-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2012,2013, by the GROMACS development team, led by
-# David van der Spoel, Berk Hess, 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.
-#
cmake_minimum_required(VERSION 2.8)
# Keep CMake suitably quiet on Cygwin
set(CMAKE_LEGACY_CYGWIN_WIN32 0) # Remove when CMake >= 2.8.4 is required
-# Allows CPack to act differently for normal tools and mdrun (e.g. because of MPI)
-set(CPACK_COMPONENT_GROUP_TOOLS_DESCRIPTION "All GROMACS executable tools")
-set(CPACK_COMPONENT_GROUP_MDRUN_DESCRIPTION "GROMACS executable for running simulations")
-
# CMake modules/macros are in a subdirectory to keep this file cleaner
# This needs to be set before project() in order to pick up toolchain files
list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Platform)
-project(Gromacs C)
+project(Gromacs)
include(Dart)
mark_as_advanced(DART_ROOT)
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+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
#
# machine with no git.
#
# NOTE: when releasing the "-dev" suffix needs to be stripped off!
-set(PROJECT_VERSION "4.6.3-dev")
+set(PROJECT_VERSION "5.0-dev")
# The version number of the regressiontest tarball against which this
# git branch can be tested. Normally, this will be the version of the
# last patch release. Comment the next line out for branches leading
# to a major/minor release.
- set(REGRESSIONTEST_VERSION "4.6.1")
+ set(REGRESSIONTEST_VERSION "4.6.2")
set(CUSTOM_VERSION_STRING ""
CACHE STRING "Custom version string (if empty, use hard-coded default)")
mark_as_advanced(CUSTOM_VERSION_STRING)
endif (CUSTOM_VERSION_STRING)
set(SOVERSION 8)
# It is a bit irritating, but this has to be set separately for now!
-SET(CPACK_PACKAGE_VERSION_MAJOR "4")
-SET(CPACK_PACKAGE_VERSION_MINOR "6")
-SET(CPACK_PACKAGE_VERSION_PATCH "1")
+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 gmx_header_config_h is set to this value.
set(API_VERSION ${NUM_VERSION})
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)
+ set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
endif()
+set(GMX_INSTALL_PREFIX "" CACHE STRING "Prefix gets appended to CMAKE_INSTALL_PREFIX. For cpack it sets the root folder of the archive.")
+mark_as_advanced(GMX_INSTALL_PREFIX)
+
include(gmxBuildTypeReference)
if(NOT CMAKE_BUILD_TYPE)
endif(NOT CMAKE_BUILD_TYPE)
enable_language(C)
-
-set(GMX_USE_RELATIVE_INSTALL_PATH OFF CACHE STRING "Use relative paths not absolute paths for cmake install. Has only an effect on cpack.")
-mark_as_advanced(GMX_USE_RELATIVE_INSTALL_PATH)
+enable_language(CXX)
set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION})
set(CPACK_PACKAGE_VENDOR "gromacs.org")
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
-if (NOT GMX_USE_RELATIVE_INSTALL_PATH)
- set(CPACK_SET_DESTDIR "ON")
-endif()
set(CPACK_RESOURCE_FILE_WELCOME "${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 "${CMAKE_SOURCE_DIR}/COPYING")
#must come after all cpack settings!
include(CPack)
+set(SOURCE_IS_GIT_REPOSITORY OFF)
+if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
+ set(SOURCE_IS_GIT_REPOSITORY ON)
+endif()
+
########################################################################
# Check and warn if cache generated on a different host is being reused
########################################################################
endif()
########################################################################
-# User input options - enable C++ - before any CXX flags are changed #
-########################################################################
-
-# decide on GPU settings based on user-settings and GPU/CUDA detection
-include(gmxManageGPU)
-
-option(GMX_FORCE_CXX "Enable C++ compilation even if not necessary" OFF)
-mark_as_advanced(GMX_FORCE_CXX)
-
option(GMX_COOL_QUOTES "Enable Gromacs cool quotes" ON)
mark_as_advanced(GMX_COOL_QUOTES)
-if(GMX_GPU OR GMX_FORCE_CXX OR GMX_OPENMM)
- enable_language(CXX)
-endif()
set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
-
-########################################################################
# User input options #
########################################################################
option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" OFF)
option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
mark_as_advanced(GMX_FAHCORE)
+# decide on GPU settings based on user-settings and GPU/CUDA detection
+include(gmxManageGPU)
+
+# TODO: move OpenMM to contrib
+option(GMX_OPENMM "Accelerated execution on GPUs through the OpenMM library (rerun cmake after changing to see relevant options)" OFF)
+mark_as_advanced(GMX_OPENMM)
+
include(gmxDetectAcceleration)
if(NOT DEFINED GMX_CPU_ACCELERATION)
if(CMAKE_CROSSCOMPILING)
option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
mark_as_advanced(GMX_LOAD_PLUGINS)
+option(GMX_GPU "Enable GPU acceleration" ON)
option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
-option(USE_VERSION_H "Generate development version string/information" ON)
-mark_as_advanced(USE_VERSION_H)
+option(GMX_GIT_VERSION_INFO "Generate git version information" ${SOURCE_IS_GIT_REPOSITORY})
+mark_as_advanced(GMX_GIT_VERSION_INFO)
option(GMX_DEFAULT_SUFFIX "Use default suffixes for GROMACS binaries and libs (_d for double, _mpi for MPI; rerun cmake after changing to see relevant options)" ON)
+if(UNIX)
+ option(GMX_SYMLINK_OLD_BINARY_NAMES "Create symbolic links for pre-5.0 binary names" ON)
+endif()
if(UNIX)
option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer static archives (not available on non-*nix platforms and it will only work if static versions of external dependencies are available and found)!" OFF)
# These files should be removed from the source tree when a CMake version that
# includes the features in question becomes required for building GROMACS.
include(CheckCCompilerFlag)
-if(CMAKE_CXX_COMPILER_LOADED)
- include(CheckCXXCompilerFlag)
-endif()
+include(CheckCXXCompilerFlag)
# Get compiler version information, needs to be done early as check that depend
# on compiler verison follow below.
# 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))
- if(CMAKE_COMPILER_IS_GNUCC AND GMX_PREFER_STATIC_OPENMP)
+ 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 "")
else()
include(gmxCFlags)
gmx_c_flags()
-# This variable should be used for additional compiler flags which are not
-# generated in gmxCFlags nor are acceleration or MPI related.
-set(EXTRA_C_FLAGS "")
-
# gcc 4.4.x is buggy and crashes when compiling some files with O3 and OpenMP on.
# Detect here whether applying a workaround is needed and will apply it later
# on the affected files.
message(FATAL_ERROR "Your compiler is clang version 3.0, which is known to be buggy for GROMACS. Use a different compiler.")
endif()
-# clang <=3.2 contains a bug that causes incorrect code to be generated for the
-# vfmaddps instruction and therefore the bug is triggered with AVX_128_FMA.
-# (see: http://llvm.org/bugs/show_bug.cgi?id=15040).
-# We can work around this by not using the integrated assembler (except on OS X
-# which has an outdated assembler that does not support AVX instructions).
-if (${CMAKE_C_COMPILER_ID} MATCHES "Clang" AND C_COMPILER_VERSION VERSION_LESS "3.3")
- set(GMX_USE_CLANG_FMA_BUG_WORKAROUND TRUE)
-endif()
-
if (CMAKE_C_COMPILER_ID STREQUAL "PGI")
message(WARNING "All tested PGI compiler versions (up to 12.9.0) generate binaries which produce incorrect results, or even fail to compile Gromacs. Highly recommended to use a different compiler. If you choose to use PGI, make sure to run the regressiontests.")
endif()
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
include(CheckIncludeFiles)
-check_include_files(string.h HAVE_STRING_H)
-check_include_files(math.h HAVE_MATH_H)
-check_include_files(limits.h HAVE_LIMITS_H)
-check_include_files(memory.h HAVE_MEMORY_H)
+include(CheckIncludeFileCXX)
check_include_files(unistd.h HAVE_UNISTD_H)
-check_include_files(direct.h HAVE_DIRECT_H)
check_include_files(pwd.h HAVE_PWD_H)
-check_include_files(stdint.h HAVE_STDINT_H)
-check_include_files(stdlib.h HAVE_STDLIB_H)
check_include_files(pthread.h HAVE_PTHREAD_H)
check_include_files(dirent.h HAVE_DIRENT_H)
-check_include_files(inttypes.h HAVE_INTTYPES_H)
-check_include_files(regex.h HAVE_REGEX_H)
-check_include_files(sys/types.h HAVE_SYS_TYPES_H)
-check_include_files(sys/stat.h HAVE_SYS_STAT_H)
check_include_files(sys/time.h HAVE_SYS_TIME_H)
-check_include_files(rpc/rpc.h HAVE_RPC_RPC_H)
-check_include_files("rpc/rpc.h;rpc/xdr.h" HAVE_RPC_XDR_H)
check_include_files(io.h HAVE_IO_H)
check_include_files(sched.h HAVE_SCHED_H)
+check_include_files(regex.h HAVE_POSIX_REGEX)
+check_include_file_cxx(regex HAVE_CXX11_REGEX)
+# TODO: It could be nice to inform the user if no regex support is found,
+# as selections won't be fully functional.
+
include(CheckFunctionExists)
-check_function_exists(strcasecmp HAVE_STRCASECMP)
check_function_exists(strdup HAVE_STRDUP)
-check_function_exists(vprintf HAVE_VPRINTF)
-check_function_exists(memcmp HAVE_MEMCMP)
check_function_exists(posix_memalign HAVE_POSIX_MEMALIGN)
check_function_exists(memalign HAVE_MEMALIGN)
check_function_exists(_aligned_malloc HAVE__ALIGNED_MALLOC)
check_function_exists(gettimeofday HAVE_GETTIMEOFDAY)
-check_function_exists(isnan HAVE_ISNAN)
-check_function_exists(_isnan HAVE__ISNAN)
check_function_exists(fsync HAVE_FSYNC)
check_function_exists(_fileno HAVE__FILENO)
check_function_exists(fileno HAVE_FILENO)
include(CheckTypeSize)
-check_type_size("bool" SIZEOF_BOOL) # will also set HAVE_BOOL
check_type_size("int" SIZEOF_INT)
check_type_size("long int" SIZEOF_LONG_INT)
check_type_size("long long int" SIZEOF_LONG_LONG_INT)
set(GMX_64_BIT FALSE)
endif (CMAKE_C_SIZEOF_DATA_PTR EQUAL 8)
-# Check for some basic types that we *need*, so set these to int if they are not present
-check_type_size(uid_t uid_t)
-if(NOT uid_t)
- set(uid_t int)
-else(NOT uid_t)
- set(uid_t 0)
-endif(NOT uid_t)
-
-check_type_size(gid_t gid_t)
-if(NOT gid_t)
- set(gid_t 1)
-else(NOT gid_t)
- set(gid_t 0)
-endif(NOT gid_t)
-
-check_type_size(size_t size_t)
-if(NOT size_t)
- set(size_t int)
-else(NOT size_t)
- set(size_t 0)
-endif(NOT size_t)
-
-check_type_size(off_t off_t)
-if(NOT off_t)
- set(off_t int)
-else(NOT off_t)
- set(off_t 0)
-endif(NOT off_t)
-
include(TestBigEndian)
test_big_endian(GMX_INTEGER_BIG_ENDIAN)
endif()
IF( WIN32 AND NOT CYGWIN)
+ # This makes windows.h not declare min/max as macros that would break
+ # C++ code using std::min/std::max.
+ add_definitions(-DNOMINMAX)
+
if (NOT BUILD_SHARED_LIBS)
option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer static system libraries (MT instead of MD)!" ON)
if(NOT GMX_PREFER_STATIC_LIBS)
message(WARNING "Shared system libraries requested, and static Gromacs libraries requested.")
endif()
else()
+ message(FATAL_ERROR "BUILD_SHARED_LIBS not yet working for Windows in the master branch")
option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer static system libraries (MT instead of MD)!" OFF)
if(GMX_PREFER_STATIC_LIBS)
#this combination segfaults (illigal passing of file handles)
ENDIF()
ENDIF()
+# Unconditionally find the package, as it is also required for unit tests
+find_package(LibXml2)
+option(GMX_XML "Use libxml2 to parse xml files (currently has no effect)" ${LIBXML2_FOUND})
+set(PKG_XML "")
+mark_as_advanced(GMX_XML)
+# Don't actually do anything, since libxml2 is currently not used by libgromacs
+#if(GMX_XML AND NOT LIBXML2_FOUND)
+# message(FATAL_ERROR "libxml2 not found. Set GMX_XML=OFF to compile without XML support")
+#endif()
+#if(GMX_XML)
+# include_directories(${LIBXML2_INCLUDE_DIR})
+# set(PKG_XML libxml-2.0)
+# set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
+#endif(GMX_XML)
+
option(GMX_GSL "Add support for gsl" OFF)
if (GMX_GSL)
find_package(GSL)
include(ThreadMPI)
set(THREAD_MPI_LIB thread_mpi)
+# Enable core threading facilities
+tmpi_enable_core("${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders")
+# Enable tMPI C++ support
+tmpi_enable_cxx()
if(GMX_THREAD_MPI)
+ # enable MPI functions
tmpi_enable()
set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_THREAD_MPI")
set(GMX_MPI 1)
endif()
# only bother with finding git and using version.h if the source is a git repo
-if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
- if(USE_VERSION_H)
- # 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)
-
- # Find out the git version
- if(GIT_FOUND AND NOT GIT_VERSION)
- execute_process(COMMAND ${GIT_EXECUTABLE} "--version"
- OUTPUT_VARIABLE _exec_out
- OUTPUT_STRIP_TRAILING_WHITESPACE)
- string(REGEX REPLACE "git version (.*)" "\\1" GIT_VERSION ${_exec_out})
- set(GIT_VERSION ${GIT_VERSION} CACHE STRING "Git version")
- mark_as_advanced(GIT_VERSION)
- endif()
-
- if(NOT GIT_FOUND OR GIT_VERSION VERSION_LESS "1.5.3")
- message("No compatible git version found, won't be able to generate proper development version information.")
- set(USE_VERSION_H OFF)
- endif()
+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)
+
+ # Find out the git version
+ if(GIT_FOUND AND NOT GIT_VERSION)
+ execute_process(COMMAND ${GIT_EXECUTABLE} "--version"
+ OUTPUT_VARIABLE _exec_out
+ OUTPUT_STRIP_TRAILING_WHITESPACE)
+ string(REGEX REPLACE "git version (.*)" "\\1" GIT_VERSION ${_exec_out})
+ set(GIT_VERSION ${GIT_VERSION} CACHE STRING "Git version")
+ mark_as_advanced(GIT_VERSION)
endif()
-else()
- set(USE_VERSION_H OFF)
+
+ if(NOT GIT_FOUND OR GIT_VERSION 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)
+ find_package(Boost 1.44.0)
+ if(Boost_FOUND AND Boost_VERSION VERSION_LESS "104400")
+ set(Boost_FOUND FALSE)
+ endif()
+ # Print the notification only on first run, when determining the default
+ if(NOT DEFINED GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
+ message("Boost >= 1.44 not found. Using minimal internal version. "
+ "This may cause trouble if you plan on compiling/linking other "
+ "software that uses Boost against Gromacs.")
+ endif()
+endif()
+option(GMX_EXTERNAL_BOOST "Use external Boost instead of minimal built-in version"
+ ${Boost_FOUND})
+if(GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
+ message(FATAL_ERROR
+ "Boost >= 1.44 not found. "
+ "You can set GMX_EXTERNAL_BOOST=OFF to compile against minimal "
+ "version of Boost included with Gromacs.")
+endif()
+
+option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING (uses Google C++ Testing and Mocking Frameworks, requires libxml2)" ${LIBXML2_FOUND})
+mark_as_advanced(GMX_BUILD_UNITTESTS)
+if (GMX_BUILD_UNITTESTS AND NOT LIBXML2_FOUND)
+ message(FATAL_ERROR
+ "Cannot build unit tests without libxml2. "
+ "Either set GMX_BUILD_UNITTESTS=OFF or tell CMake how to find libxml2.")
endif()
+set(MEMORYCHECK_SUPPRESSIONS_FILE ${CMAKE_SOURCE_DIR}/cmake/legacy_and_external.supp)
########################################################################
# Generate development version info for cache
########################################################################
add_definitions( -DHAVE_CONFIG_H )
+include_directories(${CMAKE_SOURCE_DIR}/src)
+# Required for config.h, maybe should only be set in src/CMakeLists.txt
include_directories(${CMAKE_BINARY_DIR}/src)
-include_directories(${CMAKE_BINARY_DIR}/include)
-include_directories(${CMAKE_SOURCE_DIR}/include)
+# Required for gmx_header_config_gen.h to be found before installation
+include_directories(${CMAKE_BINARY_DIR}/src/gromacs/utility)
+# Required for now to make old code compile
+include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
include(gmxTestInlineASM)
gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
gmx_test__isfinite(HAVE__ISFINITE)
gmx_test__finite(HAVE__FINITE)
+include(gmxTestCXX11)
+gmx_test_cxx11(GMX_CXX11 GMX_CXX11_FLAGS)
+if(CXX11_FLAG AND GMX_GPU)
+ #FIXME: add proper solution for progate all but cxx11 flag
+ set(CUDA_PROPAGATE_HOST_FLAGS no)
+ message(WARNING "Please manually add compiler flags to CUDA_NVCC_FLAGS. Automatic propogation temporary not working.")
+endif()
+
include(gmxTestXDR)
gmx_test_xdr(GMX_SYSTEM_XDR)
if(NOT GMX_SYSTEM_XDR)
GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
endif(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
- if (CMAKE_CXX_COMPILER_LOADED)
- GMX_TEST_CXXFLAG(GNU_SSE2_CXXFLAG "-msse2" ACCELERATION_CXX_FLAGS)
- if(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
- GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
- endif(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
- endif()
+ GMX_TEST_CXXFLAG(GNU_SSE2_CXXFLAG "-msse2" ACCELERATION_CXX_FLAGS)
+ if(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
+ GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
+ endif(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
# We dont warn for lacking SSE2 flag support, since that is probably standard today.
endif()
endif(NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
- if (CMAKE_CXX_COMPILER_LOADED)
- GMX_TEST_CXXFLAG(GNU_SSE4_CXXFLAG "-msse4.1" ACCELERATION_CXX_FLAGS)
- if (NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
- GMX_TEST_CXXFLAG(MSVC_SSE4_CXXFLAG "/arch:SSE4.1" ACCELERATION_CXX_FLAGS)
- endif(NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
- if (NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
- message(WARNING "No C++ SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance.")
- # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
- # intrinsics when SSE2 support is enabled, so we try that instead.
- if (GMX_NATIVE_WINDOWS)
- GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
- endif()
- endif(NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
- endif()
+ GMX_TEST_CXXFLAG(GNU_SSE4_CXXFLAG "-msse4.1" ACCELERATION_CXX_FLAGS)
+ if (NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
+ GMX_TEST_CXXFLAG(MSVC_SSE4_CXXFLAG "/arch:SSE4.1" ACCELERATION_CXX_FLAGS)
+ endif(NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
+ if (NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
+ message(WARNING "No C++ SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance.")
+ # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
+ # intrinsics when SSE2 support is enabled, so we try that instead.
+ if (GMX_NATIVE_WINDOWS)
+ GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
+ endif()
+ endif(NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
# This must come after we have added the -msse4.1 flag on some platforms.
check_include_file(smmintrin.h HAVE_SMMINTRIN_H ${ACCELERATION_C_FLAGS})
message(WARNING "No C AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
endif (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
- if (CMAKE_CXX_COMPILER_LOADED)
- GMX_TEST_CXXFLAG(GNU_AVX_CXXFLAG "-mavx" ACCELERATION_CXX_FLAGS)
- if (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
- GMX_TEST_CXXFLAG(MSVC_AVX_CXXFLAG "/arch:AVX" ACCELERATION_CXX_FLAGS)
- endif (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
- if (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
- message(WARNING "No C++ AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
- endif (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
- endif()
+ GMX_TEST_CXXFLAG(GNU_AVX_CXXFLAG "-mavx" ACCELERATION_CXX_FLAGS)
+ if (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
+ GMX_TEST_CXXFLAG(MSVC_AVX_CXXFLAG "/arch:AVX" ACCELERATION_CXX_FLAGS)
+ endif (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
+ if (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
+ message(WARNING "No C++ AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
+ endif (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
# Set the FMA4 flags (MSVC doesn't require any)
if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" AND NOT MSVC)
+ if (${CMAKE_COMPILER_ID} MATCHES "Clang")
+ message(FATAL_ERROR "Clang up to at least version 3.2 produces incorrect code for AVX_128_FMA. Sorry, but you will have to select a different compiler or acceleration.")
+ endif()
GMX_TEST_CFLAG(GNU_FMA_CFLAG "-mfma4" ACCELERATION_C_FLAGS)
if (NOT GNU_FMA_CFLAG)
message(WARNING "No C FMA4 flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
if (NOT ACCELERATION_QUIETLY)
message(STATUS "Enabling 128-bit AVX Gromacs acceleration (with fused-multiply add), and it will help compiler optimization.")
endif()
-
- # We don't have the full compiler version string yet (BUILD_C_COMPILER),
- # so we can't distinguish vanilla and Apple clang, but catering for AMD
- # hackintoshes is not worth the effort.
- if (APPLE AND ${CMAKE_C_COMPILER_ID} STREQUAL "Clang")
- message(WARNING "Due to a known compiler bug, Clang up to version 3.2 (and Apple Clang up to version 4.1) produces incorrect code with AVX_128_FMA acceleration. As we can not work around this bug on OS X, you will have to select a different compiler or CPU acceleration.")
- endif()
-
- if (GMX_USE_CLANG_FMA_BUG_WORKAROUND)
- # we assume that we have an external assembler that supports AVX
- message(STATUS "Clang ${C_COMPILER_VERSION} detected, enabling FMA bug workaround")
- set(EXTRA_C_FLAGS "${EXTRA_C_FLAGS} -no-integrated-as")
- endif()
-
else()
# If we are not doing AVX_128, it must be AVX_256...
set(GMX_CPU_ACCELERATION_X86_AVX_256 1)
message(WARNING "The FFTW library was compiled with --enable-avx to enable AVX SIMD instructions. That might sound like a good idea for your processor, but for FFTW versions up to 3.3.3, these are slower than the SSE/SSE2 SIMD instructions for the way GROMACS uses FFTs. Limitations in the way FFTW allows GROMACS to measure performance make it awkward for either GROMACS or FFTW to make the decision for you based on runtime performance. You should compile a different FFTW library with --enable-sse or --enable-sse2. If you have a more recent FFTW, you may like to compare the performance of GROMACS with FFTW libraries compiled with and without --enable-avx. However, the GROMACS developers do not really expect the FFTW AVX optimization to help, because the performance is limited by memory access, not computation.")
endif()
+ if(NOT "${GMX_FFT_LIBRARY}" STREQUAL "${GMX_FFT_LIBRARY_PREVIOUS_VALUE}")
+ MESSAGE(STATUS "Using external FFT library - FFTW3")
+ endif()
elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
- MESSAGE(STATUS "Using external FFT library - Intel MKL")
-
# Intel 11 and up makes life somewhat easy if you just want to use
# all their stuff. It's not easy if you only want some of their
# stuff...
set(GMX_FFT_MKL 1)
set(HAVE_LIBMKL 1)
+ if(NOT "${GMX_FFT_LIBRARY}" STREQUAL "${GMX_FFT_LIBRARY_PREVIOUS_VALUE}")
+ MESSAGE(STATUS "Using external FFT library - Intel MKL")
+ endif()
+
#elseif(${GMX_FFT_LIBRARY} STREQUAL "ACML")
# MESSAGE(STATUS "Using external FFT library - AMD core math library")
# set(GMX_FFT_ACML 1)
elseif(${GMX_FFT_LIBRARY} STREQUAL "FFTPACK")
- MESSAGE(STATUS "Using internal FFT library - fftpack")
set(GMX_FFT_FFTPACK 1)
+ if(NOT "${GMX_FFT_LIBRARY}" STREQUAL "${GMX_FFT_LIBRARY_PREVIOUS_VALUE}")
+ MESSAGE(STATUS "Using internal FFT library - fftpack")
+ endif()
else(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
MESSAGE(FATAL_ERROR "Invalid FFT library setting: ${GMX_FFT_LIBRARY}. Choose one of: fftw3, mkl, fftpack")
endif(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
+ set(GMX_FFT_LIBRARY_PREVIOUS_VALUE ${GMX_FFT_LIBRARY} CACHE INTERNAL "Previous value for GMX_FFT_LIBRARY, so that we can detect when it changes.")
# enable threaded fftw3 if we've found it
if(FFTW3_THREADS OR FFTW3F_THREADS)
# # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
# these are set after everything else
if (NOT GMX_SKIP_DEFAULT_CFLAGS)
- set(CMAKE_C_FLAGS "${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${CMAKE_C_FLAGS}")
- set(CMAKE_CXX_FLAGS "${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${CMAKE_CXX_FLAGS}")
+ set(CMAKE_C_FLAGS "${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${CMAKE_C_FLAGS}")
+ set(CMAKE_CXX_FLAGS "${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMX_CXX11_FLAGS} ${CMAKE_CXX_FLAGS}")
set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
set(CMAKE_SHARED_LINKER_FLAGS "${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
else()
message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
- message("CMAKE_C_FLAGS: ${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${GMXC_CFLAGS}")
+ message("CMAKE_C_FLAGS: ${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${GMXC_CFLAGS}")
message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
- if(CMAKE_CXX_COMPILER_LOADED)
- message("CMAKE_CXX_FLAGS: ${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMXC_CXXFLAGS}")
- message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
- message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
- endif()
+ message("CMAKE_CXX_FLAGS: ${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMX_CXX11_FLAGS} ${GMXC_CXXFLAGS}")
+ message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
+ message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
endif()
#or because it was only partially detected (e.g. only for C but not C++ compiler)
unset(OpenMP_C_FLAGS CACHE)
unset(OpenMP_CXX_FLAGS CACHE)
- unset(OpenMP_LINKER_FLAGS CACHE)
- unset(OpenMP_SHARED_LINKER_FLAGS)
+else()
+ 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} ${OpenMP_C_FLAGS}")
endif ()
########################################################################
-# Specify install locations and which subdirectories to process #
+# Specify install locations
########################################################################
-if (GMX_USE_RELATIVE_INSTALL_PATH)
- set(GMX_INSTALL_PREFIX "" CACHE STRING "Prefix gets appended to CMAKE_INSTALL_PREFIX. For cpack it sets the root folder of the archive.")
- mark_as_advanced(GMX_INSTALL_PREFIX)
-else()
- set(GMX_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}/")
-endif()
-
if ( NOT DEFINED GMXLIB )
set(GMXLIB lib)
endif()
set(GMXLIBDIR ${DATA_INSTALL_DIR}/top)
##################################################################
-# Shared library settings - Darwin uses INSTALL_NAME_DIR instead!
+# Shared library settings
##################################################################
if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
set(CMAKE_SKIP_BUILD_RPATH FALSE)
set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
set(CMAKE_INSTALL_RPATH "\\\$ORIGIN/../${GMXLIB}")
set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+else()
+ if(CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) #rpath supported for >10.4
+ set(CMAKE_INSTALL_NAME_DIR "@rpath")
+ set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} "-Wl,-rpath,@executable_path/../lib")
+ else()
+ set(CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
+ endif()
endif()
#COPYING file: Only necessary for binary distributions.
#Simpler to always install.
install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
+if(GMX_EXTERNAL_BOOST)
+ include_directories(${Boost_INCLUDE_DIRS})
+else()
+ include_directories(${CMAKE_SOURCE_DIR}/src/external/boost)
+ # typeid not supported for minimal internal version
+ # (would add significant amount of code)
+ add_definitions(-DBOOST_NO_TYPEID)
+ # TODO: Propagate the above settings to the installed CMakeFiles.txt template
+ # (from share/template/)
+ set(PKG_CFLAGS "${PKG_CFLAGS} -DBOOST_NO_TYPEID -I${INCL_INSTALL_DIR}/gromacs/external/boost")
+ install(DIRECTORY ${CMAKE_SOURCE_DIR}/src/external/boost/boost
+ DESTINATION ${INCL_INSTALL_DIR}/gromacs/external/boost
+ COMPONENT development)
+endif()
+
+add_subdirectory(doxygen)
add_subdirectory(share)
-add_subdirectory(include)
add_subdirectory(src)
add_subdirectory(scripts)
include(CTest)
mark_as_advanced(BUILD_TESTING)
#gmxtests target builds all binaries required for running gmxtest
-add_custom_target(gmxtests DEPENDS grompp mdrun pdb2gmx gmxcheck editconf)
+add_custom_target(gmxtests DEPENDS grompp mdrun pdb2gmx gmxcheck gmx links)
IF(BUILD_TESTING)
enable_testing()
add_subdirectory(tests)
- if(REGRESSIONTEST_PATH)
- #check target builds all to run tests and the runs tests
- add_custom_target(check COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure)
- add_dependencies(check gmxtests)
- else()
- add_custom_target(check COMMAND ${CMAKE_COMMAND} -E echo "WARNING: No tests are run. Running the tests requires either of the cmake variables REGRESSIONTEST_PATH or REGRESSIONTEST_DOWNLOAD to be set.")
- endif()
+ #"check" target builds and runs all tests
+ add_custom_target(check COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure)
+ add_dependencies(check gmxtests tests)
+ #TODO: Add warning if NOT REGRESSIONTEST_PATH OR NOT GMX_XML that regression/unit tests are not run.
ENDIF()
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team,
* check out http://www.gromacs.org for more information.
