndxString);
}
void
-MdrunTestFixture::useTopGroAndNdxFromDatabase(const char *name)
+SimulationRunner::useTopGroAndNdxFromDatabase(const char *name)
{
- topFileName = fileManager_.getInputFilePath((std::string(name) + ".top").c_str());
- groFileName = fileManager_.getInputFilePath((std::string(name) + ".gro").c_str());
- ndxFileName = fileManager_.getInputFilePath((std::string(name) + ".ndx").c_str());
+ topFileName_ = fixture_->fileManager_.getInputFilePath((std::string(name) + ".top").c_str());
+ groFileName_ = fixture_->fileManager_.getInputFilePath((std::string(name) + ".gro").c_str());
+ ndxFileName_ = fixture_->fileManager_.getInputFilePath((std::string(name) + ".ndx").c_str());
}
int
-MdrunTestFixture::callGromppOnThisRank()
+SimulationRunner::callGromppOnThisRank()
{
CommandLine caller;
caller.append("grompp");
- caller.addOption("-f", mdpInputFileName);
- caller.addOption("-n", ndxFileName);
- caller.addOption("-p", topFileName);
- caller.addOption("-c", groFileName);
+ caller.addOption("-f", mdpInputFileName_);
+ caller.addOption("-n", ndxFileName_);
+ caller.addOption("-p", topFileName_);
+ caller.addOption("-c", groFileName_);
- caller.addOption("-po", mdpOutputFileName);
- caller.addOption("-o", tprFileName);
+ caller.addOption("-po", mdpOutputFileName_);
+ caller.addOption("-o", tprFileName_);
return gmx_grompp(caller.argc(), caller.argv());
}
int
-MdrunTestFixture::callGrompp()
+SimulationRunner::callGrompp()
{
#ifdef GMX_LIB_MPI
// When compiled with external MPI, only call one instance of the
}
int
-MdrunTestFixture::callMdrun(const CommandLine &callerRef)
+SimulationRunner::callMdrun(const CommandLine &callerRef)
{
/* Conforming to style guide by not passing a non-const reference
to this function. Passing a non-const reference might make it
easier to write code that incorrectly re-uses callerRef after
the call to this function. */
CommandLine caller(callerRef);
- caller.addOption("-s", tprFileName);
+ caller.addOption("-s", tprFileName_);
- caller.addOption("-g", logFileName);
- caller.addOption("-e", edrFileName);
- caller.addOption("-o", fullPrecisionTrajectoryFileName);
- caller.addOption("-x", reducedPrecisionTrajectoryFileName);
+ caller.addOption("-g", logFileName_);
+ caller.addOption("-e", edrFileName_);
+ caller.addOption("-o", fullPrecisionTrajectoryFileName_);
+ caller.addOption("-x", reducedPrecisionTrajectoryFileName_);
- caller.addOption("-deffnm", fileManager_.getTemporaryFilePath("state"));
+ caller.addOption("-deffnm", fixture_->fileManager_.getTemporaryFilePath("state"));
- if (nsteps > -2)
+ if (nsteps_ > -2)
{
- caller.addOption("-nsteps", nsteps);
+ caller.addOption("-nsteps", nsteps_);
}
#ifdef GMX_THREAD_MPI
}
int
-MdrunTestFixture::callMdrun()
+SimulationRunner::callMdrun()
{
CommandLine caller;
caller.append("mdrun");
return callMdrun(caller);
}
+// ====
+
+MdrunTestFixtureBase::MdrunTestFixtureBase()
+{
+#ifdef GMX_LIB_MPI
+ GMX_RELEASE_ASSERT(gmx_mpi_initialized(), "MPI system not initialized for mdrun tests");
+#endif
+}
+
+MdrunTestFixtureBase::~MdrunTestFixtureBase()
+{
+}
+
+// ====
+
+MdrunTestFixture::MdrunTestFixture() : runner_(this)
+{
+}
+
+MdrunTestFixture::~MdrunTestFixture()
+{
+}
+
} // namespace test
} // namespace gmx
#ifndef GMX_MDRUN_TESTS_MODULETEST_H
#define GMX_MDRUN_TESTS_MODULETEST_H
-#include "testutils/integrationtests.h"
-
#include <gtest/gtest.h>
+
#include "testutils/cmdlinetest.h"
+#include "testutils/integrationtests.h"
namespace gmx
{
namespace test
{
-/*! \libinternal \brief Declares test fixture for integration tests of
- * mdrun functionality
+/*! \libinternal \brief Helper object for running grompp and mdrun in
+ * integration tests of mdrun functionality
*
- * Derived fixture classes (or individual test cases) that might have
- * specific requirements should assert that behaviour, rather than
- * hard-code the requirements. A test that (for example) can't run
- * with more than one thread should report that as a diagnostic, so the
- * person running the test (or designing the test harness) can get
- * feedback on what tests need what conditions without having to read
- * the code of lots of tests.
+ * Objects of this class are intended to be owned by
+ * IntegrationTestFixture objects, and an IntegrationTestFixture
+ * object might own more than one SimulationRunner.
*
* The setup phase creates various temporary files for input and
* output that are common for mdrun tests, using the file manager
- * object of the parent class. Individual tests should create any
- * extra filenames similarly, so that the test users's current working
- * directory does not get littered with files left over from all
- * manner of tests.
- *
- * Specifying the execution context (such as numbers of threads and
- * processors) is normally sensible to specify from the test harness
- * (i.e. when CMake/CTest/the user runs a test executable), because
- * only there is information about the hardware available. The default
- * values for such context provided in test fixtures for mdrun should
- * mirror the defaults for mdrun, but currently mdrun.c hard-codes
- * those in a gmx_hw_opt_t.
+ * object of the fixture that owns this object. Individual tests
+ * should create any extra filenames similarly, so that the test
+ * users's current working directory does not get littered with files
+ * left over from tests.
*
* Any method in this class may throw std::bad_alloc if out of memory.
*
* \ingroup module_mdrun_integration_tests
*/
-class MdrunTestFixture : public IntegrationTestFixture
+class SimulationRunner
{
- protected:
- MdrunTestFixture();
- virtual ~MdrunTestFixture();
+ public:
+ /*! \brief Constructor, which establishes the fixture that
+ * will own each object */
+ explicit SimulationRunner(IntegrationTestFixture *fixture_);
//! Use an empty .mdp file as input to grompp
void useEmptyMdpFile();
* with default command line */
int callMdrun();
+ private:
+ //! Provides access to the test fixture, e.g. for the TestFileManager
+ IntegrationTestFixture *fixture_;
+ public:
//@{
/*! \name Names for frequently used grompp and mdrun output files
*
* in a temporary directory and (by default behaviour of
* TestFileManager) deleted when the test is complete.
*/
- std::string topFileName;
- std::string groFileName;
- std::string fullPrecisionTrajectoryFileName;
- std::string reducedPrecisionTrajectoryFileName;
- std::string groOutputFileName;
- std::string ndxFileName;
- std::string mdpInputFileName;
- std::string mdpOutputFileName;
- std::string tprFileName;
- std::string logFileName;
- std::string edrFileName;
- std::string cptFileName;
- std::string swapFileName;
- int nsteps;
+ std::string topFileName_;
+ std::string groFileName_;
+ std::string fullPrecisionTrajectoryFileName_;
+ std::string reducedPrecisionTrajectoryFileName_;
+ std::string groOutputFileName_;
+ std::string ndxFileName_;
+ std::string mdpInputFileName_;
+ std::string mdpOutputFileName_;
+ std::string tprFileName_;
+ std::string logFileName_;
+ std::string edrFileName_;
+ std::string cptFileName_;
+ std::string swapFileName_;
+ int nsteps_;
//@}
};
+/*! \libinternal \brief Declares test fixture base class for
+ * integration tests of mdrun functionality
+ *
+ * Derived fixture classes (or individual test cases) that might have
+ * specific requirements should assert that behaviour, rather than
+ * hard-code the requirements. A test that (for example) can't run
+ * with more than one thread should report that as a diagnostic, so the
+ * person running the test (or designing the test harness) can get
+ * feedback on what tests need what conditions without having to read
+ * the code of lots of tests.
+ *
+ * Specifying the execution context (such as numbers of threads and
+ * processors) is normally sensible to specify from the test harness
+ * (i.e. when CMake/CTest/the user runs a test executable), because
+ * only there is information about the hardware available. The default
+ * values for such context provided in test fixtures for mdrun should
+ * mirror the defaults for mdrun, but currently mdrun.c hard-codes
+ * those in a gmx_hw_opt_t.
+ *
+ * Any method in this class may throw std::bad_alloc if out of memory.
+ *
+ * \ingroup module_mdrun_integration_tests
+ */
+class MdrunTestFixtureBase : public IntegrationTestFixture
+{
+ public:
+ MdrunTestFixtureBase();
+ virtual ~MdrunTestFixtureBase();
+};
+
+/*! \libinternal \brief Declares test fixture class for integration
+ * tests of mdrun functionality that use a single call of mdrun
+ *
+ * Any method in this class may throw std::bad_alloc if out of memory.
+ *
+ * \ingroup module_mdrun_integration_tests
+ */
+class MdrunTestFixture : public IntegrationTestFixture
+{
+ public:
+ MdrunTestFixture();
+ virtual ~MdrunTestFixture();
+
+ //! Helper object to manage the preparation for and call of mdrun
+ SimulationRunner runner_;
+};
+
/*! \libinternal \brief
* Parameterized test fixture for mdrun integration tests
*/
* \author Mark Abraham <mark.j.abraham@gmail.com>
* \ingroup module_mdrun
*/
-#include "moduletest.h"
+#include "gmxpre.h"
+
+#include "config.h"
#include <math.h>
#include <gtest/gtest.h>
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/fileio/path.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/path.h"
+#include "gromacs/utility/real.h"
#include "gromacs/utility/stringutil.h"
-
-#include "../mdrun_main.h"
+#include "programs/mdrun/mdrun_main.h"
#include "testutils/cmdlinetest.h"
+#include "moduletest.h"
+
namespace
{
/* Prepare grompp output filenames inside the new
temporary directory */
- mdpInputFileName = fileManager_.getTemporaryFilePath("input.mdp");
- mdpOutputFileName = fileManager_.getTemporaryFilePath("output.mdp");
- tprFileName = fileManager_.getTemporaryFilePath(".tpr");
+ runner_.mdpInputFileName_ = fileManager_.getTemporaryFilePath("input.mdp");
+ runner_.mdpOutputFileName_ = fileManager_.getTemporaryFilePath("output.mdp");
+ runner_.tprFileName_ = fileManager_.getTemporaryFilePath(".tpr");
mdrunCaller.addOption("-deffnm", fileManager_.getTestSpecificFileNameRoot());
}
occur. */
std::max(baseTemperature - 10 * rank, real(0)),
controlVariable);
- useStringAsMdpFile(mdpFileContents);
+ runner_.useStringAsMdpFile(mdpFileContents);
}
//! MPI process set size
organizeMultidir();
const char *pcoupl = GetParam();
organizeMdpFile(pcoupl);
- useTopGroAndNdxFromDatabase("spc2");
+ runner_.useTopGroAndNdxFromDatabase("spc2");
/* Call grompp on every rank - the standard callGrompp() only runs
grompp on rank 0. */
- EXPECT_EQ(0, callGromppOnThisRank());
+ EXPECT_EQ(0, runner_.callGromppOnThisRank());
mdrunCaller.addOption("-replex", 1);
ASSERT_EQ(0, gmx_mdrun(mdrunCaller.argc(), mdrunCaller.argv()));
* \author Mark Abraham <mark.j.abraham@gmail.com>
* \ingroup module_mdrun
*/
+#include "gmxpre.h"
+
+#include "config.h"
+
#include <gtest/gtest.h>
-#include "moduletest.h"
+
#include "gromacs/options/filenameoption.h"
+
#include "testutils/cmdlinetest.h"
-#include "config.h"
+#include "moduletest.h"
namespace
{
/* Among other things, this test ensures mdrun can read a trajectory. */
TEST_P(MdrunRerun, WithDifferentInputFormats)
{
- useEmptyMdpFile();
- useTopGroAndNdxFromDatabase("spc2");
- EXPECT_EQ(0, callGrompp());
+ runner_.useEmptyMdpFile();
+ runner_.useTopGroAndNdxFromDatabase("spc2");
+ EXPECT_EQ(0, runner_.callGrompp());
std::string rerunFileName = fileManager_.getInputFilePath(GetParam());
::gmx::test::CommandLine rerunCaller;
rerunCaller.append("mdrun");
rerunCaller.addOption("-rerun", rerunFileName);
- ASSERT_EQ(0, callMdrun(rerunCaller));
+ ASSERT_EQ(0, runner_.callMdrun(rerunCaller));
}
/*! \brief Helper array of input files present in the source repo
* \author Carsten Kutzner <ckutzne@gwdg.de>