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012, by the GROMACS development team, led by
* David van der Spoel, Berk Hess, 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 "thread_mpi/threads.h"
-#ifdef GMX_LIB_MPI
-#include <mpi.h>
-#endif
-#ifdef GMX_THREAD_MPI
-#include "tmpi.h"
-#endif
+#include "gromacs/utility/gmxmpi.h"
#ifdef GMX_FAHCORE
#include "corewrap.h"
if (inputrec->bRot)
{
- finish_rot(fplog,inputrec->rot);
+ finish_rot(inputrec->rot);
}
}
--- /dev/null
- prev.C = prev.O = -1;
+/*
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * 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 the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Green Red Orange Magenta Azure Cyan Skyblue
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdlib.h>
+
+#include "string2.h"
+#include "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 ires, i, j, k, ii;
+ t_dihatms atm, prev;
+ int nl = 0, nc[edMax];
+ char *thisres;
+ t_dlist *dl;
+
+ snew(dl, atoms->nres+1);
- atm.minC = atm.H = atm.N = atm.C = atm.O = atm.minO = -1;
++ prev.C = prev.Cn[1] = -1; /* Keep the compiler quiet */
+ for (i = 0; (i < edMax); i++)
+ {
+ nc[i] = 0;
+ }
+ ires = -1;
+ i = 0;
+ while (i < atoms->nr)
+ {
+ ires = atoms->atom[i].resind;
+
+ /* Initiate all atom numbers to -1 */
- (strcmp(*(atoms->atomname[i]), "H1") == 0) )
++ atm.minC = atm.H = atm.N = atm.C = atm.O = atm.minCalpha = -1;
+ for (j = 0; (j < MAXCHI+3); j++)
+ {
+ atm.Cn[j] = -1;
+ }
+
+ /* Look for atoms in this residue */
+ /* maybe should allow for chis to hydrogens? */
+ while ((i < atoms->nr) && (atoms->atom[i].resind == ires))
+ {
+ if ((strcmp(*(atoms->atomname[i]), "H") == 0) ||
- if (prev.O != -1)
++ (strcmp(*(atoms->atomname[i]), "H1") == 0) ||
++ (strcmp(*(atoms->atomname[i]), "HN") == 0) )
+ {
+ atm.H = i;
+ }
+ else if (strcmp(*(atoms->atomname[i]), "N") == 0)
+ {
+ atm.N = i;
+ }
+ else if (strcmp(*(atoms->atomname[i]), "C") == 0)
+ {
+ atm.C = i;
+ }
+ else if ((strcmp(*(atoms->atomname[i]), "O") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "O1") == 0))
+ {
+ atm.O = i;
+ }
+ else if (strcmp(*(atoms->atomname[i]), "CA") == 0)
+ {
+ atm.Cn[1] = i;
+ }
+ else if (strcmp(*(atoms->atomname[i]), "CB") == 0)
+ {
+ atm.Cn[2] = i;
+ }
+ else if ((strcmp(*(atoms->atomname[i]), "CG") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "CG1") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "OG") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "OG1") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "SG") == 0))
+ {
+ atm.Cn[3] = i;
+ }
+ else if ((strcmp(*(atoms->atomname[i]), "CD") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "CD1") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "SD") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "OD1") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "ND1") == 0))
+ {
+ atm.Cn[4] = i;
+ }
+ /* by grs - split the Cn[4] into 2 bits to check allowing dih to H */
+ else if (bHChi && ((strcmp(*(atoms->atomname[i]), "HG") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "HG1") == 0)) )
+ {
+ atm.Cn[4] = i;
+ }
+ else if ((strcmp(*(atoms->atomname[i]), "CE") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "CE1") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "OE1") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "NE") == 0))
+ {
+ atm.Cn[5] = i;
+ }
+ else if ((strcmp(*(atoms->atomname[i]), "CZ") == 0) ||
+ (strcmp(*(atoms->atomname[i]), "NZ") == 0))
+ {
+ atm.Cn[6] = i;
+ }
+ /* HChi flag here too */
+ else if (bHChi && (strcmp(*(atoms->atomname[i]), "NH1") == 0))
+ {
+ atm.Cn[7] = i;
+ }
+ i++;
+ }
+
+ thisres = *(atoms->resinfo[ires].name);
+
+ /* added by grs - special case for aromatics, whose chis above 2 are
+ not real and produce rubbish output - so set back to -1 */
+ if (strcmp(thisres, "PHE") == 0 ||
+ strcmp(thisres, "TYR") == 0 ||
+ strcmp(thisres, "PTR") == 0 ||
+ strcmp(thisres, "TRP") == 0 ||
+ strcmp(thisres, "HIS") == 0 ||
+ strcmp(thisres, "HISA") == 0 ||
+ strcmp(thisres, "HISB") == 0)
+ {
+ for (ii = 5; ii <= 7; ii++)
+ {
+ atm.Cn[ii] = -1;
+ }
+ }
+ /* end fixing aromatics */
+
+ /* Special case for Pro, has no H */
+ if (strcmp(thisres, "PRO") == 0)
+ {
+ atm.H = atm.Cn[4];
+ }
+ /* Carbon from previous residue */
+ if (prev.C != -1)
+ {
+ atm.minC = prev.C;
+ }
- atm.minO = prev.O;
++ /* Alpha-carbon from previous residue */
++ if (prev.Cn[1] != -1)
+ {
- if ((atm.minC != -1) && (atm.minO != -1))
++ atm.minCalpha = prev.Cn[1];
+ }
+ prev = atm;
+
+ /* Check how many dihedrals we have */
+ if ((atm.N != -1) && (atm.Cn[1] != -1) && (atm.C != -1) &&
+ (atm.O != -1) && ((atm.H != -1) || (atm.minC != -1)))
+ {
+ dl[nl].resnr = ires+1;
+ dl[nl].atm = atm;
+ dl[nl].atm.Cn[0] = atm.N;
+ if ((atm.Cn[3] != -1) && (atm.Cn[2] != -1) && (atm.Cn[1] != -1))
+ {
+ nc[0]++;
+ if (atm.Cn[4] != -1)
+ {
+ nc[1]++;
+ if (atm.Cn[5] != -1)
+ {
+ nc[2]++;
+ if (atm.Cn[6] != -1)
+ {
+ nc[3]++;
+ if (atm.Cn[7] != -1)
+ {
+ nc[4]++;
+ if (atm.Cn[8] != -1)
+ {
+ nc[5]++;
+ }
+ }
+ }
+ }
+ }
+ }
- b = ((dl->atm.minO != -1) && (dl->atm.minC != -1) && (dl->atm.N != -1) && (dl->atm.Cn[1] != -1));
++ if ((atm.minC != -1) && (atm.minCalpha != -1))
+ {
+ nc[6]++;
+ }
+ dl[nl].index = gmx_residuetype_get_index(rt, thisres);
+
+ sprintf(dl[nl].name, "%s%d", thisres, ires+r0);
+ nl++;
+ }
+ else if (debug)
+ {
+ fprintf(debug, "Could not find N atom but could find other atoms"
+ " in residue %s%d\n", thisres, ires+r0);
+ }
+ }
+ fprintf(stderr, "\n");
+ fprintf(log, "\n");
+ fprintf(log, "There are %d residues with dihedrals\n", nl);
+ j = 0;
+ if (bPhi)
+ {
+ j += nl;
+ }
+ if (bPsi)
+ {
+ j += nl;
+ }
+ if (bChi)
+ {
+ for (i = 0; (i < maxchi); i++)
+ {
+ j += nc[i];
+ }
+ }
+ fprintf(log, "There are %d dihedrals\n", j);
+ fprintf(log, "Dihedral: ");
+ if (bPhi)
+ {
+ fprintf(log, " Phi ");
+ }
+ if (bPsi)
+ {
+ fprintf(log, " Psi ");
+ }
+ if (bChi)
+ {
+ for (i = 0; (i < maxchi); i++)
+ {
+ fprintf(log, "Chi%d ", i+1);
+ }
+ }
+ fprintf(log, "\nNumber: ");
+ if (bPhi)
+ {
+ fprintf(log, "%4d ", nl);
+ }
+ if (bPsi)
+ {
+ fprintf(log, "%4d ", nl);
+ }
+ if (bChi)
+ {
+ for (i = 0; (i < maxchi); i++)
+ {
+ fprintf(log, "%4d ", nc[i]);
+ }
+ }
+ fprintf(log, "\n");
+
+ *nlist = nl;
+
+ return dl;
+}
+
+gmx_bool has_dihedral(int Dih, t_dlist *dl)
+{
+ gmx_bool b = FALSE;
+ int ddd;
+
+ switch (Dih)
+ {
+ case edPhi:
+ b = ((dl->atm.H != -1) && (dl->atm.N != -1) && (dl->atm.Cn[1] != -1) && (dl->atm.C != -1));
+ break;
+ case edPsi:
+ b = ((dl->atm.N != -1) && (dl->atm.Cn[1] != -1) && (dl->atm.C != -1) && (dl->atm.O != -1));
+ break;
+ case edOmega:
- fprintf(fp, " Omega [%5d,%5d,%5d,%5d]", 1+dl[i].atm.minO, 1+dl[i].atm.minC,
++ b = ((dl->atm.minCalpha != -1) && (dl->atm.minC != -1) && (dl->atm.N != -1) && (dl->atm.Cn[1] != -1));
+ break;
+ case edChi1:
+ case edChi2:
+ case edChi3:
+ case edChi4:
+ case edChi5:
+ case edChi6:
+ ddd = Dih - edChi1;
+ b = ((dl->atm.Cn[ddd] != -1) && (dl->atm.Cn[ddd+1] != -1) &&
+ (dl->atm.Cn[ddd+2] != -1) && (dl->atm.Cn[ddd+3] != -1));
+ break;
+ default:
+ pr_dlist(stdout, 1, dl, 1, 0, TRUE, TRUE, TRUE, TRUE, MAXCHI);
+ gmx_fatal(FARGS, "Non existant dihedral %d in file %s, line %d",
+ Dih, __FILE__, __LINE__);
+ }
+ return b;
+}
+
+static void pr_one_ro(FILE *fp, t_dlist *dl, int nDih, real dt)
+{
+ int k;
+ for (k = 0; k < NROT; k++)
+ {
+ fprintf(fp, " %6.2f", dl->rot_occ[nDih][k]);
+ }
+ fprintf(fp, "\n");
+}
+
+static void pr_ntr_s2(FILE *fp, t_dlist *dl, int nDih, real dt)
+{
+ fprintf(fp, " %6.2f %6.2f\n", (dt == 0) ? 0 : dl->ntr[nDih]/dt, dl->S2[nDih]);
+}
+
+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)
+{
+ int i, Xi;
+
+ void (*pr_props)(FILE *, t_dlist *, int, real);
+
+ /* Analysis of dihedral transitions etc */
+
+ if (printtype == edPrintST)
+ {
+ pr_props = pr_ntr_s2;
+ fprintf(stderr, "Now printing out transitions and OPs...\n");
+ }
+ else
+ {
+ pr_props = pr_one_ro;
+ fprintf(stderr, "Now printing out rotamer occupancies...\n");
+ fprintf(fp, "\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n\n");
+ }
+
+ /* change atom numbers from 0 based to 1 based */
+ for (i = 0; (i < nl); i++)
+ {
+ fprintf(fp, "Residue %s\n", dl[i].name);
+ if (printtype == edPrintST)
+ {
+ fprintf(fp, " Angle [ AI, AJ, AK, AL] #tr/ns S^2D \n"
+ "--------------------------------------------\n");
+ }
+ else
+ {
+ fprintf(fp, " Angle [ AI, AJ, AK, AL] rotamers 0 g(-) t g(+)\n"
+ "--------------------------------------------\n");
+ }
+ if (bPhi)
+ {
+ fprintf(fp, " Phi [%5d,%5d,%5d,%5d]",
+ (dl[i].atm.H == -1) ? 1+dl[i].atm.minC : 1+dl[i].atm.H,
+ 1+dl[i].atm.N, 1+dl[i].atm.Cn[1], 1+dl[i].atm.C);
+ pr_props(fp, &dl[i], edPhi, dt);
+ }
+ if (bPsi)
+ {
+ fprintf(fp, " Psi [%5d,%5d,%5d,%5d]", 1+dl[i].atm.N, 1+dl[i].atm.Cn[1],
+ 1+dl[i].atm.C, 1+dl[i].atm.O);
+ pr_props(fp, &dl[i], edPsi, dt);
+ }
+ if (bOmega && has_dihedral(edOmega, &(dl[i])))
+ {
++ fprintf(fp, " Omega [%5d,%5d,%5d,%5d]", 1+dl[i].atm.minCalpha, 1+dl[i].atm.minC,
+ 1+dl[i].atm.N, 1+dl[i].atm.Cn[1]);
+ pr_props(fp, &dl[i], edOmega, dt);
+ }
+ for (Xi = 0; Xi < MAXCHI; Xi++)
+ {
+ if (bChi && (Xi < maxchi) && (dl[i].atm.Cn[Xi+3] != -1) )
+ {
+ fprintf(fp, " Chi%d[%5d,%5d,%5d,%5d]", Xi+1, 1+dl[i].atm.Cn[Xi],
+ 1+dl[i].atm.Cn[Xi+1], 1+dl[i].atm.Cn[Xi+2],
+ 1+dl[i].atm.Cn[Xi+3]);
+ pr_props(fp, &dl[i], Xi+edChi1, dt); /* Xi+2 was wrong here */
+ }
+ }
+ fprintf(fp, "\n");
+ }
+}
+
+
+
+int pr_trans(FILE *fp, int nl, t_dlist dl[], real dt, int Xi)
+{
+ /* never called at the moment */
+
+ int i, nn, nz;
+
+ nz = 0;
+ fprintf(fp, "\\begin{table}[h]\n");
+ fprintf(fp, "\\caption{Number of dihedral transitions per nanosecond}\n");
+ fprintf(fp, "\\begin{tabular}{|l|l|}\n");
+ fprintf(fp, "\\hline\n");
+ fprintf(fp, "Residue\t&$\\chi_%d$\t\\\\\n", Xi+1);
+ for (i = 0; (i < nl); i++)
+ {
+ nn = dl[i].ntr[Xi]/dt;
+
+ if (nn == 0)
+ {
+ fprintf(fp, "%s\t&\\HL{%d}\t\\\\\n", dl[i].name, nn);
+ nz++;
+ }
+ else if (nn > 0)
+ {
+ fprintf(fp, "%s\t&\\%d\t\\\\\n", dl[i].name, nn);
+ }
+ }
+ fprintf(fp, "\\hline\n");
+ fprintf(fp, "\\end{tabular}\n");
+ fprintf(fp, "\\end{table}\n\n");
+
+ return nz;
+}
--- /dev/null
- for (i = 0; (i < nl); i++)
+/*
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * 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 the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Green Red Orange Magenta Azure Cyan Skyblue
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+#include <stdio.h>
+#include <math.h>
+
+#include "confio.h"
+#include "pdbio.h"
+#include "copyrite.h"
+#include "gmx_fatal.h"
+#include "futil.h"
+#include "gstat.h"
+#include "macros.h"
+#include "maths.h"
+#include "physics.h"
+#include "index.h"
+#include "smalloc.h"
+#include "statutil.h"
+#include "tpxio.h"
+#include <string.h>
+#include "sysstuff.h"
+#include "txtdump.h"
+#include "typedefs.h"
+#include "vec.h"
+#include "strdb.h"
+#include "xvgr.h"
+#include "matio.h"
+#include "gmx_ana.h"
+
+static gmx_bool bAllowed(real phi, real psi)
+{
+ static const char *map[] = {
+ "1100000000000000001111111000000000001111111111111111111111111",
+ "1100000000000000001111110000000000011111111111111111111111111",
+ "1100000000000000001111110000000000011111111111111111111111111",
+ "1100000000000000001111100000000000111111111111111111111111111",
+ "1100000000000000001111100000000000111111111111111111111111111",
+ "1100000000000000001111100000000001111111111111111111111111111",
+ "1100000000000000001111100000000001111111111111111111111111111",
+ "1100000000000000001111100000000011111111111111111111111111111",
+ "1110000000000000001111110000000111111111111111111111111111111",
+ "1110000000000000001111110000001111111111111111111111111111111",
+ "1110000000000000001111111000011111111111111111111111111111111",
+ "1110000000000000001111111100111111111111111111111111111111111",
+ "1110000000000000001111111111111111111111111111111111111111111",
+ "1110000000000000001111111111111111111111111111111111111111111",
+ "1110000000000000001111111111111111111111111111111111111111111",
+ "1110000000000000001111111111111111111111111111111111111111111",
+ "1110000000000000001111111111111110011111111111111111111111111",
+ "1110000000000000001111111111111100000111111111111111111111111",
+ "1110000000000000001111111111111000000000001111111111111111111",
+ "1100000000000000001111111111110000000000000011111111111111111",
+ "1100000000000000001111111111100000000000000011111111111111111",
+ "1000000000000000001111111111000000000000000001111111111111110",
+ "0000000000000000001111111110000000000000000000111111111111100",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000111111111111000000000000000",
+ "1100000000000000000000000000000001111111111111100000000000111",
+ "1100000000000000000000000000000001111111111111110000000000111",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000",
+ "0000000000000000000000000000000000000000000000000000000000000"
+ };
+#define NPP asize(map)
+ int x, y;
+
+#define INDEX(ppp) ((((int) (360+ppp*RAD2DEG)) % 360)/6)
+ x = INDEX(phi);
+ y = INDEX(psi);
+#undef INDEX
+ return (gmx_bool) map[x][y];
+}
+
+atom_id *make_chi_ind(int nl, t_dlist dl[], int *ndih)
+{
+ atom_id *id;
+ int i, Xi, n;
+
+ /* There are nl residues with max edMax dihedrals with 4 atoms each */
+ snew(id, nl*edMax*4);
+
+ n = 0;
+ for (i = 0; (i < nl); i++)
+ {
+ /* Phi, fake the first one */
+ dl[i].j0[edPhi] = n/4;
+ if (dl[i].atm.minC >= 0)
+ {
+ id[n++] = dl[i].atm.minC;
+ }
+ else
+ {
+ id[n++] = dl[i].atm.H;
+ }
+ id[n++] = dl[i].atm.N;
+ id[n++] = dl[i].atm.Cn[1];
+ id[n++] = dl[i].atm.C;
+ }
+ for (i = 0; (i < nl); i++)
+ {
+ /* Psi, fake the last one */
+ dl[i].j0[edPsi] = n/4;
+ id[n++] = dl[i].atm.N;
+ id[n++] = dl[i].atm.Cn[1];
+ id[n++] = dl[i].atm.C;
+ if (i < (nl-1) )
+ {
+ id[n++] = dl[i+1].atm.N;
+ }
+ else
+ {
+ id[n++] = dl[i].atm.O;
+ }
+ }
- id[n++] = dl[i].atm.minO;
++ for (i = 1; (i < nl); i++)
+ {
+ /* Omega */
+ if (has_dihedral(edOmega, &(dl[i])))
+ {
+ dl[i].j0[edOmega] = n/4;
- id[n++] = dl[i].atm.H;
++ id[n++] = dl[i].atm.minCalpha;
+ id[n++] = dl[i].atm.minC;
+ id[n++] = dl[i].atm.N;
++ id[n++] = dl[i].atm.Cn[1];
+ }
+ }
+ for (Xi = 0; (Xi < MAXCHI); Xi++)
+ {
+ /* Chi# */
+ for (i = 0; (i < nl); i++)
+ {
+ if (dl[i].atm.Cn[Xi+3] != -1)
+ {
+ dl[i].j0[edChi1+Xi] = n/4;
+ id[n++] = dl[i].atm.Cn[Xi];
+ id[n++] = dl[i].atm.Cn[Xi+1];
+ id[n++] = dl[i].atm.Cn[Xi+2];
+ id[n++] = dl[i].atm.Cn[Xi+3];
+ }
+ }
+ }
+ *ndih = n/4;
+
+ return id;
+}
+
+int bin(real chi, int mult)
+{
+ mult = 3;
+
+ return (int) (chi*mult/360.0);
+}
+
+
+static void do_dihcorr(const char *fn, int nf, int ndih, real **dih, real dt,
+ int nlist, t_dlist dlist[], real time[], int maxchi,
+ gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bOmega,
+ const output_env_t oenv)
+{
+ char name1[256], name2[256];
+ int i, j, Xi;
+
+ do_autocorr(fn, oenv, "Dihedral Autocorrelation Function",
+ nf, ndih, dih, dt, eacCos, FALSE);
+ /* Dump em all */
+ j = 0;
+ for (i = 0; (i < nlist); i++)
+ {
+ if (bPhi)
+ {
+ print_one(oenv, "corrphi", dlist[i].name, "Phi ACF for", "C(t)", nf/2, time,
+ dih[j]);
+ }
+ j++;
+ }
+ for (i = 0; (i < nlist); i++)
+ {
+ if (bPsi)
+ {
+ print_one(oenv, "corrpsi", dlist[i].name, "Psi ACF for", "C(t)", nf/2, time,
+ dih[j]);
+ }
+ j++;
+ }
+ for (i = 0; (i < nlist); i++)
+ {
+ if (has_dihedral(edOmega, &dlist[i]))
+ {
+ if (bOmega)
+ {
+ print_one(oenv, "corromega", dlist[i].name, "Omega ACF for", "C(t)",
+ nf/2, time, dih[j]);
+ }
+ j++;
+ }
+ }
+ for (Xi = 0; (Xi < maxchi); Xi++)
+ {
+ sprintf(name1, "corrchi%d", Xi+1);
+ sprintf(name2, "Chi%d ACF for", Xi+1);
+ for (i = 0; (i < nlist); i++)
+ {
+ if (dlist[i].atm.Cn[Xi+3] != -1)
+ {
+ if (bChi)
+ {
+ print_one(oenv, name1, dlist[i].name, name2, "C(t)", nf/2, time, dih[j]);
+ }
+ j++;
+ }
+ }
+ }
+ fprintf(stderr, "\n");
+}
+
+static void copy_dih_data(real in[], real out[], int nf, gmx_bool bLEAVE)
+{
+ /* if bLEAVE, do nothing to data in copying to out
+ * otherwise multiply by 180/pi to convert rad to deg */
+ int i;
+ real mult;
+ if (bLEAVE)
+ {
+ mult = 1;
+ }
+ else
+ {
+ mult = (180.0/M_PI);
+ }
+ for (i = 0; (i < nf); i++)
+ {
+ out[i] = in[i]*mult;
+ }
+}
+
+static void dump_em_all(int nlist, t_dlist dlist[], int nf, real time[],
+ real **dih, int maxchi,
+ gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bOmega, gmx_bool bRAD,
+ const output_env_t oenv)
+{
+ char name[256], titlestr[256], ystr[256];
+ real *data;
+ int i, j, Xi;
+
+ snew(data, nf);
+ if (bRAD)
+ {
+ strcpy(ystr, "Angle (rad)");
+ }
+ else
+ {
+ strcpy(ystr, "Angle (degrees)");
+ }
+
+ /* Dump em all */
+ j = 0;
+ for (i = 0; (i < nlist); i++)
+ {
+ /* grs debug printf("OK i %d j %d\n", i, j) ; */
+ if (bPhi)
+ {
+ copy_dih_data(dih[j], data, nf, bRAD);
+ print_one(oenv, "phi", dlist[i].name, "\\xf\\f{}", ystr, nf, time, data);
+ }
+ j++;
+ }
+ for (i = 0; (i < nlist); i++)
+ {
+ if (bPsi)
+ {
+ copy_dih_data(dih[j], data, nf, bRAD);
+ print_one(oenv, "psi", dlist[i].name, "\\xy\\f{}", ystr, nf, time, data);
+ }
+ j++;
+ }
+ for (i = 0; (i < nlist); i++)
+ {
+ if (has_dihedral(edOmega, &(dlist[i])))
+ {
+ if (bOmega)
+ {
+ copy_dih_data(dih[j], data, nf, bRAD);
+ print_one(oenv, "omega", dlist[i].name, "\\xw\\f{}", ystr, nf, time, data);
+ }
+ j++;
+ }
+ }
+
+ for (Xi = 0; (Xi < maxchi); Xi++)
+ {
+ for (i = 0; (i < nlist); i++)
+ {
+ if (dlist[i].atm.Cn[Xi+3] != -1)
+ {
+ if (bChi)
+ {
+ sprintf(name, "chi%d", Xi+1);
+ sprintf(titlestr, "\\xc\\f{}\\s%d\\N", Xi+1);
+ copy_dih_data(dih[j], data, nf, bRAD);
+ print_one(oenv, name, dlist[i].name, titlestr, ystr, nf, time, data);
+ }
+ j++;
+ }
+ }
+ }
+ fprintf(stderr, "\n");
+}
+
+static void reset_one(real dih[], int nf, real phase)
+{
+ int j;
+
+ for (j = 0; (j < nf); j++)
+ {
+ dih[j] += phase;
+ while (dih[j] < -M_PI)
+ {
+ dih[j] += 2*M_PI;
+ }
+ while (dih[j] >= M_PI)
+ {
+ dih[j] -= 2*M_PI;
+ }
+ }
+}
+
+static int reset_em_all(int nlist, t_dlist dlist[], int nf,
+ real **dih, int maxchi)
+{
+ int i, j, Xi;
+
+ /* Reset em all */
+ j = 0;
+ /* Phi */
+ for (i = 0; (i < nlist); i++)
+ {
+ if (dlist[i].atm.minC == -1)
+ {
+ reset_one(dih[j++], nf, M_PI);
+ }
+ else
+ {
+ reset_one(dih[j++], nf, 0);
+ }
+ }
+ /* Psi */
+ for (i = 0; (i < nlist-1); i++)
+ {
+ reset_one(dih[j++], nf, 0);
+ }
+ /* last Psi is faked from O */
+ reset_one(dih[j++], nf, M_PI);
+
+ /* Omega */
+ for (i = 0; (i < nlist); i++)
+ {
+ if (has_dihedral(edOmega, &dlist[i]))
+ {
+ reset_one(dih[j++], nf, 0);
+ }
+ }
+ /* Chi 1 thru maxchi */
+ for (Xi = 0; (Xi < maxchi); Xi++)
+ {
+ for (i = 0; (i < nlist); i++)
+ {
+ if (dlist[i].atm.Cn[Xi+3] != -1)
+ {
+ reset_one(dih[j], nf, 0);
+ j++;
+ }
+ }
+ }
+ fprintf(stderr, "j after resetting (nr. active dihedrals) = %d\n", j);
+ return j;
+}
+
+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[],
+ gmx_bool bPhi, gmx_bool bPsi, gmx_bool bOmega, gmx_bool bChi,
+ gmx_bool bNormalize, gmx_bool bSSHisto, const char *ssdump,
+ real bfac_max, t_atoms *atoms,
+ gmx_bool bDo_jc, const char *fn,
+ const output_env_t oenv)
+{
+ /* also gets 3J couplings and order parameters S2 */
+ t_karplus kkkphi[] = {
+ { "J_NHa1", 6.51, -1.76, 1.6, -M_PI/3, 0.0, 0.0 },
+ { "J_NHa2", 6.51, -1.76, 1.6, M_PI/3, 0.0, 0.0 },
+ { "J_HaC'", 4.0, 1.1, 0.1, 0.0, 0.0, 0.0 },
+ { "J_NHCb", 4.7, -1.5, -0.2, M_PI/3, 0.0, 0.0 },
+ { "J_Ci-1Hai", 4.5, -1.3, -1.2, 2*M_PI/3, 0.0, 0.0 }
+ };
+ t_karplus kkkpsi[] = {
+ { "J_HaN", -0.88, -0.61, -0.27, M_PI/3, 0.0, 0.0 }
+ };
+ t_karplus kkkchi1[] = {
+ { "JHaHb2", 9.5, -1.6, 1.8, -M_PI/3, 0, 0.0 },
+ { "JHaHb3", 9.5, -1.6, 1.8, 0, 0, 0.0 }
+ };
+#define NKKKPHI asize(kkkphi)
+#define NKKKPSI asize(kkkpsi)
+#define NKKKCHI asize(kkkchi1)
+#define NJC (NKKKPHI+NKKKPSI+NKKKCHI)
+
+ FILE *fp, *ssfp[3] = {NULL, NULL, NULL};
+ const char *sss[3] = { "sheet", "helix", "coil" };
+ real S2;
+ real *normhisto;
+ real **Jc, **Jcsig;
+ int ****his_aa_ss = NULL;
+ int ***his_aa, **his_aa1, *histmp;
+ int i, j, k, m, n, nn, Dih, nres, hindex, angle;
+ gmx_bool bBfac, bOccup;
+ char hisfile[256], hhisfile[256], sshisfile[256], title[256], *ss_str = NULL;
+ char **leg;
+ const char *residue_name;
+ int rt_size;
+
+ rt_size = gmx_residuetype_get_size(rt);
+ if (bSSHisto)
+ {
+ fp = ffopen(ssdump, "r");
+ if (1 != fscanf(fp, "%d", &nres))
+ {
+ gmx_fatal(FARGS, "Error reading from file %s", ssdump);
+ }
+
+ snew(ss_str, nres+1);
+ if (1 != fscanf(fp, "%s", ss_str))
+ {
+ gmx_fatal(FARGS, "Error reading from file %s", ssdump);
+ }
+
+ ffclose(fp);
+ /* Four dimensional array... Very cool */
+ snew(his_aa_ss, 3);
+ for (i = 0; (i < 3); i++)
+ {
+ snew(his_aa_ss[i], rt_size+1);
+ for (j = 0; (j <= rt_size); j++)
+ {
+ snew(his_aa_ss[i][j], edMax);
+ for (Dih = 0; (Dih < edMax); Dih++)
+ {
+ snew(his_aa_ss[i][j][Dih], nbin+1);
+ }
+ }
+ }
+ }
+ snew(his_aa, edMax);
+ for (Dih = 0; (Dih < edMax); Dih++)
+ {
+ snew(his_aa[Dih], rt_size+1);
+ for (i = 0; (i <= rt_size); i++)
+ {
+ snew(his_aa[Dih][i], nbin+1);
+ }
+ }
+ snew(histmp, nbin);
+
+ snew(Jc, nlist);
+ snew(Jcsig, nlist);
+ for (i = 0; (i < nlist); i++)
+ {
+ snew(Jc[i], NJC);
+ snew(Jcsig[i], NJC);
+ }
+
+ j = 0;
+ n = 0;
+ for (Dih = 0; (Dih < NONCHI+maxchi); Dih++)
+ {
+ for (i = 0; (i < nlist); i++)
+ {
+ if (((Dih < edOmega) ) ||
+ ((Dih == edOmega) && (has_dihedral(edOmega, &(dlist[i])))) ||
+ ((Dih > edOmega) && (dlist[i].atm.Cn[Dih-NONCHI+3] != -1)))
+ {
+ make_histo(log, nf, dih[j], nbin, histmp, -M_PI, M_PI);
+
+ if (bSSHisto)
+ {
+ /* Assume there is only one structure, the first.
+ * Compute index in histogram.
+ */
+ /* Check the atoms to see whether their B-factors are low enough
+ * Check atoms to see their occupancy is 1.
+ */
+ bBfac = bOccup = TRUE;
+ for (nn = 0; (nn < 4); nn++, n++)
+ {
+ bBfac = bBfac && (atoms->pdbinfo[index[n]].bfac <= bfac_max);
+ bOccup = bOccup && (atoms->pdbinfo[index[n]].occup == 1);
+ }
+ if (bOccup && ((bfac_max <= 0) || ((bfac_max > 0) && bBfac)))
+ {
+ hindex = ((dih[j][0]+M_PI)*nbin)/(2*M_PI);
+ range_check(hindex, 0, nbin);
+
+ /* Assign dihedral to either of the structure determined
+ * histograms
+ */
+ switch (ss_str[dlist[i].resnr])
+ {
+ case 'E':
+ his_aa_ss[0][dlist[i].index][Dih][hindex]++;
+ break;
+ case 'H':
+ his_aa_ss[1][dlist[i].index][Dih][hindex]++;
+ break;
+ default:
+ his_aa_ss[2][dlist[i].index][Dih][hindex]++;
+ break;
+ }
+ }
+ else if (debug)
+ {
+ fprintf(debug, "Res. %d has imcomplete occupancy or bfacs > %g\n",
+ dlist[i].resnr, bfac_max);
+ }
+ }
+ else
+ {
+ n += 4;
+ }
+
+ switch (Dih)
+ {
+ case edPhi:
+ calc_distribution_props(nbin, histmp, -M_PI, NKKKPHI, kkkphi, &S2);
+
+ for (m = 0; (m < NKKKPHI); m++)
+ {
+ Jc[i][m] = kkkphi[m].Jc;
+ Jcsig[i][m] = kkkphi[m].Jcsig;
+ }
+ break;
+ case edPsi:
+ calc_distribution_props(nbin, histmp, -M_PI, NKKKPSI, kkkpsi, &S2);
+
+ for (m = 0; (m < NKKKPSI); m++)
+ {
+ Jc[i][NKKKPHI+m] = kkkpsi[m].Jc;
+ Jcsig[i][NKKKPHI+m] = kkkpsi[m].Jcsig;
+ }
+ break;
+ case edChi1:
+ calc_distribution_props(nbin, histmp, -M_PI, NKKKCHI, kkkchi1, &S2);
+ for (m = 0; (m < NKKKCHI); m++)
+ {
+ Jc[i][NKKKPHI+NKKKPSI+m] = kkkchi1[m].Jc;
+ Jcsig[i][NKKKPHI+NKKKPSI+m] = kkkchi1[m].Jcsig;
+ }
+ break;
+ default: /* covers edOmega and higher Chis than Chi1 */
+ calc_distribution_props(nbin, histmp, -M_PI, 0, NULL, &S2);
+ break;
+ }
+ dlist[i].S2[Dih] = S2;
+
+ /* Sum distribution per amino acid type as well */
+ for (k = 0; (k < nbin); k++)
+ {
+ his_aa[Dih][dlist[i].index][k] += histmp[k];
+ histmp[k] = 0;
+ }
+ j++;
+ }
+ else /* dihed not defined */
+ {
+ dlist[i].S2[Dih] = 0.0;
+ }
+ }
+ }
+ sfree(histmp);
+
+ /* Print out Jcouplings */
+ fprintf(log, "\n *** J-Couplings from simulation (plus std. dev.) ***\n\n");
+ fprintf(log, "Residue ");
+ for (i = 0; (i < NKKKPHI); i++)
+ {
+ fprintf(log, "%7s SD", kkkphi[i].name);
+ }
+ for (i = 0; (i < NKKKPSI); i++)
+ {
+ fprintf(log, "%7s SD", kkkpsi[i].name);
+ }
+ for (i = 0; (i < NKKKCHI); i++)
+ {
+ fprintf(log, "%7s SD", kkkchi1[i].name);
+ }
+ fprintf(log, "\n");
+ for (i = 0; (i < NJC+1); i++)
+ {
+ fprintf(log, "------------");
+ }
+ fprintf(log, "\n");
+ for (i = 0; (i < nlist); i++)
+ {
+ fprintf(log, "%-10s", dlist[i].name);
+ for (j = 0; (j < NJC); j++)
+ {
+ fprintf(log, " %5.2f %4.2f", Jc[i][j], Jcsig[i][j]);
+ }
+ fprintf(log, "\n");
+ }
+ fprintf(log, "\n");
+
+ /* and to -jc file... */
+ if (bDo_jc)
+ {
+ fp = xvgropen(fn, "\\S3\\NJ-Couplings from Karplus Equation", "Residue",
+ "Coupling", oenv);
+ snew(leg, NJC);
+ for (i = 0; (i < NKKKPHI); i++)
+ {
+ leg[i] = strdup(kkkphi[i].name);
+ }
+ for (i = 0; (i < NKKKPSI); i++)
+ {
+ leg[i+NKKKPHI] = strdup(kkkpsi[i].name);
+ }
+ for (i = 0; (i < NKKKCHI); i++)
+ {
+ leg[i+NKKKPHI+NKKKPSI] = strdup(kkkchi1[i].name);
+ }
+ xvgr_legend(fp, NJC, (const char**)leg, oenv);
+ fprintf(fp, "%5s ", "#Res.");
+ for (i = 0; (i < NJC); i++)
+ {
+ fprintf(fp, "%10s ", leg[i]);
+ }
+ fprintf(fp, "\n");
+ for (i = 0; (i < nlist); i++)
+ {
+ fprintf(fp, "%5d ", dlist[i].resnr);
+ for (j = 0; (j < NJC); j++)
+ {
+ fprintf(fp, " %8.3f", Jc[i][j]);
+ }
+ fprintf(fp, "\n");
+ }
+ ffclose(fp);
+ for (i = 0; (i < NJC); i++)
+ {
+ sfree(leg[i]);
+ }
+ }
+ /* finished -jc stuff */
+
+ snew(normhisto, nbin);
+ for (i = 0; (i < rt_size); i++)
+ {
+ for (Dih = 0; (Dih < edMax); Dih++)
+ {
+ /* First check whether something is in there */
+ for (j = 0; (j < nbin); j++)
+ {
+ if (his_aa[Dih][i][j] != 0)
+ {
+ break;
+ }
+ }
+ if ((j < nbin) &&
+ ((bPhi && (Dih == edPhi)) ||
+ (bPsi && (Dih == edPsi)) ||
+ (bOmega && (Dih == edOmega)) ||
+ (bChi && (Dih >= edChi1))))
+ {
+ if (bNormalize)
+ {
+ normalize_histo(nbin, his_aa[Dih][i], (360.0/nbin), normhisto);
+ }
+
+ residue_name = gmx_residuetype_get_name(rt, i);
+ switch (Dih)
+ {
+ case edPhi:
+ sprintf(hisfile, "histo-phi%s", residue_name);
+ sprintf(title, "\\xf\\f{} Distribution for %s", residue_name);
+ break;
+ case edPsi:
+ sprintf(hisfile, "histo-psi%s", residue_name);
+ sprintf(title, "\\xy\\f{} Distribution for %s", residue_name);
+ break;
+ case edOmega:
+ sprintf(hisfile, "histo-omega%s", residue_name);
+ sprintf(title, "\\xw\\f{} Distribution for %s", residue_name);
+ break;
+ default:
+ sprintf(hisfile, "histo-chi%d%s", Dih-NONCHI+1, residue_name);
+ sprintf(title, "\\xc\\f{}\\s%d\\N Distribution for %s",
+ Dih-NONCHI+1, residue_name);
+ }
+ strcpy(hhisfile, hisfile);
+ strcat(hhisfile, ".xvg");
+ fp = xvgropen(hhisfile, title, "Degrees", "", oenv);
+ fprintf(fp, "@ with g0\n");
+ xvgr_world(fp, -180, 0, 180, 0.1, oenv);
+ fprintf(fp, "# this effort to set graph size fails unless you run with -autoscale none or -autoscale y flags\n");
+ fprintf(fp, "@ xaxis tick on\n");
+ fprintf(fp, "@ xaxis tick major 90\n");
+ fprintf(fp, "@ xaxis tick minor 30\n");
+ fprintf(fp, "@ xaxis ticklabel prec 0\n");
+ fprintf(fp, "@ yaxis tick off\n");
+ fprintf(fp, "@ yaxis ticklabel off\n");
+ fprintf(fp, "@ type xy\n");
+ if (bSSHisto)
+ {
+ for (k = 0; (k < 3); k++)
+ {
+ sprintf(sshisfile, "%s-%s.xvg", hisfile, sss[k]);
+ ssfp[k] = ffopen(sshisfile, "w");
+ }
+ }
+ for (j = 0; (j < nbin); j++)
+ {
+ angle = -180 + (360/nbin)*j;
+ if (bNormalize)
+ {
+ fprintf(fp, "%5d %10g\n", angle, normhisto[j]);
+ }
+ else
+ {
+ fprintf(fp, "%5d %10d\n", angle, his_aa[Dih][i][j]);
+ }
+ if (bSSHisto)
+ {
+ for (k = 0; (k < 3); k++)
+ {
+ fprintf(ssfp[k], "%5d %10d\n", angle,
+ his_aa_ss[k][i][Dih][j]);
+ }
+ }
+ }
+ fprintf(fp, "&\n");
+ ffclose(fp);
+ if (bSSHisto)
+ {
+ for (k = 0; (k < 3); k++)
+ {
+ fprintf(ssfp[k], "&\n");
+ ffclose(ssfp[k]);
+ }
+ }
+ }
+ }
+ }
+ sfree(normhisto);
+
+ if (bSSHisto)
+ {
+ /* Four dimensional array... Very cool */
+ for (i = 0; (i < 3); i++)
+ {
+ for (j = 0; (j <= rt_size); j++)
+ {
+ for (Dih = 0; (Dih < edMax); Dih++)
+ {
+ sfree(his_aa_ss[i][j][Dih]);
+ }
+ sfree(his_aa_ss[i][j]);
+ }
+ sfree(his_aa_ss[i]);
+ }
+ sfree(his_aa_ss);
+ sfree(ss_str);
+ }
+}
+
+static FILE *rama_file(const char *fn, const char *title, const char *xaxis,
+ const char *yaxis, const output_env_t oenv)
+{
+ FILE *fp;
+
+ fp = xvgropen(fn, title, xaxis, yaxis, oenv);
+ fprintf(fp, "@ with g0\n");
+ xvgr_world(fp, -180, -180, 180, 180, oenv);
+ fprintf(fp, "@ xaxis tick on\n");
+ fprintf(fp, "@ xaxis tick major 90\n");
+ fprintf(fp, "@ xaxis tick minor 30\n");
+ fprintf(fp, "@ xaxis ticklabel prec 0\n");
+ fprintf(fp, "@ yaxis tick on\n");
+ fprintf(fp, "@ yaxis tick major 90\n");
+ fprintf(fp, "@ yaxis tick minor 30\n");
+ fprintf(fp, "@ yaxis ticklabel prec 0\n");
+ fprintf(fp, "@ s0 type xy\n");
+ fprintf(fp, "@ s0 symbol 2\n");
+ fprintf(fp, "@ s0 symbol size 0.410000\n");
+ fprintf(fp, "@ s0 symbol fill 1\n");
+ fprintf(fp, "@ s0 symbol color 1\n");
+ fprintf(fp, "@ s0 symbol linewidth 1\n");
+ fprintf(fp, "@ s0 symbol linestyle 1\n");
+ fprintf(fp, "@ s0 symbol center false\n");
+ fprintf(fp, "@ s0 symbol char 0\n");
+ fprintf(fp, "@ s0 skip 0\n");
+ fprintf(fp, "@ s0 linestyle 0\n");
+ fprintf(fp, "@ s0 linewidth 1\n");
+ fprintf(fp, "@ type xy\n");
+
+ return fp;
+}
+
+static void do_rama(int nf, int nlist, t_dlist dlist[], real **dih,
+ gmx_bool bViol, gmx_bool bRamOmega, const output_env_t oenv)
+{
+ FILE *fp, *gp = NULL;
+ gmx_bool bOm;
+ char fn[256];
+ int i, j, k, Xi1, Xi2, Phi, Psi, Om = 0, nlevels;
+#define NMAT 120
+ real **mat = NULL, phi, psi, omega, axis[NMAT], lo, hi;
+ t_rgb rlo = { 1.0, 0.0, 0.0 };
+ t_rgb rmid = { 1.0, 1.0, 1.0 };
+ t_rgb rhi = { 0.0, 0.0, 1.0 };
+
+ for (i = 0; (i < nlist); i++)
+ {
+ if ((has_dihedral(edPhi, &(dlist[i]))) &&
+ (has_dihedral(edPsi, &(dlist[i]))))
+ {
+ sprintf(fn, "ramaPhiPsi%s.xvg", dlist[i].name);
+ fp = rama_file(fn, "Ramachandran Plot",
+ "\\8f\\4 (deg)", "\\8y\\4 (deg)", oenv);
+ bOm = bRamOmega && has_dihedral(edOmega, &(dlist[i]));
+ if (bOm)
+ {
+ Om = dlist[i].j0[edOmega];
+ snew(mat, NMAT);
+ for (j = 0; (j < NMAT); j++)
+ {
+ snew(mat[j], NMAT);
+ axis[j] = -180+(360*j)/NMAT;
+ }
+ }
+ if (bViol)
+ {
+ sprintf(fn, "violPhiPsi%s.xvg", dlist[i].name);
+ gp = ffopen(fn, "w");
+ }
+ Phi = dlist[i].j0[edPhi];
+ Psi = dlist[i].j0[edPsi];
+ for (j = 0; (j < nf); j++)
+ {
+ phi = RAD2DEG*dih[Phi][j];
+ psi = RAD2DEG*dih[Psi][j];
+ fprintf(fp, "%10g %10g\n", phi, psi);
+ if (bViol)
+ {
+ fprintf(gp, "%d\n", !bAllowed(dih[Phi][j], RAD2DEG*dih[Psi][j]));
+ }
+ if (bOm)
+ {
+ omega = RAD2DEG*dih[Om][j];
+ mat[(int)((phi*NMAT)/360)+NMAT/2][(int)((psi*NMAT)/360)+NMAT/2]
+ += omega;
+ }
+ }
+ if (bViol)
+ {
+ ffclose(gp);
+ }
+ ffclose(fp);
+ if (bOm)
+ {
+ sprintf(fn, "ramomega%s.xpm", dlist[i].name);
+ fp = ffopen(fn, "w");
+ lo = hi = 0;
+ for (j = 0; (j < NMAT); j++)
+ {
+ for (k = 0; (k < NMAT); k++)
+ {
+ mat[j][k] /= nf;
+ lo = min(mat[j][k], lo);
+ hi = max(mat[j][k], hi);
+ }
+ }
+ /* Symmetrise */
+ if (fabs(lo) > fabs(hi))
+ {
+ hi = -lo;
+ }
+ else
+ {
+ lo = -hi;
+ }
+ /* Add 180 */
+ for (j = 0; (j < NMAT); j++)
+ {
+ for (k = 0; (k < NMAT); k++)
+ {
+ mat[j][k] += 180;
+ }
+ }
+ lo += 180;
+ hi += 180;
+ nlevels = 20;
+ write_xpm3(fp, 0, "Omega/Ramachandran Plot", "Deg", "Phi", "Psi",
+ NMAT, NMAT, axis, axis, mat, lo, 180.0, hi, rlo, rmid, rhi, &nlevels);
+ ffclose(fp);
+ for (j = 0; (j < NMAT); j++)
+ {
+ sfree(mat[j]);
+ }
+ sfree(mat);
+ }
+ }
+ if ((has_dihedral(edChi1, &(dlist[i]))) &&
+ (has_dihedral(edChi2, &(dlist[i]))))
+ {
+ sprintf(fn, "ramaX1X2%s.xvg", dlist[i].name);
+ fp = rama_file(fn, "\\8c\\4\\s1\\N-\\8c\\4\\s2\\N Ramachandran Plot",
+ "\\8c\\4\\s1\\N (deg)", "\\8c\\4\\s2\\N (deg)", oenv);
+ Xi1 = dlist[i].j0[edChi1];
+ Xi2 = dlist[i].j0[edChi2];
+ for (j = 0; (j < nf); j++)
+ {
+ fprintf(fp, "%10g %10g\n", RAD2DEG*dih[Xi1][j], RAD2DEG*dih[Xi2][j]);
+ }
+ ffclose(fp);
+ }
+ else
+ {
+ fprintf(stderr, "No chi1 & chi2 angle for %s\n", dlist[i].name);
+ }
+ }
+}
+
+
+static void print_transitions(const char *fn, int maxchi, int nlist,
+ t_dlist dlist[], t_atoms *atoms, rvec x[],
+ matrix box, gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, real dt,
+ const output_env_t oenv)
+{
+ /* based on order_params below */
+ FILE *fp;
+ int nh[edMax];
+ int i, Dih, Xi;
+
+ /* must correspond with enum in pp2shift.h:38 */
+ 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");
+
+ /* Print order parameters */
+ fp = xvgropen(fn, "Dihedral Rotamer Transitions", "Residue", "Transitions/ns",
+ oenv);
+ xvgr_legend(fp, NONCHI+maxchi, (const char**)leg, oenv);
+
+ for (Dih = 0; (Dih < edMax); Dih++)
+ {
+ nh[Dih] = 0;
+ }
+
+ fprintf(fp, "%5s ", "#Res.");
+ fprintf(fp, "%10s %10s %10s ", leg[edPhi], leg[edPsi], leg[edOmega]);
+ for (Xi = 0; Xi < maxchi; Xi++)
+ {
+ fprintf(fp, "%10s ", leg[NONCHI+Xi]);
+ }
+ fprintf(fp, "\n");
+
+ for (i = 0; (i < nlist); i++)
+ {
+ fprintf(fp, "%5d ", dlist[i].resnr);
+ for (Dih = 0; (Dih < NONCHI+maxchi); Dih++)
+ {
+ fprintf(fp, "%10.3f ", dlist[i].ntr[Dih]/dt);
+ }
+ /* fprintf(fp,"%12s\n",dlist[i].name); this confuses xmgrace */
+ fprintf(fp, "\n");
+ }
+ ffclose(fp);
+}
+
+static void order_params(FILE *log,
+ const char *fn, int maxchi, int nlist, t_dlist dlist[],
+ const char *pdbfn, real bfac_init,
+ t_atoms *atoms, rvec x[], int ePBC, matrix box,
+ gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, const output_env_t oenv)
+{
+ FILE *fp;
+ int nh[edMax];
+ char buf[STRLEN];
+ int i, Dih, Xi;
+ real S2Max, S2Min;
+
+ /* except for S2Min/Max, must correspond with enum in pp2shift.h:38 */
+ const char *const_leg[2+edMax] = {
+ "S2Min", "S2Max", "Phi", "Psi", "Omega",
+ "Chi1", "Chi2", "Chi3", "Chi4", "Chi5",
+ "Chi6"
+ };
+#define NLEG asize(leg)
+
+ char *leg[2+edMax];
+
+ for (i = 0; i < NLEG; i++)
+ {
+ leg[i] = strdup(const_leg[i]);
+ }
+
+ /* Print order parameters */
+ fp = xvgropen(fn, "Dihedral Order Parameters", "Residue", "S2", oenv);
+ xvgr_legend(fp, 2+NONCHI+maxchi, const_leg, oenv);
+
+ for (Dih = 0; (Dih < edMax); Dih++)
+ {
+ nh[Dih] = 0;
+ }
+
+ fprintf(fp, "%5s ", "#Res.");
+ fprintf(fp, "%10s %10s ", leg[0], leg[1]);
+ fprintf(fp, "%10s %10s %10s ", leg[2+edPhi], leg[2+edPsi], leg[2+edOmega]);
+ for (Xi = 0; Xi < maxchi; Xi++)
+ {
+ fprintf(fp, "%10s ", leg[2+NONCHI+Xi]);
+ }
+ fprintf(fp, "\n");
+
+ for (i = 0; (i < nlist); i++)
+ {
+ S2Max = -10;
+ S2Min = 10;
+ for (Dih = 0; (Dih < NONCHI+maxchi); Dih++)
+ {
+ if (dlist[i].S2[Dih] != 0)
+ {
+ if (dlist[i].S2[Dih] > S2Max)
+ {
+ S2Max = dlist[i].S2[Dih];
+ }
+ if (dlist[i].S2[Dih] < S2Min)
+ {
+ S2Min = dlist[i].S2[Dih];
+ }
+ }
+ if (dlist[i].S2[Dih] > 0.8)
+ {
+ nh[Dih]++;
+ }
+ }
+ fprintf(fp, "%5d ", dlist[i].resnr);
+ fprintf(fp, "%10.3f %10.3f ", S2Min, S2Max);
+ for (Dih = 0; (Dih < NONCHI+maxchi); Dih++)
+ {
+ fprintf(fp, "%10.3f ", dlist[i].S2[Dih]);
+ }
+ fprintf(fp, "\n");
+ /* fprintf(fp,"%12s\n",dlist[i].name); this confuses xmgrace */
+ }
+ ffclose(fp);
+
+ if (NULL != pdbfn)
+ {
+ real x0, y0, z0;
+
+ if (NULL == atoms->pdbinfo)
+ {
+ snew(atoms->pdbinfo, atoms->nr);
+ }
+ for (i = 0; (i < atoms->nr); i++)
+ {
+ atoms->pdbinfo[i].bfac = bfac_init;
+ }
+
+ for (i = 0; (i < nlist); i++)
+ {
+ atoms->pdbinfo[dlist[i].atm.N].bfac = -dlist[i].S2[0]; /* Phi */
+ atoms->pdbinfo[dlist[i].atm.H].bfac = -dlist[i].S2[0]; /* Phi */
+ atoms->pdbinfo[dlist[i].atm.C].bfac = -dlist[i].S2[1]; /* Psi */
+ atoms->pdbinfo[dlist[i].atm.O].bfac = -dlist[i].S2[1]; /* Psi */
+ for (Xi = 0; (Xi < maxchi); Xi++) /* Chi's */
+ {
+ if (dlist[i].atm.Cn[Xi+3] != -1)
+ {
+ atoms->pdbinfo[dlist[i].atm.Cn[Xi+1]].bfac = -dlist[i].S2[NONCHI+Xi];
+ }
+ }
+ }
+
+ fp = ffopen(pdbfn, "w");
+ fprintf(fp, "REMARK generated by g_chi\n");
+ fprintf(fp, "REMARK "
+ "B-factor field contains negative of dihedral order parameters\n");
+ write_pdbfile(fp, NULL, atoms, x, ePBC, box, ' ', 0, NULL, TRUE);
+ x0 = y0 = z0 = 1000.0;
+ for (i = 0; (i < atoms->nr); i++)
+ {
+ x0 = min(x0, x[i][XX]);
+ y0 = min(y0, x[i][YY]);
+ z0 = min(z0, x[i][ZZ]);
+ }
+ x0 *= 10.0; /* nm -> angstrom */
+ y0 *= 10.0; /* nm -> angstrom */
+ z0 *= 10.0; /* nm -> angstrom */
+ sprintf(buf, "%s%%6.f%%6.2f\n", get_pdbformat());
+ for (i = 0; (i < 10); i++)
+ {
+ fprintf(fp, buf, "ATOM ", atoms->nr+1+i, "CA", "LEG", ' ',
+ atoms->nres+1, ' ', x0, y0, z0+(1.2*i), 0.0, -0.1*i);
+ }
+ ffclose(fp);
+ }
+
+ fprintf(log, "Dihedrals with S2 > 0.8\n");
+ fprintf(log, "Dihedral: ");
+ if (bPhi)
+ {
+ fprintf(log, " Phi ");
+ }
+ if (bPsi)
+ {
+ fprintf(log, " Psi ");
+ }
+ if (bChi)
+ {
+ for (Xi = 0; (Xi < maxchi); Xi++)
+ {
+ fprintf(log, " %s ", leg[2+NONCHI+Xi]);
+ }
+ }
+ fprintf(log, "\nNumber: ");
+ if (bPhi)
+ {
+ fprintf(log, "%4d ", nh[0]);
+ }
+ if (bPsi)
+ {
+ fprintf(log, "%4d ", nh[1]);
+ }
+ if (bChi)
+ {
+ for (Xi = 0; (Xi < maxchi); Xi++)
+ {
+ fprintf(log, "%4d ", nh[NONCHI+Xi]);
+ }
+ }
+ fprintf(log, "\n");
+
+ for (i = 0; i < NLEG; i++)
+ {
+ sfree(leg[i]);
+ }
+
+}
+
+int gmx_chi(int argc, char *argv[])
+{
+ const char *desc[] = {
+ "[TT]g_chi[tt] computes [GRK]phi[grk], [GRK]psi[grk], [GRK]omega[grk], and [GRK]chi[grk] dihedrals for all your ",
+ "amino acid backbone and sidechains.",
+ "It can compute dihedral angle as a function of time, and as",
+ "histogram distributions.",
+ "The distributions [TT](histo-(dihedral)(RESIDUE).xvg[tt]) are cumulative over all residues of each type.[PAR]",
+ "If option [TT]-corr[tt] is given, the program will",
+ "calculate dihedral autocorrelation functions. The function used",
+ "is C(t) = [CHEVRON][COS][GRK]chi[grk]([GRK]tau[grk])[cos] [COS][GRK]chi[grk]([GRK]tau[grk]+t)[cos][chevron]. The use of cosines",
+ "rather than angles themselves, resolves the problem of periodicity.",
+ "(Van der Spoel & Berendsen (1997), Biophys. J. 72, 2032-2041).",
+ "Separate files for each dihedral of each residue",
+ "[TT](corr(dihedral)(RESIDUE)(nresnr).xvg[tt]) are output, as well as a",
+ "file containing the information for all residues (argument of [TT]-corr[tt]).[PAR]",
+ "With option [TT]-all[tt], the angles themselves as a function of time for",
+ "each residue are printed to separate files [TT](dihedral)(RESIDUE)(nresnr).xvg[tt].",
+ "These can be in radians or degrees.[PAR]",
+ "A log file (argument [TT]-g[tt]) is also written. This contains [BR]",
+ "(a) information about the number of residues of each type.[BR]",
+ "(b) The NMR ^3J coupling constants from the Karplus equation.[BR]",
+ "(c) a table for each residue of the number of transitions between ",
+ "rotamers per nanosecond, and the order parameter S^2 of each dihedral.[BR]",
+ "(d) a table for each residue of the rotamer occupancy.[PAR]",
+ "All rotamers are taken as 3-fold, except for [GRK]omega[grk] and [GRK]chi[grk] dihedrals",
+ "to planar groups (i.e. [GRK]chi[grk][SUB]2[sub] of aromatics, Asp and Asn; [GRK]chi[grk][SUB]3[sub] of Glu",
+ "and Gln; and [GRK]chi[grk][SUB]4[sub] of Arg), which are 2-fold. \"rotamer 0\" means ",
+ "that the dihedral was not in the core region of each rotamer. ",
+ "The width of the core region can be set with [TT]-core_rotamer[tt][PAR]",
+
+ "The S^2 order parameters are also output to an [TT].xvg[tt] file",
+ "(argument [TT]-o[tt] ) and optionally as a [TT].pdb[tt] file with",
+ "the S^2 values as B-factor (argument [TT]-p[tt]). ",
+ "The total number of rotamer transitions per timestep",
+ "(argument [TT]-ot[tt]), the number of transitions per rotamer",
+ "(argument [TT]-rt[tt]), and the ^3J couplings (argument [TT]-jc[tt]), ",
+ "can also be written to [TT].xvg[tt] files. Note that the analysis",
+ "of rotamer transitions assumes that the supplied trajectory frames",
+ "are equally spaced in time.[PAR]",
+
+ "If [TT]-chi_prod[tt] is set (and [TT]-maxchi[tt] > 0), cumulative rotamers, e.g.",
+ "1+9([GRK]chi[grk][SUB]1[sub]-1)+3([GRK]chi[grk][SUB]2[sub]-1)+([GRK]chi[grk][SUB]3[sub]-1) (if the residue has three 3-fold ",
+ "dihedrals and [TT]-maxchi[tt] >= 3)",
+ "are calculated. As before, if any dihedral is not in the core region,",
+ "the rotamer is taken to be 0. The occupancies of these cumulative ",
+ "rotamers (starting with rotamer 0) are written to the file",
+ "that is the argument of [TT]-cp[tt], and if the [TT]-all[tt] flag",
+ "is given, the rotamers as functions of time",
+ "are written to [TT]chiproduct(RESIDUE)(nresnr).xvg[tt] ",
+ "and their occupancies to [TT]histo-chiproduct(RESIDUE)(nresnr).xvg[tt].[PAR]",
+
+ "The option [TT]-r[tt] generates a contour plot of the average [GRK]omega[grk] angle",
+ "as a function of the [GRK]phi[grk] and [GRK]psi[grk] angles, that is, in a Ramachandran plot",
+ "the average [GRK]omega[grk] angle is plotted using color coding.",
+
+ };
+
+ const char *bugs[] = {
+ "Produces MANY output files (up to about 4 times the number of residues in the protein, twice that if autocorrelation functions are calculated). Typically several hundred files are output.",
+ "[GRK]phi[grk] and [GRK]psi[grk] dihedrals are calculated in a non-standard way, using H-N-CA-C for [GRK]phi[grk] instead of C(-)-N-CA-C, and N-CA-C-O for [GRK]psi[grk] instead of N-CA-C-N(+). This causes (usually small) discrepancies with the output of other tools like [TT]g_rama[tt].",
+ "[TT]-r0[tt] option does not work properly",
+ "Rotamers with multiplicity 2 are printed in [TT]chi.log[tt] as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0"
+ };
+
+ /* defaults */
+ static int r0 = 1, ndeg = 1, maxchi = 2;
+ static gmx_bool bAll = FALSE;
+ static gmx_bool bPhi = FALSE, bPsi = FALSE, bOmega = FALSE;
+ static real bfac_init = -1.0, bfac_max = 0;
+ static const char *maxchistr[] = { NULL, "0", "1", "2", "3", "4", "5", "6", NULL };
+ static gmx_bool bRama = FALSE, bShift = FALSE, bViol = FALSE, bRamOmega = FALSE;
+ static gmx_bool bNormHisto = TRUE, bChiProduct = FALSE, bHChi = FALSE, bRAD = FALSE, bPBC = TRUE;
+ static real core_frac = 0.5;
+ t_pargs pa[] = {
+ { "-r0", FALSE, etINT, {&r0},
+ "starting residue" },
+ { "-phi", FALSE, etBOOL, {&bPhi},
+ "Output for [GRK]phi[grk] dihedral angles" },
+ { "-psi", FALSE, etBOOL, {&bPsi},
+ "Output for [GRK]psi[grk] dihedral angles" },
+ { "-omega", FALSE, etBOOL, {&bOmega},
+ "Output for [GRK]omega[grk] dihedrals (peptide bonds)" },
+ { "-rama", FALSE, etBOOL, {&bRama},
+ "Generate [GRK]phi[grk]/[GRK]psi[grk] and [GRK]chi[grk][SUB]1[sub]/[GRK]chi[grk][SUB]2[sub] Ramachandran plots" },
+ { "-viol", FALSE, etBOOL, {&bViol},
+ "Write a file that gives 0 or 1 for violated Ramachandran angles" },
+ { "-periodic", FALSE, etBOOL, {&bPBC},
+ "Print dihedral angles modulo 360 degrees" },
+ { "-all", FALSE, etBOOL, {&bAll},
+ "Output separate files for every dihedral." },
+ { "-rad", FALSE, etBOOL, {&bRAD},
+ "in angle vs time files, use radians rather than degrees."},
+ { "-shift", FALSE, etBOOL, {&bShift},
+ "Compute chemical shifts from [GRK]phi[grk]/[GRK]psi[grk] angles" },
+ { "-binwidth", FALSE, etINT, {&ndeg},
+ "bin width for histograms (degrees)" },
+ { "-core_rotamer", FALSE, etREAL, {&core_frac},
+ "only the central [TT]-core_rotamer[tt]*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)" },
+ { "-maxchi", FALSE, etENUM, {maxchistr},
+ "calculate first ndih [GRK]chi[grk] dihedrals" },
+ { "-normhisto", FALSE, etBOOL, {&bNormHisto},
+ "Normalize histograms" },
+ { "-ramomega", FALSE, etBOOL, {&bRamOmega},
+ "compute average omega as a function of [GRK]phi[grk]/[GRK]psi[grk] and plot it in an [TT].xpm[tt] plot" },
+ { "-bfact", FALSE, etREAL, {&bfac_init},
+ "B-factor value for [TT].pdb[tt] file for atoms with no calculated dihedral order parameter"},
+ { "-chi_prod", FALSE, etBOOL, {&bChiProduct},
+ "compute a single cumulative rotamer for each residue"},
+ { "-HChi", FALSE, etBOOL, {&bHChi},
+ "Include dihedrals to sidechain hydrogens"},
+ { "-bmax", FALSE, etREAL, {&bfac_max},
+ "Maximum B-factor on any of the atoms that make up a dihedral, for the dihedral angle to be considere in the statistics. Applies to database work where a number of X-Ray structures is analyzed. [TT]-bmax[tt] <= 0 means no limit." }
+ };
+
+ FILE *log;
+ int natoms, nlist, idum, nbin;
+ t_atoms atoms;
+ rvec *x;
+ int ePBC;
+ matrix box;
+ char title[256], grpname[256];
+ t_dlist *dlist;
+ gmx_bool bChi, bCorr, bSSHisto;
+ gmx_bool bDo_rt, bDo_oh, bDo_ot, bDo_jc;
+ real dt = 0, traj_t_ns;
+ output_env_t oenv;
+ gmx_residuetype_t rt;
+
+ atom_id isize, *index;
+ int ndih, nactdih, nf;
+ real **dih, *trans_frac, *aver_angle, *time;
+ int i, j, **chi_lookup, *multiplicity;
+
+ t_filenm fnm[] = {
+ { efSTX, "-s", NULL, ffREAD },
+ { efTRX, "-f", NULL, ffREAD },
+ { efXVG, "-o", "order", ffWRITE },
+ { efPDB, "-p", "order", ffOPTWR },
+ { efDAT, "-ss", "ssdump", ffOPTRD },
+ { efXVG, "-jc", "Jcoupling", ffWRITE },
+ { efXVG, "-corr", "dihcorr", ffOPTWR },
+ { efLOG, "-g", "chi", ffWRITE },
+ /* add two more arguments copying from g_angle */
+ { efXVG, "-ot", "dihtrans", ffOPTWR },
+ { efXVG, "-oh", "trhisto", ffOPTWR },
+ { efXVG, "-rt", "restrans", ffOPTWR },
+ { efXVG, "-cp", "chiprodhisto", ffOPTWR }
+ };
+#define NFILE asize(fnm)
+ int npargs;
+ t_pargs *ppa;
+
+ npargs = asize(pa);
+ ppa = add_acf_pargs(&npargs, pa);
+ parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs,
+ &oenv);
+
+ /* Handle result from enumerated type */
+ sscanf(maxchistr[0], "%d", &maxchi);
+ bChi = (maxchi > 0);
+
+ log = ffopen(ftp2fn(efLOG, NFILE, fnm), "w");
+
+ if (bRamOmega)
+ {
+ bOmega = TRUE;
+ bPhi = TRUE;
+ bPsi = TRUE;
+ }
+
+ /* set some options */
+ bDo_rt = (opt2bSet("-rt", NFILE, fnm));
+ bDo_oh = (opt2bSet("-oh", NFILE, fnm));
+ bDo_ot = (opt2bSet("-ot", NFILE, fnm));
+ bDo_jc = (opt2bSet("-jc", NFILE, fnm));
+ bCorr = (opt2bSet("-corr", NFILE, fnm));
+ if (bCorr)
+ {
+ fprintf(stderr, "Will calculate autocorrelation\n");
+ }
+
+ if (core_frac > 1.0)
+ {
+ fprintf(stderr, "core_rotamer fraction > 1.0 ; will use 1.0\n");
+ core_frac = 1.0;
+ }
+ if (core_frac < 0.0)
+ {
+ fprintf(stderr, "core_rotamer fraction < 0.0 ; will use 0.0\n");
+ core_frac = 0.0;
+ }
+
+ if (maxchi > MAXCHI)
+ {
+ fprintf(stderr,
+ "Will only calculate first %d Chi dihedrals in stead of %d.\n",
+ MAXCHI, maxchi);
+ maxchi = MAXCHI;
+ }
+ bSSHisto = ftp2bSet(efDAT, NFILE, fnm);
+ nbin = 360/ndeg;
+
+ /* Find the chi angles using atoms struct and a list of amino acids */
+ get_stx_coordnum(ftp2fn(efSTX, NFILE, fnm), &natoms);
+ init_t_atoms(&atoms, natoms, TRUE);
+ snew(x, natoms);
+ read_stx_conf(ftp2fn(efSTX, NFILE, fnm), title, &atoms, x, NULL, &ePBC, box);
+ fprintf(log, "Title: %s\n", title);
+
+ gmx_residuetype_init(&rt);
+ dlist = mk_dlist(log, &atoms, &nlist, bPhi, bPsi, bChi, bHChi, maxchi, r0, rt);
+ fprintf(stderr, "%d residues with dihedrals found\n", nlist);
+
+ if (nlist == 0)
+ {
+ gmx_fatal(FARGS, "No dihedrals in your structure!\n");
+ }
+
+ /* Make a linear index for reading all. */
+ index = make_chi_ind(nlist, dlist, &ndih);
+ isize = 4*ndih;
+ fprintf(stderr, "%d dihedrals found\n", ndih);
+
+ snew(dih, ndih);
+
+ /* COMPUTE ALL DIHEDRALS! */
+ read_ang_dih(ftp2fn(efTRX, NFILE, fnm), FALSE, TRUE, FALSE, bPBC, 1, &idum,
+ &nf, &time, isize, index, &trans_frac, &aver_angle, dih, oenv);
+
+ dt = (time[nf-1]-time[0])/(nf-1); /* might want this for corr or n. transit*/
+ if (bCorr)
+ {
+ if (nf < 2)
+ {
+ gmx_fatal(FARGS, "Need at least 2 frames for correlation");
+ }
+ }
+
+ /* put angles in -M_PI to M_PI ! and correct phase factor for phi and psi
+ * pass nactdih instead of ndih to low_ana_dih_trans and get_chi_product_traj
+ * to prevent accessing off end of arrays when maxchi < 5 or 6. */
+ nactdih = reset_em_all(nlist, dlist, nf, dih, maxchi);
+
+ if (bAll)
+ {
+ dump_em_all(nlist, dlist, nf, time, dih, maxchi, bPhi, bPsi, bChi, bOmega, bRAD, oenv);
+ }
+
+ /* Histogramming & J coupling constants & calc of S2 order params */
+ histogramming(log, nbin, rt, nf, maxchi, dih, nlist, dlist, index,
+ bPhi, bPsi, bOmega, bChi,
+ bNormHisto, bSSHisto, ftp2fn(efDAT, NFILE, fnm), bfac_max, &atoms,
+ bDo_jc, opt2fn("-jc", NFILE, fnm), oenv);
+
+ /* transitions
+ *
+ * added multiplicity */
+
+ snew(multiplicity, ndih);
+ mk_multiplicity_lookup(multiplicity, maxchi, dih, nlist, dlist, ndih);
+
+ strcpy(grpname, "All residues, ");
+ if (bPhi)
+ {
+ strcat(grpname, "Phi ");
+ }
+ if (bPsi)
+ {
+ strcat(grpname, "Psi ");
+ }
+ if (bOmega)
+ {
+ strcat(grpname, "Omega ");
+ }
+ if (bChi)
+ {
+ strcat(grpname, "Chi 1-");
+ sprintf(grpname + strlen(grpname), "%i", maxchi);
+ }
+
+
+ low_ana_dih_trans(bDo_ot, opt2fn("-ot", NFILE, fnm),
+ bDo_oh, opt2fn("-oh", NFILE, fnm), maxchi,
+ dih, nlist, dlist, nf, nactdih, grpname, multiplicity,
+ time, FALSE, core_frac, oenv);
+
+ /* Order parameters */
+ order_params(log, opt2fn("-o", NFILE, fnm), maxchi, nlist, dlist,
+ ftp2fn_null(efPDB, NFILE, fnm), bfac_init,
+ &atoms, x, ePBC, box, bPhi, bPsi, bChi, oenv);
+
+ /* Print ramachandran maps! */
+ if (bRama)
+ {
+ do_rama(nf, nlist, dlist, dih, bViol, bRamOmega, oenv);
+ }
+
+ if (bShift)
+ {
+ do_pp2shifts(log, nf, nlist, dlist, dih);
+ }
+
+ /* rprint S^2, transitions, and rotamer occupancies to log */
+ traj_t_ns = 0.001 * (time[nf-1]-time[0]);
+ pr_dlist(log, nlist, dlist, traj_t_ns, edPrintST, bPhi, bPsi, bChi, bOmega, maxchi);
+ pr_dlist(log, nlist, dlist, traj_t_ns, edPrintRO, bPhi, bPsi, bChi, bOmega, maxchi);
+ ffclose(log);
+ /* transitions to xvg */
+ if (bDo_rt)
+ {
+ print_transitions(opt2fn("-rt", NFILE, fnm), maxchi, nlist, dlist,
+ &atoms, x, box, bPhi, bPsi, bChi, traj_t_ns, oenv);
+ }
+
+ /* chi_product trajectories (ie one "rotamer number" for each residue) */
+ if (bChiProduct && bChi)
+ {
+ snew(chi_lookup, nlist);
+ for (i = 0; i < nlist; i++)
+ {
+ snew(chi_lookup[i], maxchi);
+ }
+ mk_chi_lookup(chi_lookup, maxchi, dih, nlist, dlist);
+
+ get_chi_product_traj(dih, nf, nactdih, nlist,
+ maxchi, dlist, time, chi_lookup, multiplicity,
+ FALSE, bNormHisto, core_frac, bAll,
+ opt2fn("-cp", NFILE, fnm), oenv);
+
+ for (i = 0; i < nlist; i++)
+ {
+ sfree(chi_lookup[i]);
+ }
+ }
+
+ /* Correlation comes last because it fucks up the angles */
+ if (bCorr)
+ {
+ do_dihcorr(opt2fn("-corr", NFILE, fnm), nf, ndih, dih, dt, nlist, dlist, time,
+ maxchi, bPhi, bPsi, bChi, bOmega, oenv);
+ }
+
+
+ do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
+ do_view(oenv, opt2fn("-jc", NFILE, fnm), "-nxy");
+ if (bCorr)
+ {
+ do_view(oenv, opt2fn("-corr", NFILE, fnm), "-nxy");
+ }
+
+ gmx_residuetype_destroy(rt);
+
+ thanx(stderr);
+
+ return 0;
+}
--- /dev/null
- "[TT]g_gyrate[tt] computes the radius of gyration of a group of atoms",
+/*
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * 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 the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Green Red Orange Magenta Azure Cyan Skyblue
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+#include <string.h>
+
+#include "statutil.h"
+#include "sysstuff.h"
+#include "typedefs.h"
+#include "smalloc.h"
+#include "macros.h"
+#include "vec.h"
+#include "pbc.h"
+#include "copyrite.h"
+#include "futil.h"
+#include "statutil.h"
+#include "index.h"
+#include "mshift.h"
+#include "xvgr.h"
+#include "princ.h"
+#include "rmpbc.h"
+#include "txtdump.h"
+#include "tpxio.h"
+#include "gstat.h"
+#include "gmx_ana.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)
+{
+ int i, ii, m;
+ real gyro, dx2, m0, Itot;
+ rvec comp;
+
+ if (bRot)
+ {
+ principal_comp(gnx, index, atom, x, trans, d);
+ Itot = norm(d);
+ if (bMOI)
+ {
+ return Itot;
+ }
+ for (m = 0; (m < DIM); m++)
+ {
+ d[m] = sqrt(d[m]/tm);
+ }
+#ifdef DEBUG
+ pr_rvecs(stderr, 0, "trans", trans, DIM);
+#endif
+ /* rotate_atoms(gnx,index,x,trans); */
+ }
+ clear_rvec(comp);
+ for (i = 0; (i < gnx); i++)
+ {
+ ii = index[i];
+ if (bQ)
+ {
+ m0 = fabs(atom[ii].q);
+ }
+ else
+ {
+ m0 = atom[ii].m;
+ }
+ for (m = 0; (m < DIM); m++)
+ {
+ dx2 = x[ii][m]*x[ii][m];
+ comp[m] += dx2*m0;
+ }
+ }
+ gyro = comp[XX]+comp[YY]+comp[ZZ];
+
+ for (m = 0; (m < DIM); m++)
+ {
+ gvec[m] = sqrt((gyro-comp[m])/tm);
+ }
+
+ return sqrt(gyro/tm);
+}
+
+void calc_gyro_z(rvec x[], matrix box,
+ int gnx, atom_id index[], t_atom atom[],
+ int nz, real time, FILE *out)
+{
+ static dvec *inertia = NULL;
+ static double *tm = NULL;
+ int i, ii, j, zi;
+ real zf, w, sdet, e1, e2;
+
+ if (inertia == NULL)
+ {
+ snew(inertia, nz);
+ snew(tm, nz);
+ }
+
+ for (i = 0; i < nz; i++)
+ {
+ clear_dvec(inertia[i]);
+ tm[i] = 0;
+ }
+
+ for (i = 0; (i < gnx); i++)
+ {
+ ii = index[i];
+ zf = nz*x[ii][ZZ]/box[ZZ][ZZ];
+ if (zf >= nz)
+ {
+ zf -= nz;
+ }
+ if (zf < 0)
+ {
+ zf += nz;
+ }
+ for (j = 0; j < 2; j++)
+ {
+ zi = zf + j;
+ if (zi == nz)
+ {
+ zi = 0;
+ }
+ w = atom[ii].m*(1 + cos(M_PI*(zf - zi)));
+ inertia[zi][0] += w*sqr(x[ii][YY]);
+ inertia[zi][1] += w*sqr(x[ii][XX]);
+ inertia[zi][2] -= w*x[ii][XX]*x[ii][YY];
+ tm[zi] += w;
+ }
+ }
+ fprintf(out, "%10g", time);
+ for (j = 0; j < nz; j++)
+ {
+ for (i = 0; i < 3; i++)
+ {
+ inertia[j][i] /= tm[j];
+ }
+ sdet = sqrt(sqr(inertia[j][0] - inertia[j][1]) + 4*sqr(inertia[j][2]));
+ e1 = sqrt(0.5*(inertia[j][0] + inertia[j][1] + sdet));
+ e2 = sqrt(0.5*(inertia[j][0] + inertia[j][1] - sdet));
+ fprintf(out, " %5.3f %5.3f", e1, e2);
+ }
+ fprintf(out, "\n");
+}
+
+int gmx_gyrate(int argc, char *argv[])
+{
+ const char *desc[] = {
++ "[TT]g_gyrate[tt] computes the radius of gyration of a molecule",
+ "and the radii of gyration about the [IT]x[it]-, [IT]y[it]- and [IT]z[it]-axes,",
+ "as a function of time. The atoms are explicitly mass weighted.[PAR]",
+ "With the [TT]-nmol[tt] option the radius of gyration will be calculated",
+ "for multiple molecules by splitting the analysis group in equally",
+ "sized parts.[PAR]",
+ "With the option [TT]-nz[tt] 2D radii of gyration in the [IT]x-y[it] plane",
+ "of slices along the [IT]z[it]-axis are calculated."
+ };
+ static int nmol = 1, nz = 0;
+ static gmx_bool bQ = FALSE, bRot = FALSE, bMOI = FALSE;
+ t_pargs pa[] = {
+ { "-nmol", FALSE, etINT, {&nmol},
+ "The number of molecules to analyze" },
+ { "-q", FALSE, etBOOL, {&bQ},
+ "Use absolute value of the charge of an atom as weighting factor instead of mass" },
+ { "-p", FALSE, etBOOL, {&bRot},
+ "Calculate the radii of gyration about the principal axes." },
+ { "-moi", FALSE, etBOOL, {&bMOI},
+ "Calculate the moments of inertia (defined by the principal axes)." },
+ { "-nz", FALSE, etINT, {&nz},
+ "Calculate the 2D radii of gyration of this number of slices along the z-axis" },
+ };
+ FILE *out;
+ t_trxstatus *status;
+ t_topology top;
+ int ePBC;
+ rvec *x, *x_s;
+ rvec xcm, gvec, gvec1;
+ matrix box, trans;
+ gmx_bool bACF;
+ real **moi_trans = NULL;
+ int max_moi = 0, delta_moi = 100;
+ rvec d, d1; /* eigenvalues of inertia tensor */
+ real t, t0, tm, gyro;
+ int natoms;
+ char *grpname, title[256];
+ int i, j, m, gnx, nam, mol;
+ atom_id *index;
+ output_env_t oenv;
+ gmx_rmpbc_t gpbc = NULL;
+ const char *leg[] = { "Rg", "RgX", "RgY", "RgZ" };
+ const char *legI[] = { "Itot", "I1", "I2", "I3" };
+#define NLEG asize(leg)
+ t_filenm fnm[] = {
+ { efTRX, "-f", NULL, ffREAD },
+ { efTPS, NULL, NULL, ffREAD },
+ { efNDX, NULL, NULL, ffOPTRD },
+ { efXVG, NULL, "gyrate", ffWRITE },
+ { efXVG, "-acf", "moi-acf", ffOPTWR },
+ };
+#define NFILE asize(fnm)
+ int npargs;
+ t_pargs *ppa;
+
+ npargs = asize(pa);
+ ppa = add_acf_pargs(&npargs, pa);
+
+ parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv);
+ bACF = opt2bSet("-acf", NFILE, fnm);
+ if (bACF && nmol != 1)
+ {
+ gmx_fatal(FARGS, "Can only do acf with nmol=1");
+ }
+ bRot = bRot || bMOI || bACF;
+ /*
+ if (nz > 0)
+ bMOI = TRUE;
+ */
+ if (bRot)
+ {
+ printf("Will rotate system along principal axes\n");
+ snew(moi_trans, DIM);
+ }
+ if (bMOI)
+ {
+ printf("Will print moments of inertia\n");
+ bQ = FALSE;
+ }
+ if (bQ)
+ {
+ printf("Will print radius normalised by charge\n");
+ }
+
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x, NULL, box, TRUE);
+ get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
+
+ if (nmol > gnx || gnx % nmol != 0)
+ {
+ gmx_fatal(FARGS, "The number of atoms in the group (%d) is not a multiple of nmol (%d)", gnx, nmol);
+ }
+ nam = gnx/nmol;
+
+ natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
+ snew(x_s, natoms);
+
+ j = 0;
+ t0 = t;
+ if (bQ)
+ {
+ out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
+ "Radius of Charge", "Time (ps)", "Rg (nm)", oenv);
+ }
+ else if (bMOI)
+ {
+ out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
+ "Moments of inertia", "Time (ps)", "I (a.m.u. nm\\S2\\N)", oenv);
+ }
+ else
+ {
+ out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
+ "Radius of gyration", "Time (ps)", "Rg (nm)", oenv);
+ }
+ if (bMOI)
+ {
+ xvgr_legend(out, NLEG, legI, oenv);
+ }
+ else
+ {
+ if (bRot)
+ {
+ if (output_env_get_print_xvgr_codes(oenv))
+ {
+ fprintf(out, "@ subtitle \"Axes are principal component axes\"\n");
+ }
+ }
+ xvgr_legend(out, NLEG, leg, oenv);
+ }
+ if (nz == 0)
+ {
+ gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms, box);
+ }
+ do
+ {
+ if (nz == 0)
+ {
+ gmx_rmpbc_copy(gpbc, natoms, box, x, x_s);
+ }
+ gyro = 0;
+ clear_rvec(gvec);
+ clear_rvec(d);
+ for (mol = 0; mol < nmol; mol++)
+ {
+ tm = sub_xcm(nz == 0 ? x_s : x, nam, index+mol*nam, top.atoms.atom, xcm, bQ);
+ if (nz == 0)
+ {
+ gyro += calc_gyro(x_s, nam, index+mol*nam, top.atoms.atom,
+ tm, gvec1, d1, bQ, bRot, bMOI, trans);
+ }
+ else
+ {
+ calc_gyro_z(x, box, nam, index+mol*nam, top.atoms.atom, nz, t, out);
+ }
+ rvec_inc(gvec, gvec1);
+ rvec_inc(d, d1);
+ }
+ if (nmol > 0)
+ {
+ gyro /= nmol;
+ svmul(1.0/nmol, gvec, gvec);
+ svmul(1.0/nmol, d, d);
+ }
+
+ if (nz == 0)
+ {
+ if (bRot)
+ {
+ if (j >= max_moi)
+ {
+ max_moi += delta_moi;
+ for (m = 0; (m < DIM); m++)
+ {
+ srenew(moi_trans[m], max_moi*DIM);
+ }
+ }
+ for (m = 0; (m < DIM); m++)
+ {
+ copy_rvec(trans[m], moi_trans[m]+DIM*j);
+ }
+ fprintf(out, "%10g %10g %10g %10g %10g\n",
+ t, gyro, d[XX], d[YY], d[ZZ]);
+ }
+ else
+ {
+ fprintf(out, "%10g %10g %10g %10g %10g\n",
+ t, gyro, gvec[XX], gvec[YY], gvec[ZZ]);
+ }
+ }
+ j++;
+ }
+ while (read_next_x(oenv, status, &t, natoms, x, box));
+ close_trj(status);
+ if (nz == 0)
+ {
+ gmx_rmpbc_done(gpbc);
+ }
+
+ ffclose(out);
+
+ if (bACF)
+ {
+ int mode = eacVector;
+
+ do_autocorr(opt2fn("-acf", NFILE, fnm), oenv,
+ "Moment of inertia vector ACF",
+ j, 3, moi_trans, (t-t0)/j, mode, FALSE);
+ do_view(oenv, opt2fn("-acf", NFILE, fnm), "-nxy");
+ }
+
+ do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
+
+ thanx(stderr);
+
+ return 0;
+}
#include <sched.h>
#include <sys/syscall.h>
#endif
+ #include <string.h>
+ #include <errno.h>
#include <assert.h>
#include <stdio.h>
#include "typedefs.h"
const int * pkg_id;
const int * core_id;
const int * hwthread_id;
+ gmx_bool bPickPinStride;
if (pin_offset < 0)
{
if (rc != 0)
{
+ /* topology information not available or invalid, ignore it */
nhwthreads = hwinfo->nthreads_hw_avail;
*locality_order = NULL;
{
/* We don't know anything about the hardware, don't pin */
md_print_warn(cr, fplog,
- "We don't know how many logical cores we have, will not pin threads");
+ "NOTE: We don't know how many logical cores we have, will not pin threads");
return -1;
}
}
+ if (nthreads > nhwthreads)
+ {
+ /* We are oversubscribing, don't pin */
+ md_print_warn(NULL, fplog,
+ "WARNING: Oversubscribing the CPU, will not pin threads");
+
+ return -1;
+ }
+
if (pin_offset + nthreads > nhwthreads)
{
/* We are oversubscribing, don't pin */
md_print_warn(NULL, fplog,
- "More threads requested than available logical cores, will not pin threads");
+ "WARNING: The requested pin offset is too large for the available logical cores,\n"
+ " will not pin threads");
return -1;
}
- /* Check if we need to choose the pinning stride */
- if (*pin_stride == 0)
+
+ /* do we need to choose the pinning stride? */
+ bPickPinStride = (*pin_stride == 0);
+
+ if (bPickPinStride)
{
if (rc == 0 && pin_offset + nthreads*nhwthreads_per_core <= nhwthreads)
{
*/
*pin_stride = (nhwthreads - pin_offset)/nthreads;
}
-
- if (fplog != NULL)
- {
- fprintf(fplog, "Pinning threads with a logical core stride of %d\n",
- *pin_stride);
- }
}
else
{
- if (pin_offset + nthreads*(*pin_stride) > nhwthreads)
+ /* Check the placement of the thread with the largest index to make sure
+ * that the offset & stride doesn't cause pinning beyond the last hardware thread. */
+ if (pin_offset + (nthreads-1)*(*pin_stride) >= nhwthreads)
{
/* We are oversubscribing, don't pin */
md_print_warn(NULL, fplog,
- "The requested pinning stride is too large for the available logical cores, will not pin threads");
+ "WARNING: The requested pinning stride is too large for the available logical cores,\n"
+ " will not pin threads");
return -1;
}
}
+ if (fplog != NULL)
+ {
+ fprintf(fplog, "Pinning threads with a%s logical core stride of %d\n",
+ bPickPinStride ? "n auto-selected" : " user-specified",
+ *pin_stride);
+ }
+
return 0;
}
int nth_affinity_set, thread_id_node, thread_id,
nthread_local, nthread_node, nthread_hw_max, nphyscore;
int offset;
- const int *locality_order;
- int rc;
+ /* these are inherently global properties that are shared among all threads
+ */
+ static const int *locality_order;
+ static int rc;
+ static gmx_bool have_locality_order = FALSE;
+ static tMPI_Thread_mutex_t locality_order_mtx =
+ TMPI_THREAD_MUTEX_INITIALIZER;
+ static tMPI_Thread_cond_t locality_order_cond =
+ TMPI_THREAD_COND_INITIALIZER;
if (hw_opt->thread_affinity == threadaffOFF)
{
md_print_info(cr, fplog, "Applying core pinning offset %d\n", offset);
}
- rc = get_thread_affinity_layout(fplog, cr, hwinfo,
- nthread_node,
- offset, &hw_opt->core_pinning_stride,
- &locality_order);
+ /* hw_opt is shared among tMPI threads, so for thread safety we need to do
+ * the layout detection only on master as core_pinning_stride is an in-out
+ * parameter and gets auto-set depending on its initial value.