* \ingroup module_mdrun
*/
+#include "gmxpre.h"
+
#include "moduletest.h"
namespace gmx
TEST_F(CompelTest, SwapCanRun)
{
std::string name = "OctaneSandwich";
- useTopGroAndNdxFromDatabase(name.c_str());
- mdpInputFileName = fileManager_.getInputFilePath((name + ".mdp").c_str());
+ runner_.useTopGroAndNdxFromDatabase(name.c_str());
+ runner_.mdpInputFileName_ = fileManager_.getInputFilePath((name + ".mdp").c_str());
- EXPECT_EQ(0, callGrompp());
+ EXPECT_EQ(0, runner_.callGrompp());
- cptFileName = fileManager_.getTemporaryFilePath(".cpt");
- groOutputFileName = fileManager_.getTemporaryFilePath(".gro");
- swapFileName = fileManager_.getTemporaryFilePath("swap.xvg");
+ runner_.cptFileName_ = fileManager_.getTemporaryFilePath(".cpt");
+ runner_.groOutputFileName_ = fileManager_.getTemporaryFilePath(".gro");
+ runner_.swapFileName_ = fileManager_.getTemporaryFilePath("swap.xvg");
::gmx::test::CommandLine swapCaller;
swapCaller.append("mdrun");
- swapCaller.addOption("-c", groOutputFileName);
- swapCaller.addOption("-swap", swapFileName);
+ swapCaller.addOption("-c", runner_.groOutputFileName_);
+ swapCaller.addOption("-swap", runner_.swapFileName_);
// Do an initial mdrun that writes a checkpoint file
::gmx::test::CommandLine firstCaller(swapCaller);
- firstCaller.addOption("-cpo", cptFileName);
- ASSERT_EQ(0, callMdrun(firstCaller));
+ firstCaller.addOption("-cpo", runner_.cptFileName_);
+ ASSERT_EQ(0, runner_.callMdrun(firstCaller));
// Continue mdrun from that checkpoint file
::gmx::test::CommandLine secondCaller(swapCaller);
- secondCaller.addOption("-cpi", cptFileName);
- nsteps = 2;
- ASSERT_EQ(0, callMdrun(secondCaller));
+ secondCaller.addOption("-cpi", runner_.cptFileName_);
+ runner_.nsteps_ = 2;
+ ASSERT_EQ(0, runner_.callMdrun(secondCaller));
}
* \author Mark Abraham <mark.j.abraham@gmail.com>
* \ingroup module_mdrun
*/
+#include "gmxpre.h"
+
+#include "config.h"
+
#include <gtest/gtest.h>
-#include "moduletest.h"
+
#include "gromacs/options/filenameoption.h"
#include "gromacs/utility/stringutil.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "moduletest.h"
namespace
{
//! Execute the trajectory writing test
void runTest()
{
- useStringAsMdpFile(theMdpFile);
- useTopGroAndNdxFromDatabase("spc-and-methanol");
- EXPECT_EQ(0, callGrompp());
+ runner_.useStringAsMdpFile(theMdpFile);
+ runner_.useTopGroAndNdxFromDatabase("spc-and-methanol");
+ EXPECT_EQ(0, runner_.callGrompp());
- fullPrecisionTrajectoryFileName = fileManager_.getTemporaryFilePath("spc-and-methanol.tng");
- reducedPrecisionTrajectoryFileName = fileManager_.getTemporaryFilePath("spc-and-methanol-reduced.tng");
- ASSERT_EQ(0, callMdrun());
+ runner_.fullPrecisionTrajectoryFileName_ = fileManager_.getTemporaryFilePath("spc-and-methanol.tng");
+ runner_.reducedPrecisionTrajectoryFileName_ = fileManager_.getTemporaryFilePath("spc-and-methanol-reduced.tng");
+ ASSERT_EQ(0, runner_.callMdrun());
// TODO When there is a way to sense something like the
// output of gmx check, compare the result with that from
// writing .trr and .xtc and assert the behaviour is
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "mdrun/mdrun_main.h"
+#include "gmxpre.h"
#include "gromacs/commandline/cmdlinemodulemanager.h"
+#include "mdrun/mdrun_main.h"
+
int main(int argc, char *argv[])
{
return gmx::CommandLineModuleManager::runAsMainCMain(argc, argv, &gmx_mdrun);
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "gromacs/math/3dview.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "3dview.h"
#include <math.h>
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "physics.h"
-#include "pbc.h"
-#include "vec.h"
-
-#include "gmx_fatal.h"
-#define N 4
-
-void m4_op(mat4 m, rvec x, vec4 v)
-{
- int i;
-
- for (i = 0; (i < N); i++)
- {
- v[i] = m[XX][i]*x[XX]+m[YY][i]*x[YY]+m[ZZ][i]*x[ZZ]+m[WW][i];
- }
-}
-
-void unity_m4(mat4 m)
-{
- int i, j;
-
- for (i = 0; (i < N); i++)
- {
- for (j = 0; (j < N); j++)
- {
- if (i == j)
- {
- m[i][j] = 1.0;
- }
- else
- {
- m[i][j] = 0.0;
- }
- }
- }
-}
-
-void print_m4(FILE *fp, const char *s, mat4 A)
-{
- int i, j;
-
- if (fp)
- {
- fprintf(fp, "%s: ", s);
- for (i = 0; i < N; i++)
- {
- fprintf(fp, "\t");
- for (j = 0; j < N; j++)
- {
- fprintf(fp, "%10.5f", A[i][j]);
- }
- fprintf(fp, "\n");
- }
- }
-}
-
-void print_v4(FILE *fp, char *s, int dim, real *a)
-{
- int j;
-
- if (fp)
- {
- fprintf(fp, "%s: ", s);
- for (j = 0; j < dim; j++)
- {
- fprintf(fp, "%10.5f", a[j]);
- }
- fprintf(fp, "\n");
- }
-}
+#include <algorithm>
-void mult_matrix(mat4 A, mat4 B, mat4 C)
-{
- int i, j, k;
-
- for (i = 0; i < N; i++)
- {
- for (j = 0; j < N; j++)
- {
- A[i][j] = 0;
- for (k = 0; (k < N); k++)
- {
- A[i][j] += B[i][k]*C[k][j];
- }
- }
- }
-}
-
-void rotate(int axis, real angle, mat4 A)
-{
- unity_m4(A);
-
- switch (axis)
- {
- case XX:
- A[YY][YY] = cos(angle);
- A[YY][ZZ] = -sin(angle);
- A[ZZ][YY] = sin(angle);
- A[ZZ][ZZ] = cos(angle);
- break;
- case YY:
- A[XX][XX] = cos(angle);
- A[XX][ZZ] = sin(angle);
- A[ZZ][XX] = -sin(angle);
- A[ZZ][ZZ] = cos(angle);
- break;
- case ZZ:
- A[XX][XX] = cos(angle);
- A[XX][YY] = -sin(angle);
- A[YY][XX] = sin(angle);
- A[YY][YY] = cos(angle);
- break;
- default:
- gmx_fatal(FARGS, "Error: invalid axis: %d", axis);
- }
-}
-
-void translate(real tx, real ty, real tz, mat4 A)
-{
- unity_m4(A);
- A[3][XX] = tx;
- A[3][YY] = ty;
- A[3][ZZ] = tz;
-}
+#include "gromacs/math/3dtransforms.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static void set_scale(t_3dview *view, real sx, real sy)
{
view->sc_y = sy;
}
-void calculate_view(t_3dview *view)
+static void calculate_view(t_3dview *view)
{
#define SMALL 1e-6
mat4 To, Te, T1, T2, T3, T4, T5, N1, D1, D2, D3, D4, D5;
l = sqrt(dx*dx+dy*dy+dz*dz);
r = sqrt(dx*dx+dy*dy);
#ifdef DEBUG
- print_v4(debug, "eye", N, view->eye);
+ gmx_vec4_print(debug, "eye", view->eye);
printf("del: %10.5f%10.5f%10.5f l: %10.5f, r: %10.5f\n", dx, dy, dz, l, r);
#endif
if (l < SMALL)
{
gmx_fatal(FARGS, "Error: Zero Length Vector - No View Specified");
}
- translate((real)(-view->origin[XX]),
- (real)(-view->origin[YY]), (real)(-view->origin[ZZ]), To);
- translate((real)(-view->eye[XX]),
- (real)(-view->eye[YY]), (real)(-view->eye[ZZ]), Te);
+ gmx_mat4_init_translation(-view->origin[XX], -view->origin[YY], -view->origin[ZZ], To);
+ gmx_mat4_init_translation(-view->eye[XX], -view->eye[YY], -view->eye[ZZ], Te);
- unity_m4(T2);
+ gmx_mat4_init_unity(T2);
T2[YY][YY] = 0, T2[YY][ZZ] = -1, T2[ZZ][YY] = 1, T2[ZZ][ZZ] = 0;
- unity_m4(T3);
+ gmx_mat4_init_unity(T3);
if (r > 0)
{
T3[XX][XX] = -dy/r, T3[XX][ZZ] = dx/r, T3[ZZ][XX] = -dx/r, T3[ZZ][ZZ] = -dy/r;
}
- unity_m4(T4);
+ gmx_mat4_init_unity(T4);
T4[YY][YY] = r/l, T4[YY][ZZ] = dz/l, T4[ZZ][YY] = -dz/l, T4[ZZ][ZZ] = r/l;
- unity_m4(T5);
+ gmx_mat4_init_unity(T5);
T5[ZZ][ZZ] = -1;
- unity_m4(N1);
+ gmx_mat4_init_unity(N1);
/* N1[XX][XX]=4,N1[YY][YY]=4; */
- mult_matrix(T1, To, view->Rot);
- mult_matrix(D1, Te, T2);
- mult_matrix(D2, T3, T4);
- mult_matrix(D3, T5, N1);
- mult_matrix(D4, T1, D1);
- mult_matrix(D5, D2, D3);
+ gmx_mat4_mmul(T1, To, view->Rot);
+ gmx_mat4_mmul(D1, Te, T2);
+ gmx_mat4_mmul(D2, T3, T4);
+ gmx_mat4_mmul(D3, T5, N1);
+ gmx_mat4_mmul(D4, T1, D1);
+ gmx_mat4_mmul(D5, D2, D3);
- mult_matrix(view->proj, D4, D5);
+ gmx_mat4_mmul(view->proj, D4, D5);
#ifdef DEBUG
- print_m4(debug, "T1", T1);
- print_m4(debug, "T2", T2);
- print_m4(debug, "T3", T3);
- print_m4(debug, "T4", T4);
- print_m4(debug, "T5", T5);
- print_m4(debug, "N1", N1);
- print_m4(debug, "Rot", view->Rot);
- print_m4(debug, "Proj", view->proj);
+ gmx_mat4_print(debug, "T1", T1);
+ gmx_mat4_print(debug, "T2", T2);
+ gmx_mat4_print(debug, "T3", T3);
+ gmx_mat4_print(debug, "T4", T4);
+ gmx_mat4_print(debug, "T5", T5);
+ gmx_mat4_print(debug, "N1", N1);
+ gmx_mat4_print(debug, "Rot", view->Rot);
+ gmx_mat4_print(debug, "Proj", view->proj);
#endif
}
dr1 = sqrt(dr2);
if (fac < 1)
{
- bm = max(norm(view->box[XX]), max(norm(view->box[YY]), norm(view->box[ZZ])));
+ bm = std::max(norm(view->box[XX]), std::max(norm(view->box[YY]), norm(view->box[ZZ])));
if (dr1*fac < 1.1*bm) /* Don't come to close */
{
return FALSE;
return TRUE;
}
-void init_rotate_3d(t_3dview *view)
+/* Initiates the state of 3d rotation matrices in the structure */
+static void init_rotate_3d(t_3dview *view)
{
real rot = DEG2RAD*15;
int i;
for (i = 0; (i < DIM); i++)
{
- rotate(i, rot, view->RotP[i]);
- rotate(i, (real)(-rot), view->RotM[i]);
+ gmx_mat4_init_rotation(i, rot, view->RotP[i]);
+ gmx_mat4_init_rotation(i, -rot, view->RotM[i]);
#ifdef DEBUG
- print_m4(debug, "RotP", view->RotP[i]);
- print_m4(debug, "RotM", view->RotM[i]);
+ gmx_mat4_print(debug, "RotP", view->RotP[i]);
+ gmx_mat4_print(debug, "RotM", view->RotM[i]);
#endif
}
}
void rotate_3d(t_3dview *view, int axis, gmx_bool bPositive)
{
- int i, j;
mat4 m4;
if (bPositive)
{
- mult_matrix(m4, view->Rot, view->RotP[axis]);
+ gmx_mat4_mmul(m4, view->Rot, view->RotP[axis]);
}
else
{
- mult_matrix(m4, view->Rot, view->RotM[axis]);
- }
- for (i = 0; (i < N); i++)
- {
- for (j = 0; (j < N); j++)
- {
- view->Rot[i][j] = m4[i][j];
- }
+ gmx_mat4_mmul(m4, view->Rot, view->RotM[axis]);
}
-
+ gmx_mat4_copy(m4, view->Rot);
calculate_view(view);
}
void reset_view(t_3dview *view)
{
- int i;
-
#ifdef DEBUG
printf("Reset view called\n");
#endif
set_scale(view, 4.0, 4.0);
clear_rvec(view->eye);
calc_box_center(view->ecenter, view->box, view->origin);
- view->eye[ZZ] = 3.0*max(view->box[XX][XX], view->box[YY][YY]);
+ view->eye[ZZ] = 3.0*std::max(view->box[XX][XX], view->box[YY][YY]);
zoom_3d(view, 1.0);
view->eye[WW] = view->origin[WW] = 0.0;
/* Initiate the matrix */
- unity_m4(view->Rot);
+ gmx_mat4_init_unity(view->Rot);
calculate_view(view);
init_rotate_3d(view);
t_3dview *init_view(matrix box)
{
t_3dview *view;
- int i, j;
snew(view, 1);
-
- /* Copy parameters into variables */
- for (i = 0; (i < DIM); i++)
- {
- for (j = 0; (j < DIM); j++)
- {
- view->box[i][j] = box[i][j];
- }
- }
-
+ copy_mat(box, view->box);
view->ecenter = ecenterDEF;
-
reset_view(view);
return view;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef GMX_MATH_3DVIEW_H
-#define GMX_MATH_3DVIEW_H
+#ifndef GMX_VIEW_3DVIEW_H
+#define GMX_VIEW_3DVIEW_H
-#include <stdio.h>
-
-#include "../legacyheaders/types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#define WW 3
-
-typedef real vec4[4];
-
-typedef real mat4[4][4];
+#include "gromacs/math/3dtransforms.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
typedef int iv2[2];
typedef struct {
matrix box;
- int ecenter; /* enum for centering, see pbc.h */
- vec4 eye, origin; /* The eye and origin position */
- mat4 proj; /* Projection matrix */
- mat4 Rot; /* Total rotation matrix */
- real sc_x, sc_y; /* Scaling for aspect ratio */
- mat4 RotP[DIM]; /* state for 3d rotations */
+ int ecenter; /* enum for centering, see pbc.h */
+ vec4 eye, origin; /* The eye and origin position */
+ mat4 proj; /* Projection matrix */
+ mat4 Rot; /* Total rotation matrix */
+ real sc_x, sc_y; /* Scaling for aspect ratio */
+ mat4 RotP[DIM]; /* state for 3d rotations */
mat4 RotM[DIM];
} t_3dview;
-extern void print_m4(FILE *fp, const char *s, mat4 A);
-
-extern void print_v4(FILE *fp, char *s, int dim, real *a);
-
-extern void m4_op(mat4 m, rvec x, vec4 v);
-
-extern void unity_m4(mat4 m);
-
-extern void mult_matrix(mat4 A, mat4 B, mat4 C);
-
-extern void rotate(int axis, real angle, mat4 A);
-
-extern void translate(real tx, real ty, real tz, mat4 A);
-
-extern void m4_op(mat4 m, rvec x, vec4 v);
-
-extern void calculate_view(t_3dview *view);
-
-extern t_3dview *init_view(matrix box);
+t_3dview *init_view(matrix box);
/* Generate the view matrix from the eye pos and the origin,
* applying also the scaling for the aspect ration.