+ * This
+ * This is not thread-safe with multi-simulations, but that's anyway not
+ * supported by tMPI. */
+ if (SIMMASTER(cr))
+ {
+ int ret;
+ int i;
+
+ ret = tMPI_Thread_mutex_lock(&locality_order_mtx);
+ if (ret != 0)
+ {
+ goto locality_order_err;
+ }
+ rc = get_thread_affinity_layout(fplog, cr, hwinfo,
+ nthread_node,
+ offset, &hw_opt->core_pinning_stride,
+ &locality_order);
+ have_locality_order = TRUE;
+ ret = tMPI_Thread_cond_broadcast(&locality_order_cond);
+ if (ret != 0)
+ {
+ tMPI_Thread_mutex_unlock(&locality_order_mtx);
+ goto locality_order_err;
+ }
+ ret = tMPI_Thread_mutex_unlock(&locality_order_mtx);
+ if (ret != 0)
+ {
+ goto locality_order_err;
+ }
+ }
+ else
+ {
+ int ret;
+ /* all other threads wait for the locality order data. */
+ ret = tMPI_Thread_mutex_lock(&locality_order_mtx);
+ if (ret != 0)
+ {
+ goto locality_order_err;
+ }
+
+ while (!have_locality_order)
+ {
+ ret = tMPI_Thread_cond_wait(&locality_order_cond,
+ &locality_order_mtx);
+ if (ret != 0)
+ {
+ tMPI_Thread_mutex_unlock(&locality_order_mtx);
+ goto locality_order_err;
+ }
+ }
+ ret = tMPI_Thread_mutex_unlock(&locality_order_mtx);
+ if (ret != 0)
+ {
+ goto locality_order_err;
+ }
+ }
+
if (rc != 0)
{
/* Incompatible layout, don't pin, warning was already issued */
/* sbuf1 contains rank info, while sbuf2 OpenMP thread info */
sbuf1[0] = sbuf2[0] = '\0';
+ /* Only add rank info if we have more than one rank. */
+ if (cr->nnodes > 1)
+ {
#ifdef GMX_MPI
#ifdef GMX_THREAD_MPI
- sprintf(sbuf1, "In thread-MPI thread #%d: ", cr->nodeid);
- #else /* GMX_LIB_MPI */
- sprintf(sbuf1, "In MPI process #%d: ", cr->nodeid);
+ sprintf(sbuf1, "In tMPI thread #%d: ", cr->nodeid);
+ #else /* GMX_LIB_MPI */
+ sprintf(sbuf1, "In MPI process #%d: ", cr->nodeid);
#endif
- #endif /* GMX_MPI */
+ #endif /* GMX_MPI */
+ }
if (nthread_local > 1)
{
- sprintf(sbuf2, "of %d/%d thread%s ",
+ sprintf(sbuf2, "for %d/%d thread%s ",
nthread_local - nth_affinity_set, nthread_local,
- (nthread_local - nth_affinity_set) > 1 ? "s" : "");
+ nthread_local > 1 ? "s" : "");
}
md_print_warn(NULL, fplog,
- "NOTE: %sAffinity setting %sfailed.\n"
- " This can cause performance degradation!",
+ "WARNING: %sAffinity setting %sfailed.\n"
+ " This can cause performance degradation! If you think your setting are\n"
+ " correct, contact the GROMACS developers.",
sbuf1, sbuf2);
}
}
+ return;
+
+ locality_order_err:
+ /* any error in affinity setting shouldn't be fatal, but should generate
+ a warning */
+ md_print_warn(NULL, fplog,
+ "WARNING: Obtaining affinity information failed due to a basic system error: %s.\n"
+ " This can cause performance degradation! ",
+ strerror(errno));
+ return;
}
/* Check the process affinity mask and if it is found to be non-zero,
--- /dev/null
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * 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 the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * GROningen Mixture of Alchemy and Childrens' Stories
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#ifdef GMX_THREAD_MPI
+#include <thread_mpi.h>
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include "typedefs.h"
+#include "txtdump.h"
+#include "smalloc.h"
+#include "ns.h"
+#include "vec.h"
+#include "maths.h"
+#include "macros.h"
+#include "string2.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 "smalloc.h"
+#include "nonbonded.h"
+
+#include "nb_kernel.h"
+#include "nb_free_energy.h"
+#include "nb_generic.h"
+#include "nb_generic_cg.h"
+#include "nb_generic_adress.h"
+
+/* Different default (c) and accelerated interaction-specific kernels */
+#include "nb_kernel_c/nb_kernel_c.h"
+
+#if (defined GMX_CPU_ACCELERATION_X86_SSE2) && !(defined GMX_DOUBLE)
+# include "nb_kernel_sse2_single/nb_kernel_sse2_single.h"
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_SSE4_1) && !(defined GMX_DOUBLE)
+# include "nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.h"
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_AVX_128_FMA) && !(defined GMX_DOUBLE)
+# include "nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.h"
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_AVX_256) && !(defined GMX_DOUBLE)
+# include "nb_kernel_avx_256_single/nb_kernel_avx_256_single.h"
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_SSE2 && defined GMX_DOUBLE)
+# include "nb_kernel_sse2_double/nb_kernel_sse2_double.h"
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_SSE4_1 && defined GMX_DOUBLE)
+# include "nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.h"
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_AVX_128_FMA && defined GMX_DOUBLE)
+# include "nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.h"
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_AVX_256 && defined GMX_DOUBLE)
+# include "nb_kernel_avx_256_double/nb_kernel_avx_256_double.h"
+#endif
+#if (defined GMX_CPU_ACCELERATION_SPARC64_HPC_ACE && defined GMX_DOUBLE)
+# include "nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.h"
+#endif
+
+
+#ifdef GMX_THREAD_MPI
+static tMPI_Thread_mutex_t nonbonded_setup_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+#endif
+static gmx_bool nonbonded_setup_done = FALSE;
+
+
+void
+gmx_nonbonded_setup(FILE * fplog,
+ t_forcerec * fr,
+ gmx_bool bGenericKernelOnly)
+{
+#ifdef GMX_THREAD_MPI
+ tMPI_Thread_mutex_lock(&nonbonded_setup_mutex);
+#endif
+ /* Here we are guaranteed only one thread made it. */
+ if (nonbonded_setup_done == FALSE)
+ {
+ if (bGenericKernelOnly == FALSE)
+ {
+ /* Add the generic kernels to the structure stored statically in nb_kernel.c */
+ nb_kernel_list_add_kernels(kernellist_c, kernellist_c_size);
+
+ if (!(fr != NULL && fr->use_cpu_acceleration == FALSE))
+ {
+ /* Add interaction-specific kernels for different architectures */
+ /* Single precision */
+#if (defined GMX_CPU_ACCELERATION_X86_SSE2) && !(defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_sse2_single, kernellist_sse2_single_size);
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_SSE4_1) && !(defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_sse4_1_single, kernellist_sse4_1_single_size);
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_AVX_128_FMA) && !(defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_avx_128_fma_single, kernellist_avx_128_fma_single_size);
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_AVX_256) && !(defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_avx_256_single, kernellist_avx_256_single_size);
+#endif
+ /* Double precision */
+#if (defined GMX_CPU_ACCELERATION_X86_SSE2 && defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_sse2_double, kernellist_sse2_double_size);
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_SSE4_1 && defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_sse4_1_double, kernellist_sse4_1_double_size);
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_AVX_128_FMA && defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_avx_128_fma_double, kernellist_avx_128_fma_double_size);
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_AVX_256 && defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_avx_256_double, kernellist_avx_256_double_size);
+#endif
+#if (defined GMX_CPU_ACCELERATION_SPARC64_HPC_ACE && defined GMX_DOUBLE)
+ nb_kernel_list_add_kernels(kernellist_sparc64_hpc_ace_double,kernellist_sparc64_hpc_ace_double_size);
+#endif
+ ; /* empty statement to avoid a completely empty block */
+ }
+ }
+ /* Create a hash for faster lookups */
+ nb_kernel_list_hash_init();
+
+ nonbonded_setup_done = TRUE;
+ }
+#ifdef GMX_THREAD_MPI
+ tMPI_Thread_mutex_unlock(&nonbonded_setup_mutex);
+#endif
+}
+
+
+
+void
+gmx_nonbonded_set_kernel_pointers(FILE *log, t_nblist *nl)
+{
+ const char * elec;
+ const char * elec_mod;
+ const char * vdw;
+ const char * vdw_mod;
+ const char * geom;
+ const char * other;
+ const char * vf;
+
+ struct
+ {
+ const char * arch;
+ int simd_padding_width;
+ }
+ arch_and_padding[] =
+ {
+ /* Single precision */
+#if (defined GMX_CPU_ACCELERATION_X86_AVX_256) && !(defined GMX_DOUBLE)
+ { "avx_256_single", 8 },
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_AVX_128_FMA) && !(defined GMX_DOUBLE)
+ { "avx_128_fma_single", 4 },
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_SSE4_1) && !(defined GMX_DOUBLE)
+ { "sse4_1_single", 4 },
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_SSE2) && !(defined GMX_DOUBLE)
+ { "sse2_single", 4 },
+#endif
+ /* Double precision */
+#if (defined GMX_CPU_ACCELERATION_X86_AVX_256 && defined GMX_DOUBLE)
+ { "avx_256_double", 4 },
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_AVX_128_FMA && defined GMX_DOUBLE)
+ /* Sic. Double precision 2-way SIMD does not require neighbor list padding,
+ * since the kernels execute a loop unrolled a factor 2, followed by
+ * a possible single odd-element epilogue.
+ */
+ { "avx_128_fma_double", 1 },
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_SSE2 && defined GMX_DOUBLE)
+ /* No padding - see comment above */
+ { "sse2_double", 1 },
+#endif
+#if (defined GMX_CPU_ACCELERATION_X86_SSE4_1 && defined GMX_DOUBLE)
+ /* No padding - see comment above */
+ { "sse4_1_double", 1 },
+#endif
+#if (defined GMX_CPU_ACCELERATION_SPARC64_HPC_ACE && defined GMX_DOUBLE)
+ /* No padding - see comment above */
+ { "sparc64_hpc_ace_double", 1 },
+#endif
+ { "c", 1 },
+ };
+ int narch = asize(arch_and_padding);
+ int i;
+
+ if (nonbonded_setup_done == FALSE)
+ {
+ /* We typically call this setup routine before starting timers,
+ * but if that has not been done for whatever reason we do it now.
+ */
+ gmx_nonbonded_setup(NULL, NULL, FALSE);
+ }
+
+ /* Not used yet */
+ other = "";
+
+ nl->kernelptr_vf = NULL;
+ nl->kernelptr_v = NULL;
+ nl->kernelptr_f = NULL;
+
+ elec = gmx_nbkernel_elec_names[nl->ielec];
+ elec_mod = eintmod_names[nl->ielecmod];
+ vdw = gmx_nbkernel_vdw_names[nl->ivdw];
+ vdw_mod = eintmod_names[nl->ivdwmod];
+ geom = gmx_nblist_geometry_names[nl->igeometry];
+
+ if (nl->type == GMX_NBLIST_INTERACTION_ADRESS)
+ {
+ nl->kernelptr_vf = (void *) gmx_nb_generic_adress_kernel;
+ nl->kernelptr_f = (void *) gmx_nb_generic_adress_kernel;
+ nl->simd_padding_width = 1;
+ return;
+ }
+
+ if (nl->type == GMX_NBLIST_INTERACTION_FREE_ENERGY)
+ {
+ nl->kernelptr_vf = (void *) gmx_nb_free_energy_kernel;
+ nl->kernelptr_f = (void *) gmx_nb_free_energy_kernel;
+ nl->simd_padding_width = 1;
+ }
+ else if (!gmx_strcasecmp_min(geom, "CG-CG"))
+ {
+ nl->kernelptr_vf = (void *) gmx_nb_generic_cg_kernel;
+ nl->kernelptr_f = (void *) gmx_nb_generic_cg_kernel;
+ nl->simd_padding_width = 1;
+ }
+ else
+ {
+ /* Try to find a specific kernel first */
+
+ for (i = 0; i < narch && nl->kernelptr_vf == NULL; i++)
+ {
+ nl->kernelptr_vf = (void *) nb_kernel_list_findkernel(log, arch_and_padding[i].arch, elec, elec_mod, vdw, vdw_mod, geom, other, "PotentialAndForce");
+ nl->simd_padding_width = arch_and_padding[i].simd_padding_width;
+ }
+ for (i = 0; i < narch && nl->kernelptr_f == NULL; i++)
+ {
+ nl->kernelptr_f = (void *) nb_kernel_list_findkernel(log, arch_and_padding[i].arch, elec, elec_mod, vdw, vdw_mod, geom, other, "Force");
+ nl->simd_padding_width = arch_and_padding[i].simd_padding_width;
+
+ /* If there is not force-only optimized kernel, is there a potential & force one? */
+ if (nl->kernelptr_f == NULL)
+ {
+ nl->kernelptr_f = (void *) nb_kernel_list_findkernel(NULL, arch_and_padding[i].arch, elec, elec_mod, vdw, vdw_mod, geom, other, "PotentialAndForce");
+ nl->simd_padding_width = arch_and_padding[i].simd_padding_width;
+ }
+ }
+
+ /* Give up, pick a generic one instead */
+ if (nl->kernelptr_vf == NULL)
+ {
+ nl->kernelptr_vf = (void *) gmx_nb_generic_kernel;
+ nl->kernelptr_f = (void *) gmx_nb_generic_kernel;
+ nl->simd_padding_width = 1;
+ if (debug)
+ {
+ fprintf(debug,
+ "WARNING - Slow generic NB kernel used for neighborlist with\n"
+ " Elec: '%s', Modifier: '%s'\n"
+ " Vdw: '%s', Modifier: '%s'\n"
+ " Geom: '%s', Other: '%s'\n\n",
+ elec, elec_mod, vdw, vdw_mod, geom, other);
+ }
+ }
+ }
+
+ return;
+}
+
+void do_nonbonded(t_commrec *cr, t_forcerec *fr,
+ rvec x[], rvec f_shortrange[], rvec f_longrange[], t_mdatoms *mdatoms, t_blocka *excl,
+ gmx_grppairener_t *grppener, rvec box_size,
+ t_nrnb *nrnb, real *lambda, real *dvdl,
+ int nls, int eNL, int flags)
+{
+ t_nblist * nlist;
+ int n, n0, n1, i, i0, i1, sz, range;
+ t_nblists * nblists;
+ nb_kernel_data_t kernel_data;
+ nb_kernel_t * kernelptr = NULL;
+ rvec * f;
+
+ kernel_data.flags = flags;
+ kernel_data.exclusions = excl;
+ kernel_data.lambda = lambda;
+ kernel_data.dvdl = dvdl;
+
+ if (fr->bAllvsAll)
+ {
++ gmx_incons("All-vs-all kernels have not been implemented in version 4.6");
+ return;
+ }
+
+ if (eNL >= 0)
+ {
+ i0 = eNL;
+ i1 = i0+1;
+ }
+ else
+ {
+ i0 = 0;
+ i1 = eNL_NR;
+ }
+
+ if (nls >= 0)
+ {
+ n0 = nls;
+ n1 = nls+1;
+ }
+ else
+ {
+ n0 = 0;
+ n1 = fr->nnblists;
+ }
+
+ for (n = n0; (n < n1); n++)
+ {
+ nblists = &fr->nblists[n];
+
+ kernel_data.table_elec = &nblists->table_elec;
+ kernel_data.table_vdw = &nblists->table_vdw;
+ kernel_data.table_elec_vdw = &nblists->table_elec_vdw;
+
+ for (range = 0; range < 2; range++)
+ {
+ /* Are we doing short/long-range? */
+ if (range == 0)
+ {
+ /* Short-range */
+ if (!(flags & GMX_NONBONDED_DO_SR))
+ {
+ continue;
+ }
+ kernel_data.energygrp_elec = grppener->ener[egCOULSR];
+ kernel_data.energygrp_vdw = grppener->ener[fr->bBHAM ? egBHAMSR : egLJSR];
+ kernel_data.energygrp_polarization = grppener->ener[egGB];
+ nlist = nblists->nlist_sr;
+ f = f_shortrange;
+ }
+ else if (range == 1)
+ {
+ /* Long-range */
+ if (!(flags & GMX_NONBONDED_DO_LR))
+ {
+ continue;
+ }
+ kernel_data.energygrp_elec = grppener->ener[egCOULLR];
+ kernel_data.energygrp_vdw = grppener->ener[fr->bBHAM ? egBHAMLR : egLJLR];
+ kernel_data.energygrp_polarization = grppener->ener[egGB];
+ nlist = nblists->nlist_lr;
+ f = f_longrange;
+ }
+
+ for (i = i0; (i < i1); i++)
+ {
+ if (nlist[i].nri > 0)
+ {
+ if (flags & GMX_NONBONDED_DO_POTENTIAL)
+ {
+ /* Potential and force */
+ kernelptr = (nb_kernel_t *)nlist[i].kernelptr_vf;
+ }
+ else
+ {
+ /* Force only, no potential */
+ kernelptr = (nb_kernel_t *)nlist[i].kernelptr_f;
+ }
+
+ if (nlist[i].type != GMX_NBLIST_INTERACTION_FREE_ENERGY && (flags & GMX_NONBONDED_DO_FOREIGNLAMBDA))
+ {
+ /* We don't need the non-perturbed interactions */
+ continue;
+ }
+ (*kernelptr)(&(nlist[i]), x, f, fr, mdatoms, &kernel_data, nrnb);
+ }
+ }
+ }
+ }
+}
+
+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;
+}
}
}
+
+ /* Set the thread id var for this thread
+ Returns a pointer to the thread object if succesful, NULL if ENOMEM */
+ static struct tMPI_Thread* tMPI_Set_thread_id_key(int started_by_tmpi)
+ {
+ struct tMPI_Thread *th;
+
+ th = (struct tMPI_Thread*)malloc(sizeof(struct tMPI_Thread)*1);
+ if (th == NULL)
+ {
+ return NULL;
+ }
+ th->th = pthread_self();
+ th->started_by_tmpi = started_by_tmpi;
+ /* we ignore errors because any thread that needs this value will
+ re-generate it in the next iteration. */
+ pthread_setspecific(thread_id_key, th);
+ return th;
+ }
+
/* initialize the thread id vars if not already initialized */
static int tMPI_Init_thread_ids(void)
{
if (!thread_id_key_initialized)
{
/* initialize and set the thread id thread-specific variable */
- struct tMPI_Thread *main_thread;
+ struct tMPI_Thread *th;
thread_id_key_initialized = 1;
ret = pthread_key_create(&thread_id_key, tMPI_Destroy_thread_id);
{
goto err;
}
- main_thread = (struct tMPI_Thread*)malloc(sizeof(struct tMPI_Thread)*1);
- if (main_thread == NULL)
+ th = tMPI_Set_thread_id_key(0);
+ if (th == NULL)
{
ret = ENOMEM;
goto err;
}
- main_thread->th = pthread_self();
- main_thread->started_by_tmpi = 0;
- ret = pthread_setspecific(thread_id_key, main_thread);
- if (ret != 0)
- {
- goto err;
- }
}
ret = pthread_mutex_unlock( &thread_id_mutex );
struct tMPI_Thread *thread;
void *(*start_routine)(void*);
void *arg;
+ pthread_mutex_t cond_lock; /* lock for initialization of thread
+ structure */
};
/* the thread_starter function that sets the thread id */
void *parg;
int ret;
+ /* first wait for the parent thread to signal that the starter->thread
+ structure is ready. That's done by unlocking the starter->cond_lock */
+ ret = pthread_mutex_lock(&(starter->cond_lock));
+ if (ret != 0)
+ {
+ return NULL;
+ }
+ ret = pthread_mutex_unlock(&(starter->cond_lock));
+ if (ret != 0)
+ {
+ return NULL;
+ }
+
+ /* now remember the tMPI_thread_t structure for this thread */
ret = pthread_setspecific(thread_id_key, starter->thread);
if (ret != 0)
{
start_routine = starter->start_routine;
parg = starter->arg;
+ /* deallocate the starter structure. Errors here are non-fatal. */
+ pthread_mutex_destroy(&(starter->cond_lock));
free(starter);
return (*start_routine)(parg);
}
starter->start_routine = start_routine;
starter->arg = arg;
+ ret = pthread_mutex_init(&(starter->cond_lock), NULL);
+ if (ret != 0)
+ {
+ return ret;
+ }
+ /* now lock the mutex so we can unlock it once we know the data in
+ thread->th is safe. */
+ ret = pthread_mutex_lock(&(starter->cond_lock));
+ if (ret != 0)
+ {
+ return ret;
+ }
+
ret = pthread_create(&((*thread)->th), NULL, tMPI_Thread_starter,
(void*)starter);
+ if (ret != 0)
+ {
+ return ret;
+ }
+
+ /* Here we know thread->th is safe. */
+ ret = pthread_mutex_unlock(&(starter->cond_lock));
return ret;
}
/* check if it is already in our list */
if (th == NULL)
{
- /* if not, create an ID, set it and return it */
- th = (struct tMPI_Thread*)malloc(sizeof(struct tMPI_Thread)*1);
- if (th == NULL)
- {
- return NULL;
- }
- th->th = pthread_self();
- th->started_by_tmpi = 0;
- /* we ignore errors here because they're not important -
- the next iteration will do the same thing. */
- pthread_setspecific(thread_id_key, th);
+ th = tMPI_Set_thread_id_key(0);
}
return th;
}
--- /dev/null
- if (file_version < 72)
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * 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 the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * GROningen Mixture of Alchemy and Childrens' Stories
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+/* This file is completely threadsafe - keep it that way! */
+#ifdef GMX_THREAD_MPI
+#include <thread_mpi.h>
+#endif
+
+
+#include <ctype.h>
+#include "sysstuff.h"
+#include "smalloc.h"
+#include "string2.h"
+#include "gmx_fatal.h"
+#include "macros.h"
+#include "names.h"
+#include "symtab.h"
+#include "futil.h"
+#include "filenm.h"
+#include "gmxfio.h"
+#include "topsort.h"
+#include "tpxio.h"
+#include "txtdump.h"
+#include "confio.h"
+#include "atomprop.h"
+#include "copyrite.h"
+#include "vec.h"
+#include "mtop_util.h"
+
+#define TPX_TAG_RELEASE "release"
+
+/* This is the tag string which is stored in the tpx file.
+ * Change this if you want to change the tpx format in a feature branch.
+ * This ensures that there will not be different tpx formats around which
+ * can not be distinguished.
+ */
+static const char *tpx_tag = TPX_TAG_RELEASE;
+
+/* This number should be increased whenever the file format changes! */
+static const int tpx_version = 92;
+
+/* This number should only be increased when you edit the TOPOLOGY section
+ * or the HEADER of the tpx format.
+ * This way we can maintain forward compatibility too for all analysis tools
+ * and/or external programs that only need to know the atom/residue names,
+ * charges, and bond connectivity.
+ *
+ * It first appeared in tpx version 26, when I also moved the inputrecord
+ * to the end of the tpx file, so we can just skip it if we only
+ * want the topology.
+ */
+static const int tpx_generation = 25;
+
+/* This number should be the most recent backwards incompatible version
+ * I.e., if this number is 9, we cannot read tpx version 9 with this code.
+ */
+static const int tpx_incompatible_version = 9;
+
+
+
+/* Struct used to maintain tpx compatibility when function types are added */
+typedef struct {
+ int fvnr; /* file version number in which the function type first appeared */
+ int ftype; /* function type */
+} t_ftupd;
+
+/*
+ * The entries should be ordered in:
+ * 1. ascending file version number
+ * 2. ascending function type number
+ */
+/*static const t_ftupd ftupd[] = {
+ { 20, F_CUBICBONDS },
+ { 20, F_CONNBONDS },
+ { 20, F_HARMONIC },
+ { 20, F_EQM, },
+ { 22, F_DISRESVIOL },
+ { 22, F_ORIRES },
+ { 22, F_ORIRESDEV },
+ { 26, F_FOURDIHS },
+ { 26, F_PIDIHS },
+ { 26, F_DIHRES },
+ { 26, F_DIHRESVIOL },
+ { 30, F_CROSS_BOND_BONDS },
+ { 30, F_CROSS_BOND_ANGLES },
+ { 30, F_UREY_BRADLEY },
+ { 30, F_POLARIZATION },
+ { 54, F_DHDL_CON },
+ };*/
+/*
+ * The entries should be ordered in:
+ * 1. ascending function type number
+ * 2. ascending file version number
+ */
+/* question; what is the purpose of the commented code above? */
+static const t_ftupd ftupd[] = {
+ { 20, F_CUBICBONDS },
+ { 20, F_CONNBONDS },
+ { 20, F_HARMONIC },
+ { 34, F_FENEBONDS },
+ { 43, F_TABBONDS },
+ { 43, F_TABBONDSNC },
+ { 70, F_RESTRBONDS },
+ { 76, F_LINEAR_ANGLES },
+ { 30, F_CROSS_BOND_BONDS },
+ { 30, F_CROSS_BOND_ANGLES },
+ { 30, F_UREY_BRADLEY },
+ { 34, F_QUARTIC_ANGLES },
+ { 43, F_TABANGLES },
+ { 26, F_FOURDIHS },
+ { 26, F_PIDIHS },
+ { 43, F_TABDIHS },
+ { 65, F_CMAP },
+ { 60, F_GB12 },
+ { 61, F_GB13 },
+ { 61, F_GB14 },
+ { 72, F_GBPOL },
+ { 72, F_NPSOLVATION },
+ { 41, F_LJC14_Q },
+ { 41, F_LJC_PAIRS_NB },
+ { 32, F_BHAM_LR },
+ { 32, F_RF_EXCL },
+ { 32, F_COUL_RECIP },
+ { 46, F_DPD },
+ { 30, F_POLARIZATION },
+ { 36, F_THOLE_POL },
+ { 90, F_FBPOSRES },
+ { 22, F_DISRESVIOL },
+ { 22, F_ORIRES },
+ { 22, F_ORIRESDEV },
+ { 26, F_DIHRES },
+ { 26, F_DIHRESVIOL },
+ { 49, F_VSITE4FDN },
+ { 50, F_VSITEN },
+ { 46, F_COM_PULL },
+ { 20, F_EQM },
+ { 46, F_ECONSERVED },
+ { 69, F_VTEMP_NOLONGERUSED},
+ { 66, F_PDISPCORR },
+ { 54, F_DVDL_CONSTR },
+ { 76, F_ANHARM_POL },
+ { 79, F_DVDL_COUL },
+ { 79, F_DVDL_VDW, },
+ { 79, F_DVDL_BONDED, },
+ { 79, F_DVDL_RESTRAINT },
+ { 79, F_DVDL_TEMPERATURE },
+};
+#define NFTUPD asize(ftupd)
+
+/* 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
+ *
+ **************************************************************/
+static void do_pullgrp(t_fileio *fio, t_pullgrp *pgrp, gmx_bool bRead,
+ int file_version)
+{
+ gmx_bool bDum = TRUE;
+ int i;
+
+ gmx_fio_do_int(fio, pgrp->nat);
+ if (bRead)
+ {
+ snew(pgrp->ind, pgrp->nat);
+ }
+ bDum = gmx_fio_ndo_int(fio, pgrp->ind, pgrp->nat);
+ gmx_fio_do_int(fio, pgrp->nweight);
+ if (bRead)
+ {
+ snew(pgrp->weight, pgrp->nweight);
+ }
+ bDum = gmx_fio_ndo_real(fio, pgrp->weight, pgrp->nweight);
+ gmx_fio_do_int(fio, pgrp->pbcatom);
+ gmx_fio_do_rvec(fio, pgrp->vec);
+ gmx_fio_do_rvec(fio, pgrp->init);
+ gmx_fio_do_real(fio, pgrp->rate);
+ gmx_fio_do_real(fio, pgrp->k);
+ if (file_version >= 56)
+ {
+ gmx_fio_do_real(fio, pgrp->kB);
+ }
+ else
+ {
+ pgrp->kB = pgrp->k;
+ }
+}
+
+static void do_expandedvals(t_fileio *fio, t_expanded *expand, t_lambda *fepvals, gmx_bool bRead, int file_version)
+{
+ /* i is used in the ndo_double macro*/
+ int i;
+ real fv;
+ gmx_bool bDum = TRUE;
+ real rdum;
+ int n_lambda = fepvals->n_lambda;
+
+ /* reset the lambda calculation window */
+ fepvals->lambda_start_n = 0;
+ fepvals->lambda_stop_n = n_lambda;
+ if (file_version >= 79)
+ {
+ if (n_lambda > 0)
+ {
+ if (bRead)
+ {
+ snew(expand->init_lambda_weights, n_lambda);
+ }
+ bDum = gmx_fio_ndo_real(fio, expand->init_lambda_weights, n_lambda);
+ gmx_fio_do_gmx_bool(fio, expand->bInit_weights);
+ }
+
+ gmx_fio_do_int(fio, expand->nstexpanded);
+ gmx_fio_do_int(fio, expand->elmcmove);
+ gmx_fio_do_int(fio, expand->elamstats);
+ gmx_fio_do_int(fio, expand->lmc_repeats);
+ gmx_fio_do_int(fio, expand->gibbsdeltalam);
+ gmx_fio_do_int(fio, expand->lmc_forced_nstart);
+ gmx_fio_do_int(fio, expand->lmc_seed);
+ gmx_fio_do_real(fio, expand->mc_temp);
+ gmx_fio_do_int(fio, expand->bSymmetrizedTMatrix);
+ gmx_fio_do_int(fio, expand->nstTij);
+ gmx_fio_do_int(fio, expand->minvarmin);
+ gmx_fio_do_int(fio, expand->c_range);
+ gmx_fio_do_real(fio, expand->wl_scale);
+ gmx_fio_do_real(fio, expand->wl_ratio);
+ gmx_fio_do_real(fio, expand->init_wl_delta);
+ gmx_fio_do_gmx_bool(fio, expand->bWLoneovert);
+ gmx_fio_do_int(fio, expand->elmceq);
+ gmx_fio_do_int(fio, expand->equil_steps);
+ gmx_fio_do_int(fio, expand->equil_samples);
+ gmx_fio_do_int(fio, expand->equil_n_at_lam);
+ gmx_fio_do_real(fio, expand->equil_wl_delta);
+ gmx_fio_do_real(fio, expand->equil_ratio);
+ }
+}
+
+static void do_simtempvals(t_fileio *fio, t_simtemp *simtemp, int n_lambda, gmx_bool bRead,
+ int file_version)
+{
+ gmx_bool bDum = TRUE;
+
+ if (file_version >= 79)
+ {
+ gmx_fio_do_int(fio, simtemp->eSimTempScale);
+ gmx_fio_do_real(fio, simtemp->simtemp_high);
+ gmx_fio_do_real(fio, simtemp->simtemp_low);
+ if (n_lambda > 0)
+ {
+ if (bRead)
+ {
+ snew(simtemp->temperatures, n_lambda);
+ }
+ bDum = gmx_fio_ndo_real(fio, simtemp->temperatures, n_lambda);
+ }
+ }
+}
+
+static void do_fepvals(t_fileio *fio, t_lambda *fepvals, gmx_bool bRead, int file_version)
+{
+ /* i is defined in the ndo_double macro; use g to iterate. */
+ int i, g;
+ real fv;
+ gmx_bool bDum = TRUE;
+ real rdum;
+
+ /* free energy values */
+
+ if (file_version >= 79)
+ {
+ gmx_fio_do_int(fio, fepvals->init_fep_state);
+ gmx_fio_do_double(fio, fepvals->init_lambda);
+ gmx_fio_do_double(fio, fepvals->delta_lambda);
+ }
+ else if (file_version >= 59)
+ {
+ gmx_fio_do_double(fio, fepvals->init_lambda);
+ gmx_fio_do_double(fio, fepvals->delta_lambda);
+ }
+ else
+ {
+ gmx_fio_do_real(fio, rdum);
+ fepvals->init_lambda = rdum;
+ gmx_fio_do_real(fio, rdum);
+ fepvals->delta_lambda = rdum;
+ }
+ if (file_version >= 79)
+ {
+ gmx_fio_do_int(fio, fepvals->n_lambda);
+ if (bRead)
+ {
+ snew(fepvals->all_lambda, efptNR);
+ }
+ for (g = 0; g < efptNR; g++)
+ {
+ if (fepvals->n_lambda > 0)
+ {
+ if (bRead)
+ {
+ snew(fepvals->all_lambda[g], fepvals->n_lambda);
+ }
+ bDum = gmx_fio_ndo_double(fio, fepvals->all_lambda[g], fepvals->n_lambda);
+ bDum = gmx_fio_ndo_int(fio, fepvals->separate_dvdl, efptNR);
+ }
+ else if (fepvals->init_lambda >= 0)
+ {
+ fepvals->separate_dvdl[efptFEP] = TRUE;
+ }
+ }
+ }
+ else if (file_version >= 64)
+ {
+ gmx_fio_do_int(fio, fepvals->n_lambda);
+ if (bRead)
+ {
+ int g;
+
+ snew(fepvals->all_lambda, efptNR);
+ /* still allocate the all_lambda array's contents. */
+ for (g = 0; g < efptNR; g++)
+ {
+ if (fepvals->n_lambda > 0)
+ {
+ snew(fepvals->all_lambda[g], fepvals->n_lambda);
+ }
+ }
+ }
+ bDum = gmx_fio_ndo_double(fio, fepvals->all_lambda[efptFEP],
+ fepvals->n_lambda);
+ if (fepvals->init_lambda >= 0)
+ {
+ int g, h;
+
+ fepvals->separate_dvdl[efptFEP] = TRUE;
+
+ if (bRead)
+ {
+ /* copy the contents of the efptFEP lambda component to all
+ the other components */
+ for (g = 0; g < efptNR; g++)
+ {
+ for (h = 0; h < fepvals->n_lambda; h++)
+ {
+ if (g != efptFEP)
+ {
+ fepvals->all_lambda[g][h] =
+ fepvals->all_lambda[efptFEP][h];
+ }
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ fepvals->n_lambda = 0;
+ fepvals->all_lambda = NULL;
+ if (fepvals->init_lambda >= 0)
+ {
+ fepvals->separate_dvdl[efptFEP] = TRUE;
+ }
+ }
+ if (file_version >= 13)
+ {
+ gmx_fio_do_real(fio, fepvals->sc_alpha);
+ }
+ else
+ {
+ fepvals->sc_alpha = 0;
+ }
+ if (file_version >= 38)
+ {
+ gmx_fio_do_int(fio, fepvals->sc_power);
+ }
+ else
+ {
+ fepvals->sc_power = 2;
+ }
+ if (file_version >= 79)
+ {
+ gmx_fio_do_real(fio, fepvals->sc_r_power);
+ }
+ else
+ {
+ fepvals->sc_r_power = 6.0;
+ }
+ if (file_version >= 15)
+ {
+ gmx_fio_do_real(fio, fepvals->sc_sigma);
+ }
+ else
+ {
+ fepvals->sc_sigma = 0.3;
+ }
+ if (bRead)
+ {
+ if (file_version >= 71)
+ {
+ fepvals->sc_sigma_min = fepvals->sc_sigma;
+ }
+ else
+ {
+ fepvals->sc_sigma_min = 0;
+ }
+ }
+ if (file_version >= 79)
+ {
+ gmx_fio_do_int(fio, fepvals->bScCoul);
+ }
+ else
+ {
+ fepvals->bScCoul = TRUE;
+ }
+ if (file_version >= 64)
+ {
+ gmx_fio_do_int(fio, fepvals->nstdhdl);
+ }
+ else
+ {
+ fepvals->nstdhdl = 1;
+ }
+
+ if (file_version >= 73)
+ {
+ gmx_fio_do_int(fio, fepvals->separate_dhdl_file);
+ gmx_fio_do_int(fio, fepvals->dhdl_derivatives);
+ }
+ else
+ {
+ fepvals->separate_dhdl_file = esepdhdlfileYES;
+ fepvals->dhdl_derivatives = edhdlderivativesYES;
+ }
+ if (file_version >= 71)
+ {
+ gmx_fio_do_int(fio, fepvals->dh_hist_size);
+ gmx_fio_do_double(fio, fepvals->dh_hist_spacing);
+ }
+ else
+ {
+ fepvals->dh_hist_size = 0;
+ fepvals->dh_hist_spacing = 0.1;
+ }
+ if (file_version >= 79)
+ {
+ gmx_fio_do_int(fio, fepvals->bPrintEnergy);
+ }
+ else
+ {
+ fepvals->bPrintEnergy = FALSE;
+ }
+
+ /* handle lambda_neighbors */
+ if ((file_version >= 83 && file_version < 90) || file_version >= 92)
+ {
+ gmx_fio_do_int(fio, fepvals->lambda_neighbors);
+ if ( (fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0) &&
+ (fepvals->init_lambda < 0) )
+ {
+ fepvals->lambda_start_n = (fepvals->init_fep_state -
+ fepvals->lambda_neighbors);
+ fepvals->lambda_stop_n = (fepvals->init_fep_state +
+ fepvals->lambda_neighbors + 1);
+ if (fepvals->lambda_start_n < 0)
+ {
+ fepvals->lambda_start_n = 0;;
+ }
+ if (fepvals->lambda_stop_n >= fepvals->n_lambda)
+ {
+ fepvals->lambda_stop_n = fepvals->n_lambda;
+ }
+ }
+ else
+ {
+ fepvals->lambda_start_n = 0;
+ fepvals->lambda_stop_n = fepvals->n_lambda;
+ }
+ }
+ else
+ {
+ fepvals->lambda_start_n = 0;
+ fepvals->lambda_stop_n = fepvals->n_lambda;
+ }
+}
+
+static void do_pull(t_fileio *fio, t_pull *pull, gmx_bool bRead, int file_version)
+{
+ int g;
+
+ gmx_fio_do_int(fio, pull->ngrp);
+ gmx_fio_do_int(fio, pull->eGeom);
+ gmx_fio_do_ivec(fio, pull->dim);
+ gmx_fio_do_real(fio, pull->cyl_r1);
+ gmx_fio_do_real(fio, pull->cyl_r0);
+ gmx_fio_do_real(fio, pull->constr_tol);
+ gmx_fio_do_int(fio, pull->nstxout);
+ gmx_fio_do_int(fio, pull->nstfout);
+ if (bRead)
+ {
+ snew(pull->grp, pull->ngrp+1);
+ }
+ for (g = 0; g < pull->ngrp+1; g++)
+ {
+ do_pullgrp(fio, &pull->grp[g], bRead, file_version);
+ }
+}
+
+
+static void do_rotgrp(t_fileio *fio, t_rotgrp *rotg, gmx_bool bRead, int file_version)
+{
+ gmx_bool bDum = TRUE;
+ int i;
+
+ gmx_fio_do_int(fio, rotg->eType);
+ gmx_fio_do_int(fio, rotg->bMassW);
+ gmx_fio_do_int(fio, rotg->nat);
+ if (bRead)
+ {
+ snew(rotg->ind, rotg->nat);
+ }
+ gmx_fio_ndo_int(fio, rotg->ind, rotg->nat);
+ if (bRead)
+ {
+ snew(rotg->x_ref, rotg->nat);
+ }
+ gmx_fio_ndo_rvec(fio, rotg->x_ref, rotg->nat);
+ gmx_fio_do_rvec(fio, rotg->vec);
+ gmx_fio_do_rvec(fio, rotg->pivot);
+ gmx_fio_do_real(fio, rotg->rate);
+ gmx_fio_do_real(fio, rotg->k);
+ gmx_fio_do_real(fio, rotg->slab_dist);
+ gmx_fio_do_real(fio, rotg->min_gaussian);
+ gmx_fio_do_real(fio, rotg->eps);
+ gmx_fio_do_int(fio, rotg->eFittype);
+ gmx_fio_do_int(fio, rotg->PotAngle_nstep);
+ gmx_fio_do_real(fio, rotg->PotAngle_step);
+}
+
+static void do_rot(t_fileio *fio, t_rot *rot, gmx_bool bRead, int file_version)
+{
+ int g;
+
+ gmx_fio_do_int(fio, rot->ngrp);
+ gmx_fio_do_int(fio, rot->nstrout);
+ gmx_fio_do_int(fio, rot->nstsout);
+ if (bRead)
+ {
+ snew(rot->grp, rot->ngrp);
+ }
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ do_rotgrp(fio, &rot->grp[g], bRead, file_version);
+ }
+}
+
+
+static void do_inputrec(t_fileio *fio, t_inputrec *ir, gmx_bool bRead,
+ int file_version, real *fudgeQQ)
+{
+ int i, j, k, *tmp, idum = 0;
+ gmx_bool bDum = TRUE;
+ real rdum, bd_temp;
+ rvec vdum;
+ gmx_bool bSimAnn;
+ real zerotemptime, finish_t, init_temp, finish_temp;
+
+ if (file_version != tpx_version)
+ {
+ /* Give a warning about features that are not accessible */
+ fprintf(stderr, "Note: file tpx version %d, software tpx version %d\n",
+ file_version, tpx_version);
+ }
+
+ if (bRead)
+ {
+ init_inputrec(ir);
+ }
+
+ if (file_version == 0)
+ {
+ return;
+ }
+
+ /* Basic inputrec stuff */
+ gmx_fio_do_int(fio, ir->eI);
+ if (file_version >= 62)
+ {
+ gmx_fio_do_gmx_large_int(fio, ir->nsteps);
+ }
+ else
+ {
+ gmx_fio_do_int(fio, idum);
+ ir->nsteps = idum;
+ }
+ if (file_version > 25)
+ {
+ if (file_version >= 62)
+ {
+ gmx_fio_do_gmx_large_int(fio, ir->init_step);
+ }
+ else
+ {
+ gmx_fio_do_int(fio, idum);
+ ir->init_step = idum;
+ }
+ }
+ else
+ {
+ ir->init_step = 0;
+ }
+
+ if (file_version >= 58)
+ {
+ gmx_fio_do_int(fio, ir->simulation_part);
+ }
+ else
+ {
+ ir->simulation_part = 1;
+ }
+
+ if (file_version >= 67)
+ {
+ gmx_fio_do_int(fio, ir->nstcalcenergy);
+ }
+ else
+ {
+ ir->nstcalcenergy = 1;
+ }
+ if (file_version < 53)
+ {
+ /* The pbc info has been moved out of do_inputrec,
+ * since we always want it, also without reading the inputrec.
+ */
+ gmx_fio_do_int(fio, ir->ePBC);
+ if ((file_version <= 15) && (ir->ePBC == 2))
+ {
+ ir->ePBC = epbcNONE;
+ }
+ if (file_version >= 45)
+ {
+ gmx_fio_do_int(fio, ir->bPeriodicMols);
+ }
+ else
+ {
+ if (ir->ePBC == 2)
+ {
+ ir->ePBC = epbcXYZ;
+ ir->bPeriodicMols = TRUE;
+ }
+ else
+ {
+ ir->bPeriodicMols = FALSE;
+ }
+ }
+ }
+ if (file_version >= 81)
+ {
+ gmx_fio_do_int(fio, ir->cutoff_scheme);
+ }
+ else
+ {
+ ir->cutoff_scheme = ecutsGROUP;
+ }
+ gmx_fio_do_int(fio, ir->ns_type);
+ gmx_fio_do_int(fio, ir->nstlist);
+ gmx_fio_do_int(fio, ir->ndelta);
+ if (file_version < 41)
+ {
+ gmx_fio_do_int(fio, idum);
+ gmx_fio_do_int(fio, idum);
+ }
+ if (file_version >= 45)
+ {
+ gmx_fio_do_real(fio, ir->rtpi);
+ }
+ else
+ {
+ ir->rtpi = 0.05;
+ }
+ gmx_fio_do_int(fio, ir->nstcomm);
+ if (file_version > 34)
+ {
+ gmx_fio_do_int(fio, ir->comm_mode);
+ }
+ else if (ir->nstcomm < 0)
+ {
+ ir->comm_mode = ecmANGULAR;
+ }
+ else
+ {
+ ir->comm_mode = ecmLINEAR;
+ }
+ ir->nstcomm = abs(ir->nstcomm);
+
+ if (file_version > 25)
+ {
+ gmx_fio_do_int(fio, ir->nstcheckpoint);
+ }
+ else
+ {
+ ir->nstcheckpoint = 0;
+ }
+
+ gmx_fio_do_int(fio, ir->nstcgsteep);
+
+ if (file_version >= 30)
+ {
+ gmx_fio_do_int(fio, ir->nbfgscorr);
+ }
+ else if (bRead)
+ {
+ ir->nbfgscorr = 10;
+ }
+
+ gmx_fio_do_int(fio, ir->nstlog);
+ gmx_fio_do_int(fio, ir->nstxout);
+ gmx_fio_do_int(fio, ir->nstvout);
+ gmx_fio_do_int(fio, ir->nstfout);
+ gmx_fio_do_int(fio, ir->nstenergy);
+ gmx_fio_do_int(fio, ir->nstxtcout);
+ if (file_version >= 59)
+ {
+ gmx_fio_do_double(fio, ir->init_t);
+ gmx_fio_do_double(fio, ir->delta_t);
+ }
+ else
+ {
+ gmx_fio_do_real(fio, rdum);
+ ir->init_t = rdum;
+ gmx_fio_do_real(fio, rdum);
+ ir->delta_t = rdum;
+ }
+ gmx_fio_do_real(fio, ir->xtcprec);
+ if (file_version < 19)
+ {
+ gmx_fio_do_int(fio, idum);
+ gmx_fio_do_int(fio, idum);
+ }
+ if (file_version < 18)
+ {
+ gmx_fio_do_int(fio, idum);
+ }
+ if (file_version >= 81)
+ {
+ gmx_fio_do_real(fio, ir->verletbuf_drift);
+ }
+ else
+ {
+ ir->verletbuf_drift = 0;
+ }
+ gmx_fio_do_real(fio, ir->rlist);
+ if (file_version >= 67)
+ {
+ gmx_fio_do_real(fio, ir->rlistlong);
+ }
+ if (file_version >= 82 && file_version != 90)
+ {
+ gmx_fio_do_int(fio, ir->nstcalclr);
+ }
+ else
+ {
+ /* Calculate at NS steps */
+ ir->nstcalclr = ir->nstlist;
+ }
+ gmx_fio_do_int(fio, ir->coulombtype);
+ if (file_version < 32 && ir->coulombtype == eelRF)
+ {
+ ir->coulombtype = eelRF_NEC;
+ }
+ if (file_version >= 81)
+ {
+ gmx_fio_do_int(fio, ir->coulomb_modifier);
+ }
+ else
+ {
+ ir->coulomb_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
+ }
+ gmx_fio_do_real(fio, ir->rcoulomb_switch);
+ gmx_fio_do_real(fio, ir->rcoulomb);
+ gmx_fio_do_int(fio, ir->vdwtype);
+ if (file_version >= 81)
+ {
+ gmx_fio_do_int(fio, ir->vdw_modifier);
+ }
+ else
+ {
+ ir->vdw_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
+ }
+ gmx_fio_do_real(fio, ir->rvdw_switch);
+ gmx_fio_do_real(fio, ir->rvdw);
+ if (file_version < 67)
+ {
+ ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
+ }
+ gmx_fio_do_int(fio, ir->eDispCorr);
+ gmx_fio_do_real(fio, ir->epsilon_r);
+ if (file_version >= 37)
+ {
+ gmx_fio_do_real(fio, ir->epsilon_rf);
+ }
+ else
+ {
+ if (EEL_RF(ir->coulombtype))
+ {
+ ir->epsilon_rf = ir->epsilon_r;
+ ir->epsilon_r = 1.0;
+ }
+ else
+ {
+ ir->epsilon_rf = 1.0;
+ }
+ }
+ if (file_version >= 29)
+ {
+ gmx_fio_do_real(fio, ir->tabext);
+ }
+ else
+ {
+ ir->tabext = 1.0;
+ }
+
+ if (file_version > 25)
+ {
+ gmx_fio_do_int(fio, ir->gb_algorithm);
+ gmx_fio_do_int(fio, ir->nstgbradii);
+ gmx_fio_do_real(fio, ir->rgbradii);
+ gmx_fio_do_real(fio, ir->gb_saltconc);
+ gmx_fio_do_int(fio, ir->implicit_solvent);
+ }
+ else
+ {
+ ir->gb_algorithm = egbSTILL;
+ ir->nstgbradii = 1;
+ ir->rgbradii = 1.0;
+ ir->gb_saltconc = 0;
+ ir->implicit_solvent = eisNO;
+ }
+ if (file_version >= 55)
+ {
+ gmx_fio_do_real(fio, ir->gb_epsilon_solvent);
+ gmx_fio_do_real(fio, ir->gb_obc_alpha);
+ gmx_fio_do_real(fio, ir->gb_obc_beta);
+ gmx_fio_do_real(fio, ir->gb_obc_gamma);
+ if (file_version >= 60)
+ {
+ gmx_fio_do_real(fio, ir->gb_dielectric_offset);
+ gmx_fio_do_int(fio, ir->sa_algorithm);
+ }
+ else
+ {
+ ir->gb_dielectric_offset = 0.009;
+ ir->sa_algorithm = esaAPPROX;
+ }
+ gmx_fio_do_real(fio, ir->sa_surface_tension);
+
+ /* Override sa_surface_tension if it is not changed in the mpd-file */
+ if (ir->sa_surface_tension < 0)
+ {
+ if (ir->gb_algorithm == egbSTILL)
+ {
+ ir->sa_surface_tension = 0.0049 * 100 * CAL2JOULE;
+ }
+ else if (ir->gb_algorithm == egbHCT || ir->gb_algorithm == egbOBC)
+ {
+ ir->sa_surface_tension = 0.0054 * 100 * CAL2JOULE;
+ }
+ }
+
+ }
+ else
+ {
+ /* Better use sensible values than insane (0.0) ones... */
+ ir->gb_epsilon_solvent = 80;
+ ir->gb_obc_alpha = 1.0;
+ ir->gb_obc_beta = 0.8;
+ ir->gb_obc_gamma = 4.85;
+ ir->sa_surface_tension = 2.092;
+ }
+
+
+ if (file_version >= 81)
+ {
+ gmx_fio_do_real(fio, ir->fourier_spacing);
+ }
+ else
+ {
+ ir->fourier_spacing = 0.0;
+ }
+ gmx_fio_do_int(fio, ir->nkx);
+ gmx_fio_do_int(fio, ir->nky);
+ gmx_fio_do_int(fio, ir->nkz);
+ gmx_fio_do_int(fio, ir->pme_order);
+ gmx_fio_do_real(fio, ir->ewald_rtol);
+
+ if (file_version >= 24)
+ {
+ gmx_fio_do_int(fio, ir->ewald_geometry);
+ }
+ else
+ {
+ ir->ewald_geometry = eewg3D;
+ }
+
+ if (file_version <= 17)
+ {
+ ir->epsilon_surface = 0;
+ if (file_version == 17)
+ {
+ gmx_fio_do_int(fio, idum);
+ }
+ }
+ else
+ {
+ gmx_fio_do_real(fio, ir->epsilon_surface);
+ }
+
+ gmx_fio_do_gmx_bool(fio, ir->bOptFFT);
+
+ gmx_fio_do_gmx_bool(fio, ir->bContinuation);
+ gmx_fio_do_int(fio, ir->etc);
+ /* before version 18, ir->etc was a gmx_bool (ir->btc),
+ * but the values 0 and 1 still mean no and
+ * berendsen temperature coupling, respectively.
+ */
+ if (file_version >= 79)
+ {
+ gmx_fio_do_gmx_bool(fio, ir->bPrintNHChains);
+ }
+ if (file_version >= 71)
+ {
+ gmx_fio_do_int(fio, ir->nsttcouple);
+ }
+ else
+ {
+ ir->nsttcouple = ir->nstcalcenergy;
+ }
+ if (file_version <= 15)
+ {
+ gmx_fio_do_int(fio, idum);
+ }
+ if (file_version <= 17)
+ {
+ gmx_fio_do_int(fio, ir->epct);
+ if (file_version <= 15)
+ {
+ if (ir->epct == 5)
+ {
+ ir->epct = epctSURFACETENSION;
+ }
+ gmx_fio_do_int(fio, idum);
+ }
+ ir->epct -= 1;
+ /* we have removed the NO alternative at the beginning */
+ if (ir->epct == -1)
+ {
+ ir->epc = epcNO;
+ ir->epct = epctISOTROPIC;
+ }
+ else
+ {
+ ir->epc = epcBERENDSEN;
+ }
+ }
+ else
+ {
+ gmx_fio_do_int(fio, ir->epc);
+ gmx_fio_do_int(fio, ir->epct);
+ }
+ if (file_version >= 71)
+ {
+ gmx_fio_do_int(fio, ir->nstpcouple);
+ }
+ else
+ {
+ ir->nstpcouple = ir->nstcalcenergy;
+ }
+ gmx_fio_do_real(fio, ir->tau_p);
+ if (file_version <= 15)
+ {
+ gmx_fio_do_rvec(fio, vdum);
+ clear_mat(ir->ref_p);
+ for (i = 0; i < DIM; i++)
+ {
+ ir->ref_p[i][i] = vdum[i];
+ }
+ }
+ else
+ {
+ gmx_fio_do_rvec(fio, ir->ref_p[XX]);
+ gmx_fio_do_rvec(fio, ir->ref_p[YY]);
+ gmx_fio_do_rvec(fio, ir->ref_p[ZZ]);
+ }
+ if (file_version <= 15)
+ {
+ gmx_fio_do_rvec(fio, vdum);
+ clear_mat(ir->compress);
+ for (i = 0; i < DIM; i++)
+ {
+ ir->compress[i][i] = vdum[i];
+ }
+ }
+ else
+ {
+ gmx_fio_do_rvec(fio, ir->compress[XX]);
+ gmx_fio_do_rvec(fio, ir->compress[YY]);
+ gmx_fio_do_rvec(fio, ir->compress[ZZ]);
+ }
+ if (file_version >= 47)
+ {
+ gmx_fio_do_int(fio, ir->refcoord_scaling);
+ gmx_fio_do_rvec(fio, ir->posres_com);
+ gmx_fio_do_rvec(fio, ir->posres_comB);
+ }
+ else
+ {
+ ir->refcoord_scaling = erscNO;
+ clear_rvec(ir->posres_com);
+ clear_rvec(ir->posres_comB);
+ }
+ if ((file_version > 25) && (file_version < 79))
+ {
+ gmx_fio_do_int(fio, ir->andersen_seed);
+ }
+ else
+ {
+ ir->andersen_seed = 0;
+ }
+ if (file_version < 26)
+ {
+ gmx_fio_do_gmx_bool(fio, bSimAnn);
+ gmx_fio_do_real(fio, zerotemptime);
+ }
+
+ if (file_version < 37)
+ {
+ gmx_fio_do_real(fio, rdum);
+ }
+
+ gmx_fio_do_real(fio, ir->shake_tol);
+ if (file_version < 54)
+ {
+ gmx_fio_do_real(fio, *fudgeQQ);
+ }
+
+ gmx_fio_do_int(fio, ir->efep);
+ if (file_version <= 14 && ir->efep != efepNO)
+ {
+ ir->efep = efepYES;
+ }
+ do_fepvals(fio, ir->fepvals, bRead, file_version);
+
+ if (file_version >= 79)
+ {
+ gmx_fio_do_gmx_bool(fio, ir->bSimTemp);
+ if (ir->bSimTemp)
+ {
+ ir->bSimTemp = TRUE;
+ }
+ }
+ else
+ {
+ ir->bSimTemp = FALSE;
+ }
+ if (ir->bSimTemp)
+ {
+ do_simtempvals(fio, ir->simtempvals, ir->fepvals->n_lambda, bRead, file_version);
+ }
+
+ if (file_version >= 79)
+ {
+ gmx_fio_do_gmx_bool(fio, ir->bExpanded);
+ if (ir->bExpanded)
+ {
+ ir->bExpanded = TRUE;
+ }
+ else
+ {
+ ir->bExpanded = FALSE;
+ }
+ }
+ if (ir->bExpanded)
+ {
+ do_expandedvals(fio, ir->expandedvals, ir->fepvals, bRead, file_version);
+ }
+ if (file_version >= 57)
+ {
+ gmx_fio_do_int(fio, ir->eDisre);
+ }
+ gmx_fio_do_int(fio, ir->eDisreWeighting);
+ if (file_version < 22)
+ {
+ if (ir->eDisreWeighting == 0)
+ {
+ ir->eDisreWeighting = edrwEqual;
+ }
+ else
+ {
+ ir->eDisreWeighting = edrwConservative;
+ }
+ }
+ gmx_fio_do_gmx_bool(fio, ir->bDisreMixed);
+ gmx_fio_do_real(fio, ir->dr_fc);
+ gmx_fio_do_real(fio, ir->dr_tau);
+ gmx_fio_do_int(fio, ir->nstdisreout);
+ if (file_version >= 22)
+ {
+ gmx_fio_do_real(fio, ir->orires_fc);
+ gmx_fio_do_real(fio, ir->orires_tau);
+ gmx_fio_do_int(fio, ir->nstorireout);
+ }
+ else
+ {
+ ir->orires_fc = 0;
+ ir->orires_tau = 0;
+ ir->nstorireout = 0;
+ }
+ if (file_version >= 26 && file_version < 79)
+ {
+ gmx_fio_do_real(fio, ir->dihre_fc);
+ if (file_version < 56)
+ {
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_int(fio, idum);
+ }
+ }
+ else
+ {
+ ir->dihre_fc = 0;
+ }
+
+ gmx_fio_do_real(fio, ir->em_stepsize);
+ gmx_fio_do_real(fio, ir->em_tol);
+ if (file_version >= 22)
+ {
+ gmx_fio_do_gmx_bool(fio, ir->bShakeSOR);
+ }
+ else if (bRead)
+ {
+ ir->bShakeSOR = TRUE;
+ }
+ if (file_version >= 11)
+ {
+ gmx_fio_do_int(fio, ir->niter);
+ }
+ else if (bRead)
+ {
+ ir->niter = 25;
+ fprintf(stderr, "Note: niter not in run input file, setting it to %d\n",
+ ir->niter);
+ }
+ if (file_version >= 21)
+ {
+ gmx_fio_do_real(fio, ir->fc_stepsize);
+ }
+ else
+ {
+ ir->fc_stepsize = 0;
+ }
+ gmx_fio_do_int(fio, ir->eConstrAlg);
+ gmx_fio_do_int(fio, ir->nProjOrder);
+ gmx_fio_do_real(fio, ir->LincsWarnAngle);
+ if (file_version <= 14)
+ {
+ gmx_fio_do_int(fio, idum);
+ }
+ if (file_version >= 26)
+ {
+ gmx_fio_do_int(fio, ir->nLincsIter);
+ }
+ else if (bRead)
+ {
+ ir->nLincsIter = 1;
+ fprintf(stderr, "Note: nLincsIter not in run input file, setting it to %d\n",
+ ir->nLincsIter);
+ }
+ if (file_version < 33)
+ {
+ gmx_fio_do_real(fio, bd_temp);
+ }
+ gmx_fio_do_real(fio, ir->bd_fric);
+ gmx_fio_do_int(fio, ir->ld_seed);
+ if (file_version >= 33)
+ {
+ for (i = 0; i < DIM; i++)
+ {
+ gmx_fio_do_rvec(fio, ir->deform[i]);
+ }
+ }
+ else
+ {
+ for (i = 0; i < DIM; i++)
+ {
+ clear_rvec(ir->deform[i]);
+ }
+ }
+ if (file_version >= 14)
+ {
+ gmx_fio_do_real(fio, ir->cos_accel);
+ }
+ else if (bRead)
+ {
+ ir->cos_accel = 0;
+ }
+ gmx_fio_do_int(fio, ir->userint1);
+ gmx_fio_do_int(fio, ir->userint2);
+ gmx_fio_do_int(fio, ir->userint3);
+ gmx_fio_do_int(fio, ir->userint4);
+ gmx_fio_do_real(fio, ir->userreal1);
+ gmx_fio_do_real(fio, ir->userreal2);
+ gmx_fio_do_real(fio, ir->userreal3);
+ gmx_fio_do_real(fio, ir->userreal4);
+
+ /* AdResS stuff */
+ if (file_version >= 77)
+ {
+ gmx_fio_do_gmx_bool(fio, ir->bAdress);
+ if (ir->bAdress)
+ {
+ if (bRead)
+ {
+ snew(ir->adress, 1);
+ }
+ gmx_fio_do_int(fio, ir->adress->type);
+ gmx_fio_do_real(fio, ir->adress->const_wf);
+ gmx_fio_do_real(fio, ir->adress->ex_width);
+ gmx_fio_do_real(fio, ir->adress->hy_width);
+ gmx_fio_do_int(fio, ir->adress->icor);
+ gmx_fio_do_int(fio, ir->adress->site);
+ gmx_fio_do_rvec(fio, ir->adress->refs);
+ gmx_fio_do_int(fio, ir->adress->n_tf_grps);
+ gmx_fio_do_real(fio, ir->adress->ex_forcecap);
+ gmx_fio_do_int(fio, ir->adress->n_energy_grps);
+ gmx_fio_do_int(fio, ir->adress->do_hybridpairs);
+
+ if (bRead)
+ {
+ snew(ir->adress->tf_table_index, ir->adress->n_tf_grps);
+ }
+ if (ir->adress->n_tf_grps > 0)
+ {
+ bDum = gmx_fio_ndo_int(fio, ir->adress->tf_table_index, ir->adress->n_tf_grps);
+ }
+ if (bRead)
+ {
+ snew(ir->adress->group_explicit, ir->adress->n_energy_grps);
+ }
+ if (ir->adress->n_energy_grps > 0)
+ {
+ bDum = gmx_fio_ndo_int(fio, ir->adress->group_explicit, ir->adress->n_energy_grps);
+ }
+ }
+ }
+ else
+ {
+ ir->bAdress = FALSE;
+ }
+
+ /* pull stuff */
+ if (file_version >= 48)
+ {
+ gmx_fio_do_int(fio, ir->ePull);
+ if (ir->ePull != epullNO)
+ {
+ if (bRead)
+ {
+ snew(ir->pull, 1);
+ }
+ do_pull(fio, ir->pull, bRead, file_version);
+ }
+ }
+ else
+ {
+ ir->ePull = epullNO;
+ }
+
+ /* Enforced rotation */
+ if (file_version >= 74)
+ {
+ gmx_fio_do_int(fio, ir->bRot);
+ if (ir->bRot == TRUE)
+ {
+ if (bRead)
+ {
+ snew(ir->rot, 1);
+ }
+ do_rot(fio, ir->rot, bRead, file_version);
+ }
+ }
+ else
+ {
+ ir->bRot = FALSE;
+ }
+
+ /* grpopts stuff */
+ gmx_fio_do_int(fio, ir->opts.ngtc);
+ if (file_version >= 69)
+ {
+ gmx_fio_do_int(fio, ir->opts.nhchainlength);
+ }
+ else
+ {
+ ir->opts.nhchainlength = 1;
+ }
+ gmx_fio_do_int(fio, ir->opts.ngacc);
+ gmx_fio_do_int(fio, ir->opts.ngfrz);
+ gmx_fio_do_int(fio, ir->opts.ngener);
+
+ if (bRead)
+ {
+ snew(ir->opts.nrdf, ir->opts.ngtc);
+ snew(ir->opts.ref_t, ir->opts.ngtc);
+ snew(ir->opts.annealing, ir->opts.ngtc);
+ snew(ir->opts.anneal_npoints, ir->opts.ngtc);
+ snew(ir->opts.anneal_time, ir->opts.ngtc);
+ snew(ir->opts.anneal_temp, ir->opts.ngtc);
+ snew(ir->opts.tau_t, ir->opts.ngtc);
+ snew(ir->opts.nFreeze, ir->opts.ngfrz);
+ snew(ir->opts.acc, ir->opts.ngacc);
+ snew(ir->opts.egp_flags, ir->opts.ngener*ir->opts.ngener);
+ }
+ if (ir->opts.ngtc > 0)
+ {
+ if (bRead && file_version < 13)
+ {
+ snew(tmp, ir->opts.ngtc);
+ bDum = gmx_fio_ndo_int(fio, tmp, ir->opts.ngtc);
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ ir->opts.nrdf[i] = tmp[i];
+ }
+ sfree(tmp);
+ }
+ else
+ {
+ bDum = gmx_fio_ndo_real(fio, ir->opts.nrdf, ir->opts.ngtc);
+ }
+ bDum = gmx_fio_ndo_real(fio, ir->opts.ref_t, ir->opts.ngtc);
+ bDum = gmx_fio_ndo_real(fio, ir->opts.tau_t, ir->opts.ngtc);
+ if (file_version < 33 && ir->eI == eiBD)
+ {
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ ir->opts.tau_t[i] = bd_temp;
+ }
+ }
+ }
+ if (ir->opts.ngfrz > 0)
+ {
+ bDum = gmx_fio_ndo_ivec(fio, ir->opts.nFreeze, ir->opts.ngfrz);
+ }
+ if (ir->opts.ngacc > 0)
+ {
+ gmx_fio_ndo_rvec(fio, ir->opts.acc, ir->opts.ngacc);
+ }
+ if (file_version >= 12)
+ {
+ bDum = gmx_fio_ndo_int(fio, ir->opts.egp_flags,
+ ir->opts.ngener*ir->opts.ngener);
+ }
+
+ if (bRead && file_version < 26)
+ {
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ if (bSimAnn)
+ {
+ ir->opts.annealing[i] = eannSINGLE;
+ ir->opts.anneal_npoints[i] = 2;
+ snew(ir->opts.anneal_time[i], 2);
+ snew(ir->opts.anneal_temp[i], 2);
+ /* calculate the starting/ending temperatures from reft, zerotemptime, and nsteps */
+ finish_t = ir->init_t + ir->nsteps * ir->delta_t;
+ init_temp = ir->opts.ref_t[i]*(1-ir->init_t/zerotemptime);
+ finish_temp = ir->opts.ref_t[i]*(1-finish_t/zerotemptime);
+ ir->opts.anneal_time[i][0] = ir->init_t;
+ ir->opts.anneal_time[i][1] = finish_t;
+ ir->opts.anneal_temp[i][0] = init_temp;
+ ir->opts.anneal_temp[i][1] = finish_temp;
+ }
+ else
+ {
+ ir->opts.annealing[i] = eannNO;
+ ir->opts.anneal_npoints[i] = 0;
+ }
+ }
+ }
+ else
+ {
+ /* file version 26 or later */
+ /* First read the lists with annealing and npoints for each group */
+ bDum = gmx_fio_ndo_int(fio, ir->opts.annealing, ir->opts.ngtc);
+ bDum = gmx_fio_ndo_int(fio, ir->opts.anneal_npoints, ir->opts.ngtc);
+ for (j = 0; j < (ir->opts.ngtc); j++)
+ {
+ k = ir->opts.anneal_npoints[j];
+ if (bRead)
+ {
+ snew(ir->opts.anneal_time[j], k);
+ snew(ir->opts.anneal_temp[j], k);
+ }
+ bDum = gmx_fio_ndo_real(fio, ir->opts.anneal_time[j], k);
+ bDum = gmx_fio_ndo_real(fio, ir->opts.anneal_temp[j], k);
+ }
+ }
+ /* Walls */
+ if (file_version >= 45)
+ {
+ gmx_fio_do_int(fio, ir->nwall);
+ gmx_fio_do_int(fio, ir->wall_type);
+ if (file_version >= 50)
+ {
+ gmx_fio_do_real(fio, ir->wall_r_linpot);
+ }
+ else
+ {
+ ir->wall_r_linpot = -1;
+ }
+ gmx_fio_do_int(fio, ir->wall_atomtype[0]);
+ gmx_fio_do_int(fio, ir->wall_atomtype[1]);
+ gmx_fio_do_real(fio, ir->wall_density[0]);
+ gmx_fio_do_real(fio, ir->wall_density[1]);
+ gmx_fio_do_real(fio, ir->wall_ewald_zfac);
+ }
+ else
+ {
+ ir->nwall = 0;
+ ir->wall_type = 0;
+ ir->wall_atomtype[0] = -1;
+ ir->wall_atomtype[1] = -1;
+ ir->wall_density[0] = 0;
+ ir->wall_density[1] = 0;
+ ir->wall_ewald_zfac = 3;
+ }
+ /* Cosine stuff for electric fields */
+ for (j = 0; (j < DIM); j++)
+ {
+ gmx_fio_do_int(fio, ir->ex[j].n);
+ gmx_fio_do_int(fio, ir->et[j].n);
+ if (bRead)
+ {
+ snew(ir->ex[j].a, ir->ex[j].n);
+ snew(ir->ex[j].phi, ir->ex[j].n);
+ snew(ir->et[j].a, ir->et[j].n);
+ snew(ir->et[j].phi, ir->et[j].n);
+ }
+ bDum = gmx_fio_ndo_real(fio, ir->ex[j].a, ir->ex[j].n);
+ bDum = gmx_fio_ndo_real(fio, ir->ex[j].phi, ir->ex[j].n);
+ bDum = gmx_fio_ndo_real(fio, ir->et[j].a, ir->et[j].n);
+ bDum = gmx_fio_ndo_real(fio, ir->et[j].phi, ir->et[j].n);
+ }
+
+ /* QMMM stuff */
+ if (file_version >= 39)
+ {
+ gmx_fio_do_gmx_bool(fio, ir->bQMMM);
+ gmx_fio_do_int(fio, ir->QMMMscheme);
+ gmx_fio_do_real(fio, ir->scalefactor);
+ gmx_fio_do_int(fio, ir->opts.ngQM);
+ if (bRead)
+ {
+ snew(ir->opts.QMmethod, ir->opts.ngQM);
+ snew(ir->opts.QMbasis, ir->opts.ngQM);
+ snew(ir->opts.QMcharge, ir->opts.ngQM);
+ snew(ir->opts.QMmult, ir->opts.ngQM);
+ snew(ir->opts.bSH, ir->opts.ngQM);
+ snew(ir->opts.CASorbitals, ir->opts.ngQM);
+ snew(ir->opts.CASelectrons, ir->opts.ngQM);
+ snew(ir->opts.SAon, ir->opts.ngQM);
+ snew(ir->opts.SAoff, ir->opts.ngQM);
+ snew(ir->opts.SAsteps, ir->opts.ngQM);
+ snew(ir->opts.bOPT, ir->opts.ngQM);
+ snew(ir->opts.bTS, ir->opts.ngQM);
+ }
+ if (ir->opts.ngQM > 0)
+ {
+ bDum = gmx_fio_ndo_int(fio, ir->opts.QMmethod, ir->opts.ngQM);
+ bDum = gmx_fio_ndo_int(fio, ir->opts.QMbasis, ir->opts.ngQM);
+ bDum = gmx_fio_ndo_int(fio, ir->opts.QMcharge, ir->opts.ngQM);
+ bDum = gmx_fio_ndo_int(fio, ir->opts.QMmult, ir->opts.ngQM);
+ bDum = gmx_fio_ndo_gmx_bool(fio, ir->opts.bSH, ir->opts.ngQM);
+ bDum = gmx_fio_ndo_int(fio, ir->opts.CASorbitals, ir->opts.ngQM);
+ bDum = gmx_fio_ndo_int(fio, ir->opts.CASelectrons, ir->opts.ngQM);
+ bDum = gmx_fio_ndo_real(fio, ir->opts.SAon, ir->opts.ngQM);
+ bDum = gmx_fio_ndo_real(fio, ir->opts.SAoff, ir->opts.ngQM);
+ bDum = gmx_fio_ndo_int(fio, ir->opts.SAsteps, ir->opts.ngQM);
+ bDum = gmx_fio_ndo_gmx_bool(fio, ir->opts.bOPT, ir->opts.ngQM);
+ bDum = gmx_fio_ndo_gmx_bool(fio, ir->opts.bTS, ir->opts.ngQM);
+ }
+ /* end of QMMM stuff */
+ }
+}
+
+
+static void do_harm(t_fileio *fio, t_iparams *iparams, gmx_bool bRead)
+{
+ gmx_fio_do_real(fio, iparams->harmonic.rA);
+ gmx_fio_do_real(fio, iparams->harmonic.krA);
+ gmx_fio_do_real(fio, iparams->harmonic.rB);
+ gmx_fio_do_real(fio, iparams->harmonic.krB);
+}
+
+void do_iparams(t_fileio *fio, t_functype ftype, t_iparams *iparams,
+ gmx_bool bRead, int file_version)
+{
+ int idum;
+ gmx_bool bDum;
+ real rdum;
+
+ if (!bRead)
+ {
+ gmx_fio_set_comment(fio, interaction_function[ftype].name);
+ }
+ switch (ftype)
+ {
+ case F_ANGLES:
+ case F_G96ANGLES:
+ case F_BONDS:
+ case F_G96BONDS:
+ case F_HARMONIC:
+ case F_IDIHS:
+ do_harm(fio, iparams, bRead);
+ if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && bRead)
+ {
+ /* Correct incorrect storage of parameters */
+ iparams->pdihs.phiB = iparams->pdihs.phiA;
+ iparams->pdihs.cpB = iparams->pdihs.cpA;
+ }
+ break;
+ case F_LINEAR_ANGLES:
+ gmx_fio_do_real(fio, iparams->linangle.klinA);
+ gmx_fio_do_real(fio, iparams->linangle.aA);
+ gmx_fio_do_real(fio, iparams->linangle.klinB);
+ gmx_fio_do_real(fio, iparams->linangle.aB);
+ break;
+ case F_FENEBONDS:
+ gmx_fio_do_real(fio, iparams->fene.bm);
+ gmx_fio_do_real(fio, iparams->fene.kb);
+ break;
+ case F_RESTRBONDS:
+ gmx_fio_do_real(fio, iparams->restraint.lowA);
+ gmx_fio_do_real(fio, iparams->restraint.up1A);
+ gmx_fio_do_real(fio, iparams->restraint.up2A);
+ gmx_fio_do_real(fio, iparams->restraint.kA);
+ gmx_fio_do_real(fio, iparams->restraint.lowB);
+ gmx_fio_do_real(fio, iparams->restraint.up1B);
+ gmx_fio_do_real(fio, iparams->restraint.up2B);
+ gmx_fio_do_real(fio, iparams->restraint.kB);
+ break;
+ case F_TABBONDS:
+ case F_TABBONDSNC:
+ case F_TABANGLES:
+ case F_TABDIHS:
+ gmx_fio_do_real(fio, iparams->tab.kA);
+ gmx_fio_do_int(fio, iparams->tab.table);
+ gmx_fio_do_real(fio, iparams->tab.kB);
+ break;
+ case F_CROSS_BOND_BONDS:
+ gmx_fio_do_real(fio, iparams->cross_bb.r1e);
+ gmx_fio_do_real(fio, iparams->cross_bb.r2e);
+ gmx_fio_do_real(fio, iparams->cross_bb.krr);
+ break;
+ case F_CROSS_BOND_ANGLES:
+ gmx_fio_do_real(fio, iparams->cross_ba.r1e);
+ gmx_fio_do_real(fio, iparams->cross_ba.r2e);
+ gmx_fio_do_real(fio, iparams->cross_ba.r3e);
+ gmx_fio_do_real(fio, iparams->cross_ba.krt);
+ break;
+ case F_UREY_BRADLEY:
+ gmx_fio_do_real(fio, iparams->u_b.thetaA);
+ gmx_fio_do_real(fio, iparams->u_b.kthetaA);
+ gmx_fio_do_real(fio, iparams->u_b.r13A);
+ gmx_fio_do_real(fio, iparams->u_b.kUBA);
+ if (file_version >= 79)
+ {
+ gmx_fio_do_real(fio, iparams->u_b.thetaB);
+ gmx_fio_do_real(fio, iparams->u_b.kthetaB);
+ gmx_fio_do_real(fio, iparams->u_b.r13B);
+ gmx_fio_do_real(fio, iparams->u_b.kUBB);
+ }
+ else
+ {
+ iparams->u_b.thetaB = iparams->u_b.thetaA;
+ iparams->u_b.kthetaB = iparams->u_b.kthetaA;
+ iparams->u_b.r13B = iparams->u_b.r13A;
+ iparams->u_b.kUBB = iparams->u_b.kUBA;
+ }
+ break;
+ case F_QUARTIC_ANGLES:
+ gmx_fio_do_real(fio, iparams->qangle.theta);
+ bDum = gmx_fio_ndo_real(fio, iparams->qangle.c, 5);
+ break;
+ case F_BHAM:
+ gmx_fio_do_real(fio, iparams->bham.a);
+ gmx_fio_do_real(fio, iparams->bham.b);
+ gmx_fio_do_real(fio, iparams->bham.c);
+ break;
+ case F_MORSE:
+ gmx_fio_do_real(fio, iparams->morse.b0A);
+ gmx_fio_do_real(fio, iparams->morse.cbA);
+ gmx_fio_do_real(fio, iparams->morse.betaA);
+ if (file_version >= 79)
+ {
+ gmx_fio_do_real(fio, iparams->morse.b0B);
+ gmx_fio_do_real(fio, iparams->morse.cbB);
+ gmx_fio_do_real(fio, iparams->morse.betaB);
+ }
+ else
+ {
+ iparams->morse.b0B = iparams->morse.b0A;
+ iparams->morse.cbB = iparams->morse.cbA;
+ iparams->morse.betaB = iparams->morse.betaA;
+ }
+ break;
+ case F_CUBICBONDS:
+ gmx_fio_do_real(fio, iparams->cubic.b0);
+ gmx_fio_do_real(fio, iparams->cubic.kb);
+ gmx_fio_do_real(fio, iparams->cubic.kcub);
+ break;
+ case F_CONNBONDS:
+ break;
+ case F_POLARIZATION:
+ gmx_fio_do_real(fio, iparams->polarize.alpha);
+ break;
+ case F_ANHARM_POL:
+ gmx_fio_do_real(fio, iparams->anharm_polarize.alpha);
+ gmx_fio_do_real(fio, iparams->anharm_polarize.drcut);
+ gmx_fio_do_real(fio, iparams->anharm_polarize.khyp);
+ break;
+ case F_WATER_POL:
+ if (file_version < 31)
+ {
+ gmx_fatal(FARGS, "Old tpr files with water_polarization not supported. Make a new.");
+ }
+ gmx_fio_do_real(fio, iparams->wpol.al_x);
+ gmx_fio_do_real(fio, iparams->wpol.al_y);
+ gmx_fio_do_real(fio, iparams->wpol.al_z);
+ gmx_fio_do_real(fio, iparams->wpol.rOH);
+ gmx_fio_do_real(fio, iparams->wpol.rHH);
+ gmx_fio_do_real(fio, iparams->wpol.rOD);
+ break;
+ case F_THOLE_POL:
+ gmx_fio_do_real(fio, iparams->thole.a);
+ gmx_fio_do_real(fio, iparams->thole.alpha1);
+ gmx_fio_do_real(fio, iparams->thole.alpha2);
+ gmx_fio_do_real(fio, iparams->thole.rfac);
+ break;
+ case F_LJ:
+ gmx_fio_do_real(fio, iparams->lj.c6);
+ gmx_fio_do_real(fio, iparams->lj.c12);
+ break;
+ case F_LJ14:
+ gmx_fio_do_real(fio, iparams->lj14.c6A);
+ gmx_fio_do_real(fio, iparams->lj14.c12A);
+ gmx_fio_do_real(fio, iparams->lj14.c6B);
+ gmx_fio_do_real(fio, iparams->lj14.c12B);
+ break;
+ case F_LJC14_Q:
+ gmx_fio_do_real(fio, iparams->ljc14.fqq);
+ gmx_fio_do_real(fio, iparams->ljc14.qi);
+ gmx_fio_do_real(fio, iparams->ljc14.qj);
+ gmx_fio_do_real(fio, iparams->ljc14.c6);
+ gmx_fio_do_real(fio, iparams->ljc14.c12);
+ break;
+ case F_LJC_PAIRS_NB:
+ gmx_fio_do_real(fio, iparams->ljcnb.qi);
+ gmx_fio_do_real(fio, iparams->ljcnb.qj);
+ gmx_fio_do_real(fio, iparams->ljcnb.c6);
+ gmx_fio_do_real(fio, iparams->ljcnb.c12);
+ break;
+ case F_PDIHS:
+ case F_PIDIHS:
+ case F_ANGRES:
+ case F_ANGRESZ:
+ gmx_fio_do_real(fio, iparams->pdihs.phiA);
+ gmx_fio_do_real(fio, iparams->pdihs.cpA);
+ if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && file_version < 42)
+ {
+ /* Read the incorrectly stored multiplicity */
+ gmx_fio_do_real(fio, iparams->harmonic.rB);
+ gmx_fio_do_real(fio, iparams->harmonic.krB);
+ iparams->pdihs.phiB = iparams->pdihs.phiA;
+ iparams->pdihs.cpB = iparams->pdihs.cpA;
+ }
+ else
+ {
+ gmx_fio_do_real(fio, iparams->pdihs.phiB);
+ gmx_fio_do_real(fio, iparams->pdihs.cpB);
+ gmx_fio_do_int(fio, iparams->pdihs.mult);
+ }
+ break;
+ case F_DISRES:
+ gmx_fio_do_int(fio, iparams->disres.label);
+ gmx_fio_do_int(fio, iparams->disres.type);
+ gmx_fio_do_real(fio, iparams->disres.low);
+ gmx_fio_do_real(fio, iparams->disres.up1);
+ gmx_fio_do_real(fio, iparams->disres.up2);
+ gmx_fio_do_real(fio, iparams->disres.kfac);
+ break;
+ case F_ORIRES:
+ gmx_fio_do_int(fio, iparams->orires.ex);
+ gmx_fio_do_int(fio, iparams->orires.label);
+ gmx_fio_do_int(fio, iparams->orires.power);
+ gmx_fio_do_real(fio, iparams->orires.c);
+ gmx_fio_do_real(fio, iparams->orires.obs);
+ gmx_fio_do_real(fio, iparams->orires.kfac);
+ break;
+ case F_DIHRES:
- if (file_version >= 72)
++ if (file_version < 82)
+ {
+ gmx_fio_do_int(fio, idum);
+ gmx_fio_do_int(fio, idum);
+ }
+ gmx_fio_do_real(fio, iparams->dihres.phiA);
+ gmx_fio_do_real(fio, iparams->dihres.dphiA);
+ gmx_fio_do_real(fio, iparams->dihres.kfacA);
++ if (file_version >= 82)
+ {
+ gmx_fio_do_real(fio, iparams->dihres.phiB);
+ gmx_fio_do_real(fio, iparams->dihres.dphiB);
+ gmx_fio_do_real(fio, iparams->dihres.kfacB);
+ }
+ else
+ {
+ iparams->dihres.phiB = iparams->dihres.phiA;
+ iparams->dihres.dphiB = iparams->dihres.dphiA;
+ iparams->dihres.kfacB = iparams->dihres.kfacA;
+ }
+ break;
+ case F_POSRES:
+ gmx_fio_do_rvec(fio, iparams->posres.pos0A);
+ gmx_fio_do_rvec(fio, iparams->posres.fcA);
+ if (bRead && file_version < 27)
+ {
+ copy_rvec(iparams->posres.pos0A, iparams->posres.pos0B);
+ copy_rvec(iparams->posres.fcA, iparams->posres.fcB);
+ }
+ else
+ {
+ gmx_fio_do_rvec(fio, iparams->posres.pos0B);
+ gmx_fio_do_rvec(fio, iparams->posres.fcB);
+ }
+ break;
+ case F_FBPOSRES:
+ gmx_fio_do_int(fio, iparams->fbposres.geom);
+ gmx_fio_do_rvec(fio, iparams->fbposres.pos0);
+ gmx_fio_do_real(fio, iparams->fbposres.r);
+ gmx_fio_do_real(fio, iparams->fbposres.k);
+ break;
+ case F_RBDIHS:
+ bDum = gmx_fio_ndo_real(fio, iparams->rbdihs.rbcA, NR_RBDIHS);
+ if (file_version >= 25)
+ {
+ bDum = gmx_fio_ndo_real(fio, iparams->rbdihs.rbcB, NR_RBDIHS);
+ }
+ break;
+ case F_FOURDIHS:
+ /* Fourier dihedrals are internally represented
+ * as Ryckaert-Bellemans since those are faster to compute.