* There is no accompanying done_view routine: the struct can simply
* reset the view
*/
-extern gmx_bool zoom_3d(t_3dview *view, real fac);
+gmx_bool zoom_3d(t_3dview *view, real fac);
/* Zoom in or out with factor fac, returns TRUE when zoom successful,
* FALSE otherwise.
*/
-extern void init_rotate_3d(t_3dview *view);
-/* Initiates the state of 3d rotation matrices in the structure */
-
-extern void rotate_3d(t_3dview *view, int axis, gmx_bool bPositive);
+void rotate_3d(t_3dview *view, int axis, gmx_bool bPositive);
/* Rotate the eye around the center of the box, around axis */
-extern void translate_view(t_3dview *view, int axis, gmx_bool bPositive);
+void translate_view(t_3dview *view, int axis, gmx_bool bPositive);
/* Translate the origin at which one is looking */
-extern void reset_view(t_3dview *view);
+void reset_view(t_3dview *view);
/* Reset the viewing to the initial view */
-#ifdef __cplusplus
-}
-#endif
-
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#endif
#include <X11/Xlib.h>
+#include <X11/Xresource.h>
#include <X11/Xutil.h>
-#include <X11/keysym.h>
#include <X11/cursorfont.h>
-#include <X11/Xresource.h>
+#include <X11/keysym.h>
#ifdef _acc_
typedef unsigned char bmchar;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "buttons.h"
+
+#include <stdlib.h>
#include <string.h>
#include <algorithm>
-#include "macros.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-
-#include "x11.h"
-#include "xutil.h"
-#include "buttons.h"
-#include "stop_ani.bm"
-#include "play.bm"
#include "ff.bm"
+#include "play.bm"
#include "rewind.bm"
+#include "stop_ani.bm"
+#include "x11.h"
+#include "xutil.h"
static void move_bbox(t_x11 *x11, t_butbox *bbox)
{
void set_vbtime(t_x11 *x11, t_butbox *vbox, char *text)
{
sfree(vbox->wd.text);
- vbox->wd.text = strdup(text);
+ vbox->wd.text = gmx_strdup(text);
ExposeWin(x11->disp, vbox->wd.self);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
+#include <stdlib.h>
#ifdef HAVE_UNISTD_H
#include <unistd.h> // for fork()
#endif
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "macros.h"
+#include "dialogs.h"
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/dir_separator.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "manager.h"
+#include "nmol.h"
#include "x11.h"
#include "xdlghi.h"
#include "xmb.h"
-#include "dialogs.h"
-#include "names.h"
-#include "nmol.h"
-#include "manager.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
#define MBFLAGS /* MB_APPLMODAL | */ MB_DONTSHOW
fprintf(stderr, "command: %s\n", command);
#endif
-#ifdef GMX_NO_SYSTEM
- printf("Warning-- No calls to system(3) supported on this platform.");
- printf("Warning-- Skipping execution of 'system(\"%s\")'.", buf);
-#else
if (0 != system(command))
{
gmx_fatal(FARGS, "Failed to execute command: %s", command);
}
-#endif
#ifdef DEBUG
unlink(tmp)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _dialogs_h
#define _dialogs_h
-#include "xdlg.h"
-#include "pulldown.h"
-#include "manager.h"
#include "logo.h"
+#include "manager.h"
+#include "pulldown.h"
+#include "xdlg.h"
typedef struct {
bool bMapped;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+#include "fgrid.h"
+
+#include <ctype.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include <ctype.h>
+
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "fgrid.h"
-#include "gromacs/fileio/futil.h"
static const char *type[] = {
"button", "radiobuttons", "groupbox", "checkbox",
static void ReadAccOpen(const char *infile, FILE *in)
{
char buf[STRLEN];
+ int result;
- fscanf(in, "%4s", buf);
- if (strcmp(buf, "{") != 0)
+ result = fscanf(in, "%4s", buf);
+ if ((1 != result) || strcmp(buf, "{") != 0)
{
ReadDlgErr(infile, eACCOEXP, buf);
}
static void ReadAccClose(const char *infile, FILE *in)
{
char buf[STRLEN];
+ int result;
- fscanf(in, "%4s", buf);
- if (strcmp(buf, "}") != 0)
+ result = fscanf(in, "%4s", buf);
+ if ((1 != result) || strcmp(buf, "}") != 0)
{
ReadDlgErr(infile, eACCCEXP, buf);
}
static void AddFItemName(t_fitem *fitem, char *name)
{
srenew(fitem->name, ++fitem->nname);
- fitem->name[fitem->nname-1] = strdup(name);
+ fitem->name[fitem->nname-1] = gmx_strdup(name);
}
static t_fgroup *NewFGroup(void)
ReadQuoteString(infile, in, get);
ReadQuoteString(infile, in, def);
ReadQuoteString(infile, in, help);
- fitem->set = strdup(set);
- fitem->get = strdup(get);
- fitem->def = strdup(def);
- fitem->help = strdup(help);
+ fitem->set = gmx_strdup(set);
+ fitem->get = gmx_strdup(get);
+ fitem->def = gmx_strdup(def);
+ fitem->help = gmx_strdup(help);
return fitem;
}
{
FILE *in;
char buf[STRLEN];
+ int result;
t_fgrid *fgrid;
t_fgroup *fgroup;
t_fsimple *fsimple;
int gridx, gridy;
- in = libopen(infile);
- fscanf(in, "%6s", buf);
- if (strcmp(buf, "grid") != 0)
+ in = libopen(infile);
+ result = fscanf(in, "%6s", buf);
+ if ((1 != result) || strcmp(buf, "grid") != 0)
{
ReadDlgErr(infile, eGRIDEXP, buf);
}
fgrid->w = gridx;
fgrid->h = gridy;
ReadAccOpen(infile, in);
- fscanf(in, "%15s", buf);
- while (bNotAccClose(buf))
+ result = fscanf(in, "%15s", buf);
+ while ((1 == result) && bNotAccClose(buf))
{
if (strcmp(buf, "group") == 0)
{
fgroup = AddFGridFGroup(fgrid);
ReadQuoteString(infile, in, buf);
- fgroup->name = strdup(buf);
+ fgroup->name = gmx_strdup(buf);
if ((fscanf(in, "%5d%5d%5d%5d", &fgroup->x, &fgroup->y, &fgroup->w, &fgroup->h)) != 4)
{
ReadDlgErr(infile, eNOVALS, "group x,y,w,h");
ReadDlgErr(infile, eTOOHIGH, buf);
}
ReadAccOpen(infile, in);
- fscanf(in, "%15s", buf);
- while (bNotAccClose(buf))
+ result = fscanf(in, "%15s", buf);
+ while ((1 == result) && bNotAccClose(buf))
{
AddFGroupFItem(fgroup, ScanFItem(infile, in, buf));
- fscanf(in, "%15s", buf);
+ result = fscanf(in, "%15s", buf);
}
}
else if (strcmp(buf, "simple") == 0)
ReadDlgErr(infile, eTOOHIGH, "simple");
}
ReadAccOpen(infile, in);
- fscanf(in, "%15s", buf);
- fsimple->fitem = ScanFItem(infile, in, buf);
- ReadAccClose(infile, in);
+ result = fscanf(in, "%15s", buf);
+ if (1 == result)
+ {
+ fsimple->fitem = ScanFItem(infile, in, buf);
+ ReadAccClose(infile, in);
+ }
+ }
+ if (1 == result)
+ {
+ result = fscanf(in, "%15s", buf);
}
- fscanf(in, "%15s", buf);
}
gmx_ffclose(in);
+ /* Since we always read one variable at a time the result from
+ * fscanf should always be 1.
+ */
+ if (1 != result)
+ {
+ ReadDlgErr(infile, eNOVALS, "fgrid");
+ }
return fgrid;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <string.h>
#include <algorithm>
-#include "sysstuff.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/dir_separator.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "index.h"
-#include "xdlghi.h"
+
#include "dialogs.h"
-#include "index.h"
-#include "gmx_fatal.h"
+#include "xdlghi.h"
t_filter *init_filter(t_atoms *atoms, const char *fn, int natom_trx)
{
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "sysstuff.h"
-#include "macros.h"
-#include "xutil.h"
-#include "Xstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "copyrite.h"
#include "logo.h"
+#include <stdlib.h>
+
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/real.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "Xstuff.h"
+#include "xutil.h"
+
typedef struct {
int x, y, rad;
unsigned long *col;
};
#define NMESS asize(Mess)
int i;
- real wfac, hfac;
t_logo *logo;
t_windata *wd;
wd = &(logo->wd);
if (bFirst)
{
- wfac = wd->width/110.0;
- hfac = wd->height/110.0;
+ const real wfac = wd->width/110.0;
+ const real hfac = wd->height/110.0;
for (i = 0; (i < asize(c)); i++)
{
c[i].x *= wfac;
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <ctype.h>
+#include <stdlib.h>
#include <string.h>
#ifdef HAVE_UNISTD_H
#include <unistd.h> // for usleep()
#endif
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "atomprop.h"
-#include "names.h"
#include "manager.h"
-#include "pbc.h"
-#include "nmol.h"
-#include "copyrite.h"
-#include "vec.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/tpxio.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "3dview.h"
+#include "nmol.h"
static void add_object(t_manager *man, eObject eO, atom_id ai, atom_id aj)
{
man->natom =
read_first_x(man->oenv, &man->status, trajectory, &(man->time), &(man->x),
man->box);
- man->trajfile = strdup(trajectory);
+ man->trajfile = gmx_strdup(trajectory);
if (man->natom > man->top.atoms.nr)
{
gmx_fatal(FARGS, "Topology %s (%d atoms) and trajectory %s (%d atoms) "
cool_quote(quote, 255, NULL);
sprintf(buf, "%s: %s", *man->top.name, quote);
- man->title.text = strdup(buf);
+ man->title.text = gmx_strdup(buf);
man->view = init_view(man->box);
at = &(man->top.atoms);
aps = gmx_atomprop_init();
#define _manager_h
#include <stdio.h>
-#include "typedefs.h"
+
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/pbcutil/rmpbc.h"
+
+#include "3dview.h"
+#include "buttons.h"
+#include "nleg.h"
#include "x11.h"
#include "xutil.h"
-#include "gromacs/math/3dview.h"
-#include "nleg.h"
-#include "buttons.h"
-#include "rmpbc.h"
-#include "gromacs/fileio/trxio.h"
/* Some window sizes */
#define EWIDTH 200
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include "sysstuff.h"
+#include <stdlib.h>
#include <string.h>
+
+#include "gromacs/fileio/writeps.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "xutil.h"
+
+#include "3dview.h"
#include "buttons.h"
#include "manager.h"
-#include "nmol.h"
#include "nleg.h"
-
-#include "gromacs/fileio/writeps.h"
-#include "gromacs/math/3dview.h"
+#include "nmol.h"
+#include "xutil.h"
#define MSIZE 4
{
corner[i][j] = ivec[i][j]*box[j][j];
}
- m4_op(view->proj, corner[i], x4);
+ gmx_mat4_transform_point(view->proj, corner[i], x4);
v4_to_iv2(x4, vec2[i], x0, y0, sx, sy);
}
ps_color(ps, 0, 0, 0.5);
{
if (man->bVis[i])
{
- m4_op(view->proj, man->x[i], x4);
+ gmx_mat4_transform_point(view->proj, man->x[i], x4);
man->zz[i] = x4[ZZ];
v4_to_iv2(x4, vec2[i], x0, y0, sx, sy);
}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "nleg.h"
#include <string.h>
#include <algorithm>
-#include "macros.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/types/rgb.h"
#include "gromacs/utility/smalloc.h"
#include "buttons.h"
-#include "nleg.h"
typedef struct {
const char *tp;
#ifndef _nleg_h
#define _nleg_h
+#include "gromacs/legacyheaders/types/rgb.h"
+
#include "x11.h"
#include "xutil.h"
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "nmol.h"
#include <math.h>
-#include "sysstuff.h"
+#include <stdlib.h>
#include <string.h>
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "xutil.h"
-#include "gromacs/math/3dview.h"
-#include "gmx_fatal.h"
+
+#include "3dview.h"
#include "buttons.h"
#include "manager.h"
-#include "nmol.h"
-#include "vec.h"
-#include "txtdump.h"
-#include "pbc.h"
+#include "xutil.h"
#define MSIZE 4
for (i = 0; (i < NCUCEDGE); i++)
{
- m4_op(view->proj, corner[i], x4);
+ gmx_mat4_transform_point(view->proj, corner[i], x4);
v4_to_iv2(x4, vec2[i], x0, y0, sx, sy);
}
XSetForeground(x11->disp, x11->gc, YELLOW);
}
}
rvec_inc(corner[i], box_center);
- m4_op(view->proj, corner[i], x4);
+ gmx_mat4_transform_point(view->proj, corner[i], x4);
v4_to_iv2(x4, vec2[i], x0, y0, sx, sy);
}
if (debug)
{
if (man->bVis[i])
{
- m4_op(view->proj, man->x[i], x4);
+ gmx_mat4_transform_point(view->proj, man->x[i], x4);
man->zz[i] = x4[ZZ];
v4_to_iv2(x4, vec2[i], x0, y0, sx, sy);
}
#ifndef _nmol_h
#define _nmol_h
+#include "manager.h"
#include "x11.h"
#include "xutil.h"
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "popup.h"
#include <math.h>
#include <string.h>
#include <algorithm>
-#include "macros.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/utility/smalloc.h"
#include "x11.h"
#include "xutil.h"
-#include "popup.h"
bool ChildCallBack(t_x11 *x11, XEvent *event, Window w, void *data)
{
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "pulldown.h"
#include <string.h>
#include <algorithm>
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "x11.h"
#include "popup.h"
-#include "pulldown.h"
+#include "x11.h"
static bool PDCallBack(t_x11 *x11, XEvent *event, Window w, void *data)
{
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
#include <stdio.h>
#include <string.h>
-#include "sysstuff.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "typedefs.h"
#include "gromacs/commandline/pargs.h"
-#include "copyrite.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/tpxio.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#ifdef GMX_X11
#include "gromacs/fileio/writeps.h"
#include "Xstuff.h"
-#include "gromacs.bm"
-#include "xutil.h"
#include "dialogs.h"
+#include "gromacs.bm"
#include "molps.h"
#include "nmol.h"
+#include "xutil.h"
static void dump_it(t_manager *man)
{
snew(gmx, 1);
snew(gmx->wd, 1);
- ePBC = read_tpx_top(ftp2fn(efTPX, nfile, fnm),
+ ePBC = read_tpx_top(ftp2fn(efTPR, nfile, fnm),
NULL, box, &natom, NULL, NULL, NULL, &top);
read_first_frame(oenv, &status, ftp2fn(efTRX, nfile, fnm), &fr, TRX_DONT_SKIP);
init_dlgs(x11, gmx);
/* Now do file operations */
- set_file(x11, gmx->man, ftp2fn(efTRX, nfile, fnm), ftp2fn(efTPX, nfile, fnm));
+ set_file(x11, gmx->man, ftp2fn(efTRX, nfile, fnm), ftp2fn(efTPR, nfile, fnm));
ShowDlg(gmx->dlgs[edFilter]);
}
output_env_t oenv;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD }
};
#define NFILE asize(fnm)
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "x11.h"
+#include <stdlib.h>
#include <string.h>
-#include "typedefs.h"
-#include "sysstuff.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
+
#include "Xstuff.h"
-#include "x11.h"
/* These colours will be mapped to black on a monochrome screen */
unsigned long BLACK, BLUE, GREEN, CYAN, RED, BROWN, GREY, DARKGREY;
bool bVerbose = false;
int i;
- title = strdup(argv[0]);
+ title = gmx_strdup(argv[0]);
/* First check environment */
fontname = getenv("GMX_FONT");
break;
case 't':
sfree(title);
- title = strdup(argv[++i]);
+ title = gmx_strdup(argv[++i]);
break;
case 'v':
bVerbose = true;
{
x11->bg = LIGHTGREY;
}
- x11->title = strdup(title);
+ x11->title = gmx_strdup(title);
sfree(title);
x11->wlist = NULL;
x11->GetNamedColor = &GetNamedColor;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define _x11_h
#include <stdio.h>
-#include "typedefs.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
+
#include "Xstuff.h"
/* These colours will be mapped to black on a monochrome screen */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "xdlg.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
+
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/utility/cstringutil.h"
-#include "macros.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
+
#include "Xstuff.h"
-#include "xutil.h"
-#include "xdlg.h"
#include "xmb.h"
-#include "gmx_fatal.h"
+#include "xutil.h"
/*****************************
*
* Helpful routines
if (gmx_strcasecmp(buf, "nok") == 0)
{
/* An error occurred */
- for (i = 0; (i < nlines); i++)
+ if (lines)
{
- sfree(lines[i]);
+ for (i = 0; (i < nlines); i++)
+ {
+ sfree(lines[i]);
+ }
+ sfree(lines);
}
- sfree(lines);
NoHelp(dlg);
return;
}
if (bCont)
{
srenew(lines, ++nlines);
- lines[nlines-1] = strdup(buf);
+ lines[nlines-1] = gmx_strdup(buf);
}
}
}
dlg->data = data;
if (title)
{
- dlg->title = strdup(title);
+ dlg->title = gmx_strdup(title);
}
else
{
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "xdlghi.h"
+#include <stdlib.h>
#include <string.h>
#include <algorithm>
-#include "gmx_fatal.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gromacs/utility/cstringutil.h"
-#include "sysstuff.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "macros.h"
-#include "xutil.h"
-#include "xdlghi.h"
+
#include "fgrid.h"
+#include "xutil.h"
t_dlgitem **CreateRadioButtonGroup(t_x11 *x11, char *szTitle,
t_id GroupID, int nrb, t_id rb[],
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define _xdlghi_h
#include <stdarg.h>
+
#include "Xstuff.h"
#include "x11.h"
#include "xdlg.h"
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "xdlgitem.h"
#include <ctype.h>
#include <stdio.h>
#include <algorithm>
-#include "gmx_fatal.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-#include "macros.h"
+
#include "Xstuff.h"
-#include "xdlgitem.h"
#define BUFSIZE 16
case ButtonPress:
/* Calculate new position for caret */
et->pos = strlen(et->buf);
- bp = strdup(et->buf);
+ bp = gmx_strdup(et->buf);
xp = event->xbutton.x-XTextWidth(x11->font, win->text, strlen(win->text))-
XCARET;
while ((et->pos > 0) && (XTextWidth(x11->font, bp, strlen(bp)) > xp))
}
else
{
- lab = strdup(szLab);
+ lab = gmx_strdup(szLab);
}
InitWin(&(dlgitem->win), x0, y0, w, h, bw, szLab);
sfree(lab);
snew(dlgitem->u.statictext.lines, nlines);
for (i = 0; (i < nlines); i++)
{
- dlgitem->u.statictext.lines[i] = strdup(lines[i]);
+ dlgitem->u.statictext.lines[i] = gmx_strdup(lines[i]);
}
dlgitem->WndProc = WndProcST;
return dlgitem;
}
-#define SC(src) (strlen(src) ? strdup(src) : NULL)
+#define SC(src) (strlen(src) ? gmx_strdup(src) : NULL)
void SetDlgitemOpts(t_dlgitem *dlgitem, bool bUseMon,
char *set, char *get, char *help)
#define _xdlgitem_h
#include "Xstuff.h"
-#include "xutil.h"
#include "x11.h"
+#include "xutil.h"
typedef enum {
edlgBN, edlgRB, edlgGB, edlgCB, edlgPM, edlgST, edlgET, edlgNR
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "xmb.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include "typedefs.h"
-#include "macros.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/fatalerror.h"
+
#include "Xstuff.h"
-#include "x11.h"
-#include "xutil.h"
-#include "xdlg.h"
-#include "xmb.h"
-#include "gmx_fatal.h"
+#include "alert.bm"
#include "gromacs.bm"
-#include "stop.bm"
#include "info.bm"
-#include "alert.bm"
+#include "stop.bm"
+#include "x11.h"
+#include "xdlg.h"
+#include "xutil.h"
#define ID_BOX -3
#define ID_ICON -2
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _xmb_h
#define _xmb_h
+#include "manager.h"
#include "x11.h"
+#include "xdlg.h"
+#include "xmb.h"
#define MB_OK 1
#define MB_CANCEL (1<<1)
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "xutil.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "xutil.h"
+
#include "Xstuff.h"
int CheckWin(Window win, const char *file, int line)
win->cursor = 0;
if (text)
{
- win->text = strdup(text);
+ win->text = gmx_strdup(text);
}
else
{
#ifndef _xutil_h
#define _xutil_h
-#include "typedefs.h"
+#include "gromacs/legacyheaders/typedefs.h"
/* TODO: This include is needed here, because this header reuses eXPos and
* eYPos. It has nothing to do with PostScript output. */
#include "gromacs/fileio/writeps.h"
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
add_executable(${EXENAME} ${UNITTEST_TARGET_OPTIONS} ${ARGN} ${TESTUTILS_DIR}/unittest_main.cpp)
set_property(TARGET ${EXENAME} APPEND PROPERTY COMPILE_DEFINITIONS "${GMOCK_COMPILE_DEFINITIONS}")
target_link_libraries(${EXENAME} ${TESTUTILS_LIBS} libgromacs ${GMOCK_LIBRARIES} ${GMX_EXE_LINKER_FLAGS})
+ file(RELATIVE_PATH _input_files_path ${CMAKE_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR})
set(_temporary_files_path "${CMAKE_CURRENT_BINARY_DIR}/Testing/Temporary")
file(MAKE_DIRECTORY ${_temporary_files_path})
-
# Note that the quotation marks in the next line form part of
# the defined symbol, so that the macro replacement in the
# source file is as a string.
- set(EXTRA_COMPILE_DEFINITIONS TEST_DATA_PATH="${CMAKE_CURRENT_SOURCE_DIR}" TEST_TEMP_PATH="${_temporary_files_path}")
+ set(EXTRA_COMPILE_DEFINITIONS
+ TEST_DATA_PATH="${_input_files_path}"
+ TEST_TEMP_PATH="${_temporary_files_path}")
set_property(TARGET ${EXENAME} APPEND PROPERTY COMPILE_DEFINITIONS "${EXTRA_COMPILE_DEFINITIONS}")
endif()
*/
/*! \internal \file
* \brief
- * Implements gmx::test::CommandLine.
+ * Implements classes from cmdlinetest.h.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_testutils
*/
+#include "gmxpre.h"
+
#include "cmdlinetest.h"
#include <cstdlib>
#include <cstring>
-#include <sstream>
#include <new>
+#include <sstream>
#include <vector>
+#include <boost/scoped_ptr.hpp>
+
+#include "gromacs/commandline/cmdlineoptionsmodule.h"
#include "gromacs/commandline/cmdlineprogramcontext.h"
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/file.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testfilemanager.h"
namespace gmx
{
return ss.str();
}
-}
+} // namespace
-void CommandLine::addOption(const char *name,
- const char *value)
+void CommandLine::addOption(const char *name, const char *value)
{
append(name);
append(value);
}
-void CommandLine::addOption(const char *name,
- const std::string &value)
+void CommandLine::addOption(const char *name, const std::string &value)
{
addOption(name, value.c_str());
}
-void CommandLine::addOption(const char *name,
- int value)
+void CommandLine::addOption(const char *name, int value)
{
append(name);
append(value2string(value));
}
-void CommandLine::addOption(const char *name,
- double value)
+void CommandLine::addOption(const char *name, double value)
{
append(name);
append(value2string(value));
}
+void CommandLine::merge(const CommandLine &args)
+{
+ // Skip first argument if it is the module name.
+ const int firstArg = (args.arg(0)[0] == '-' ? 0 : 1);
+ for (int i = firstArg; i < args.argc(); ++i)
+ {
+ append(args.arg(i));
+ }
+}
+
int &CommandLine::argc()
{
return impl_->argc_;
return CommandLineProgramContext(argc(), argv()).commandLine();
}
+/********************************************************************
+ * CommandLineTestHelper::Impl
+ */
+
+class CommandLineTestHelper::Impl
+{
+ public:
+ struct OutputFileInfo
+ {
+ OutputFileInfo(const char *option, const std::string &path)
+ : option(option), path(path)
+ {
+ }
+
+ std::string option;
+ std::string path;
+ };
+
+ typedef std::vector<OutputFileInfo> OutputFileList;
+
+ explicit Impl(TestFileManager *fileManager)
+ : fileManager_(*fileManager)
+ {
+ }
+
+ TestFileManager &fileManager_;
+ OutputFileList outputFiles_;
+};
+
+/********************************************************************
+ * CommandLineTestHelper
+ */
+
+// static
+int CommandLineTestHelper::runModule(
+ CommandLineModuleInterface *module, CommandLine *commandLine)
+{
+ CommandLineModuleSettings settings;
+ module->init(&settings);
+ return module->run(commandLine->argc(), commandLine->argv());
+}
+
+// static
+int CommandLineTestHelper::runModule(
+ CommandLineOptionsModuleInterface::FactoryMethod factory,
+ CommandLine *commandLine)
+{
+ // The name and description are not used in the tests, so they can be NULL.
+ boost::scoped_ptr<CommandLineModuleInterface> module(
+ CommandLineOptionsModuleInterface::createModule(NULL, NULL, factory));
+ return runModule(module.get(), commandLine);
+}
+
+CommandLineTestHelper::CommandLineTestHelper(TestFileManager *fileManager)
+ : impl_(new Impl(fileManager))
+{
+}
+
+CommandLineTestHelper::~CommandLineTestHelper()
+{
+}
+
+void CommandLineTestHelper::setInputFileContents(
+ CommandLine *args, const char *option, const char *extension,
+ const std::string &contents)
+{
+ GMX_ASSERT(extension[0] != '.', "Extension should not contain a dot");
+ std::string fullFilename = impl_->fileManager_.getTemporaryFilePath(
+ formatString("%d.%s", args->argc(), extension));
+ File::writeFileFromString(fullFilename, contents);
+ args->addOption(option, fullFilename);
+}
+
+void CommandLineTestHelper::setInputFileContents(
+ CommandLine *args, const char *option, const char *extension,
+ const ConstArrayRef<const char *> &contents)
+{
+ GMX_ASSERT(extension[0] != '.', "Extension should not contain a dot");
+ std::string fullFilename = impl_->fileManager_.getTemporaryFilePath(
+ formatString("%d.%s", args->argc(), extension));
+ File file(fullFilename, "w");
+ ConstArrayRef<const char *>::const_iterator i;
+ for (i = contents.begin(); i != contents.end(); ++i)
+ {
+ file.writeLine(*i);
+ }
+ file.close();
+ args->addOption(option, fullFilename);
+}
+
+void CommandLineTestHelper::setOutputFile(
+ CommandLine *args, const char *option, const char *filename)
+{
+ std::string fullFilename = impl_->fileManager_.getTemporaryFilePath(filename);
+ args->addOption(option, fullFilename);
+ impl_->outputFiles_.push_back(Impl::OutputFileInfo(option, fullFilename));
+}
+
+void CommandLineTestHelper::setOutputFileNoTest(
+ CommandLine *args, const char *option, const char *extension)
+{
+ std::string fullFilename = impl_->fileManager_.getTemporaryFilePath(
+ formatString("%d.%s", args->argc(), extension));
+ args->addOption(option, fullFilename);
+}
+
+void CommandLineTestHelper::checkOutputFiles(TestReferenceChecker checker) const
+{
+ if (!impl_->outputFiles_.empty())
+ {
+ TestReferenceChecker outputChecker(
+ checker.checkCompound("OutputFiles", "Files"));
+ Impl::OutputFileList::const_iterator outfile;
+ for (outfile = impl_->outputFiles_.begin();
+ outfile != impl_->outputFiles_.end();
+ ++outfile)
+ {
+ std::string output = File::readToString(outfile->path);
+ outputChecker.checkStringBlock(output, outfile->option.c_str());
+ }
+ }
+}
+
+/********************************************************************
+ * CommandLineTestBase::Impl
+ */
+
+class CommandLineTestBase::Impl
+{
+ public:
+ Impl() : helper_(&tempFiles_)
+ {
+ cmdline_.append("module");
+ }
+
+ TestReferenceData data_;
+ TestFileManager tempFiles_;
+ CommandLineTestHelper helper_;
+ CommandLine cmdline_;
+};
+
+/********************************************************************
+ * CommandLineTestBase
+ */
+
+CommandLineTestBase::CommandLineTestBase()
+ : impl_(new Impl)
+{
+}
+
+CommandLineTestBase::~CommandLineTestBase()
+{
+}
+
+void CommandLineTestBase::setInputFile(
+ const char *option, const char *filename)
+{
+ impl_->cmdline_.addOption(option, TestFileManager::getInputFilePath(filename));
+}
+
+void CommandLineTestBase::setInputFileContents(
+ const char *option, const char *extension, const std::string &contents)
+{
+ impl_->helper_.setInputFileContents(&impl_->cmdline_, option, extension,
+ contents);
+}
+
+void CommandLineTestBase::setInputFileContents(
+ const char *option, const char *extension,
+ const ConstArrayRef<const char *> &contents)
+{
+ impl_->helper_.setInputFileContents(&impl_->cmdline_, option, extension,
+ contents);
+}
+
+void CommandLineTestBase::setOutputFile(
+ const char *option, const char *filename)
+{
+ impl_->helper_.setOutputFile(&impl_->cmdline_, option, filename);
+}
+
+void CommandLineTestBase::setOutputFileNoTest(
+ const char *option, const char *extension)
+{
+ impl_->helper_.setOutputFileNoTest(&impl_->cmdline_, option, extension);
+}
+
+CommandLine &CommandLineTestBase::commandLine()
+{
+ return impl_->cmdline_;
+}
+
+TestFileManager &CommandLineTestBase::fileManager()
+{
+ return impl_->tempFiles_;
+}
+
+TestReferenceChecker CommandLineTestBase::rootChecker()
+{
+ return impl_->data_.rootChecker();
+}
+
+void CommandLineTestBase::checkOutputFiles()
+{
+ impl_->helper_.checkOutputFiles(rootChecker());
+}
+
} // namespace test
} // namespace gmx
*/
/*! \libinternal \file
* \brief
- * Declares gmx::test::CommandLine.