+ */
+ bDum = gmx_fio_ndo_real(fio, iparams->rbdihs.rbcA, NR_RBDIHS);
+ bDum = gmx_fio_ndo_real(fio, iparams->rbdihs.rbcB, NR_RBDIHS);
+ break;
+ case F_CONSTR:
+ case F_CONSTRNC:
+ gmx_fio_do_real(fio, iparams->constr.dA);
+ gmx_fio_do_real(fio, iparams->constr.dB);
+ break;
+ case F_SETTLE:
+ gmx_fio_do_real(fio, iparams->settle.doh);
+ gmx_fio_do_real(fio, iparams->settle.dhh);
+ break;
+ case F_VSITE2:
+ gmx_fio_do_real(fio, iparams->vsite.a);
+ break;
+ case F_VSITE3:
+ case F_VSITE3FD:
+ case F_VSITE3FAD:
+ gmx_fio_do_real(fio, iparams->vsite.a);
+ gmx_fio_do_real(fio, iparams->vsite.b);
+ break;
+ case F_VSITE3OUT:
+ case F_VSITE4FD:
+ case F_VSITE4FDN:
+ gmx_fio_do_real(fio, iparams->vsite.a);
+ gmx_fio_do_real(fio, iparams->vsite.b);
+ gmx_fio_do_real(fio, iparams->vsite.c);
+ break;
+ case F_VSITEN:
+ gmx_fio_do_int(fio, iparams->vsiten.n);
+ gmx_fio_do_real(fio, iparams->vsiten.a);
+ break;
+ case F_GB12:
+ case F_GB13:
+ case F_GB14:
+ /* We got rid of some parameters in version 68 */
+ if (bRead && file_version < 68)
+ {
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ }
+ gmx_fio_do_real(fio, iparams->gb.sar);
+ gmx_fio_do_real(fio, iparams->gb.st);
+ gmx_fio_do_real(fio, iparams->gb.pi);
+ gmx_fio_do_real(fio, iparams->gb.gbr);
+ gmx_fio_do_real(fio, iparams->gb.bmlt);
+ break;
+ case F_CMAP:
+ gmx_fio_do_int(fio, iparams->cmap.cmapA);
+ gmx_fio_do_int(fio, iparams->cmap.cmapB);
+ break;
+ default:
+ gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d",
+ ftype, interaction_function[ftype].name, __FILE__, __LINE__);
+ }
+ if (!bRead)
+ {
+ gmx_fio_unset_comment(fio);
+ }
+}
+
+static void do_ilist(t_fileio *fio, t_ilist *ilist, gmx_bool bRead, int file_version,
+ int ftype)
+{
+ int i, k, idum;
+ gmx_bool bDum = TRUE;
+
+ if (!bRead)
+ {
+ gmx_fio_set_comment(fio, interaction_function[ftype].name);
+ }
+ if (file_version < 44)
+ {
+ for (i = 0; i < MAXNODES; i++)
+ {
+ gmx_fio_do_int(fio, idum);
+ }
+ }
+ gmx_fio_do_int(fio, ilist->nr);
+ if (bRead)
+ {
+ snew(ilist->iatoms, ilist->nr);
+ }
+ bDum = gmx_fio_ndo_int(fio, ilist->iatoms, ilist->nr);
+ if (!bRead)
+ {
+ gmx_fio_unset_comment(fio);
+ }
+}
+
+static void do_ffparams(t_fileio *fio, gmx_ffparams_t *ffparams,
+ gmx_bool bRead, int file_version)
+{
+ int idum, i, j;
+ gmx_bool bDum = TRUE;
+ unsigned int k;
+
+ gmx_fio_do_int(fio, ffparams->atnr);
+ if (file_version < 57)
+ {
+ gmx_fio_do_int(fio, idum);
+ }
+ gmx_fio_do_int(fio, ffparams->ntypes);
+ if (bRead && debug)
+ {
+ fprintf(debug, "ffparams->atnr = %d, ntypes = %d\n",
+ ffparams->atnr, ffparams->ntypes);
+ }
+ if (bRead)
+ {
+ snew(ffparams->functype, ffparams->ntypes);
+ snew(ffparams->iparams, ffparams->ntypes);
+ }
+ /* Read/write all the function types */
+ bDum = gmx_fio_ndo_int(fio, ffparams->functype, ffparams->ntypes);
+ if (bRead && debug)
+ {
+ pr_ivec(debug, 0, "functype", ffparams->functype, ffparams->ntypes, TRUE);
+ }
+
+ if (file_version >= 66)
+ {
+ gmx_fio_do_double(fio, ffparams->reppow);
+ }
+ else
+ {
+ ffparams->reppow = 12.0;
+ }
+
+ if (file_version >= 57)
+ {
+ gmx_fio_do_real(fio, ffparams->fudgeQQ);
+ }
+
+ /* Check whether all these function types are supported by the code.
+ * In practice the code is backwards compatible, which means that the
+ * numbering may have to be altered from old numbering to new numbering
+ */
+ for (i = 0; (i < ffparams->ntypes); i++)
+ {
+ if (bRead)
+ {
+ /* Loop over file versions */
+ for (k = 0; (k < NFTUPD); k++)
+ {
+ /* Compare the read file_version to the update table */
+ if ((file_version < ftupd[k].fvnr) &&
+ (ffparams->functype[i] >= ftupd[k].ftype))
+ {
+ ffparams->functype[i] += 1;
+ if (debug)
+ {
+ fprintf(debug, "Incrementing function type %d to %d (due to %s)\n",
+ i, ffparams->functype[i],
+ interaction_function[ftupd[k].ftype].longname);
+ fflush(debug);
+ }
+ }
+ }
+ }
+
+ do_iparams(fio, ffparams->functype[i], &ffparams->iparams[i], bRead,
+ file_version);
+ if (bRead && debug)
+ {
+ pr_iparams(debug, ffparams->functype[i], &ffparams->iparams[i]);
+ }
+ }
+}
+
+static void add_settle_atoms(t_ilist *ilist)
+{
+ int i;
+
+ /* Settle used to only store the first atom: add the other two */
+ srenew(ilist->iatoms, 2*ilist->nr);
+ for (i = ilist->nr/2-1; i >= 0; i--)
+ {
+ ilist->iatoms[4*i+0] = ilist->iatoms[2*i+0];
+ ilist->iatoms[4*i+1] = ilist->iatoms[2*i+1];
+ ilist->iatoms[4*i+2] = ilist->iatoms[2*i+1] + 1;
+ ilist->iatoms[4*i+3] = ilist->iatoms[2*i+1] + 2;
+ }
+ ilist->nr = 2*ilist->nr;
+}
+
+static void do_ilists(t_fileio *fio, t_ilist *ilist, gmx_bool bRead,
+ int file_version)
+{
+ int i, j, renum[F_NRE];
+ gmx_bool bDum = TRUE, bClear;
+ unsigned int k;
+
+ for (j = 0; (j < F_NRE); j++)
+ {
+ bClear = FALSE;
+ if (bRead)
+ {
+ for (k = 0; k < NFTUPD; k++)
+ {
+ if ((file_version < ftupd[k].fvnr) && (j == ftupd[k].ftype))
+ {
+ bClear = TRUE;
+ }
+ }
+ }
+ if (bClear)
+ {
+ ilist[j].nr = 0;
+ ilist[j].iatoms = NULL;
+ }
+ else
+ {
+ do_ilist(fio, &ilist[j], bRead, file_version, j);
+ if (file_version < 78 && j == F_SETTLE && ilist[j].nr > 0)
+ {
+ add_settle_atoms(&ilist[j]);
+ }
+ }
+ /*
+ if (bRead && gmx_debug_at)
+ pr_ilist(debug,0,interaction_function[j].longname,
+ functype,&ilist[j],TRUE);
+ */
+ }
+}
+
+static void do_idef(t_fileio *fio, gmx_ffparams_t *ffparams, gmx_moltype_t *molt,
+ gmx_bool bRead, int file_version)
+{
+ do_ffparams(fio, ffparams, bRead, file_version);
+
+ if (file_version >= 54)
+ {
+ gmx_fio_do_real(fio, ffparams->fudgeQQ);
+ }
+
+ do_ilists(fio, molt->ilist, bRead, file_version);
+}
+
+static void do_block(t_fileio *fio, t_block *block, gmx_bool bRead, int file_version)
+{
+ int i, idum, dum_nra, *dum_a;
+ gmx_bool bDum = TRUE;
+
+ if (file_version < 44)
+ {
+ for (i = 0; i < MAXNODES; i++)
+ {
+ gmx_fio_do_int(fio, idum);
+ }
+ }
+ gmx_fio_do_int(fio, block->nr);
+ if (file_version < 51)
+ {
+ gmx_fio_do_int(fio, dum_nra);
+ }
+ if (bRead)
+ {
+ if ((block->nalloc_index > 0) && (NULL != block->index))
+ {
+ sfree(block->index);
+ }
+ block->nalloc_index = block->nr+1;
+ snew(block->index, block->nalloc_index);
+ }
+ bDum = gmx_fio_ndo_int(fio, block->index, block->nr+1);
+
+ if (file_version < 51 && dum_nra > 0)
+ {
+ snew(dum_a, dum_nra);
+ bDum = gmx_fio_ndo_int(fio, dum_a, dum_nra);
+ sfree(dum_a);
+ }
+}
+
+static void do_blocka(t_fileio *fio, t_blocka *block, gmx_bool bRead,
+ int file_version)
+{
+ int i, idum;
+ gmx_bool bDum = TRUE;
+
+ if (file_version < 44)
+ {
+ for (i = 0; i < MAXNODES; i++)
+ {
+ gmx_fio_do_int(fio, idum);
+ }
+ }
+ gmx_fio_do_int(fio, block->nr);
+ gmx_fio_do_int(fio, block->nra);
+ if (bRead)
+ {
+ block->nalloc_index = block->nr+1;
+ snew(block->index, block->nalloc_index);
+ block->nalloc_a = block->nra;
+ snew(block->a, block->nalloc_a);
+ }
+ bDum = gmx_fio_ndo_int(fio, block->index, block->nr+1);
+ bDum = gmx_fio_ndo_int(fio, block->a, block->nra);
+}
+
+static void do_atom(t_fileio *fio, t_atom *atom, int ngrp, gmx_bool bRead,
+ int file_version, gmx_groups_t *groups, int atnr)
+{
+ int i, myngrp;
+
+ gmx_fio_do_real(fio, atom->m);
+ gmx_fio_do_real(fio, atom->q);
+ gmx_fio_do_real(fio, atom->mB);
+ gmx_fio_do_real(fio, atom->qB);
+ gmx_fio_do_ushort(fio, atom->type);
+ gmx_fio_do_ushort(fio, atom->typeB);
+ gmx_fio_do_int(fio, atom->ptype);
+ gmx_fio_do_int(fio, atom->resind);
+ if (file_version >= 52)
+ {
+ gmx_fio_do_int(fio, atom->atomnumber);
+ }
+ else if (bRead)
+ {
+ atom->atomnumber = NOTSET;
+ }
+ if (file_version < 23)
+ {
+ myngrp = 8;
+ }
+ else if (file_version < 39)
+ {
+ myngrp = 9;
+ }
+ else
+ {
+ myngrp = ngrp;
+ }
+
+ if (file_version < 57)
+ {
+ unsigned char uchar[egcNR];
+ gmx_fio_ndo_uchar(fio, uchar, myngrp);
+ for (i = myngrp; (i < ngrp); i++)
+ {
+ uchar[i] = 0;
+ }
+ /* Copy the old data format to the groups struct */
+ for (i = 0; i < ngrp; i++)
+ {
+ groups->grpnr[i][atnr] = uchar[i];
+ }
+ }
+}
+
+static void do_grps(t_fileio *fio, int ngrp, t_grps grps[], gmx_bool bRead,
+ int file_version)
+{
+ int i, j, myngrp;
+ gmx_bool bDum = TRUE;
+
+ if (file_version < 23)
+ {
+ myngrp = 8;
+ }
+ else if (file_version < 39)
+ {
+ myngrp = 9;
+ }
+ else
+ {
+ myngrp = ngrp;
+ }
+
+ for (j = 0; (j < ngrp); j++)
+ {
+ if (j < myngrp)
+ {
+ gmx_fio_do_int(fio, grps[j].nr);
+ if (bRead)
+ {
+ snew(grps[j].nm_ind, grps[j].nr);
+ }
+ bDum = gmx_fio_ndo_int(fio, grps[j].nm_ind, grps[j].nr);
+ }
+ else
+ {
+ grps[j].nr = 1;
+ snew(grps[j].nm_ind, grps[j].nr);
+ }
+ }
+}
+
+static void do_symstr(t_fileio *fio, char ***nm, gmx_bool bRead, t_symtab *symtab)
+{
+ int ls;
+
+ if (bRead)
+ {
+ gmx_fio_do_int(fio, ls);
+ *nm = get_symtab_handle(symtab, ls);
+ }
+ else
+ {
+ ls = lookup_symtab(symtab, *nm);
+ gmx_fio_do_int(fio, ls);
+ }
+}
+
+static void do_strstr(t_fileio *fio, int nstr, char ***nm, gmx_bool bRead,
+ t_symtab *symtab)
+{
+ int j;
+
+ for (j = 0; (j < nstr); j++)
+ {
+ do_symstr(fio, &(nm[j]), bRead, symtab);
+ }
+}
+
+static void do_resinfo(t_fileio *fio, int n, t_resinfo *ri, gmx_bool bRead,
+ t_symtab *symtab, int file_version)
+{
+ int j;
+
+ for (j = 0; (j < n); j++)
+ {
+ do_symstr(fio, &(ri[j].name), bRead, symtab);
+ if (file_version >= 63)
+ {
+ gmx_fio_do_int(fio, ri[j].nr);
+ gmx_fio_do_uchar(fio, ri[j].ic);
+ }
+ else
+ {
+ ri[j].nr = j + 1;
+ ri[j].ic = ' ';
+ }
+ }
+}
+
+static void do_atoms(t_fileio *fio, t_atoms *atoms, gmx_bool bRead, t_symtab *symtab,
+ int file_version,
+ gmx_groups_t *groups)
+{
+ int i;
+
+ gmx_fio_do_int(fio, atoms->nr);
+ gmx_fio_do_int(fio, atoms->nres);
+ if (file_version < 57)
+ {
+ gmx_fio_do_int(fio, groups->ngrpname);
+ for (i = 0; i < egcNR; i++)
+ {
+ groups->ngrpnr[i] = atoms->nr;
+ snew(groups->grpnr[i], groups->ngrpnr[i]);
+ }
+ }
+ if (bRead)
+ {
+ snew(atoms->atom, atoms->nr);
+ snew(atoms->atomname, atoms->nr);
+ snew(atoms->atomtype, atoms->nr);
+ snew(atoms->atomtypeB, atoms->nr);
+ snew(atoms->resinfo, atoms->nres);
+ if (file_version < 57)
+ {
+ snew(groups->grpname, groups->ngrpname);
+ }
+ atoms->pdbinfo = NULL;
+ }
+ for (i = 0; (i < atoms->nr); i++)
+ {
+ do_atom(fio, &atoms->atom[i], egcNR, bRead, file_version, groups, i);
+ }
+ do_strstr(fio, atoms->nr, atoms->atomname, bRead, symtab);
+ if (bRead && (file_version <= 20))
+ {
+ for (i = 0; i < atoms->nr; i++)
+ {
+ atoms->atomtype[i] = put_symtab(symtab, "?");
+ atoms->atomtypeB[i] = put_symtab(symtab, "?");
+ }
+ }
+ else
+ {
+ do_strstr(fio, atoms->nr, atoms->atomtype, bRead, symtab);
+ do_strstr(fio, atoms->nr, atoms->atomtypeB, bRead, symtab);
+ }
+ do_resinfo(fio, atoms->nres, atoms->resinfo, bRead, symtab, file_version);
+
+ if (file_version < 57)
+ {
+ do_strstr(fio, groups->ngrpname, groups->grpname, bRead, symtab);
+
+ do_grps(fio, egcNR, groups->grps, bRead, file_version);
+ }
+}
+
+static void do_groups(t_fileio *fio, gmx_groups_t *groups,
+ gmx_bool bRead, t_symtab *symtab,
+ int file_version)
+{
+ int g, n, i;
+ gmx_bool bDum = TRUE;
+
+ do_grps(fio, egcNR, groups->grps, bRead, file_version);
+ gmx_fio_do_int(fio, groups->ngrpname);
+ if (bRead)
+ {
+ snew(groups->grpname, groups->ngrpname);
+ }
+ do_strstr(fio, groups->ngrpname, groups->grpname, bRead, symtab);
+ for (g = 0; g < egcNR; g++)
+ {
+ gmx_fio_do_int(fio, groups->ngrpnr[g]);
+ if (groups->ngrpnr[g] == 0)
+ {
+ if (bRead)
+ {
+ groups->grpnr[g] = NULL;
+ }
+ }
+ else
+ {
+ if (bRead)
+ {
+ snew(groups->grpnr[g], groups->ngrpnr[g]);
+ }
+ bDum = gmx_fio_ndo_uchar(fio, groups->grpnr[g], groups->ngrpnr[g]);
+ }
+ }
+}
+
+static void do_atomtypes(t_fileio *fio, t_atomtypes *atomtypes, gmx_bool bRead,
+ t_symtab *symtab, int file_version)
+{
+ int i, j;
+ gmx_bool bDum = TRUE;
+
+ if (file_version > 25)
+ {
+ gmx_fio_do_int(fio, atomtypes->nr);
+ j = atomtypes->nr;
+ if (bRead)
+ {
+ snew(atomtypes->radius, j);
+ snew(atomtypes->vol, j);
+ snew(atomtypes->surftens, j);
+ snew(atomtypes->atomnumber, j);
+ snew(atomtypes->gb_radius, j);
+ snew(atomtypes->S_hct, j);
+ }
+ bDum = gmx_fio_ndo_real(fio, atomtypes->radius, j);
+ bDum = gmx_fio_ndo_real(fio, atomtypes->vol, j);
+ bDum = gmx_fio_ndo_real(fio, atomtypes->surftens, j);
+ if (file_version >= 40)
+ {
+ bDum = gmx_fio_ndo_int(fio, atomtypes->atomnumber, j);
+ }
+ if (file_version >= 60)
+ {
+ bDum = gmx_fio_ndo_real(fio, atomtypes->gb_radius, j);
+ bDum = gmx_fio_ndo_real(fio, atomtypes->S_hct, j);
+ }
+ }
+ else
+ {
+ /* File versions prior to 26 cannot do GBSA,
+ * so they dont use this structure
+ */
+ atomtypes->nr = 0;
+ atomtypes->radius = NULL;
+ atomtypes->vol = NULL;
+ atomtypes->surftens = NULL;
+ atomtypes->atomnumber = NULL;
+ atomtypes->gb_radius = NULL;
+ atomtypes->S_hct = NULL;
+ }
+}
+
+static void do_symtab(t_fileio *fio, t_symtab *symtab, gmx_bool bRead)
+{
+ int i, nr;
+ t_symbuf *symbuf;
+ char buf[STRLEN];
+
+ gmx_fio_do_int(fio, symtab->nr);
+ nr = symtab->nr;
+ if (bRead)
+ {
+ snew(symtab->symbuf, 1);
+ symbuf = symtab->symbuf;
+ symbuf->bufsize = nr;
+ snew(symbuf->buf, nr);
+ for (i = 0; (i < nr); i++)
+ {
+ gmx_fio_do_string(fio, buf);
+ symbuf->buf[i] = strdup(buf);
+ }
+ }
+ else
+ {
+ symbuf = symtab->symbuf;
+ while (symbuf != NULL)
+ {
+ for (i = 0; (i < symbuf->bufsize) && (i < nr); i++)
+ {
+ gmx_fio_do_string(fio, symbuf->buf[i]);
+ }
+ nr -= i;
+ symbuf = symbuf->next;
+ }
+ if (nr != 0)
+ {
+ gmx_fatal(FARGS, "nr of symtab strings left: %d", nr);
+ }
+ }
+}
+
+static void do_cmap(t_fileio *fio, gmx_cmap_t *cmap_grid, gmx_bool bRead)
+{
+ int i, j, ngrid, gs, nelem;
+
+ gmx_fio_do_int(fio, cmap_grid->ngrid);
+ gmx_fio_do_int(fio, cmap_grid->grid_spacing);
+
+ ngrid = cmap_grid->ngrid;
+ gs = cmap_grid->grid_spacing;
+ nelem = gs * gs;
+
+ if (bRead)
+ {
+ snew(cmap_grid->cmapdata, ngrid);
+
+ for (i = 0; i < cmap_grid->ngrid; i++)
+ {
+ snew(cmap_grid->cmapdata[i].cmap, 4*nelem);
+ }
+ }
+
+ for (i = 0; i < cmap_grid->ngrid; i++)
+ {
+ for (j = 0; j < nelem; j++)
+ {
+ gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4]);
+ gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+1]);
+ gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+2]);
+ gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+3]);
+ }
+ }
+}
+
+
+void tpx_make_chain_identifiers(t_atoms *atoms, t_block *mols)
+{
+ int m, a, a0, a1, r;
+ char c, chainid;
+ int chainnum;
+
+ /* We always assign a new chain number, but save the chain id characters
+ * for larger molecules.
+ */
+#define CHAIN_MIN_ATOMS 15
+
+ chainnum = 0;
+ chainid = 'A';
+ for (m = 0; m < mols->nr; m++)
+ {
+ a0 = mols->index[m];
+ a1 = mols->index[m+1];
+ if ((a1-a0 >= CHAIN_MIN_ATOMS) && (chainid <= 'Z'))
+ {
+ c = chainid;
+ chainid++;
+ }
+ else
+ {
+ c = ' ';
+ }
+ for (a = a0; a < a1; a++)
+ {
+ atoms->resinfo[atoms->atom[a].resind].chainnum = chainnum;
+ atoms->resinfo[atoms->atom[a].resind].chainid = c;
+ }
+ chainnum++;
+ }
+
+ /* Blank out the chain id if there was only one chain */
+ if (chainid == 'B')
+ {
+ for (r = 0; r < atoms->nres; r++)
+ {
+ atoms->resinfo[r].chainid = ' ';
+ }
+ }
+}
+
+static void do_moltype(t_fileio *fio, gmx_moltype_t *molt, gmx_bool bRead,
+ t_symtab *symtab, int file_version,
+ gmx_groups_t *groups)
+{
+ int i;
+
+ if (file_version >= 57)
+ {
+ do_symstr(fio, &(molt->name), bRead, symtab);
+ }
+
+ do_atoms(fio, &molt->atoms, bRead, symtab, file_version, groups);
+
+ if (bRead && gmx_debug_at)
+ {
+ pr_atoms(debug, 0, "atoms", &molt->atoms, TRUE);
+ }
+
+ if (file_version >= 57)
+ {
+ do_ilists(fio, molt->ilist, bRead, file_version);
+
+ do_block(fio, &molt->cgs, bRead, file_version);
+ if (bRead && gmx_debug_at)
+ {
+ pr_block(debug, 0, "cgs", &molt->cgs, TRUE);
+ }
+ }
+
+ /* This used to be in the atoms struct */
+ do_blocka(fio, &molt->excls, bRead, file_version);
+}
+
+static void do_molblock(t_fileio *fio, gmx_molblock_t *molb, gmx_bool bRead,
+ int file_version)
+{
+ int i;
+
+ gmx_fio_do_int(fio, molb->type);
+ gmx_fio_do_int(fio, molb->nmol);
+ gmx_fio_do_int(fio, molb->natoms_mol);
+ /* Position restraint coordinates */
+ gmx_fio_do_int(fio, molb->nposres_xA);
+ if (molb->nposres_xA > 0)
+ {
+ if (bRead)
+ {
+ snew(molb->posres_xA, molb->nposres_xA);
+ }
+ gmx_fio_ndo_rvec(fio, molb->posres_xA, molb->nposres_xA);
+ }
+ gmx_fio_do_int(fio, molb->nposres_xB);
+ if (molb->nposres_xB > 0)
+ {
+ if (bRead)
+ {
+ snew(molb->posres_xB, molb->nposres_xB);
+ }
+ gmx_fio_ndo_rvec(fio, molb->posres_xB, molb->nposres_xB);
+ }
+
+}
+
+static t_block mtop_mols(gmx_mtop_t *mtop)
+{
+ int mb, m, a, mol;
+ t_block mols;
+
+ mols.nr = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ mols.nr += mtop->molblock[mb].nmol;
+ }
+ mols.nalloc_index = mols.nr + 1;
+ snew(mols.index, mols.nalloc_index);
+
+ a = 0;
+ m = 0;
+ mols.index[m] = a;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ for (mol = 0; mol < mtop->molblock[mb].nmol; mol++)
+ {
+ a += mtop->molblock[mb].natoms_mol;
+ m++;
+ mols.index[m] = a;
+ }
+ }
+
+ return mols;
+}
+
+static void add_posres_molblock(gmx_mtop_t *mtop)
+{
+ t_ilist *il, *ilfb;
+ int am, i, mol, a;
+ gmx_bool bFE;
+ gmx_molblock_t *molb;
+ t_iparams *ip;
+
+ /* posres reference positions are stored in ip->posres (if present) and
+ in ip->fbposres (if present). If normal and flat-bottomed posres are present,
+ posres.pos0A are identical to fbposres.pos0. */
+ il = &mtop->moltype[0].ilist[F_POSRES];
+ ilfb = &mtop->moltype[0].ilist[F_FBPOSRES];
+ if (il->nr == 0 && ilfb->nr == 0)
+ {
+ return;
+ }
+ am = 0;
+ bFE = FALSE;
+ for (i = 0; i < il->nr; i += 2)
+ {
+ ip = &mtop->ffparams.iparams[il->iatoms[i]];
+ am = max(am, il->iatoms[i+1]);
+ if (ip->posres.pos0B[XX] != ip->posres.pos0A[XX] ||
+ ip->posres.pos0B[YY] != ip->posres.pos0A[YY] ||
+ ip->posres.pos0B[ZZ] != ip->posres.pos0A[ZZ])
+ {
+ bFE = TRUE;
+ }
+ }
+ /* This loop is required if we have only flat-bottomed posres:
+ - set am
+ - bFE == FALSE (no B-state for flat-bottomed posres) */
+ if (il->nr == 0)
+ {
+ for (i = 0; i < ilfb->nr; i += 2)
+ {
+ ip = &mtop->ffparams.iparams[ilfb->iatoms[i]];
+ am = max(am, ilfb->iatoms[i+1]);
+ }
+ }
+ /* Make the posres coordinate block end at a molecule end */
+ mol = 0;
+ while (am >= mtop->mols.index[mol+1])
+ {
+ mol++;
+ }
+ molb = &mtop->molblock[0];
+ molb->nposres_xA = mtop->mols.index[mol+1];
+ snew(molb->posres_xA, molb->nposres_xA);
+ if (bFE)
+ {
+ molb->nposres_xB = molb->nposres_xA;
+ snew(molb->posres_xB, molb->nposres_xB);
+ }
+ else
+ {
+ molb->nposres_xB = 0;
+ }
+ for (i = 0; i < il->nr; i += 2)
+ {
+ ip = &mtop->ffparams.iparams[il->iatoms[i]];
+ a = il->iatoms[i+1];
+ molb->posres_xA[a][XX] = ip->posres.pos0A[XX];
+ molb->posres_xA[a][YY] = ip->posres.pos0A[YY];
+ molb->posres_xA[a][ZZ] = ip->posres.pos0A[ZZ];
+ if (bFE)
+ {
+ molb->posres_xB[a][XX] = ip->posres.pos0B[XX];
+ molb->posres_xB[a][YY] = ip->posres.pos0B[YY];
+ molb->posres_xB[a][ZZ] = ip->posres.pos0B[ZZ];
+ }
+ }
+ if (il->nr == 0)
+ {
+ /* If only flat-bottomed posres are present, take reference pos from them.
+ Here: bFE == FALSE */
+ for (i = 0; i < ilfb->nr; i += 2)
+ {
+ ip = &mtop->ffparams.iparams[ilfb->iatoms[i]];
+ a = ilfb->iatoms[i+1];
+ molb->posres_xA[a][XX] = ip->fbposres.pos0[XX];
+ molb->posres_xA[a][YY] = ip->fbposres.pos0[YY];
+ molb->posres_xA[a][ZZ] = ip->fbposres.pos0[ZZ];
+ }
+ }
+}
+
+static void set_disres_npair(gmx_mtop_t *mtop)
+{
+ int mt, i, npair;
+ t_iparams *ip;
+ t_ilist *il;
+ t_iatom *a;
+
+ ip = mtop->ffparams.iparams;
+
+ for (mt = 0; mt < mtop->nmoltype; mt++)
+ {
+ il = &mtop->moltype[mt].ilist[F_DISRES];
+ if (il->nr > 0)
+ {
+ a = il->iatoms;
+ npair = 0;
+ for (i = 0; i < il->nr; i += 3)
+ {
+ npair++;
+ if (i+3 == il->nr || ip[a[i]].disres.label != ip[a[i+3]].disres.label)
+ {
+ ip[a[i]].disres.npair = npair;
+ npair = 0;
+ }
+ }
+ }
+ }
+}
+
+static void do_mtop(t_fileio *fio, gmx_mtop_t *mtop, gmx_bool bRead,
+ int file_version)
+{
+ int mt, mb, i;
+ t_blocka dumb;
+
+ if (bRead)
+ {
+ init_mtop(mtop);
+ }
+ do_symtab(fio, &(mtop->symtab), bRead);
+ if (bRead && debug)
+ {
+ pr_symtab(debug, 0, "symtab", &mtop->symtab);
+ }
+
+ do_symstr(fio, &(mtop->name), bRead, &(mtop->symtab));
+
+ if (file_version >= 57)
+ {
+ do_ffparams(fio, &mtop->ffparams, bRead, file_version);
+
+ gmx_fio_do_int(fio, mtop->nmoltype);
+ }
+ else
+ {
+ mtop->nmoltype = 1;
+ }
+ if (bRead)
+ {
+ snew(mtop->moltype, mtop->nmoltype);
+ if (file_version < 57)
+ {
+ mtop->moltype[0].name = mtop->name;
+ }
+ }
+ for (mt = 0; mt < mtop->nmoltype; mt++)
+ {
+ do_moltype(fio, &mtop->moltype[mt], bRead, &mtop->symtab, file_version,
+ &mtop->groups);
+ }
+
+ if (file_version >= 57)
+ {
+ gmx_fio_do_int(fio, mtop->nmolblock);
+ }
+ else
+ {
+ mtop->nmolblock = 1;
+ }
+ if (bRead)
+ {
+ snew(mtop->molblock, mtop->nmolblock);
+ }
+ if (file_version >= 57)
+ {
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ do_molblock(fio, &mtop->molblock[mb], bRead, file_version);
+ }
+ gmx_fio_do_int(fio, mtop->natoms);
+ }
+ else
+ {
+ mtop->molblock[0].type = 0;
+ mtop->molblock[0].nmol = 1;
+ mtop->molblock[0].natoms_mol = mtop->moltype[0].atoms.nr;
+ mtop->molblock[0].nposres_xA = 0;
+ mtop->molblock[0].nposres_xB = 0;
+ }
+
+ do_atomtypes (fio, &(mtop->atomtypes), bRead, &(mtop->symtab), file_version);
+ if (bRead && debug)
+ {
+ pr_atomtypes(debug, 0, "atomtypes", &mtop->atomtypes, TRUE);
+ }
+
+ if (file_version < 57)
+ {
+ /* Debug statements are inside do_idef */
+ do_idef (fio, &mtop->ffparams, &mtop->moltype[0], bRead, file_version);
+ mtop->natoms = mtop->moltype[0].atoms.nr;
+ }
+
+ if (file_version >= 65)
+ {
+ do_cmap(fio, &mtop->ffparams.cmap_grid, bRead);
+ }
+ else
+ {
+ mtop->ffparams.cmap_grid.ngrid = 0;
+ mtop->ffparams.cmap_grid.grid_spacing = 0;
+ mtop->ffparams.cmap_grid.cmapdata = NULL;
+ }
+
+ if (file_version >= 57)
+ {
+ do_groups(fio, &mtop->groups, bRead, &(mtop->symtab), file_version);
+ }
+
+ if (file_version < 57)
+ {
+ do_block(fio, &mtop->moltype[0].cgs, bRead, file_version);
+ if (bRead && gmx_debug_at)
+ {
+ pr_block(debug, 0, "cgs", &mtop->moltype[0].cgs, TRUE);
+ }
+ do_block(fio, &mtop->mols, bRead, file_version);
+ /* Add the posres coordinates to the molblock */
+ add_posres_molblock(mtop);
+ }
+ if (bRead)
+ {
+ if (file_version >= 57)
+ {
+ done_block(&mtop->mols);
+ mtop->mols = mtop_mols(mtop);
+ }
+ if (gmx_debug_at)
+ {
+ pr_block(debug, 0, "mols", &mtop->mols, TRUE);
+ }
+ }
+
+ if (file_version < 51)
+ {
+ /* Here used to be the shake blocks */
+ do_blocka(fio, &dumb, bRead, file_version);
+ if (dumb.nr > 0)
+ {
+ sfree(dumb.index);
+ }
+ if (dumb.nra > 0)
+ {
+ sfree(dumb.a);
+ }
+ }
+
+ if (bRead)
+ {
+ close_symtab(&(mtop->symtab));
+ }
+}
+
+/* If TopOnlyOK is TRUE then we can read even future versions
+ * of tpx files, provided the file_generation hasn't changed.
+ * If it is FALSE, we need the inputrecord too, and bail out
+ * if the file is newer than the program.
+ *
+ * The version and generation if the topology (see top of this file)
+ * are returned in the two last arguments.
+ *
+ * If possible, we will read the inputrec even when TopOnlyOK is TRUE.
+ */
+static void do_tpxheader(t_fileio *fio, gmx_bool bRead, t_tpxheader *tpx,
+ gmx_bool TopOnlyOK, int *file_version,
+ int *file_generation)
+{
+ char buf[STRLEN];
+ char file_tag[STRLEN];
+ gmx_bool bDouble;
+ int precision;
+ int fver, fgen;
+ int idum = 0;
+ real rdum = 0;
+
+ gmx_fio_checktype(fio);
+ gmx_fio_setdebug(fio, bDebugMode());
+
+ /* NEW! XDR tpb file */
+ precision = sizeof(real);
+ if (bRead)
+ {
+ gmx_fio_do_string(fio, buf);
+ if (strncmp(buf, "VERSION", 7))
+ {
+ gmx_fatal(FARGS, "Can not read file %s,\n"
+ " this file is from a Gromacs version which is older than 2.0\n"
+ " Make a new one with grompp or use a gro or pdb file, if possible",
+ gmx_fio_getname(fio));
+ }
+ gmx_fio_do_int(fio, precision);
+ bDouble = (precision == sizeof(double));
+ if ((precision != sizeof(float)) && !bDouble)
+ {
+ gmx_fatal(FARGS, "Unknown precision in file %s: real is %d bytes "
+ "instead of %d or %d",
+ gmx_fio_getname(fio), precision, sizeof(float), sizeof(double));
+ }
+ gmx_fio_setprecision(fio, bDouble);
+ fprintf(stderr, "Reading file %s, %s (%s precision)\n",
+ gmx_fio_getname(fio), buf, bDouble ? "double" : "single");
+ }
+ else
+ {
+ gmx_fio_write_string(fio, GromacsVersion());
+ bDouble = (precision == sizeof(double));
+ gmx_fio_setprecision(fio, bDouble);
+ gmx_fio_do_int(fio, precision);
+ fver = tpx_version;
+ sprintf(file_tag, "%s", tpx_tag);
+ fgen = tpx_generation;
+ }
+
+ /* Check versions! */
+ gmx_fio_do_int(fio, fver);
+
+ /* This is for backward compatibility with development versions 77-79
+ * where the tag was, mistakenly, placed before the generation,
+ * which would cause a segv instead of a proper error message
+ * when reading the topology only from tpx with <77 code.
+ */
+ if (fver >= 77 && fver <= 79)
+ {
+ gmx_fio_do_string(fio, file_tag);
+ }
+
+ if (fver >= 26)
+ {
+ gmx_fio_do_int(fio, fgen);
+ }
+ else
+ {
+ fgen = 0;
+ }
+
+ if (fver >= 81)
+ {
+ gmx_fio_do_string(fio, file_tag);
+ }
+ if (bRead)
+ {
+ if (fver < 77)
+ {
+ /* Versions before 77 don't have the tag, set it to release */
+ sprintf(file_tag, "%s", TPX_TAG_RELEASE);
+ }
+
+ if (strcmp(file_tag, tpx_tag) != 0)
+ {
+ fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n",
+ file_tag, tpx_tag);
+
+ /* We only support reading tpx files with the same tag as the code
+ * or tpx files with the release tag and with lower version number.
+ */
+ if (!strcmp(file_tag, TPX_TAG_RELEASE) == 0 && fver < tpx_version)
+ {
+ gmx_fatal(FARGS, "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' with program for tpx version %d, tag '%s'",
+ gmx_fio_getname(fio), fver, file_tag,
+ tpx_version, tpx_tag);
+ }
+ }
+ }
+
+ if (file_version != NULL)
+ {
+ *file_version = fver;
+ }
+ if (file_generation != NULL)
+ {
+ *file_generation = fgen;
+ }
+
+
+ if ((fver <= tpx_incompatible_version) ||
+ ((fver > tpx_version) && !TopOnlyOK) ||
+ (fgen > tpx_generation) ||
+ tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
+ {
+ gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program",
+ gmx_fio_getname(fio), fver, tpx_version);
+ }
+
+ do_section(fio, eitemHEADER, bRead);
+ gmx_fio_do_int(fio, tpx->natoms);
+ if (fver >= 28)
+ {
+ gmx_fio_do_int(fio, tpx->ngtc);
+ }
+ else
+ {
+ tpx->ngtc = 0;
+ }
+ if (fver < 62)
+ {
+ gmx_fio_do_int(fio, idum);
+ gmx_fio_do_real(fio, rdum);
+ }
+ /*a better decision will eventually (5.0 or later) need to be made
+ on how to treat the alchemical state of the system, which can now
+ vary through a simulation, and cannot be completely described
+ though a single lambda variable, or even a single state
+ index. Eventually, should probably be a vector. MRS*/
+ if (fver >= 79)
+ {
+ gmx_fio_do_int(fio, tpx->fep_state);
+ }
+ gmx_fio_do_real(fio, tpx->lambda);
+ gmx_fio_do_int(fio, tpx->bIr);
+ gmx_fio_do_int(fio, tpx->bTop);
+ gmx_fio_do_int(fio, tpx->bX);
+ gmx_fio_do_int(fio, tpx->bV);
+ gmx_fio_do_int(fio, tpx->bF);
+ gmx_fio_do_int(fio, tpx->bBox);
+
+ if ((fgen > tpx_generation))
+ {
+ /* This can only happen if TopOnlyOK=TRUE */
+ tpx->bIr = FALSE;
+ }
+}
+
+static int do_tpx(t_fileio *fio, gmx_bool bRead,
+ t_inputrec *ir, t_state *state, rvec *f, gmx_mtop_t *mtop,
+ gmx_bool bXVallocated)
+{
+ t_tpxheader tpx;
+ t_inputrec dum_ir;
+ gmx_mtop_t dum_top;
+ gmx_bool TopOnlyOK, bDum = TRUE;
+ int file_version, file_generation;
+ int i;
+ rvec *xptr, *vptr;
+ int ePBC;
+ gmx_bool bPeriodicMols;
+
+ if (!bRead)
+ {
+ tpx.natoms = state->natoms;
+ tpx.ngtc = state->ngtc; /* need to add nnhpres here? */
+ tpx.fep_state = state->fep_state;
+ tpx.lambda = state->lambda[efptFEP];
+ tpx.bIr = (ir != NULL);
+ tpx.bTop = (mtop != NULL);
+ tpx.bX = (state->x != NULL);
+ tpx.bV = (state->v != NULL);
+ tpx.bF = (f != NULL);
+ tpx.bBox = TRUE;
+ }
+
+ TopOnlyOK = (ir == NULL);
+
+ do_tpxheader(fio, bRead, &tpx, TopOnlyOK, &file_version, &file_generation);
+
+ if (bRead)
+ {
+ state->flags = 0;
+ /* state->lambda = tpx.lambda;*/ /*remove this eventually? */
+ /* The init_state calls initialize the Nose-Hoover xi integrals to zero */
+ if (bXVallocated)
+ {
+ xptr = state->x;
+ vptr = state->v;
+ init_state(state, 0, tpx.ngtc, 0, 0, 0); /* nose-hoover chains */ /* eventually, need to add nnhpres here? */
+ state->natoms = tpx.natoms;
+ state->nalloc = tpx.natoms;
+ state->x = xptr;
+ state->v = vptr;
+ }
+ else
+ {
+ init_state(state, tpx.natoms, tpx.ngtc, 0, 0, 0); /* nose-hoover chains */
+ }
+ }
+
+#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 >= 51)
+ {
+ gmx_fio_ndo_rvec(fio, state->box_rel, DIM);
+ }
+ else
+ {
+ /* We initialize box_rel after reading the inputrec */
+ clear_mat(state->box_rel);
+ }
+ if (file_version >= 28)
+ {
+ gmx_fio_ndo_rvec(fio, state->boxv, DIM);
+ if (file_version < 56)
+ {
+ matrix mdum;
+ gmx_fio_ndo_rvec(fio, mdum, DIM);
+ }
+ }
+ }
+
+ if (state->ngtc > 0 && file_version >= 28)
+ {
+ real *dumv;
+ /*ndo_double(state->nosehoover_xi,state->ngtc,bDum);*/
+ /*ndo_double(state->nosehoover_vxi,state->ngtc,bDum);*/
+ /*ndo_double(state->therm_integral,state->ngtc,bDum);*/
+ snew(dumv, state->ngtc);
+ if (file_version < 69)
+ {
+ bDum = gmx_fio_ndo_real(fio, dumv, state->ngtc);
+ }
+ /* These used to be the Berendsen tcoupl_lambda's */
+ bDum = gmx_fio_ndo_real(fio, dumv, state->ngtc);
+ sfree(dumv);
+ }
+
+ /* Prior to tpx version 26, the inputrec was here.
+ * I moved it to enable partial forward-compatibility
+ * for analysis/viewer programs.
+ */
+ if (file_version < 26)
+ {
+ do_test(fio, tpx.bIr, ir);
+ do_section(fio, eitemIR, bRead);
+ if (tpx.bIr)
+ {
+ if (ir)
+ {
+ do_inputrec(fio, ir, bRead, file_version,
+ mtop ? &mtop->ffparams.fudgeQQ : NULL);
+ if (bRead && debug)
+ {
+ pr_inputrec(debug, 0, "inputrec", ir, FALSE);
+ }
+ }
+ else
+ {
+ do_inputrec(fio, &dum_ir, bRead, file_version,
+ mtop ? &mtop->ffparams.fudgeQQ : NULL);
+ if (bRead && debug)
+ {
+ pr_inputrec(debug, 0, "inputrec", &dum_ir, FALSE);
+ }
+ done_inputrec(&dum_ir);
+ }
+
+ }
+ }
+
+ do_test(fio, tpx.bTop, mtop);
+ do_section(fio, eitemTOP, bRead);
+ if (tpx.bTop)
+ {
+ if (mtop)
+ {
+ do_mtop(fio, mtop, bRead, file_version);
+ }
+ else
+ {
+ do_mtop(fio, &dum_top, bRead, file_version);
+ done_mtop(&dum_top, TRUE);
+ }
+ }
+ do_test(fio, tpx.bX, state->x);
+ do_section(fio, eitemX, bRead);
+ if (tpx.bX)
+ {
+ if (bRead)
+ {
+ state->flags |= (1<<estX);
+ }
+ gmx_fio_ndo_rvec(fio, state->x, state->natoms);
+ }
+
+ do_test(fio, tpx.bV, state->v);
+ do_section(fio, eitemV, bRead);
+ if (tpx.bV)
+ {
+ if (bRead)
+ {
+ state->flags |= (1<<estV);
+ }
+ gmx_fio_ndo_rvec(fio, state->v, state->natoms);
+ }
+
+ do_test(fio, tpx.bF, f);
+ do_section(fio, eitemF, bRead);
+ if (tpx.bF)
+ {
+ gmx_fio_ndo_rvec(fio, f, state->natoms);
+ }
+
+ /* Starting with tpx version 26, we have the inputrec
+ * at the end of the file, so we can ignore it
+ * if the file is never than the software (but still the
+ * same generation - see comments at the top of this file.
+ *
+ *
+ */
+ ePBC = -1;
+ bPeriodicMols = FALSE;
+ if (file_version >= 26)
+ {
+ do_test(fio, tpx.bIr, ir);
+ do_section(fio, eitemIR, bRead);
+ if (tpx.bIr)
+ {
+ if (file_version >= 53)
+ {
+ /* Removed the pbc info from do_inputrec, since we always want it */
+ if (!bRead)
+ {
+ ePBC = ir->ePBC;
+ bPeriodicMols = ir->bPeriodicMols;
+ }
+ gmx_fio_do_int(fio, ePBC);
+ gmx_fio_do_gmx_bool(fio, bPeriodicMols);
+ }
+ if (file_generation <= tpx_generation && ir)
+ {
+ do_inputrec(fio, ir, bRead, file_version, mtop ? &mtop->ffparams.fudgeQQ : NULL);
+ if (bRead && debug)
+ {
+ pr_inputrec(debug, 0, "inputrec", ir, FALSE);
+ }
+ if (file_version < 51)
+ {
+ set_box_rel(ir, state);
+ }
+ if (file_version < 53)
+ {
+ ePBC = ir->ePBC;
+ bPeriodicMols = ir->bPeriodicMols;
+ }
+ }
+ if (bRead && ir && file_version >= 53)
+ {
+ /* We need to do this after do_inputrec, since that initializes ir */
+ ir->ePBC = ePBC;
+ ir->bPeriodicMols = bPeriodicMols;
+ }
+ }
+ }
+
+ if (bRead)
+ {
+ if (tpx.bIr && ir)
+ {
+ if (state->ngtc == 0)
+ {
+ /* Reading old version without tcoupl state data: set it */
+ init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength);
+ }
+ if (tpx.bTop && mtop)
+ {
+ if (file_version < 57)
+ {
+ if (mtop->moltype[0].ilist[F_DISRES].nr > 0)
+ {
+ ir->eDisre = edrSimple;
+ }
+ else
+ {
+ ir->eDisre = edrNone;
+ }
+ }
+ set_disres_npair(mtop);
+ }
+ }
+
+ if (tpx.bTop && mtop)
+ {
+ gmx_mtop_finalize(mtop);
+ }
+
+ if (file_version >= 57)
+ {
+ char *env;
+ int ienv;
+ env = getenv("GMX_NOCHARGEGROUPS");
+ if (env != NULL)
+ {
+ sscanf(env, "%d", &ienv);
+ fprintf(stderr, "\nFound env.var. GMX_NOCHARGEGROUPS = %d\n",
+ ienv);
+ if (ienv > 0)
+ {
+ fprintf(stderr,
+ "Will make single atomic charge groups in non-solvent%s\n",
+ ienv > 1 ? " and solvent" : "");
+ gmx_mtop_make_atomic_charge_groups(mtop, ienv == 1);
+ }
+ fprintf(stderr, "\n");
+ }
+ }
+ }
+
+ return ePBC;
+}
+
+/************************************************************
+ *
+ * The following routines are the exported ones
+ *
+ ************************************************************/
+
+t_fileio *open_tpx(const char *fn, const char *mode)
+{
+ return gmx_fio_open(fn, mode);
+}
+
+void close_tpx(t_fileio *fio)
+{
+ gmx_fio_close(fio);
+}
+
+void read_tpxheader(const char *fn, t_tpxheader *tpx, gmx_bool TopOnlyOK,
+ int *file_version, int *file_generation)
+{
+ t_fileio *fio;
+
+ fio = open_tpx(fn, "r");
+ do_tpxheader(fio, TRUE, tpx, TopOnlyOK, file_version, file_generation);
+ close_tpx(fio);
+}
+
+void write_tpx_state(const char *fn,
+ t_inputrec *ir, t_state *state, gmx_mtop_t *mtop)
+{
+ t_fileio *fio;
+
+ fio = open_tpx(fn, "w");
+ do_tpx(fio, FALSE, ir, state, NULL, mtop, FALSE);
+ close_tpx(fio);
+}
+
+void read_tpx_state(const char *fn,
+ t_inputrec *ir, t_state *state, rvec *f, gmx_mtop_t *mtop)
+{
+ t_fileio *fio;
+
+ fio = open_tpx(fn, "r");
+ do_tpx(fio, TRUE, ir, state, f, mtop, FALSE);
+ close_tpx(fio);
+}
+
+int read_tpx(const char *fn,
+ t_inputrec *ir, matrix box, int *natoms,
+ rvec *x, rvec *v, rvec *f, gmx_mtop_t *mtop)
+{
+ t_fileio *fio;
+ t_state state;
+ int ePBC;
+
+ state.x = x;
+ state.v = v;
+ fio = open_tpx(fn, "r");
+ ePBC = do_tpx(fio, TRUE, ir, &state, f, mtop, TRUE);
+ close_tpx(fio);
+ *natoms = state.natoms;
+ if (box)
+ {
+ copy_mat(state.box, box);
+ }
+ state.x = NULL;
+ state.v = NULL;
+ done_state(&state);
+
+ return ePBC;
+}
+
+int read_tpx_top(const char *fn,
+ t_inputrec *ir, matrix box, int *natoms,
+ rvec *x, rvec *v, rvec *f, t_topology *top)
+{
+ gmx_mtop_t mtop;
+ t_topology *ltop;
+ int ePBC;
+
+ ePBC = read_tpx(fn, ir, box, natoms, x, v, f, &mtop);
+
+ *top = gmx_mtop_t_to_t_topology(&mtop);
+
+ return ePBC;
+}
+
+gmx_bool fn2bTPX(const char *file)
+{
+ switch (fn2ftp(file))
+ {
+ case efTPR:
+ case efTPB:
+ case efTPA:
+ return TRUE;
+ default:
+ return FALSE;
+ }
+}
+
+static void done_gmx_groups_t(gmx_groups_t *g)
+{
+ int i;
+
+ for (i = 0; (i < egcNR); i++)
+ {
+ if (NULL != g->grps[i].nm_ind)
+ {
+ sfree(g->grps[i].nm_ind);
+ g->grps[i].nm_ind = NULL;
+ }
+ if (NULL != g->grpnr[i])
+ {
+ sfree(g->grpnr[i]);
+ g->grpnr[i] = NULL;
+ }
+ }
+ /* The contents of this array is in symtab, don't free it here */
+ sfree(g->grpname);
+}
+
+gmx_bool read_tps_conf(const char *infile, char *title, t_topology *top, int *ePBC,
+ rvec **x, rvec **v, matrix box, gmx_bool bMass)
+{
+ t_tpxheader header;
+ int natoms, i, version, generation;
+ gmx_bool bTop, bXNULL = FALSE;
+ gmx_mtop_t *mtop;
+ t_topology *topconv;
+ gmx_atomprop_t aps;
+
+ bTop = fn2bTPX(infile);
+ *ePBC = -1;
+ if (bTop)
+ {
+ read_tpxheader(infile, &header, TRUE, &version, &generation);
+ if (x)
+ {
+ snew(*x, header.natoms);
+ }
+ if (v)
+ {
+ snew(*v, header.natoms);
+ }
+ snew(mtop, 1);
+ *ePBC = read_tpx(infile, NULL, box, &natoms,
+ (x == NULL) ? NULL : *x, (v == NULL) ? NULL : *v, NULL, mtop);
+ *top = gmx_mtop_t_to_t_topology(mtop);
+ /* In this case we need to throw away the group data too */
+ done_gmx_groups_t(&mtop->groups);
+ sfree(mtop);
+ strcpy(title, *top->name);
+ tpx_make_chain_identifiers(&top->atoms, &top->mols);
+ }
+ else
+ {
+ get_stx_coordnum(infile, &natoms);
+ init_t_atoms(&top->atoms, natoms, (fn2ftp(infile) == efPDB));
+ if (x == NULL)
+ {
+ snew(x, 1);
+ bXNULL = TRUE;
+ }
+ snew(*x, natoms);
+ if (v)
+ {
+ snew(*v, natoms);
+ }
+ read_stx_conf(infile, title, &top->atoms, *x, (v == NULL) ? NULL : *v, ePBC, box);
+ if (bXNULL)
+ {
+ sfree(*x);
+ sfree(x);
+ }
+ if (bMass)
+ {
+ aps = gmx_atomprop_init();
+ for (i = 0; (i < natoms); i++)
+ {
+ if (!gmx_atomprop_query(aps, epropMass,
+ *top->atoms.resinfo[top->atoms.atom[i].resind].name,
+ *top->atoms.atomname[i],
+ &(top->atoms.atom[i].m)))
+ {
+ if (debug)
+ {
+ fprintf(debug, "Can not find mass for atom %s %d %s, setting to 1\n",
+ *top->atoms.resinfo[top->atoms.atom[i].resind].name,
+ top->atoms.resinfo[top->atoms.atom[i].resind].nr,
+ *top->atoms.atomname[i]);
+ }
+ }
+ }
+ gmx_atomprop_destroy(aps);
+ }
+ top->idef.ntypes = -1;
+ }
+
+ return bTop;
+}
--- /dev/null
- int minO, minC, H, N, C, O, Cn[MAXCHI+3];
+/*
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * 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 the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gromacs Runs On Most of All Computer Systems
+ */
+
+#ifndef _gstat_h
+#define _gstat_h
+
+#include "typedefs.h"
+#include "statutil.h"
+#include "mshift.h"
+#include "rmpbc.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
+};
+
+/* must correspond with 'leg' g_chi.c:727 */
+enum {
+ edPhi = 0, edPsi, edOmega, edChi1, edChi2, edChi3, edChi4, edChi5, edChi6, edMax
+};
+
+enum {
+ edPrintST = 0, edPrintRO
+};
+
+#define NHISTO 360
+#define NONCHI 3
+#define MAXCHI edMax-NONCHI
+#define NROT 4 /* number of rotamers: 1=g(-), 2=t, 3=g(+), 0=other */
+
+typedef struct {
++ int minCalpha, minC, H, N, C, O, Cn[MAXCHI+3];
+} t_dihatms; /* Cn[0]=N, Cn[1]=Ca, Cn[2]=Cb etc. */
+
+typedef struct {
+ char name[12];
+ int resnr;
+ int index; /* Index for amino acids (histograms) */
+ int j0[edMax]; /* Index in dih array (phi angle is first...) */
+ t_dihatms atm;
+ int b[edMax];
+ int ntr[edMax];
+ real S2[edMax];
+ real rot_occ[edMax][NROT];
+
+} 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, int nskip);
+/*
+ * 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 */
+ real offset; /* Offset for dihedral angle in histogram (e.g. -M_PI/3) */
+ real Jc; /* Resulting Jcoupling */
+ real Jcsig; /* Standard deviation in Jc */
+} t_karplus;
+
+void calc_distribution_props(int nh, int histo[],
+ real start, int nkkk, t_karplus kkk[],
+ real *S2);
+/* This routine takes a dihedral distribution and calculates
+ * coupling constants and dihedral order parameters of it.
+ *
+ * nh is the number of points
+ * histo is the array of datapoints which is assumed to span
+ * 2 M_PI radians
+ * start is the starting angle of the histogram, this can be either 0
+ * or -M_PI
+ * nkkk is the number of karplus sets (multiple coupling constants may be
+ * derived from a single angle)
+ * kkk are the constants for calculating J coupling constants using a
+ * Karplus equation according to
+ *
+ * 2
+ * J = A cos theta + B cos theta + C
+ *
+ * where theta is phi - offset (phi is the angle in the histogram)
+ * offset is subtracted from phi before substitution in the Karplus
+ * equation
+ * S2 is the resulting dihedral order parameter
+ *
+ */
+
+
+/***********************************************
+ *
+ * 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,
+ const output_env_t oenv);
+/*
+ * Analyse dihedral transitions, by counting transitions per dihedral
+ * and per frame. The total number of transitions is printed to
+ * stderr, as well as the average time between transitions.
+ *
+ * is wrapper to low_ana_dih_trans, which also passes in and out the
+ number of transitions per dihedral per residue. that uses struc dlist
+ which is not external, so pp2shift.h must be included.
+
+ * Dihedrals are supposed to be in either of three minima,
+ * (trans, gauche+, gauche-)
+ *
+ * fn_trans output file name for #transitions per timeframe
+ * fn_histo output file name for transition time histogram
+ * dih the actual dihedral angles
+ * nframes number of times frames
+ * nangles number of angles
+ * grpname a string for the header of plots
+ * time array (size nframes) of times of trajectory frames
+ * bRb determines whether the polymer convention is used
+ * (trans = 0)
+ */
+
+void low_ana_dih_trans(gmx_bool bTrans, const char *fn_trans,
+ gmx_bool bHisto, const char *fn_histo, int maxchi,
+ real **dih, int nlist, t_dlist dlist[],
+ int nframes, int nangles, const char *grpname,
+ int multiplicity[], real *time, gmx_bool bRb,
+ real core_frac, const output_env_t oenv);
+/* as above but passes dlist so can copy occupancies into it, and multiplicity[]
+ * (1..nangles, corresp to dih[this][], so can have non-3 multiplicity of
+ * rotamers. Also production of xvg output files is conditional
+ * and the fractional width of each rotamer can be set ie for a 3 fold
+ * dihedral with core_frac = 0.5 only the central 60 degrees is assigned
+ * to each rotamer, the rest goes to rotamer zero */
+
+
+
+void read_ang_dih(const char *trj_fn,
+ gmx_bool bAngles, gmx_bool bSaveAll, gmx_bool bRb, gmx_bool bPBC,
+ int maxangstat, int angstat[],
+ int *nframes, real **time,
+ int isize, atom_id index[],
+ real **trans_frac,
+ real **aver_angle,
+ real *dih[],
+ const output_env_t oenv);
+/*
+ * 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)
+ * bPBC compute angles module 2 Pi
+ * maxangstat number of entries in distribution array
+ * angstat angle distribution
+ * *nframes number of frames read
+ * time simulation time at each time frame
+ * isize number of entries in the index, when angles 3*number of angles
+ * else 4*number of angles
+ * index atom numbers that define the angles or dihedrals
+ * (i,j,k) resp (i,j,k,l)
+ * trans_frac number of dihedrals in trans
+ * aver_angle average angle at each time frame
+ * dih all angles at each time frame
+ */
+
+void make_histo(FILE *log,
+ int ndata, real data[], int npoints, int histo[],
+ real minx, real maxx);
+/*
+ * Make a histogram from data. The min and max of the data array can
+ * be determined (if minx == 0 and maxx == 0)
+ * and the index in the histogram is computed from
+ * ind = npoints/(max(data) - min(data))
+ *
+ * log write error output to this file
+ * ndata number of points in data
+ * data data points
+ * npoints number of points in histogram
+ * histo histogram array. This is NOT set to zero, to allow you
+ * to add multiple histograms
+ * minx start of the histogram
+ * maxx end of the histogram
+ * if both are 0, these values are computed by the routine itself
+ */
+
+void normalize_histo(int npoints, int histo[], real dx, real normhisto[]);
+/*
+ * Normalize a histogram so that the integral over the histo is 1
+ *
+ * npoints number of points in the histo array
+ * histo input histogram
+ * dx distance between points on the X-axis
+ * 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,
+ int nlist, t_dlist dlist[], real **dih);
+
+gmx_bool has_dihedral(int Dih, t_dlist *dl);
+
+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);
+
+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);
+
+int pr_trans(FILE *fp, int nl, t_dlist dl[], real dt, int Xi);
+
+void mk_chi_lookup (int **lookup, int maxchi, real **dih,
+ int nlist, t_dlist dlist[]);
+
+void mk_multiplicity_lookup (int *multiplicity, int maxchi, real **dih,
+ int nlist, t_dlist dlist[], int nangle);
+
+void get_chi_product_traj (real **dih, int nframes, int nangles,
+ int nlist, int maxchi, t_dlist dlist[],
+ real time[], int **lookup, int *multiplicity,
+ gmx_bool bRb, gmx_bool bNormalize,
+ real core_frac, gmx_bool bAll, const char *fnall,
+ const output_env_t oenv);
+
+void print_one (const output_env_t oenv, const char *base,
+ const char *name,
+ const char *title, const char *ylabel, int nf,
+ real time[], real data[]);
+
+/* Routines from g_hbond */
+void analyse_corr(int n, real t[], real ct[], real nt[], real kt[],
+ real sigma_ct[], real sigma_nt[], real sigma_kt[],
+ real fit_start, real temp, real smooth_tail_start,
+ const output_env_t oenv);
+
+void compute_derivative(int nn, real x[], real y[], real dydx[]);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
--- /dev/null
- void nbnxn_cuda_init_const(nbnxn_cuda_ptr_t p_cu_nb,
- const interaction_const_t *ic,
- const nonbonded_verlet_t *nbv) FUNC_TERM
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2012, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+ *
+ * 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 the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
+#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"
+
+#ifdef GMX_GPU
+#define FUNC_TERM ;
+#define FUNC_QUALIFIER
+#else
+#define FUNC_TERM {}
+#define FUNC_QUALIFIER static
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*! Initializes the data structures related to CUDA nonbonded calculations. */
+FUNC_QUALIFIER
+void nbnxn_cuda_init(FILE *fplog,
+ nbnxn_cuda_ptr_t *p_cu_nb,
+ gmx_gpu_info_t *gpu_info, int my_gpu_index,
+ /* true of both local and non-local are don on GPU */
+ gmx_bool bLocalAndNonlocal) FUNC_TERM
+
+/*! Initializes simulation constant data. */
+FUNC_QUALIFIER
++void nbnxn_cuda_init_const(nbnxn_cuda_ptr_t cu_nb,
++ const interaction_const_t *ic,
++ const nonbonded_verlet_group_t *nbv_group) FUNC_TERM
+
+/*! Initializes pair-list data for GPU, called at every pair search step. */
+FUNC_QUALIFIER
+void nbnxn_cuda_init_pairlist(nbnxn_cuda_ptr_t cu_nb,
+ const nbnxn_pairlist_t *h_nblist,
+ int iloc) FUNC_TERM
+
+/*! Initializes atom-data on the GPU, called at every pair search step. */
+FUNC_QUALIFIER
+void nbnxn_cuda_init_atomdata(nbnxn_cuda_ptr_t cu_nb,
+ const nbnxn_atomdata_t *atomdata) FUNC_TERM
+
+/*! \brief Update parameters during PP-PME load balancing. */
+FUNC_QUALIFIER
+void nbnxn_cuda_pme_loadbal_update_param(nbnxn_cuda_ptr_t cu_nb,
+ const interaction_const_t *ic) FUNC_TERM
+
+/*! 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 cu_nb,
+ const nbnxn_atomdata_t *nbatom) FUNC_TERM
+
+/*! Clears GPU outputs: nonbonded force, shift force and energy. */
+FUNC_QUALIFIER
+void nbnxn_cuda_clear_outputs(nbnxn_cuda_ptr_t cu_nb,
+ int flags) FUNC_TERM
+
+/*! Frees all GPU resources used for the nonbonded calculations. */
+FUNC_QUALIFIER
+void nbnxn_cuda_free(FILE *fplog,
+ nbnxn_cuda_ptr_t cu_nb) FUNC_TERM
+
+/*! 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 cu_nb)
+#ifdef GMX_GPU
+;
+#else
+{
+ return NULL;
+}
+#endif
+
+/*! Resets nonbonded GPU timings. */
+FUNC_QUALIFIER
+void nbnxn_cuda_reset_timings(nbnxn_cuda_ptr_t cu_nb) FUNC_TERM
+
+/*! 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 cu_nb)
+#ifdef GMX_GPU
+;
+#else
+{
+ return -1;
+}
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+
+#undef FUNC_TERM
+#undef FUNC_QUALIFIER
+
+#endif /* NBNXN_CUDA_DATA_MGMT_H */
--- /dev/null
- * \param box Simulation box, needed to make group whole.
+/*
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * 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 the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
+/*! \file pull_rotation.h
+ *
+ * @brief Enforced rotation of protein parts or other groups of particles.
+ *
+ * This file contains routines that are used to enforce rotational motion
+ * upon a subgroup of particles.
+ *
+ */
+
+#ifndef _pull_rotation_h
+#define _pull_rotation_h
+
+#include "vec.h"
+#include "typedefs.h"
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+/*! \brief Initialize the enforced rotation groups.
+ *
+ * This routine does the memory allocation for various helper arrays, opens
+ * the output files etc.
+ *
+ * \param fplog General output file, normally md.log.
+ * \param ir Struct containing MD input parameters, among those
+ * also the enforced rotation parameters.
+ * \param nfile Number of entries in the fnm structure.
+ * \param fnm The filenames struct containing also the names
+ * of the rotation output files.
+ * \param cr Pointer to MPI communication data.
+ * \param x The positions of all MD particles.
- * \param fplog General output file, normally md.log.
++ * \param box The simulation box.
+ * \param mtop Molecular topology.
+ * \param oenv Needed to open the rotation output xvgr file.
+ * \param bVerbose Whether to print extra status information.
+ * \param Flags Flags passed over from main, used to determine
+ * whether or not we are doing a rerun.
+ */
+extern void init_rot(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
+ t_commrec *cr, rvec *x, matrix box, gmx_mtop_t *mtop, const output_env_t oenv,
+ gmx_bool bVerbose, unsigned long Flags);
+
+
+/*! \brief Make a selection of the home atoms for all enforced rotation groups.
+ *
+ * This routine is similar to dd_make_local_pull_groups, but works only with
+ * domain decomposition. It should be called at every domain decomposition.
+ *
+ * \param dd Structure containing domain decomposition data.
+ * \param rot Pointer to all the enforced rotation data.
+ */
+extern void dd_make_local_rotation_groups(gmx_domdec_t *dd, t_rot *rot);
+
+
+/*! \brief Calculation of the enforced rotation potential.
+ *
+ * This is the main enforced rotation module which is called during every time
+ * step. Here the rotation potential as well as the resulting forces are
+ * calculated.
+ *
+ * \param cr Pointer to MPI communication data.
+ * \param ir Struct containing MD input parameters, among those
+ * \param box Simulation box, needed to make group whole.
+ * \param x The positions of all the local particles.
+ * \param t Time.
+ * \param step The time step.
+ * \param wcycle During the potential calculation the wallcycles are
+ * counted. Later they enter the dynamic load balancing.
+ * \param bNS After domain decomposition / neighborsearching several
+ * local arrays have to be updated (masses, shifts)
+ */
+extern void do_rotation(t_commrec *cr, t_inputrec *ir, matrix box, rvec x[], real t,
+ gmx_large_int_t step, gmx_wallcycle_t wcycle, gmx_bool bNS);
+
+
+/*! \brief Add the enforced rotation forces to the official force array.
+ *
+ * Adds the forces from enforced rotation potential to the local forces and
+ * sums up the contributions to the rotation potential from all the nodes. Since
+ * this needs communication, this routine should be called after the SR forces
+ * have been evaluated (in order not to spoil cycle counts).
+ * This routine also outputs data to the various rotation output files (e.g.
+ * the potential, the angle of the group, torques and more).
+ *
+ * \param rot Pointer to all the enforced rotation data.
+ * \param f The local forces to which the rotational forces have
+ * to be added.
+ * \param cr Pointer to MPI communication data.
+ * \param step The time step, used for output.
+ * \param t Time, used for output.
+ */
+extern real add_rot_forces(t_rot *rot, rvec f[], t_commrec *cr, gmx_large_int_t step, real t);
+
+
+/*! \brief Close the enforced rotation output files.
+ *
- extern void finish_rot(FILE *fplog, t_rot *rot);
+ * \param rot Pointer to all the enforced rotation data.
+ */
++extern void finish_rot(t_rot *rot);
+
+
+#ifdef __cplusplus
+}
+#endif
+
+
+#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2012, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+ *
+ * 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 the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * GROwing Monsters And Cloning Shrimps
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#ifdef GMX_CRAY_XT3
+#include <catamount/dclock.h>
+#endif
+
+
+#include <stdio.h>
+#include <time.h>
+#ifdef HAVE_SYS_TIME_H
+#include <sys/time.h>
+#endif
+#include <math.h>
+#include "typedefs.h"
+#include "string2.h"
+#include "gmxfio.h"
+#include "smalloc.h"
+#include "names.h"
+#include "confio.h"
+#include "mvdata.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 "trnio.h"
+#include "xtcio.h"
+#include "copyrite.h"
+#include "gmx_random.h"
+#include "domdec.h"
+#include "partdec.h"
+#include "gmx_wallcycle.h"
+#include "macros.h"
+
+#include "gromacs/utility/gmxmpi.h"
+
+void GenerateGibbsProbabilities(real *ene, real *p_k, real *pks, int minfep, int maxfep)
+{
+
+ int i;
+ real maxene;
+
+ *pks = 0.0;
+ maxene = ene[minfep];
+ /* find the maximum value */
+ for (i = minfep; i <= maxfep; i++)
+ {
+ if (ene[i] > maxene)
+ {
+ maxene = ene[i];
+ }
+ }
+ /* find the denominator */
+ for (i = minfep; i <= maxfep; i++)
+ {
+ *pks += exp(ene[i]-maxene);
+ }
+ /*numerators*/
+ for (i = minfep; i <= maxfep; i++)
+ {
+ p_k[i] = exp(ene[i]-maxene) / *pks;
+ }
+}
+
+void GenerateWeightedGibbsProbabilities(real *ene, real *p_k, real *pks, int nlim, real *nvals, real delta)
+{
+
+ int i;
+ real maxene;
+ real *nene;
+ *pks = 0.0;
+
+ snew(nene, nlim);
+ for (i = 0; i < nlim; i++)
+ {
+ if (nvals[i] == 0)
+ {
+ /* add the delta, since we need to make sure it's greater than zero, and
+ we need a non-arbitrary number? */
+ nene[i] = ene[i] + log(nvals[i]+delta);
+ }
+ else
+ {
+ nene[i] = ene[i] + log(nvals[i]);
+ }
+ }
+
+ /* find the maximum value */
+ maxene = nene[0];
+ for (i = 0; i < nlim; i++)
+ {
+ if (nene[i] > maxene)
+ {
+ maxene = nene[i];
+ }
+ }
+
+ /* subtract off the maximum, avoiding overflow */
+ for (i = 0; i < nlim; i++)
+ {
+ nene[i] -= maxene;
+ }
+
+ /* find the denominator */
+ for (i = 0; i < nlim; i++)
+ {
+ *pks += exp(nene[i]);
+ }
+
+ /*numerators*/
+ for (i = 0; i < nlim; i++)
+ {
+ p_k[i] = exp(nene[i]) / *pks;
+ }
+ sfree(nene);
+}
+
+real do_logsum(int N, real *a_n)
+{
+
+ /* RETURN VALUE */
+ /* log(\sum_{i=0}^(N-1) exp[a_n]) */
+ real maxarg;
+ real sum;
+ int i;
+ real logsum;
+ /* compute maximum argument to exp(.) */
+
+ maxarg = a_n[0];
+ for (i = 1; i < N; i++)
+ {
+ maxarg = max(maxarg, a_n[i]);
+ }
+
+ /* compute sum of exp(a_n - maxarg) */
+ sum = 0.0;
+ for (i = 0; i < N; i++)
+ {
+ sum = sum + exp(a_n[i] - maxarg);
+ }
+
+ /* compute log sum */
+ logsum = log(sum) + maxarg;
+ return logsum;
+}
+
+int FindMinimum(real *min_metric, int N)
+{
+
+ real min_val;
+ int min_nval, nval;
+
+ min_nval = 0;
+ min_val = min_metric[0];
+
+ for (nval = 0; nval < N; nval++)
+ {
+ if (min_metric[nval] < min_val)
+ {
+ min_val = min_metric[nval];
+ min_nval = nval;
+ }
+ }
+ return min_nval;
+}
+
+static gmx_bool CheckHistogramRatios(int nhisto, real *histo, real ratio)
+{
+
+ int i;
+ real nmean;
+ gmx_bool bIfFlat;
+
+ nmean = 0;
+ for (i = 0; i < nhisto; i++)
+ {
+ nmean += histo[i];
+ }
+
+ if (nmean == 0)
+ {
+ /* no samples! is bad!*/
+ bIfFlat = FALSE;
+ return bIfFlat;
+ }
+ nmean /= (real)nhisto;
+
+ bIfFlat = TRUE;
+ for (i = 0; i < nhisto; i++)
+ {
+ /* make sure that all points are in the ratio < x < 1/ratio range */
+ if (!((histo[i]/nmean < 1.0/ratio) && (histo[i]/nmean > ratio)))
+ {
+ bIfFlat = FALSE;
+ break;
+ }
+ }
+ return bIfFlat;
+}
+
+static gmx_bool CheckIfDoneEquilibrating(int nlim, t_expanded *expand, df_history_t *dfhist, gmx_large_int_t step)
+{
+
+ int i, totalsamples;
+ gmx_bool bDoneEquilibrating = TRUE;
+ gmx_bool bIfFlat;
+
+ /* assume we have equilibrated the weights, then check to see if any of the conditions are not met */
+
+ /* calculate the total number of samples */
+ switch (expand->elmceq)
+ {
+ case elmceqNO:
+ /* We have not equilibrated, and won't, ever. */
+ return FALSE;
+ case elmceqYES:
+ /* we have equilibrated -- we're done */
+ return TRUE;
+ case elmceqSTEPS:
+ /* first, check if we are equilibrating by steps, if we're still under */
+ if (step < expand->equil_steps)
+ {
+ bDoneEquilibrating = FALSE;
+ }
+ break;
+ case elmceqSAMPLES:
+ totalsamples = 0;
+ for (i = 0; i < nlim; i++)
+ {
+ totalsamples += dfhist->n_at_lam[i];
+ }
+ if (totalsamples < expand->equil_samples)
+ {
+ bDoneEquilibrating = FALSE;
+ }
+ break;
+ case elmceqNUMATLAM:
+ for (i = 0; i < nlim; i++)
+ {
+ if (dfhist->n_at_lam[i] < expand->equil_n_at_lam) /* we are still doing the initial sweep, so we're definitely not
+ done equilibrating*/
+ {
+ bDoneEquilibrating = FALSE;
+ break;
+ }
+ }
+ break;
+ case elmceqWLDELTA:
+ if (EWL(expand->elamstats)) /* This check is in readir as well, but
+ just to be sure */
+ {
+ if (dfhist->wl_delta > expand->equil_wl_delta)
+ {
+ bDoneEquilibrating = FALSE;
+ }
+ }
+ break;
+ case elmceqRATIO:
+ /* we can use the flatness as a judge of good weights, as long as
+ we're not doing minvar, or Wang-Landau.
+ But turn off for now until we figure out exactly how we do this.