+ * Declares utilities testing command-line programs.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \inlibraryapi
#include <string>
+#include <gtest/gtest.h>
+
// arrayref.h is not strictly necessary for this header, but nearly all
// callers will need it to use the constructor that takes ConstArrayRef.
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/common.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
+
+class CommandLineModuleInterface;
+class CommandLineOptionsModuleInterface;
+
namespace test
{
+class TestFileManager;
+class TestReferenceChecker;
+
/*! \libinternal \brief
- * Helper class for tests that check command-line handling.
+ * Helper class for tests that need to construct command lines.
*
* This class helps in writing tests for command-line handling.
* The constructor method takes an array of const char pointers, specifying the
* parameters are actually modified. Reading the command line is possible
* afterwards, but modification is not.
*
+ * If you need to construct command lines that refer to files on the file
+ * system, see CommandLineTestHelper and CommandLineTestBase for additional
+ * convenience utilities.
+ *
* All constructors and methods that modify this class may throw an
* std::bad_alloc. Const methods and accessors do not throw.
*
void initFromArray(const ConstArrayRef<const char *> &cmdline);
/*! \brief
- * Append an argument to the command line.
+ * Appends an argument to the command line.
*
* \param[in] arg Argument to append.
*
//! Convenience overload taking a std::string.
void append(const std::string &arg) { append(arg.c_str()); }
/*! \brief
- * Add an option-value pair to the command line.
+ * Adds an option-value pair to the command line.
*
* \param[in] name Name of the option to append, which
* should start with "-".
void addOption(const char *name, int value);
//! Overload taking a double.
void addOption(const char *name, double value);
+ /*! \brief
+ * Appends all arguments from \p args to the command line.
+ *
+ * If the first argument of \p args does not start with a `-`, it is
+ * skipped.
+ */
+ void merge(const CommandLine &args);
+
//! Returns argc for passing into C-style command-line handling.
int &argc();
//! Returns argv for passing into C-style command-line handling.
PrivateImplPointer<Impl> impl_;
};
+/*! \libinternal \brief
+ * Helper class for tests that construct command lines that need to reference
+ * existing files.
+ *
+ * This class provides helper methods for:
+ *
+ * 1. Adding input files to a CommandLine instance by generating them from a
+ * string provided in the test (setInputFileContents()).
+ * 2. Adding output files to a CommandLine instance (setOutputFile() and
+ * setOutputFileNoTest()).
+ * 3. Checking the contents of some of the output files using
+ * TestReferenceData (setOutputFile() and checkOutputFiles()).
+ * 4. Static methods for easily executing command-line modules
+ * (various overloads of runModule()).
+ *
+ * All files created during the test are cleaned up at the end of the test.
+ *
+ * All methods can throw std::bad_alloc.
+ *
+ * \see TestFileManager
+ * \inlibraryapi
+ * \ingroup module_testutils
+ */
+class CommandLineTestHelper
+{
+ public:
+ /*! \brief
+ * Runs a command-line program that implements CommandLineModuleInterface.
+ *
+ * \param[in,out] module Module to run.
+ * The function does not take ownership.
+ * \param[in,out] commandLine Command line parameters to pass.
+ * This is only modified if \p module modifies it.
+ * \returns The return value of the module.
+ * \throws unspecified Any exception thrown by the module.
+ */
+ static int
+ runModule(CommandLineModuleInterface *module, CommandLine *commandLine);
+ /*! \brief
+ * Runs a command-line program that implements
+ * CommandLineOptionsModuleInterface.
+ *
+ * \param[in] factory Factory method for the module to run.
+ * \param[in,out] commandLine Command line parameters to pass.
+ * This is only modified if the module modifies it.
+ * \returns The return value of the module.
+ * \throws unspecified Any exception thrown by the factory or the
+ * module.
+ */
+ static int
+ runModule(CommandLineOptionsModuleInterface *(*factory)(),
+ CommandLine *commandLine);
+
+ /*! \brief
+ * Initializes an instance.
+ *
+ * \param fileManager File manager to use for generating temporary
+ * file names and to track temporary files.
+ */
+ explicit CommandLineTestHelper(TestFileManager *fileManager);
+ ~CommandLineTestHelper();
+
+ /*! \brief
+ * Generates and sets an input file.
+ *
+ * \param[in,out] args CommandLine to which to add the option.
+ * \param[in] option Option to set.
+ * \param[in] extension Extension for the file to create.
+ * \param[in] contents Text to write to the input file.
+ *
+ * Creates a temporary file with contents from \p contents, and adds
+ * \p option to \p args with a value that points to the generated file.
+ */
+ void setInputFileContents(CommandLine *args, const char *option,
+ const char *extension,
+ const std::string &contents);
+ /*! \brief
+ * Generates and sets an input file.
+ *
+ * \param[in,out] args CommandLine to which to add the option.
+ * \param[in] option Option to set.
+ * \param[in] extension Extension for the file to create.
+ * \param[in] contents Text to write to the input file.
+ *
+ * Creates a temporary file with contents from \p contents (each array
+ * entry on its own line), and adds \p option to \p args with a value
+ * that points to the generated file.
+ */
+ void setInputFileContents(CommandLine *args, const char *option,
+ const char *extension,
+ const ConstArrayRef<const char *> &contents);
+ /*! \brief
+ * Sets an output file parameter and adds it to the set of tested files.
+ *
+ * \param[in,out] args CommandLine to which to add the option.
+ * \param[in] option Option to set.
+ * \param[in] filename Name of the output file.
+ *
+ * This method:
+ * - Adds \p option to \p args to point a temporary file name
+ * constructed from \p filename.
+ * - Makes checkOutputFiles() to check the contents of the file
+ * against reference data.
+ * - Marks the temporary file for removal at test teardown.
+ *
+ * \p filename is given to TestTemporaryFileManager to make a unique
+ * filename for the temporary file, but is not otherwise used.
+ *
+ * Currently, this method should not be called for an XVG file, because
+ * the comments in the beginning of the file contain timestamps and
+ * other variable information, causing the test to fail. Best used
+ * only for custom data formats.
+ */
+ void setOutputFile(CommandLine *args, const char *option,
+ const char *filename);
+ /*! \brief
+ * Sets an output file parameter.
+ *
+ * \param[in,out] args CommandLine to which to add the option.
+ * \param[in] option Option to set.
+ * \param[in] extension Extension for the file to create.
+ *
+ * This method:
+ * - Adds \p option to \p args to point to a temporary file name with
+ * extension \p extension.
+ * - Marks the temporary file for removal at test teardown.
+ *
+ * This method provides the mechanism to set output files that are
+ * required to trigger computation of values that are required for
+ * the test. The contents of the output file are not tested.
+ *
+ * Another use case is to mark files that are unconditionally produced
+ * by the code under test, but do not need to be tested. This method
+ * makes the test code aware of those files such that it can remove
+ * them at the end of the test.
+ */
+ void setOutputFileNoTest(CommandLine *args, const char *option,
+ const char *extension);
+
+ /*! \brief
+ * Checks output files added with setOutputFile() against reference
+ * data.
+ *
+ * \param checker Reference data root location where the reference
+ * data is stored.
+ *
+ * The file contents are tested verbatim, using direct string
+ * comparison. The text can be found verbatim in the reference data
+ * XML files for manual inspection.
+ *
+ * Generates non-fatal test failures if some output file contents do
+ * not match the reference data.
+ */
+ void checkOutputFiles(TestReferenceChecker checker) const;
+
+ private:
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
+};
+
+/*! \libinternal \brief
+ * Test fixture for tests that call a single command-line program with
+ * input/output files.
+ *
+ * This class provides a convenient package for using CommandLineTestHelper in
+ * a test that do not need special customization. It takes care of creating
+ * the other necessary objects (like TestFileManager, TestReferenceData, and
+ * CommandLine) and wrapping the methods from CommandLineTestHelper such that
+ * extra parameters are not needed. Additionally, it provides setInputFile()
+ * as a convenience function for adding a fixed input file, pointing to a file
+ * that resides in the source tree.
+ *
+ * \see CommandLineTestHelper
+ * \inlibraryapi
+ * \ingroup module_testutils
+ */
+class CommandLineTestBase : public ::testing::Test
+{
+ public:
+ CommandLineTestBase();
+ ~CommandLineTestBase();
+
+ /*! \brief
+ * Sets an input file.
+ *
+ * \param[in] option Option to set.
+ * \param[in] filename Name of the input file.
+ *
+ * \see TestFileManager::getInputFilePath()
+ */
+ void setInputFile(const char *option, const char *filename);
+ /*! \brief
+ * Generates and sets an input file.
+ *
+ * \see CommandLineTestHelper::setInputFileContents()
+ */
+ void setInputFileContents(const char *option,
+ const char *extension,
+ const std::string &contents);
+ /*! \brief
+ * Generates and sets an input file.
+ *
+ * \see CommandLineTestHelper::setInputFileContents()
+ */
+ void setInputFileContents(const char *option,
+ const char *extension,
+ const ConstArrayRef<const char *> &contents);
+ /*! \brief
+ * Sets an output file parameter and adds it to the set of tested files.
+ *
+ * \see CommandLineTestHelper::setOutputFile()
+ */
+ void setOutputFile(const char *option, const char *filename);
+ /*! \brief
+ * Sets an output file parameter.
+ *
+ * \see CommandLineTestHelper::setOutputFileNoTest()
+ */
+ void setOutputFileNoTest(const char *option, const char *extension);
+
+ /*! \brief
+ * Returns the internal CommandLine object used to construct the
+ * command line for the test.
+ *
+ * Derived test fixtures can use this to add additional options, and
+ * to access the final command line to do the actual call that is being
+ * tested.
+ *
+ * Does not throw.
+ */
+ CommandLine &commandLine();
+ /*! \brief
+ * Returns the internal TestFileManager object used to manage the
+ * files.
+ *
+ * Derived test fixtures can use this to manage files in cases the
+ * canned methods are not sufficient.
+ *
+ * Does not throw.
+ */
+ TestFileManager &fileManager();
+ /*! \brief
+ * Returns the root reference data checker.
+ *
+ * Derived test fixtures can use this to check other things than output
+ * file contents.
+ */
+ TestReferenceChecker rootChecker();
+
+ /*! \brief
+ * Checks output files added with setOutputFile() against reference
+ * data.
+ *
+ * \see CommandLineTestHelper::checkOutputFiles()
+ */
+ void checkOutputFiles();
+
+ private:
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
+};
+
} // namespace test
} // namespace gmx
* \author Mark Abraham <mark.j.abraham@gmail.com>
* \ingroup module_testutils
*/
+#include "gmxpre.h"
+
#include "integrationtests.h"
-#include "testutils/testoptions.h"
-#include "gromacs/utility/stringutil.h"
+#include <stdio.h>
+
#include "gromacs/utility/exceptions.h"
-#include "gromacs/options/options.h"
-#include "gromacs/options/basicoptions.h"
#include "gromacs/utility/file.h"
-#include <stdlib.h>
-#include <stdio.h>
namespace gmx
{
* IntegrationTestFixture
*/
-std::string IntegrationTestFixture::s_maxBackup("-1");
-
-//! \cond
-GMX_TEST_OPTIONS(IntegrationTestOptions, options)
-{
- options->addOption(StringOption("max-backup")
- .store(&IntegrationTestFixture::s_maxBackup)
- .description("Maximum number of backup files of old test output to write (-1 prevents backups being created)"));
-}
-//! \endcond
-
IntegrationTestFixture::IntegrationTestFixture()
{
- // TODO fix this when we have an encapsulation layer for handling
- // environment variables
-#ifdef GMX_NATIVE_WINDOWS
- _putenv(("GMX_MAXBACKUP="+s_maxBackup).c_str());
-#else
- setenv("GMX_MAXBACKUP", s_maxBackup.c_str(), true);
-#endif
}
IntegrationTestFixture::~IntegrationTestFixture()
* sufficiently modular to permit it to work. */
void redirectStderrToDevNull();
- /* TEST_F() constructs derived classes, and those classes
- * might need to access implementation details, so we
- * cannot use the private access specifer here. */
- protected:
+ /* TEST_F() constructs derived classes, and those classes and
+ * their member objects might need to access implementation
+ * details, so we cannot use the private access specifer
+ * here. */
+ public:
/*! \brief Object that manages finding input files, writing
* temporary output files and cleaning up files.
*/
::gmx::test::TestFileManager fileManager_;
-
- public:
- //! Number of backup files to write
- static std::string s_maxBackup;
};
} // namespace test
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
#include "mpi-printer.h"
#include "config.h"
+
#include "gromacs/utility/gmxmpi.h"
#ifdef GMX_LIB_MPI
#include <boost/scoped_ptr.hpp>
#include <gtest/gtest.h>
-#include "gromacs/utility/common.h"
+#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/gmxassert.h"
#define FORWARD_TO_DEFAULT_PRINTER1(MethodName, Param1Type) \
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_testutils
*/
+#include "gmxpre.h"
+
#include "refdata.h"
#include <cstdio>
#include <libxml/parser.h>
#include <libxml/xmlmemory.h>
-#include "gromacs/fileio/path.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/path.h"
#include "gromacs/utility/stringutil.h"
#include "testutils/testasserts.h"
#include <iterator>
#include <string>
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/utility/common.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_testutils
*/
-#include "testutils/stringtest.h"
+#include "gmxpre.h"
+
+#include "stringtest.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <boost/scoped_ptr.hpp>
#include <gtest/gtest.h>
-#include "refdata.h"
+#include "testutils/refdata.h"
namespace gmx
{
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_testutils
*/
-#include "testutils/testasserts.h"
+#include "gmxpre.h"
+
+#include "testasserts.h"
#include <cmath>
#include <gtest/gtest.h>
-#include "gromacs/legacyheaders/types/simple.h"
-
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/stringutil.h"
namespace gmx
}
/*! \brief
- * Computes difference in ULPs between two numbers, treating also values of
- * different sign.
+ * Computes the magnitude of the difference in ULPs between two numbers,
+ * treating also values of different sign.
*/
template <typename FloatType>
gmx_uint64_t calculateUlpDifference(const FloatingPoint<FloatType> &value1,
*ulpDifference = calculateUlpDifference(value1, value2);
}
+/*! \brief
+ * Converts a relative tolerance into an ULP difference.
+ */
+template <typename FloatType>
+gmx_uint64_t relativeToleranceToUlp(FloatType tolerance)
+{
+ FloatingPoint<FloatType> m(1.0);
+ FloatingPoint<FloatType> t(1.0 + tolerance);
+ return calculateUlpDifference<FloatType>(m, t);
+}
+
//! \}
//! \}
std::string FloatingPointDifference::toString() const
{
- return formatString("%g (%" GMX_PRIu64 " %s-prec. ULPs)%s",
+ const double eps = isDouble() ? GMX_DOUBLE_EPS : GMX_FLOAT_EPS;
+ return formatString("%g (%" GMX_PRIu64 " %s-prec. ULPs, rel. %.3g)%s",
absoluteDifference_, ulpDifference_,
- bDouble_ ? "double" : "single",
+ isDouble() ? "double" : "single",
+ ulpDifference_ * eps,
bSignDifference_ ? ", signs differ" : "");
}
return false;
}
- if (difference.asAbsolute() < absoluteTolerance_)
+ const double absoluteTolerance
+ = difference.isDouble() ? doubleAbsoluteTolerance_ : singleAbsoluteTolerance_;
+ if (difference.asAbsolute() < absoluteTolerance)
{
return true;
}
- if (ulpTolerance_ >= 0
- && difference.asUlps() <= static_cast<gmx_uint64_t>(ulpTolerance_))
+ const gmx_uint64_t ulpTolerance
+ = difference.isDouble() ? doubleUlpTolerance_ : singleUlpTolerance_;
+ if (ulpTolerance < GMX_UINT64_MAX && difference.asUlps() <= ulpTolerance)
{
return true;
}
return false;
}
-std::string FloatingPointTolerance::toString() const
+std::string FloatingPointTolerance::toString(const FloatingPointDifference &difference) const
{
- std::string result;
- if (absoluteTolerance_ > 0.0)
+ std::string result;
+ const double absoluteTolerance
+ = difference.isDouble() ? doubleAbsoluteTolerance_ : singleAbsoluteTolerance_;
+ const gmx_uint64_t ulpTolerance
+ = difference.isDouble() ? doubleUlpTolerance_ : singleUlpTolerance_;
+ const double eps
+ = difference.isDouble() ? GMX_DOUBLE_EPS : GMX_FLOAT_EPS;
+
+ if (absoluteTolerance > 0.0)
{
- result.append(formatString("abs. %g", absoluteTolerance_));
+ result.append(formatString("abs. %g", absoluteTolerance));
}
- if (ulpTolerance_ >= 0)
+ if (ulpTolerance < GMX_UINT64_MAX)
{
if (!result.empty())
{
result.append(", ");
}
- result.append(formatString("%d ULPs", ulpTolerance_));
+ result.append(formatString("%" GMX_PRIu64 " ULPs (rel. %.3g)", ulpTolerance, ulpTolerance * eps));
}
if (bSignMustMatch_)
{
return result;
}
+// Doxygen does not recognize this as the same function as in the header...
+//! \cond
+FloatingPointTolerance
+relativeToleranceAsFloatingPoint(double magnitude, double tolerance)
+{
+ const double absoluteTolerance = magnitude * tolerance;
+ return FloatingPointTolerance(absoluteTolerance, absoluteTolerance,
+ relativeToleranceToUlp<float>(tolerance),
+ relativeToleranceToUlp<double>(tolerance),
+ false);
+}
+//! \endcond
+
} // namespace test
} // namespace gmx
* assertions for:
* - exceptions
* - floating-point comparison
+ * - comparison against NULL
*
* \if internal
* \todo
#include <gtest/gtest.h>
-#include "gromacs/legacyheaders/types/simple.h"
-
+#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/real.h"
namespace gmx
{
* 0.0 and -0.0 are treated as positive and negative, respectively.
*/
bool signsDiffer() const { return bSignDifference_; }
-
+ /*! \brief
+ * Whether the difference is between single- or double-precision
+ * numbers.
+ */
+ bool isDouble() const { return bDouble_; }
//! Formats the difference as a string for assertion failure messages.
std::string toString() const;
* Specifies a floating-point comparison tolerance and checks whether a
* difference is within the tolerance.
*
+ * The related functions section lists methods that can be construct methods
+ * using less parameters than the full constructor, and with more obvious
+ * semantics. These should be preferred over using the constructor directly.
+ *
* Several types of tolerances are possible:
* - _absolute tolerance_: difference between the values must be smaller than
* the given tolerance for the check to pass.
* - _ULP tolerance_: ULP (units of least precision) difference between the
* values must be smaller than the given tolerance for the check to pass.
* Setting the ULP tolerance to zero requires exact match.
- * Setting the ULP tolerance to negative disables the ULP check.
+ * Setting the ULP tolerance to GMX_UINT64_MAX disables the ULP check.
* `0.0` and `-0.0` are treated as equal for the ULP check.
* - _sign check_: if set, any values that are of different signs fail the
* check (note that this also applies to `0.0` and `-0.0`: a value with a
* check. In this case, the sign check must succeed for the check to pass,
* even if other tolerances are satisfied.
*
- * Currently, the ULP tolerance is not in any particular precision, but the
- * interpretation depends on the compared numbers: if floats are compared, then
- * the ULP tolerance specifies single-precision ULPs, and if doubles are
- * compared, then the same number is interpreted as double-precision ULPs.
- *
- * The related functions section lists methods that can be construct methods
- * using less parameters than the full constructor, and with more obvious
- * semantics.
+ * The tolerances can be specified separately for single and double precision
+ * comparison. Different initialization functions have different semantics on
+ * how the provided tolerance values are interpreted; check their
+ * documentation.
*
* Methods in this class do not throw, except for toString(), which may throw
* std::bad_alloc.
*
+ * \todo
+ * The factory methods that take ULP difference could be better formulated as
+ * methods that take the acceptable number of incorrect bits and/or the number
+ * of accurate bits.
+ *
* \see FloatingPointDifference
*/
class FloatingPointTolerance
/*! \brief
* Creates a tolerance with the specified values.
*
- * \param[in] absolute Allowed absolute difference.
- * \param[in] ulp Allowed ULP difference.
- * \param[in] bSignMustMatch Whether sign mismatch fails the comparison.
+ * \param[in] singleAbsoluteTolerance
+ * Allowed absolute difference in a single-precision number.
+ * \param[in] doubleAbsoluteTolerance
+ * Allowed absolute difference in a double-precision number.
+ * \param[in] singleUlpTolerance
+ * Allowed ULP difference in a single-precision number.
+ * \param[in] doubleUlpTolerance
+ * Allowed ULP difference in a double-precision number.
+ * \param[in] bSignMustMatch
+ * Whether sign mismatch fails the comparison.
*/
- FloatingPointTolerance(double absolute, int ulp,
- bool bSignMustMatch)
- : absoluteTolerance_(absolute), ulpTolerance_(ulp),
+ FloatingPointTolerance(float singleAbsoluteTolerance,
+ double doubleAbsoluteTolerance,
+ gmx_uint64_t singleUlpTolerance,
+ gmx_uint64_t doubleUlpTolerance,
+ bool bSignMustMatch)
+ : singleAbsoluteTolerance_(singleAbsoluteTolerance),
+ doubleAbsoluteTolerance_(doubleAbsoluteTolerance),
+ singleUlpTolerance_(singleUlpTolerance),
+ doubleUlpTolerance_(doubleUlpTolerance),
bSignMustMatch_(bSignMustMatch)
{
}
bool isWithin(const FloatingPointDifference &difference) const;
//! Formats the tolerance as a string for assertion failure messages.
- std::string toString() const;
+ std::string toString(const FloatingPointDifference &difference) const;
private:
- double absoluteTolerance_;
- int ulpTolerance_;
+ float singleAbsoluteTolerance_;
+ double doubleAbsoluteTolerance_;
+ gmx_uint64_t singleUlpTolerance_;
+ gmx_uint64_t doubleUlpTolerance_;
bool bSignMustMatch_;
};
/*! \brief
* Creates a tolerance that only allows a specified ULP difference.
*
+ * The tolerance uses the given ULP value for both precisions, i.e., double
+ * precision will have much stricter tolerance.
+ *
+ * \related FloatingPointTolerance
+ */
+static inline FloatingPointTolerance
+ulpTolerance(gmx_uint64_t ulpDiff)
+{
+ return FloatingPointTolerance(0.0, 0.0, ulpDiff, ulpDiff, false);
+}
+
+/*! \brief
+ * Creates a tolerance that allows a difference in two compared values that is
+ * relative to the given magnitude.
+ *
+ * \param[in] magnitude Magnitude of the numbers the computation operates in.
+ * \param[in] tolerance Relative tolerance permitted (e.g. 1e-4).
+ *
+ * In addition to setting an ULP tolerance equivalent to \p tolerance for both
+ * precisions, this sets the absolute tolerance such that values close to zero
+ * (in general, smaller than \p magnitude) do not fail the check if they
+ * differ by less than \p tolerance evaluated at \p magnitude. This accounts
+ * for potential loss of precision for small values, and should be used when
+ * accuracy of values much less than \p magnitude do not matter for
+ * correctness.
+ *
+ * The ULP tolerance for different precisions will be different to make them
+ * both match \p tolerance.
+ *
+ * \related FloatingPointTolerance
+ */
+FloatingPointTolerance
+ relativeToleranceAsFloatingPoint(double magnitude, double tolerance);
+
+/*! \brief
+ * Creates a tolerance that allows a precision-dependent relative difference in
+ * a complex computation.
+ *
+ * \param[in] magnitude Magnitude of the numbers the computation operates in.
+ * \param[in] singleUlpDiff Expected accuracy of single-precision
+ * computation (in ULPs).
+ * \param[in] doubleUlpDiff Expected accuracy of double-precision
+ * computation (in ULPs).
+ *
+ * This works as relativeToleranceAsUlp(), but allows setting the ULP
+ * difference separately for the different precisions. This supports
+ * cases where the double-precision calculation can acceptably has a higher ULP
+ * difference, but relaxing the single-precision tolerance would lead to an
+ * unnecessarily loose test.
+ *
+ * \related FloatingPointTolerance
+ */
+static inline FloatingPointTolerance
+relativeToleranceAsPrecisionDependentUlp(double magnitude,
+ gmx_uint64_t singleUlpDiff,
+ gmx_uint64_t doubleUlpDiff)
+{
+ return FloatingPointTolerance(magnitude*singleUlpDiff*GMX_FLOAT_EPS,
+ magnitude*doubleUlpDiff*GMX_DOUBLE_EPS,
+ singleUlpDiff, doubleUlpDiff, false);
+}
+
+/*! \brief
+ * Creates a tolerance that allows a specified absolute difference.
+ *
* \related FloatingPointTolerance
*/
static inline FloatingPointTolerance
-ulpTolerance(gmx_int64_t ulpDiff)
+absoluteTolerance(double tolerance)
{
- return FloatingPointTolerance(0.0, ulpDiff, false);
+ return FloatingPointTolerance(tolerance, tolerance,
+ GMX_UINT64_MAX, GMX_UINT64_MAX, false);
}
/*! \brief
* \param[in] magnitude Magnitude of the numbers the computation operates in.
* \param[in] ulpDiff Expected accuracy of the computation (in ULPs).
*
- * In addition to setting the ULP tolerance, this sets the absolute tolerance
- * such that values close to zero (in general, smaller than \p magnitude) do
- * not fail the check if they differ by less than \p ulpDiff evaluated at
- * \p magniture. This accounts for potential loss of precision for small
- * values, and should be used when accuracy of values much less than
- * \p magniture do not matter for correctness.