+ */
+
+ if (!(EWL(expand->elamstats) || expand->elamstats == elamstatsMINVAR))
+ {
+ /* we want to use flatness -avoiding- the forced-through samples. Plus, we need to convert to
+ floats for this histogram function. */
+
+ real *modhisto;
+ snew(modhisto, nlim);
+ for (i = 0; i < nlim; i++)
+ {
+ modhisto[i] = 1.0*(dfhist->n_at_lam[i]-expand->lmc_forced_nstart);
+ }
+ bIfFlat = CheckHistogramRatios(nlim, modhisto, expand->equil_ratio);
+ sfree(modhisto);
+ if (!bIfFlat)
+ {
+ bDoneEquilibrating = FALSE;
+ }
+ }
+ default:
+ bDoneEquilibrating = TRUE;
+ }
+ /* one last case to go though, if we are doing slow growth to get initial values, we haven't finished equilibrating */
+
+ if (expand->lmc_forced_nstart > 0)
+ {
+ for (i = 0; i < nlim; i++)
+ {
+ if (dfhist->n_at_lam[i] < expand->lmc_forced_nstart) /* we are still doing the initial sweep, so we're definitely not
+ done equilibrating*/
+ {
+ bDoneEquilibrating = FALSE;
+ break;
+ }
+ }
+ }
+ return bDoneEquilibrating;
+}
+
+static gmx_bool UpdateWeights(int nlim, t_expanded *expand, df_history_t *dfhist,
+ int fep_state, real *scaled_lamee, real *weighted_lamee, gmx_large_int_t step)
+{
+ real maxdiff = 0.000000001;
+ gmx_bool bSufficientSamples;
+ int i, k, n, nz, indexi, indexk, min_n, max_n, nlam, totali;
+ int n0, np1, nm1, nval, min_nvalm, min_nvalp, maxc;
+ real omega_m1_0, omega_p1_m1, omega_m1_p1, omega_p1_0, clam_osum;
+ real de, de_function, dr, denom, maxdr, pks = 0;
+ real min_val, cnval, zero_sum_weights;
+ real *omegam_array, *weightsm_array, *omegap_array, *weightsp_array, *varm_array, *varp_array, *dwp_array, *dwm_array;
+ real clam_varm, clam_varp, clam_weightsm, clam_weightsp, clam_minvar;
+ real *lam_weights, *lam_minvar_corr, *lam_variance, *lam_dg, *p_k;
+ real *numweighted_lamee, *logfrac;
+ int *nonzero;
+ real chi_m1_0, chi_p1_0, chi_m2_0, chi_p2_0, chi_p1_m1, chi_p2_m1, chi_m1_p1, chi_m2_p1;
+
+ /* if we have equilibrated the weights, exit now */
+ if (dfhist->bEquil)
+ {
+ return FALSE;
+ }
+
+ if (CheckIfDoneEquilibrating(nlim, expand, dfhist, step))
+ {
+ dfhist->bEquil = TRUE;
+ /* zero out the visited states so we know how many equilibrated states we have
+ from here on out.*/
+ for (i = 0; i < nlim; i++)
+ {
+ dfhist->n_at_lam[i] = 0;
+ }
+ return TRUE;
+ }
+
+ /* If we reached this far, we have not equilibrated yet, keep on
+ going resetting the weights */
+
+ if (EWL(expand->elamstats))
+ {
+ if (expand->elamstats == elamstatsWL) /* Standard Wang-Landau */
+ {
+ dfhist->sum_weights[fep_state] -= dfhist->wl_delta;
+ dfhist->wl_histo[fep_state] += 1.0;
+ }
+ else if (expand->elamstats == elamstatsWWL) /* Weighted Wang-Landau */
+ {
+ snew(p_k, nlim);
+
+ /* first increment count */
+ GenerateGibbsProbabilities(weighted_lamee, p_k, &pks, 0, nlim-1);
+ for (i = 0; i < nlim; i++)
+ {
+ dfhist->wl_histo[i] += p_k[i];
+ }
+
+ /* then increment weights (uses count) */
+ pks = 0.0;
+ GenerateWeightedGibbsProbabilities(weighted_lamee, p_k, &pks, nlim, dfhist->wl_histo, dfhist->wl_delta);
+
+ for (i = 0; i < nlim; i++)
+ {
+ dfhist->sum_weights[i] -= dfhist->wl_delta*p_k[i];
+ }
+ /* Alternate definition, using logarithms. Shouldn't make very much difference! */
+ /*
+ real di;
+ for (i=0;i<nlim;i++)
+ {
+ di = 1+dfhist->wl_delta*p_k[i];
+ dfhist->sum_weights[i] -= log(di);
+ }
+ */
+ sfree(p_k);
+ }
+
+ zero_sum_weights = dfhist->sum_weights[0];
+ for (i = 0; i < nlim; i++)
+ {
+ dfhist->sum_weights[i] -= zero_sum_weights;
+ }
+ }
+
+ if (expand->elamstats == elamstatsBARKER || expand->elamstats == elamstatsMETROPOLIS || expand->elamstats == elamstatsMINVAR)
+ {
+
+ de_function = 0; /* to get rid of warnings, but this value will not be used because of the logic */
+ maxc = 2*expand->c_range+1;
+
+ snew(lam_dg, nlim);
+ snew(lam_variance, nlim);
+
+ snew(omegap_array, maxc);
+ snew(weightsp_array, maxc);
+ snew(varp_array, maxc);
+ snew(dwp_array, maxc);
+
+ snew(omegam_array, maxc);
+ snew(weightsm_array, maxc);
+ snew(varm_array, maxc);
+ snew(dwm_array, maxc);
+
+ /* unpack the current lambdas -- we will only update 2 of these */
+
+ for (i = 0; i < nlim-1; i++)
+ { /* only through the second to last */
+ lam_dg[i] = dfhist->sum_dg[i+1] - dfhist->sum_dg[i];
+ lam_variance[i] = pow(dfhist->sum_variance[i+1], 2) - pow(dfhist->sum_variance[i], 2);
+ }
+
+ /* accumulate running averages */
+ for (nval = 0; nval < maxc; nval++)
+ {
+ /* constants for later use */
+ cnval = (real)(nval-expand->c_range);
+ /* actually, should be able to rewrite it w/o exponential, for better numerical stability */
+ if (fep_state > 0)
+ {
+ de = exp(cnval - (scaled_lamee[fep_state]-scaled_lamee[fep_state-1]));
+ if (expand->elamstats == elamstatsBARKER || expand->elamstats == elamstatsMINVAR)
+ {
+ de_function = 1.0/(1.0+de);
+ }
+ else if (expand->elamstats == elamstatsMETROPOLIS)
+ {
+ if (de < 1.0)
+ {
+ de_function = 1.0;
+ }
+ else
+ {
+ de_function = 1.0/de;
+ }
+ }
+ dfhist->accum_m[fep_state][nval] += de_function;
+ dfhist->accum_m2[fep_state][nval] += de_function*de_function;
+ }
+
+ if (fep_state < nlim-1)
+ {
+ de = exp(-cnval + (scaled_lamee[fep_state+1]-scaled_lamee[fep_state]));
+ if (expand->elamstats == elamstatsBARKER || expand->elamstats == elamstatsMINVAR)
+ {
+ de_function = 1.0/(1.0+de);
+ }
+ else if (expand->elamstats == elamstatsMETROPOLIS)
+ {
+ if (de < 1.0)
+ {
+ de_function = 1.0;
+ }
+ else
+ {
+ de_function = 1.0/de;
+ }
+ }
+ dfhist->accum_p[fep_state][nval] += de_function;
+ dfhist->accum_p2[fep_state][nval] += de_function*de_function;
+ }
+
+ /* Metropolis transition and Barker transition (unoptimized Bennett) acceptance weight determination */
+
+ n0 = dfhist->n_at_lam[fep_state];
+ if (fep_state > 0)
+ {
+ nm1 = dfhist->n_at_lam[fep_state-1];
+ }
+ else
+ {
+ nm1 = 0;
+ }
+ if (fep_state < nlim-1)
+ {
+ np1 = dfhist->n_at_lam[fep_state+1];
+ }
+ else
+ {
+ np1 = 0;
+ }
+
+ /* logic SHOULD keep these all set correctly whatever the logic, but apparently it can't figure it out. */
+ chi_m1_0 = chi_p1_0 = chi_m2_0 = chi_p2_0 = chi_p1_m1 = chi_p2_m1 = chi_m1_p1 = chi_m2_p1 = 0;
+
+ if (n0 > 0)
+ {
+ chi_m1_0 = dfhist->accum_m[fep_state][nval]/n0;
+ chi_p1_0 = dfhist->accum_p[fep_state][nval]/n0;
+ chi_m2_0 = dfhist->accum_m2[fep_state][nval]/n0;
+ chi_p2_0 = dfhist->accum_p2[fep_state][nval]/n0;
+ }
+
+ if ((fep_state > 0 ) && (nm1 > 0))
+ {
+ chi_p1_m1 = dfhist->accum_p[fep_state-1][nval]/nm1;
+ chi_p2_m1 = dfhist->accum_p2[fep_state-1][nval]/nm1;
+ }
+
+ if ((fep_state < nlim-1) && (np1 > 0))
+ {
+ chi_m1_p1 = dfhist->accum_m[fep_state+1][nval]/np1;
+ chi_m2_p1 = dfhist->accum_m2[fep_state+1][nval]/np1;
+ }
+
+ omega_m1_0 = 0;
+ omega_p1_0 = 0;
+ clam_weightsm = 0;
+ clam_weightsp = 0;
+ clam_varm = 0;
+ clam_varp = 0;
+
+ if (fep_state > 0)
+ {
+ if (n0 > 0)
+ {
+ omega_m1_0 = chi_m2_0/(chi_m1_0*chi_m1_0) - 1.0;
+ }
+ if (nm1 > 0)
+ {
+ omega_p1_m1 = chi_p2_m1/(chi_p1_m1*chi_p1_m1) - 1.0;
+ }
+ if ((n0 > 0) && (nm1 > 0))
+ {
+ clam_weightsm = (log(chi_m1_0) - log(chi_p1_m1)) + cnval;
+ clam_varm = (1.0/n0)*(omega_m1_0) + (1.0/nm1)*(omega_p1_m1);
+ }
+ }
+
+ if (fep_state < nlim-1)
+ {
+ if (n0 > 0)
+ {
+ omega_p1_0 = chi_p2_0/(chi_p1_0*chi_p1_0) - 1.0;
+ }
+ if (np1 > 0)
+ {
+ omega_m1_p1 = chi_m2_p1/(chi_m1_p1*chi_m1_p1) - 1.0;
+ }
+ if ((n0 > 0) && (np1 > 0))
+ {
+ clam_weightsp = (log(chi_m1_p1) - log(chi_p1_0)) + cnval;
+ clam_varp = (1.0/np1)*(omega_m1_p1) + (1.0/n0)*(omega_p1_0);
+ }
+ }
+
+ if (n0 > 0)
+ {
+ omegam_array[nval] = omega_m1_0;
+ }
+ else
+ {
+ omegam_array[nval] = 0;
+ }
+ weightsm_array[nval] = clam_weightsm;
+ varm_array[nval] = clam_varm;
+ if (nm1 > 0)
+ {
+ dwm_array[nval] = fabs( (cnval + log((1.0*n0)/nm1)) - lam_dg[fep_state-1] );
+ }
+ else
+ {
+ dwm_array[nval] = fabs( cnval - lam_dg[fep_state-1] );
+ }
+
+ if (n0 > 0)
+ {
+ omegap_array[nval] = omega_p1_0;
+ }
+ else
+ {
+ omegap_array[nval] = 0;
+ }
+ weightsp_array[nval] = clam_weightsp;
+ varp_array[nval] = clam_varp;
+ if ((np1 > 0) && (n0 > 0))
+ {
+ dwp_array[nval] = fabs( (cnval + log((1.0*np1)/n0)) - lam_dg[fep_state] );
+ }
+ else
+ {
+ dwp_array[nval] = fabs( cnval - lam_dg[fep_state] );
+ }
+
+ }
+
+ /* find the C's closest to the old weights value */
+
+ min_nvalm = FindMinimum(dwm_array, maxc);
+ omega_m1_0 = omegam_array[min_nvalm];
+ clam_weightsm = weightsm_array[min_nvalm];
+ clam_varm = varm_array[min_nvalm];
+
+ min_nvalp = FindMinimum(dwp_array, maxc);
+ omega_p1_0 = omegap_array[min_nvalp];
+ clam_weightsp = weightsp_array[min_nvalp];
+ clam_varp = varp_array[min_nvalp];
+
+ clam_osum = omega_m1_0 + omega_p1_0;
+ clam_minvar = 0;
+ if (clam_osum > 0)
+ {
+ clam_minvar = 0.5*log(clam_osum);
+ }
+
+ if (fep_state > 0)
+ {
+ lam_dg[fep_state-1] = clam_weightsm;
+ lam_variance[fep_state-1] = clam_varm;
+ }
+
+ if (fep_state < nlim-1)
+ {
+ lam_dg[fep_state] = clam_weightsp;
+ lam_variance[fep_state] = clam_varp;
+ }
+
+ if (expand->elamstats == elamstatsMINVAR)
+ {
+ bSufficientSamples = TRUE;
+ /* make sure they are all past a threshold */
+ for (i = 0; i < nlim; i++)
+ {
+ if (dfhist->n_at_lam[i] < expand->minvarmin)
+ {
+ bSufficientSamples = FALSE;
+ }
+ }
+ if (bSufficientSamples)
+ {
+ dfhist->sum_minvar[fep_state] = clam_minvar;
+ if (fep_state == 0)
+ {
+ for (i = 0; i < nlim; i++)
+ {
+ dfhist->sum_minvar[i] += (expand->minvar_const-clam_minvar);
+ }
+ expand->minvar_const = clam_minvar;
+ dfhist->sum_minvar[fep_state] = 0.0;
+ }
+ else
+ {
+ dfhist->sum_minvar[fep_state] -= expand->minvar_const;
+ }
+ }
+ }
+
+ /* we need to rezero minvar now, since it could change at fep_state = 0 */
+ dfhist->sum_dg[0] = 0.0;
+ dfhist->sum_variance[0] = 0.0;
+ dfhist->sum_weights[0] = dfhist->sum_dg[0] + dfhist->sum_minvar[0]; /* should be zero */
+
+ for (i = 1; i < nlim; i++)
+ {
+ dfhist->sum_dg[i] = lam_dg[i-1] + dfhist->sum_dg[i-1];
+ dfhist->sum_variance[i] = sqrt(lam_variance[i-1] + pow(dfhist->sum_variance[i-1], 2));
+ dfhist->sum_weights[i] = dfhist->sum_dg[i] + dfhist->sum_minvar[i];
+ }
+
+ sfree(lam_dg);
+ sfree(lam_variance);
+
+ sfree(omegam_array);
+ sfree(weightsm_array);
+ sfree(varm_array);
+ sfree(dwm_array);
+
+ sfree(omegap_array);
+ sfree(weightsp_array);
+ sfree(varp_array);
+ sfree(dwp_array);
+ }
+ return FALSE;
+}
+
+static int ChooseNewLambda(FILE *log, int nlim, t_expanded *expand, df_history_t *dfhist, int fep_state, real *weighted_lamee, real *p_k, gmx_rng_t rng)
+{
+ /* Choose new lambda value, and update transition matrix */
+
+ int i, ifep, jfep, minfep, maxfep, lamnew, lamtrial, starting_fep_state;
+ real r1, r2, pks, de_old, de_new, de, trialprob, tprob = 0;
+ real **Tij;
+ real *propose, *accept, *remainder;
+ real sum, pnorm;
+ gmx_bool bRestricted;
+
+ starting_fep_state = fep_state;
+ lamnew = fep_state; /* so that there is a default setting -- stays the same */
+
+ if (!EWL(expand->elamstats)) /* ignore equilibrating the weights if using WL */
+ {
+ if ((expand->lmc_forced_nstart > 0) && (dfhist->n_at_lam[nlim-1] <= expand->lmc_forced_nstart))
+ {
+ /* Use a marching method to run through the lambdas and get preliminary free energy data,
+ before starting 'free' sampling. We start free sampling when we have enough at each lambda */
+
+ /* if we have enough at this lambda, move on to the next one */
+
+ if (dfhist->n_at_lam[fep_state] == expand->lmc_forced_nstart)
+ {
+ lamnew = fep_state+1;
+ if (lamnew == nlim) /* whoops, stepped too far! */
+ {
+ lamnew -= 1;
+ }
+ }
+ else
+ {
+ lamnew = fep_state;
+ }
+ return lamnew;
+ }
+ }
+
+ snew(propose, nlim);
+ snew(accept, nlim);
+ snew(remainder, nlim);
+
+ for (i = 0; i < expand->lmc_repeats; i++)
+ {
+
+ for (ifep = 0; ifep < nlim; ifep++)
+ {
+ propose[ifep] = 0;
+ accept[ifep] = 0;
+ }
+
+ if ((expand->elmcmove == elmcmoveGIBBS) || (expand->elmcmove == elmcmoveMETGIBBS))
+ {
+ bRestricted = TRUE;
+ /* use the Gibbs sampler, with restricted range */
+ if (expand->gibbsdeltalam < 0)
+ {
+ minfep = 0;
+ maxfep = nlim-1;
+ bRestricted = FALSE;
+ }
+ else
+ {
+ minfep = fep_state - expand->gibbsdeltalam;
+ maxfep = fep_state + expand->gibbsdeltalam;
+ if (minfep < 0)
+ {
+ minfep = 0;
+ }
+ if (maxfep > nlim-1)
+ {
+ maxfep = nlim-1;
+ }
+ }
+
+ GenerateGibbsProbabilities(weighted_lamee, p_k, &pks, minfep, maxfep);
+
+ if (expand->elmcmove == elmcmoveGIBBS)
+ {
+ for (ifep = minfep; ifep <= maxfep; ifep++)
+ {
+ propose[ifep] = p_k[ifep];
+ accept[ifep] = 1.0;
+ }
+ /* Gibbs sampling */
+ r1 = gmx_rng_uniform_real(rng);
+ for (lamnew = minfep; lamnew <= maxfep; lamnew++)
+ {
+ if (r1 <= p_k[lamnew])
+ {
+ break;
+ }
+ r1 -= p_k[lamnew];
+ }
+ }
+ else if (expand->elmcmove == elmcmoveMETGIBBS)
+ {
+
+ /* Metropolized Gibbs sampling */
+ for (ifep = minfep; ifep <= maxfep; ifep++)
+ {
+ remainder[ifep] = 1 - p_k[ifep];
+ }
+
+ /* find the proposal probabilities */
+
+ if (remainder[fep_state] == 0)
+ {
+ /* only the current state has any probability */
+ /* we have to stay at the current state */
+ lamnew = fep_state;
+ }
+ else
+ {
+ for (ifep = minfep; ifep <= maxfep; ifep++)
+ {
+ if (ifep != fep_state)
+ {
+ propose[ifep] = p_k[ifep]/remainder[fep_state];
+ }
+ else
+ {
+ propose[ifep] = 0;
+ }
+ }
+
+ r1 = gmx_rng_uniform_real(rng);
+ for (lamtrial = minfep; lamtrial <= maxfep; lamtrial++)
+ {
+ pnorm = p_k[lamtrial]/remainder[fep_state];
+ if (lamtrial != fep_state)
+ {
+ if (r1 <= pnorm)
+ {
+ break;
+ }
+ r1 -= pnorm;
+ }
+ }
+
+ /* we have now selected lamtrial according to p(lamtrial)/1-p(fep_state) */
+ tprob = 1.0;
+ /* trial probability is min{1,\frac{1 - p(old)}{1-p(new)} MRS 1/8/2008 */
+ trialprob = (remainder[fep_state])/(remainder[lamtrial]);
+ if (trialprob < tprob)
+ {
+ tprob = trialprob;
+ }
+ r2 = gmx_rng_uniform_real(rng);
+ if (r2 < tprob)
+ {
+ lamnew = lamtrial;
+ }
+ else
+ {
+ lamnew = fep_state;
+ }
+ }
+
+ /* now figure out the acceptance probability for each */
+ for (ifep = minfep; ifep <= maxfep; ifep++)
+ {
+ tprob = 1.0;
+ if (remainder[ifep] != 0)
+ {
+ trialprob = (remainder[fep_state])/(remainder[ifep]);
+ }
+ else
+ {
+ trialprob = 1.0; /* this state is the only choice! */
+ }
+ if (trialprob < tprob)
+ {
+ tprob = trialprob;
+ }
+ /* probability for fep_state=0, but that's fine, it's never proposed! */
+ accept[ifep] = tprob;
+ }
+ }
+
+ if (lamnew > maxfep)
+ {
+ /* it's possible some rounding is failing */
+ if (remainder[fep_state] < 2.0e-15)
+ {
+ /* probably numerical rounding error -- no state other than the original has weight */
+ lamnew = fep_state;
+ }
+ else
+ {
+ /* probably not a numerical issue */
+ int loc = 0;
+ int nerror = 200+(maxfep-minfep+1)*60;
+ char *errorstr;
+ snew(errorstr, nerror);
+ /* if its greater than maxfep, then something went wrong -- probably underflow in the calculation
+ of sum weights. Generated detailed info for failure */
+ loc += sprintf(errorstr, "Something wrong in choosing new lambda state with a Gibbs move -- probably underflow in weight determination.\nDenominator is: %3d%17.10e\n i dE numerator weights\n", 0, pks);
+ for (ifep = minfep; ifep <= maxfep; ifep++)
+ {
+ loc += sprintf(&errorstr[loc], "%3d %17.10e%17.10e%17.10e\n", ifep, weighted_lamee[ifep], p_k[ifep], dfhist->sum_weights[ifep]);
+ }
+ gmx_fatal(FARGS, errorstr);
+ }
+ }
+ }
+ else if ((expand->elmcmove == elmcmoveMETROPOLIS) || (expand->elmcmove == elmcmoveBARKER))
+ {
+ /* use the metropolis sampler with trial +/- 1 */
+ r1 = gmx_rng_uniform_real(rng);
+ if (r1 < 0.5)
+ {
+ if (fep_state == 0)
+ {
+ lamtrial = fep_state;
+ }
+ else
+ {
+ lamtrial = fep_state-1;
+ }
+ }
+ else
+ {
+ if (fep_state == nlim-1)
+ {
+ lamtrial = fep_state;
+ }
+ else
+ {
+ lamtrial = fep_state+1;
+ }
+ }
+
+ de = weighted_lamee[lamtrial] - weighted_lamee[fep_state];
+ if (expand->elmcmove == elmcmoveMETROPOLIS)
+ {
+ tprob = 1.0;
+ trialprob = exp(de);
+ if (trialprob < tprob)
+ {
+ tprob = trialprob;
+ }
+ propose[fep_state] = 0;
+ propose[lamtrial] = 1.0; /* note that this overwrites the above line if fep_state = ntrial, which only occurs at the ends */
+ accept[fep_state] = 1.0; /* doesn't actually matter, never proposed unless fep_state = ntrial, in which case it's 1.0 anyway */
+ accept[lamtrial] = tprob;
+
+ }
+ else if (expand->elmcmove == elmcmoveBARKER)
+ {
+ tprob = 1.0/(1.0+exp(-de));
+
+ propose[fep_state] = (1-tprob);
+ propose[lamtrial] += tprob; /* we add, to account for the fact that at the end, they might be the same point */
+ accept[fep_state] = 1.0;
+ accept[lamtrial] = 1.0;
+ }
+
+ r2 = gmx_rng_uniform_real(rng);
+ if (r2 < tprob)
+ {
+ lamnew = lamtrial;
+ }
+ else
+ {
+ lamnew = fep_state;
+ }
+ }
+
+ for (ifep = 0; ifep < nlim; ifep++)
+ {
+ dfhist->Tij[fep_state][ifep] += propose[ifep]*accept[ifep];
+ dfhist->Tij[fep_state][fep_state] += propose[ifep]*(1.0-accept[ifep]);
+ }
+ fep_state = lamnew;
+ }
+
+ dfhist->Tij_empirical[starting_fep_state][lamnew] += 1.0;
+
+ sfree(propose);
+ sfree(accept);
+ sfree(remainder);
+
+ return lamnew;
+}
+
+/* print out the weights to the log, along with current state */
+extern void PrintFreeEnergyInfoToFile(FILE *outfile, t_lambda *fep, t_expanded *expand, t_simtemp *simtemp, df_history_t *dfhist,
+ int nlam, int frequency, gmx_large_int_t step)
+{
+ int nlim, i, ifep, jfep;
+ real dw, dg, dv, dm, Tprint;
+ real *temps;
+ const char *print_names[efptNR] = {" FEPL", "MassL", "CoulL", " VdwL", "BondL", "RestT", "Temp.(K)"};
+ gmx_bool bSimTemp = FALSE;
+
+ nlim = fep->n_lambda;
+ if (simtemp != NULL)
+ {
+ bSimTemp = TRUE;
+ }
+
+ if (mod(step, frequency) == 0)
+ {
+ fprintf(outfile, " MC-lambda information\n");
+ if (EWL(expand->elamstats) && (!(dfhist->bEquil)))
+ {
+ fprintf(outfile, " Wang-Landau incrementor is: %11.5g\n", dfhist->wl_delta);
+ }
+ fprintf(outfile, " N");
+ for (i = 0; i < efptNR; i++)
+ {
+ if (fep->separate_dvdl[i])
+ {
+ fprintf(outfile, "%7s", print_names[i]);
+ }
+ else if ((i == efptTEMPERATURE) && bSimTemp)
+ {
+ fprintf(outfile, "%10s", print_names[i]); /* more space for temperature formats */
+ }
+ }
+ fprintf(outfile, " Count ");
+ if (expand->elamstats == elamstatsMINVAR)
+ {
+ fprintf(outfile, "W(in kT) G(in kT) dG(in kT) dV(in kT)\n");
+ }
+ else
+ {
+ fprintf(outfile, "G(in kT) dG(in kT)\n");
+ }
+ for (ifep = 0; ifep < nlim; ifep++)
+ {
+ if (ifep == nlim-1)
+ {
+ dw = 0.0;
+ dg = 0.0;
+ dv = 0.0;
+ dm = 0.0;
+ }
+ else
+ {
+ dw = dfhist->sum_weights[ifep+1] - dfhist->sum_weights[ifep];
+ dg = dfhist->sum_dg[ifep+1] - dfhist->sum_dg[ifep];
+ dv = sqrt(pow(dfhist->sum_variance[ifep+1], 2) - pow(dfhist->sum_variance[ifep], 2));
+ dm = dfhist->sum_minvar[ifep+1] - dfhist->sum_minvar[ifep];
+
+ }
+ fprintf(outfile, "%3d", (ifep+1));
+ for (i = 0; i < efptNR; i++)
+ {
+ if (fep->separate_dvdl[i])
+ {
+ fprintf(outfile, "%7.3f", fep->all_lambda[i][ifep]);
+ }
+ else if (i == efptTEMPERATURE && bSimTemp)
+ {
+ fprintf(outfile, "%9.3f", simtemp->temperatures[ifep]);
+ }
+ }
+ if (EWL(expand->elamstats) && (!(dfhist->bEquil))) /* if performing WL and still haven't equilibrated */
+ {
+ if (expand->elamstats == elamstatsWL)
+ {
+ fprintf(outfile, " %8d", (int)dfhist->wl_histo[ifep]);
+ }
+ else
+ {
+ fprintf(outfile, " %8.3f", dfhist->wl_histo[ifep]);
+ }
+ }
+ else /* we have equilibrated weights */
+ {
+ fprintf(outfile, " %8d", dfhist->n_at_lam[ifep]);
+ }
+ if (expand->elamstats == elamstatsMINVAR)
+ {
+ fprintf(outfile, " %10.5f %10.5f %10.5f %10.5f", dfhist->sum_weights[ifep], dfhist->sum_dg[ifep], dg, dv);
+ }
+ else
+ {
+ fprintf(outfile, " %10.5f %10.5f", dfhist->sum_weights[ifep], dw);
+ }
+ if (ifep == nlam)
+ {
+ fprintf(outfile, " <<\n");
+ }
+ else
+ {
+ fprintf(outfile, " \n");
+ }
+ }
+ fprintf(outfile, "\n");
+
+ if ((mod(step, expand->nstTij) == 0) && (expand->nstTij > 0) && (step > 0))
+ {
+ fprintf(outfile, " Transition Matrix\n");
+ for (ifep = 0; ifep < nlim; ifep++)
+ {
+ fprintf(outfile, "%12d", (ifep+1));
+ }
+ fprintf(outfile, "\n");
+ for (ifep = 0; ifep < nlim; ifep++)
+ {
+ for (jfep = 0; jfep < nlim; jfep++)
+ {
+ if (dfhist->n_at_lam[ifep] > 0)
+ {
+ if (expand->bSymmetrizedTMatrix)
+ {
+ Tprint = (dfhist->Tij[ifep][jfep]+dfhist->Tij[jfep][ifep])/(dfhist->n_at_lam[ifep]+dfhist->n_at_lam[jfep]);
+ }
+ else
+ {
+ Tprint = (dfhist->Tij[ifep][jfep])/(dfhist->n_at_lam[ifep]);
+ }
+ }
+ else
+ {
+ Tprint = 0.0;
+ }
+ fprintf(outfile, "%12.8f", Tprint);
+ }
+ fprintf(outfile, "%3d\n", (ifep+1));
+ }
+
+ fprintf(outfile, " Empirical Transition Matrix\n");
+ for (ifep = 0; ifep < nlim; ifep++)
+ {
+ fprintf(outfile, "%12d", (ifep+1));
+ }
+ fprintf(outfile, "\n");
+ for (ifep = 0; ifep < nlim; ifep++)
+ {
+ for (jfep = 0; jfep < nlim; jfep++)
+ {
+ if (dfhist->n_at_lam[ifep] > 0)
+ {
+ if (expand->bSymmetrizedTMatrix)
+ {
+ Tprint = (dfhist->Tij_empirical[ifep][jfep]+dfhist->Tij_empirical[jfep][ifep])/(dfhist->n_at_lam[ifep]+dfhist->n_at_lam[jfep]);
+ }
+ else
+ {
+ Tprint = dfhist->Tij_empirical[ifep][jfep]/(dfhist->n_at_lam[ifep]);
+ }
+ }
+ else
+ {
+ Tprint = 0.0;
+ }
+ fprintf(outfile, "%12.8f", Tprint);
+ }
+ fprintf(outfile, "%3d\n", (ifep+1));
+ }
+ }
+ }
+}
+
+extern void get_mc_state(gmx_rng_t rng, t_state *state)
+{
+ gmx_rng_get_state(rng, state->mc_rng, state->mc_rngi);
+}
+
+extern void set_mc_state(gmx_rng_t rng, t_state *state)
+{
+ gmx_rng_set_state(rng, state->mc_rng, state->mc_rngi[0]);
+}
+
+extern int ExpandedEnsembleDynamics(FILE *log, t_inputrec *ir, gmx_enerdata_t *enerd,
+ t_state *state, t_extmass *MassQ, df_history_t *dfhist,
+ gmx_large_int_t step, gmx_rng_t mcrng,
+ rvec *v, t_mdatoms *mdatoms)
+{
+ real *pfep_lamee, *p_k, *scaled_lamee, *weighted_lamee;
+ int i, nlam, nlim, lamnew, totalsamples;
+ real oneovert, maxscaled = 0, maxweighted = 0;
+ t_expanded *expand;
+ t_simtemp *simtemp;
+ double *temperature_lambdas;
+ gmx_bool bIfReset, bSwitchtoOneOverT, bDoneEquilibrating = FALSE;
+
+ expand = ir->expandedvals;
+ simtemp = ir->simtempvals;
+ nlim = ir->fepvals->n_lambda;
+ nlam = state->fep_state;
+
+ snew(scaled_lamee, nlim);
+ snew(weighted_lamee, nlim);
+ snew(pfep_lamee, nlim);
+ snew(p_k, nlim);
+
+ if (expand->bInit_weights) /* if initialized weights, we need to fill them in */
+ {
+ dfhist->wl_delta = expand->init_wl_delta; /* MRS -- this would fit better somewhere else? */
+ for (i = 0; i < nlim; i++)
+ {
+ dfhist->sum_weights[i] = expand->init_lambda_weights[i];
+ dfhist->sum_dg[i] = expand->init_lambda_weights[i];
+ }
+ expand->bInit_weights = FALSE;
+ }
+
+ /* update the count at the current lambda*/
+ dfhist->n_at_lam[nlam]++;
+
+ /* need to calculate the PV term somewhere, but not needed here? Not until there's a lambda state that's
+ pressure controlled.*/
+ /*
+ pVTerm = 0;
+ where does this PV term go?
+ for (i=0;i<nlim;i++)
+ {
+ fep_lamee[i] += pVTerm;
+ }
+ */
+
+ /* determine the minimum value to avoid overflow. Probably a better way to do this */
+ /* we don't need to include the pressure term, since the volume is the same between the two.
+ is there some term we are neglecting, however? */
+
+ if (ir->efep != efepNO)
+ {
+ for (i = 0; i < nlim; i++)
+ {
+ if (ir->bSimTemp)
+ {
+ /* Note -- this assumes no mass changes, since kinetic energy is not added . . . */
+ scaled_lamee[i] = (enerd->enerpart_lambda[i+1]-enerd->enerpart_lambda[0])/(simtemp->temperatures[i]*BOLTZ)
+ + enerd->term[F_EPOT]*(1.0/(simtemp->temperatures[i])- 1.0/(simtemp->temperatures[nlam]))/BOLTZ;
+ }
+ else
+ {
+ scaled_lamee[i] = (enerd->enerpart_lambda[i+1]-enerd->enerpart_lambda[0])/(expand->mc_temp*BOLTZ);
+ /* mc_temp is currently set to the system reft unless otherwise defined */
+ }
+
+ /* save these energies for printing, so they don't get overwritten by the next step */
+ /* they aren't overwritten in the non-free energy case, but we always print with these
+ for simplicity */
+ }
+ }
+ else
+ {
+ if (ir->bSimTemp)
+ {
+ for (i = 0; i < nlim; i++)
+ {
+ scaled_lamee[i] = enerd->term[F_EPOT]*(1.0/simtemp->temperatures[i] - 1.0/simtemp->temperatures[nlam])/BOLTZ;
+ }
+ }
+ }
+
+ for (i = 0; i < nlim; i++)
+ {
+ pfep_lamee[i] = scaled_lamee[i];
+
+ weighted_lamee[i] = dfhist->sum_weights[i] - scaled_lamee[i];
+ if (i == 0)
+ {
+ maxscaled = scaled_lamee[i];
+ maxweighted = weighted_lamee[i];
+ }
+ else
+ {
+ if (scaled_lamee[i] > maxscaled)
+ {
+ maxscaled = scaled_lamee[i];
+ }
+ if (weighted_lamee[i] > maxweighted)
+ {
+ maxweighted = weighted_lamee[i];
+ }
+ }
+ }
+
+ for (i = 0; i < nlim; i++)
+ {
+ scaled_lamee[i] -= maxscaled;
+ weighted_lamee[i] -= maxweighted;
+ }
+
+ /* update weights - we decide whether or not to actually do this inside */
+
+ bDoneEquilibrating = UpdateWeights(nlim, expand, dfhist, nlam, scaled_lamee, weighted_lamee, step);
+ if (bDoneEquilibrating)
+ {
+ if (log)
+ {
+ fprintf(log, "\nStep %d: Weights have equilibrated, using criteria: %s\n", (int)step, elmceq_names[expand->elmceq]);
+ }
+ }
+
+ lamnew = ChooseNewLambda(log, nlim, expand, dfhist, nlam, weighted_lamee, p_k, mcrng);
+ /* if using simulated tempering, we need to adjust the temperatures */
+ if (ir->bSimTemp && (lamnew != nlam)) /* only need to change the temperatures if we change the state */
+ {
+ int i, j, n, d;
+ real *buf_ngtc;
+ real told;
+ int nstart, nend, gt;
+
+ snew(buf_ngtc, ir->opts.ngtc);
+
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ if (ir->opts.ref_t[i] > 0)
+ {
+ told = ir->opts.ref_t[i];
+ ir->opts.ref_t[i] = simtemp->temperatures[lamnew];
+ buf_ngtc[i] = sqrt(ir->opts.ref_t[i]/told); /* using the buffer as temperature scaling */
+ }
+ }
+
+ /* we don't need to manipulate the ekind information, as it isn't due to be reset until the next step anyway */
+
+ nstart = mdatoms->start;
+ nend = nstart + mdatoms->homenr;
+ for (n = nstart; n < nend; n++)
+ {
+ gt = 0;
+ if (mdatoms->cTC)
+ {
+ gt = mdatoms->cTC[n];
+ }
+ for (d = 0; d < DIM; d++)
+ {
+ v[n][d] *= buf_ngtc[gt];
+ }
+ }
+
+ if (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir) || IR_NVT_TROTTER(ir))
+ {
+ /* we need to recalculate the masses if the temperature has changed */
+ init_npt_masses(ir, state, MassQ, FALSE);
+ for (i = 0; i < state->nnhpres; i++)
+ {
+ for (j = 0; j < ir->opts.nhchainlength; j++)
+ {
+ state->nhpres_vxi[i+j] *= buf_ngtc[i];
+ }
+ }
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ for (j = 0; j < ir->opts.nhchainlength; j++)
+ {
+ state->nosehoover_vxi[i+j] *= buf_ngtc[i];
+ }
+ }
+ }
+ sfree(buf_ngtc);
+ }
+
+ /* now check on the Wang-Landau updating critera */
+
+ if (EWL(expand->elamstats))
+ {
+ bSwitchtoOneOverT = FALSE;
+ if (expand->bWLoneovert)
+ {
+ totalsamples = 0;
+ for (i = 0; i < nlim; i++)
+ {
+ totalsamples += dfhist->n_at_lam[i];
+ }
+ oneovert = (1.0*nlim)/totalsamples;
+ /* oneovert has decreasd by a bit since last time, so we actually make sure its within one of this number */
+ /* switch to 1/t incrementing when wl_delta has decreased at least once, and wl_delta is now less than 1/t */
+ if ((dfhist->wl_delta <= ((totalsamples)/(totalsamples-1.00001))*oneovert) &&
+ (dfhist->wl_delta < expand->init_wl_delta))
+ {
+ bSwitchtoOneOverT = TRUE;
+ }
+ }
+ if (bSwitchtoOneOverT)
+ {
+ dfhist->wl_delta = oneovert; /* now we reduce by this each time, instead of only at flatness */
+ }
+ else
+ {
+ bIfReset = CheckHistogramRatios(nlim, dfhist->wl_histo, expand->wl_ratio);
+ if (bIfReset)
+ {
+ for (i = 0; i < nlim; i++)
+ {
+ dfhist->wl_histo[i] = 0;
+ }
+ dfhist->wl_delta *= expand->wl_scale;
+ if (log)
+ {
+ fprintf(log, "\nStep %d: weights are now:", (int)step);
+ for (i = 0; i < nlim; i++)
+ {
+ fprintf(log, " %.5f", dfhist->sum_weights[i]);
+ }
+ fprintf(log, "\n");
+ }
+ }
+ }
+ }
++ sfree(pfep_lamee);
+ sfree(scaled_lamee);
+ sfree(weighted_lamee);
+ sfree(p_k);
+
+ return lamnew;
+}
--- /dev/null
- enerd->term[F_DVDL_BONDED] += enerd->term[F_DVDL_CONSTR];
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * 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 the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * GROwing Monsters And Cloning Shrimps
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+#include <string.h>
+#include <assert.h>
+#include "sysstuff.h"
+#include "typedefs.h"
+#include "macros.h"
+#include "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 "partdec.h"
+#include "qmmm.h"
+#include "gmx_omp_nthreads.h"
+
+
+void ns(FILE *fp,
+ t_forcerec *fr,
+ rvec x[],
+ matrix box,
+ gmx_groups_t *groups,
+ t_grpopts *opts,
+ gmx_localtop_t *top,
+ t_mdatoms *md,
+ t_commrec *cr,
+ t_nrnb *nrnb,
+ real *lambda,
+ real *dvdlambda,
+ gmx_grppairener_t *grppener,
+ gmx_bool bFillGrid,
+ gmx_bool bDoLongRangeNS)
+{
+ char *ptr;
+ int nsearch;
+
+
+ if (!fr->ns.nblist_initialized)
+ {
+ init_neighbor_list(fp, fr, md->homenr);
+ }
+
+ if (fr->bTwinRange)
+ {
+ fr->nlr = 0;
+ }
+
+ nsearch = search_neighbours(fp, fr, x, box, top, groups, cr, nrnb, md,
+ lambda, dvdlambda, grppener,
+ bFillGrid, bDoLongRangeNS, TRUE);
+ if (debug)
+ {
+ fprintf(debug, "nsearch = %d\n", nsearch);
+ }
+
+ /* Check whether we have to do dynamic load balancing */
+ /*if ((nsb->nstDlb > 0) && (mod(step,nsb->nstDlb) == 0))
+ count_nb(cr,nsb,&(top->blocks[ebCGS]),nns,fr->nlr,
+ &(top->idef),opts->ngener);
+ */
+ if (fr->ns.dump_nl > 0)
+ {
+ dump_nblist(fp, cr, fr, fr->ns.dump_nl);
+ }
+}
+
+static void reduce_thread_forces(int n, rvec *f,
+ tensor vir,
+ real *Vcorr,
+ int efpt_ind, real *dvdl,
+ int nthreads, f_thread_t *f_t)
+{
+ int t, i;
+
+ /* This reduction can run over any number of threads */
+#pragma omp parallel for num_threads(gmx_omp_nthreads_get(emntBonded)) private(t) schedule(static)
+ for (i = 0; i < n; i++)
+ {
+ for (t = 1; t < nthreads; t++)
+ {
+ rvec_inc(f[i], f_t[t].f[i]);
+ }
+ }
+ for (t = 1; t < nthreads; t++)
+ {
+ *Vcorr += f_t[t].Vcorr;
+ *dvdl += f_t[t].dvdl[efpt_ind];
+ m_add(vir, f_t[t].vir, vir);
+ }
+}
+
+void do_force_lowlevel(FILE *fplog, gmx_large_int_t step,
+ t_forcerec *fr, t_inputrec *ir,
+ t_idef *idef, t_commrec *cr,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ t_mdatoms *md,
+ t_grpopts *opts,
+ rvec x[], history_t *hist,
+ rvec f[],
+ rvec f_longrange[],
+ gmx_enerdata_t *enerd,
+ t_fcdata *fcd,
+ gmx_mtop_t *mtop,
+ gmx_localtop_t *top,
+ gmx_genborn_t *born,
+ t_atomtypes *atype,
+ gmx_bool bBornRadii,
+ matrix box,
+ t_lambda *fepvals,
+ real *lambda,
+ t_graph *graph,
+ t_blocka *excl,
+ rvec mu_tot[],
+ int flags,
+ float *cycles_pme)
+{
+ int i, j, status;
+ int donb_flags;
+ gmx_bool bDoEpot, bSepDVDL, bSB;
+ int pme_flags;
+ matrix boxs;
+ rvec box_size;
+ real Vsr, Vlr, Vcorr = 0;
+ t_pbc pbc;
+ real dvdgb;
+ char buf[22];
+ double clam_i, vlam_i;
+ real dvdl_dum[efptNR], dvdl, dvdl_nb[efptNR], lam_i[efptNR];
+ real dvdlsum;
+
+#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) {fprintf(fplog, sepdvdlformat, s, v, dvdlambda); }
+
+
+ set_pbc(&pbc, fr->ePBC, box);
+
+ /* reset free energy components */
+ for (i = 0; i < efptNR; i++)
+ {
+ dvdl_nb[i] = 0;
+ dvdl_dum[i] = 0;
+ }
+
+ /* Reset box */
+ for (i = 0; (i < DIM); i++)
+ {