+ * In addition to setting the ULP tolerance as ulpTolerance(), this sets the
+ * absolute tolerance such that values close to zero (in general, smaller than
+ * \p magnitude) do not fail the check if they differ by less than \p ulpDiff
+ * evaluated at \p magnitude. This accounts for potential loss of precision
+ * for small values, and should be used when accuracy of values much less than
+ * \p magnitude do not matter for correctness.
*
* \related FloatingPointTolerance
*/
static inline FloatingPointTolerance
-relativeRealTolerance(double magnitude, gmx_int64_t ulpDiff)
+relativeToleranceAsUlp(double magnitude, gmx_uint64_t ulpDiff)
{
- return FloatingPointTolerance(magnitude*ulpDiff*GMX_REAL_EPS, ulpDiff, false);
+ return relativeToleranceAsPrecisionDependentUlp(magnitude, ulpDiff, ulpDiff);
}
/*! \brief
*/
static inline FloatingPointTolerance defaultRealTolerance()
{
- return relativeRealTolerance(1.0, 4);
+ return relativeToleranceAsUlp(1.0, 4);
}
/*! \name Assertions for floating-point comparison
<< " Expected: " << expr1 << std::endl
<< " Which is: " << value1 << std::endl
<< "Difference: " << diff.toString() << std::endl
- << " Tolerance: " << tolerance.toString();
+ << " Tolerance: " << tolerance.toString(diff);
}
//! \endcond
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_testutils
*/
+#include "gmxpre.h"
+
#include "testfilemanager.h"
#include <cstdio>
#include <gtest/gtest.h>
-#include "gromacs/fileio/path.h"
-#include "gromacs/options/options.h"
#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/options.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/path.h"
#include "testutils/testoptions.h"
{
public:
//! Global test input data path set with setDataInputDirectory().
- static const char *s_inputDirectory;
+ static std::string s_inputDirectory;
//! Global temporary output directory for tests, set with setGlobalOutputTempDirectory().
static const char *s_globalOutputTempDirectory;
std::string outputTempDirectory_;
};
-const char *TestFileManager::Impl::s_inputDirectory = NULL;
+std::string TestFileManager::Impl::s_inputDirectory;
const char *TestFileManager::Impl::s_globalOutputTempDirectory = NULL;
/** Controls whether TestFileManager should delete temporary files
after the test finishes. */
const char *TestFileManager::getInputDataDirectory()
{
- GMX_RELEASE_ASSERT(Impl::s_inputDirectory != NULL, "Path for test input files is not set");
- return Impl::s_inputDirectory;
+ GMX_RELEASE_ASSERT(!Impl::s_inputDirectory.empty(), "Path for test input files is not set");
+ return Impl::s_inputDirectory.c_str();
}
const char *TestFileManager::getGlobalOutputTempDirectory()
return impl_->outputTempDirectory_.c_str();
}
-void TestFileManager::setInputDataDirectory(const char *path)
+void TestFileManager::setInputDataDirectory(const std::string &path)
{
// There is no need to protect this by a mutex, as this is called in early
// initialization of the tests.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
-#include "gromacs/utility/common.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
* This function is automatically called by unittest_main.cpp through
* initTestUtils().
*/
- static void setInputDataDirectory(const char *path);
+ static void setInputDataDirectory(const std::string &path);
/*! \brief Returns the path to the global test output
* temporary directory for future TestFileManager objects.
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements functions in testinit.h.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_testutils
+ */
+#include "gmxpre.h"
+
+#include "testinit.h"
+
+#include "config.h"
+
+#include <cstdio>
+#include <cstdlib>
+
+#include <boost/scoped_ptr.hpp>
+#include <gmock/gmock.h>
+
+#include "gromacs/commandline/cmdlinehelpcontext.h"
+#include "gromacs/commandline/cmdlinehelpwriter.h"
+#include "gromacs/commandline/cmdlineinit.h"
+#include "gromacs/commandline/cmdlineparser.h"
+#include "gromacs/commandline/cmdlineprogramcontext.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/options.h"
+#include "gromacs/utility/errorcodes.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/file.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/path.h"
+#include "gromacs/utility/programcontext.h"
+
+#include "testutils/mpi-printer.h"
+#include "testutils/refdata.h"
+#include "testutils/testfilemanager.h"
+#include "testutils/testoptions.h"
+
+namespace gmx
+{
+namespace test
+{
+
+namespace
+{
+
+/*! \brief
+ * Custom program context for test binaries.
+ *
+ * This context overrides the installationPrefix() implementation to always
+ * load data files from the source directory, as the test binaries are never
+ * installed. It also support overriding the directory through a command-line
+ * option to the test binary.
+ *
+ * \ingroup module_testutils
+ */
+class TestProgramContext : public ProgramContextInterface
+{
+ public:
+ /*! \brief
+ * Initializes a test program context.
+ *
+ * \param[in] context Current \Gromacs program context.
+ */
+ explicit TestProgramContext(const ProgramContextInterface &context)
+ : context_(context), dataPath_(CMAKE_SOURCE_DIR)
+ {
+ }
+
+ /*! \brief
+ * Sets the source directory root from which to look for data files.
+ */
+ void overrideSourceRoot(const std::string &sourceRoot)
+ {
+ dataPath_ = sourceRoot;
+ }
+
+ virtual const char *programName() const
+ {
+ return context_.programName();
+ }
+ virtual const char *displayName() const
+ {
+ return context_.displayName();
+ }
+ virtual const char *fullBinaryPath() const
+ {
+ return context_.fullBinaryPath();
+ }
+ virtual InstallationPrefixInfo installationPrefix() const
+ {
+ return InstallationPrefixInfo(dataPath_.c_str(), true);
+ }
+ virtual const char *commandLine() const
+ {
+ return context_.commandLine();
+ }
+
+ private:
+ const ProgramContextInterface &context_;
+ std::string dataPath_;
+};
+
+//! Prints the command-line options for the unit test binary.
+void printHelp(const Options &options)
+{
+ std::fprintf(stderr,
+ "\nYou can use the following GROMACS-specific command-line flags\n"
+ "to control the behavior of the tests:\n\n");
+ CommandLineHelpContext context(&File::standardError(),
+ eHelpOutputFormat_Console, NULL);
+ context.setModuleDisplayName(getProgramContext().displayName());
+ CommandLineHelpWriter(options).writeHelp(context);
+}
+
+//! Global program context instance for test binaries.
+boost::scoped_ptr<TestProgramContext> g_testContext;
+
+} // namespace
+
+//! \cond internal
+void initTestUtils(const char *dataPath, const char *tempPath, int *argc, char ***argv)
+{
+#ifndef NDEBUG
+ gmx_feenableexcept();
+#endif
+ const CommandLineProgramContext &context = initForCommandLine(argc, argv);
+ try
+ {
+ g_testContext.reset(new TestProgramContext(context));
+ setProgramContext(g_testContext.get());
+ // Use the default finder that does not respect GMXLIB, since the tests
+ // generally can only get confused by a different set of data files.
+ setLibraryFileFinder(NULL);
+ ::testing::InitGoogleMock(argc, *argv);
+ if (dataPath != NULL)
+ {
+ TestFileManager::setInputDataDirectory(
+ Path::join(CMAKE_SOURCE_DIR, dataPath));
+ }
+ if (tempPath != NULL)
+ {
+ TestFileManager::setGlobalOutputTempDirectory(tempPath);
+ }
+ bool bHelp = false;
+ std::string sourceRoot;
+ Options options(NULL, NULL);
+ // TODO: A single option that accepts multiple names would be nicer.
+ // Also, we recognize -help, but GTest doesn't, which leads to a bit
+ // unintuitive behavior.
+ options.addOption(BooleanOption("h").store(&bHelp)
+ .description("Print GROMACS-specific unit test options"));
+ options.addOption(BooleanOption("help").store(&bHelp).hidden());
+ options.addOption(BooleanOption("?").store(&bHelp).hidden());
+ // TODO: Make this into a FileNameOption (or a DirectoryNameOption).
+ options.addOption(StringOption("src-root").store(&sourceRoot)
+ .description("Override source tree location (for data files)"));
+ // TODO: Consider removing this option from test binaries that do not need it.
+ initReferenceData(&options);
+ initTestOptions(&options);
+ try
+ {
+ CommandLineParser(&options).parse(argc, *argv);
+ options.finish();
+ }
+ catch (const UserInputError &)
+ {
+ printHelp(options);
+ throw;
+ }
+ if (bHelp)
+ {
+ printHelp(options);
+ }
+ if (!sourceRoot.empty())
+ {
+ g_testContext->overrideSourceRoot(sourceRoot);
+ TestFileManager::setInputDataDirectory(
+ Path::join(sourceRoot, dataPath));
+ }
+ setFatalErrorHandler(NULL);
+ initMPIOutput();
+ }
+ catch (const std::exception &ex)
+ {
+ printFatalErrorMessage(stderr, ex);
+ int retcode = processExceptionAtExitForCommandLine(ex);
+ // TODO: It could be nice to destroy things in proper order such that
+ // g_testContext would not contain hanging references at this point,
+ // but in practice that should not matter.
+ g_testContext.reset();
+ std::exit(retcode);
+ }
+}
+
+void finalizeTestUtils()
+{
+ setProgramContext(NULL);
+ g_testContext.reset();
+ finalizeForCommandLine();
+}
+//! \endcond
+
+} // namespace test
+} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/*! \defgroup module_onlinehelp Help Formatting for Online Help (onlinehelp)
- * \ingroup group_utilitymodules
+/*! \internal \file
* \brief
- * Provides functionality for formatting help text for console and other
- * formats.
- *
- * This module provides helper functions and classes for formatting console
- * help, as well as man pages and HTML help from the source code. It should
- * not be necessary to call any methods in this module outside the \Gromacs
- * library.
+ * Functions for initialing \Gromacs unit test executables.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_testutils
*/
-/*! \file
+#ifndef GMX_TESTUTILS_TESTINIT_H
+#define GMX_TESTUTILS_TESTINIT_H
+
+namespace gmx
+{
+
+namespace test
+{
+
+//! \cond internal
+/*! \internal
* \brief
- * Public API convenience header for help formatting.
+ * Initializes the test utilities library.
*
- * This module does not provide any classes that are intended to be used
- * outside the library. It only contains some type declarations that are
- * necessary for implementation reasons in other public API headers.
+ * Does not throw. Terminates the program with a non-zero error code if an
+ * error occurs.
*
- * \author Teemu Murtola <teemu.murtola@gmail.com>
- * \inlibraryapi
- * \ingroup module_onlinehelp
+ * This function is automatically called by unittest_main.cpp.
+ *
+ * \ingroup module_testutils
+ */
+void initTestUtils(const char *dataPath, const char *tempPath, int *argc, char ***argv);
+
+/*! \internal
+ * \brief
+ * Finalizes the test utilities library.
+ *
+ * Does not throw. Terminates the program with a non-zero error code if an
+ * error occurs.
+ *
+ * This function is automatically called by unittest_main.cpp.
+ *
+ * \ingroup module_testutils
*/
-#ifndef GMX_ONLINEHELP_H
-#define GMX_ONLINEHELP_H
+void finalizeTestUtils();
+//! \endcond
-#include "onlinehelp/helptopicinterface.h"
+} // namespace test
+} // namespace gmx
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_testutils
*/
-#include "testoptions.h"
+#include "gmxpre.h"
-#include <cstdio>
-#include <cstdlib>
+#include "testoptions.h"
#include <list>
-#include <gmock/gmock.h>
-
#include "thread_mpi/mutex.h"
-#include "gromacs/commandline/cmdlinehelpcontext.h"
-#include "gromacs/commandline/cmdlinehelpwriter.h"
-#include "gromacs/commandline/cmdlineinit.h"
-#include "gromacs/commandline/cmdlineparser.h"
-#include "gromacs/options/basicoptions.h"
-#include "gromacs/options/options.h"
-#include "gromacs/utility/common.h"
-#include "gromacs/utility/errorcodes.h"
-#include "gromacs/utility/exceptions.h"
-#include "gromacs/utility/file.h"
-#include "gromacs/utility/programcontext.h"
-
-#include "refdata.h"
-#include "testfilemanager.h"
-#include "mpi-printer.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
}
}
-//! Prints the command-line options for the unit test binary.
-void printHelp(const Options &options)
-{
- std::fprintf(stderr,
- "\nYou can use the following GROMACS-specific command-line flags\n"
- "to control the behavior of the tests:\n\n");
- CommandLineHelpContext context(&File::standardError(),
- eHelpOutputFormat_Console, NULL);
- context.setModuleDisplayName(getProgramContext().displayName());
- CommandLineHelpWriter(options).writeHelp(context);
-}
-
} // namespace
void registerTestOptions(const char *name, TestOptionsProvider *provider)
TestOptionsRegistry::getInstance().add(name, provider);
}
-void initTestUtils(const char *dataPath, const char *tempPath, int *argc, char ***argv)
-{
- gmx::initForCommandLine(argc, argv);
- try
- {
- ::testing::InitGoogleMock(argc, *argv);
- if (dataPath != NULL)
- {
- TestFileManager::setInputDataDirectory(dataPath);
- }
- if (tempPath != NULL)
- {
- TestFileManager::setGlobalOutputTempDirectory(tempPath);
- }
- bool bHelp = false;
- Options options(NULL, NULL);
- // TODO: A single option that accepts multiple names would be nicer.
- // Also, we recognize -help, but GTest doesn't, which leads to a bit
- // unintuitive behavior.
- options.addOption(BooleanOption("h").store(&bHelp)
- .description("Print GROMACS-specific unit test options"));
- options.addOption(BooleanOption("help").store(&bHelp).hidden());
- options.addOption(BooleanOption("?").store(&bHelp).hidden());
- // TODO: Consider removing this option from test binaries that do not need it.
- initReferenceData(&options);
- TestOptionsRegistry::getInstance().initOptions(&options);
- try
- {
- CommandLineParser(&options).parse(argc, *argv);
- options.finish();
- }
- catch (const UserInputError &)
- {
- printHelp(options);
- throw;
- }
- if (bHelp)
- {
- printHelp(options);
- }
- setFatalErrorHandler(NULL);
- initMPIOutput();
- }
- catch (const std::exception &ex)
- {
- printFatalErrorMessage(stderr, ex);
- std::exit(processExceptionAtExit(ex));
- }
-}
-
-void finalizeTestUtils()
+void initTestOptions(Options *options)
{
- gmx::finalizeForCommandLine();
+ TestOptionsRegistry::getInstance().initOptions(options);
}
} // namespace test
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \ingroup module_testutils
*/
void registerTestOptions(const char *name, TestOptionsProvider *provider);
+/*! \libinternal \brief
+ * Initializes the options from all registered test providers.
+ *
+ * \param options The options are added here.
+ *
+ * This is called automatically by initTestUtils().
+ *
+ * \ingroup module_testutils
+ */
+void initTestOptions(Options *options);
// Uncrustify screws up the indentation for the example otherwise.
/* *INDENT-OFF* */
* \code
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
+
#include "testutils/testoptions.h"
namespace gmx
\
void name::initOptions(::gmx::Options *options)
-/*! \libinternal \brief
- * Initializes the test utilities library.
- *
- * Does not throw. Terminates the program with a non-zero error code if an
- * error occurs.
- *
- * This function is automatically called by unittest_main.cpp.
- */
-void initTestUtils(const char *dataPath, const char *tempPath, int *argc, char ***argv);
-
-/*! \libinternal \brief
- * Finalizes the test utilities library.
- *
- * Does not throw. Terminates the program with a non-zero error code if an
- * error occurs.
- *
- * This function is automatically called by unittest_main.cpp.
- */
-void finalizeTestUtils();
-
} // namespace test
} // namespace gmx
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_testutils
*/
+#include "gmxpre.h"
+
#include "testutils/refdata.h"
#include <vector>
-#include <gtest/gtest.h>
#include <gtest/gtest-spi.h>
+#include <gtest/gtest.h>
namespace
{
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_testutils
*/
+#include "gmxpre.h"
+
#include "testutils/testasserts.h"
#include <gtest/gtest.h>
TEST(FloatingPointDifferenceTest, HandlesEqualValues)
{
FloatingPointDifference diff(1.2, 1.2);
+ EXPECT_TRUE(diff.isDouble());
+ EXPECT_FALSE(diff.isNaN());
+ EXPECT_EQ(0.0, diff.asAbsolute());
+ EXPECT_EQ(0U, diff.asUlps());
+ EXPECT_FALSE(diff.signsDiffer());
+}
+
+// TODO: Use typed tests to run all the tests for single and double.
+TEST(FloatingPointDifferenceTest, HandlesFloatValues)
+{
+ FloatingPointDifference diff(1.2f, 1.2f);
+ EXPECT_FALSE(diff.isDouble());
EXPECT_FALSE(diff.isNaN());
EXPECT_EQ(0.0, diff.asAbsolute());
EXPECT_EQ(0U, diff.asUlps());
EXPECT_TRUE(diff.isNaN());
}
+TEST(FloatingPointToleranceTest, UlpTolerance)
+{
+ using gmx::test::ulpTolerance;
+
+ FloatingPointDifference fequal(1.0, 1.0);
+ FloatingPointDifference fulp2(1.0f, addUlps(1.0f, 2));
+ EXPECT_TRUE(ulpTolerance(0).isWithin(fequal));
+ EXPECT_FALSE(ulpTolerance(1).isWithin(fulp2));
+ EXPECT_TRUE(ulpTolerance(2).isWithin(fulp2));
+
+ FloatingPointDifference dequal(1.0, 1.0);
+ FloatingPointDifference dulp2(1.0, addUlps(1.0, 2));
+ FloatingPointDifference dulp2f(1.0, static_cast<double>(addUlps(1.0f, 2)));
+ EXPECT_TRUE(ulpTolerance(0).isWithin(dequal));
+ EXPECT_TRUE(ulpTolerance(2).isWithin(dulp2));
+ EXPECT_FALSE(ulpTolerance(2).isWithin(dulp2f));
+}
+
+TEST(FloatingPointToleranceTest, RelativeToleranceAsFloatingPoint)
+{
+ using gmx::test::relativeToleranceAsFloatingPoint;
+
+ FloatingPointDifference fequal(1.0f, 1.0f);
+ FloatingPointDifference fulp2(1.0f, addUlps(1.0f, 2));
+ FloatingPointDifference fdiff(1.0f, 1.011f);
+ FloatingPointDifference fsmall(0.1f, 0.111f);
+ FloatingPointDifference fsmall2(0.1f, 0.121f);
+ EXPECT_TRUE(relativeToleranceAsFloatingPoint(1.0, 1e-2).isWithin(fequal));
+ EXPECT_TRUE(relativeToleranceAsFloatingPoint(1.0, 1e-9).isWithin(fequal));
+ EXPECT_TRUE(relativeToleranceAsFloatingPoint(1.0, 1e-2).isWithin(fulp2));
+ EXPECT_FALSE(relativeToleranceAsFloatingPoint(1.0, 1e-9).isWithin(fulp2));
+ EXPECT_FALSE(relativeToleranceAsFloatingPoint(1.0, 1e-2).isWithin(fdiff));
+ EXPECT_TRUE(relativeToleranceAsFloatingPoint(1.0, 2e-2).isWithin(fdiff));
+ EXPECT_TRUE(relativeToleranceAsFloatingPoint(1.0, 2e-2).isWithin(fsmall));
+ EXPECT_FALSE(relativeToleranceAsFloatingPoint(0.1, 2e-2).isWithin(fsmall));
+ EXPECT_FALSE(relativeToleranceAsFloatingPoint(1.0, 2e-2).isWithin(fsmall2));
+
+ FloatingPointDifference dequal(1.0, 1.0);
+ FloatingPointDifference dulp2f(1.0, static_cast<double>(addUlps(1.0f, 2)));
+ FloatingPointDifference ddiff(1.0, 1.011);
+ FloatingPointDifference dsmall(0.1, 0.111);
+ FloatingPointDifference dsmall2(0.1, 0.121);
+ EXPECT_TRUE(relativeToleranceAsFloatingPoint(1.0, 1e-2).isWithin(dequal));
+ EXPECT_TRUE(relativeToleranceAsFloatingPoint(1.0, 1e-9).isWithin(dequal));
+ EXPECT_TRUE(relativeToleranceAsFloatingPoint(1.0, 1e-2).isWithin(dulp2f));
+ EXPECT_FALSE(relativeToleranceAsFloatingPoint(1.0, 1e-9).isWithin(dulp2f));
+ EXPECT_FALSE(relativeToleranceAsFloatingPoint(1.0, 1e-2).isWithin(ddiff));
+ EXPECT_TRUE(relativeToleranceAsFloatingPoint(1.0, 2e-2).isWithin(ddiff));
+ EXPECT_TRUE(relativeToleranceAsFloatingPoint(1.0, 2e-2).isWithin(dsmall));
+ EXPECT_FALSE(relativeToleranceAsFloatingPoint(0.1, 2e-2).isWithin(dsmall));
+ EXPECT_FALSE(relativeToleranceAsFloatingPoint(1.0, 2e-2).isWithin(dsmall2));
+}
+
+TEST(FloatingPointToleranceTest, RelativeToleranceAsUlp)
+{
+ using gmx::test::relativeToleranceAsUlp;
+
+ FloatingPointDifference fequal(1.0f, 1.0f);
+ FloatingPointDifference fulp4(1.0f, addUlps(1.0f, 4));
+ FloatingPointDifference fsmall(0.1f, addUlps(1.0f, 2) - 0.9f);
+ FloatingPointDifference fsmall2(0.1f, addUlps(1.0f, 6) - 0.9f);
+ EXPECT_TRUE(relativeToleranceAsUlp(1.0, 2).isWithin(fequal));
+ EXPECT_FALSE(relativeToleranceAsUlp(1.0, 2).isWithin(fulp4));
+ EXPECT_TRUE(relativeToleranceAsUlp(1.0, 4).isWithin(fulp4));
+ EXPECT_TRUE(relativeToleranceAsUlp(1.0, 4).isWithin(fsmall));
+ EXPECT_FALSE(relativeToleranceAsUlp(0.1, 4).isWithin(fsmall));
+ EXPECT_FALSE(relativeToleranceAsUlp(1.0, 4).isWithin(fsmall2));
+
+ FloatingPointDifference dequal(1.0, 1.0);
+ FloatingPointDifference dulp4(1.0, addUlps(1.0, 4));
+ FloatingPointDifference dulp4f(1.0, static_cast<double>(addUlps(1.0f, 4)));
+ FloatingPointDifference dsmall(0.1, addUlps(1.0, 2) - 0.9);
+ FloatingPointDifference dsmall2(0.1, addUlps(1.0, 6) - 0.9);
+ EXPECT_TRUE(relativeToleranceAsUlp(1.0, 2).isWithin(dequal));
+ EXPECT_FALSE(relativeToleranceAsUlp(1.0, 2).isWithin(dulp4));
+ EXPECT_TRUE(relativeToleranceAsUlp(1.0, 4).isWithin(dulp4));
+ EXPECT_FALSE(relativeToleranceAsUlp(1.0, 4).isWithin(dulp4f));
+ EXPECT_TRUE(relativeToleranceAsUlp(1.0, 4).isWithin(dsmall));
+ EXPECT_FALSE(relativeToleranceAsUlp(0.1, 4).isWithin(dsmall));
+ EXPECT_FALSE(relativeToleranceAsUlp(1.0, 4).isWithin(dsmall2));
+}
+
} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_testutils
*/
+#include "gmxpre.h"
+
#include <gtest/gtest.h>
-#include "testutils/testoptions.h"
+#include "testutils/testinit.h"
#ifndef TEST_DATA_PATH
//! Path to test input data directory (needs to be set by the build system).
"Automatically download regressiontests. Tests can be run with ctest." OFF)
if(REGRESSIONTEST_DOWNLOAD)
- if("${PROJECT_VERSION}" MATCHES "-dev")
- set(REGRESSIONTEST_URL http://gerrit.gromacs.org/snapshot/${REGRESSIONTEST_BRANCH})
- set(REGRESSIONTEST_PATH "${CMAKE_CURRENT_BINARY_DIR}/regressiontests"
- CACHE PATH "Path to auto-downloaded regressiontests" FORCE)
+ if (NOT SOURCE_IS_SOURCE_DISTRIBUTION)
+ set(REGRESSIONTEST_URL http://gerrit.gromacs.org/snapshot/${REGRESSIONTEST_BRANCH})
+ set(REGRESSIONTEST_PATH "${CMAKE_CURRENT_BINARY_DIR}/regressiontests"
+ CACHE PATH "Path to auto-downloaded regressiontests" FORCE)
else()
set(REGRESSIONTEST_URL http://gerrit.gromacs.org/download/regressiontests-${REGRESSIONTEST_VERSION}.tar.gz)
set(REGRESSIONTEST_PATH
- "${CMAKE_CURRENT_BINARY_DIR}/regressiontests-${REGRESSIONTEST_VERSION}"
- CACHE PATH "Path to auto-downloaded regressiontests" FORCE)
+ "${CMAKE_CURRENT_BINARY_DIR}/regressiontests-${REGRESSIONTEST_VERSION}"
+ CACHE PATH "Path to auto-downloaded regressiontests" FORCE)
endif()
set(REGRESSIONTEST_FILE "${CMAKE_CURRENT_BINARY_DIR}/regressiontests.tgz")
message("Downloading: ${REGRESSIONTEST_URL}")
status_string: ${status_string}
log: ${log}")
endif()
- if(NOT "${PROJECT_VERSION}" MATCHES "-dev")
+ if (SOURCE_IS_SOURCE_DISTRIBUTION)
file(MD5 ${REGRESSIONTEST_FILE} COMPUTED_MD5SUM)
if(NOT ${REGRESSIONTEST_MD5SUM} STREQUAL ${COMPUTED_MD5SUM})
message(FATAL_ERROR "Download of regressiontests failed. Expected MD5 of ${REGRESSIONTEST_MD5SUM} but download has ${COMPUTED_MD5SUM}")
${CMAKE_SOURCE_DIR}/src/external/*.c
${CMAKE_SOURCE_DIR}/src/external/*.cpp
${CMAKE_SOURCE_DIR}/src/external/*.cu
+ ${CMAKE_SOURCE_DIR}/src/gromacs/selection/scanner.cpp
+ ${CMAKE_SOURCE_DIR}/src/gromacs/selection/parser.cpp
)
list(REMOVE_ITEM _inputfiles ${_files_to_ignore})
set(_outputopt --template=gcc)
if (CPPCHECK_XML_OUTPUT)
set(_outputext xml)
- set(_outputopt --xml)
+ set(_outputopt --xml --xml-version=2)
endif()
set(_common_flags
- --enable=style -DLINUX
- -I src/gromacs/legacyheaders -I src
+ --enable=style -DLINUX -DHAVE_UNISTD_H
+ -I src
-I src/external/thread_mpi/include
-I src/external/tng_io/include
- -I ${CMAKE_BINARY_DIR}/src -I ${CMAKE_BINARY_DIR}/src/gromacs/utility
+ -I ${CMAKE_BINARY_DIR}/src
--quiet
+ --inline-suppr
${_outputopt})
set(_c_flags
--suppress=variableScope
--suppress=unusedStructMember
--suppress=invalidscanf
--suppress=sizeofCalculation
+ --suppress=invalidscanf_libc
--suppress=missingInclude:src/programs/mdrun/gmx_gpu_utils/gmx_gpu_utils.cu
--suppress=*:src/external/Random123-1.08/include/Random123/features/compilerfeatures.h
- --inline-suppr)
+ --suppress=invalidPointerCast:src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh
+ --suppress=passedByValue:src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh
+ --suppress=passedByValue:src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh
+ )
set(_cxx_flags
-D__cplusplus
--suppress=variableScope
--suppress=unnecessaryForwardDeclaration
- --suppress=invalidscanf:src/gromacs/fileio/matio.cpp
- --suppress=invalidscanf:src/gromacs/gmxlib/xvgr.cpp
- --suppress=invalidscanf:src/gromacs/gmxpreprocess/pdb2top.cpp
- --suppress=*:src/gromacs/selection/scanner.cpp)
+ --suppress=memsetClassFloat #we assume IEEE754
+ --suppress=invalidscanf_libc #seems only important for security on non-std libc
+ --suppress=invalidscanf #same as last (style and portability checker have the same warning)
+ --suppress=passedByValue:src/gromacs/simd/tests/*
+ )
# This list will hold the list of all files with cppcheck errors
# (one per input file)
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff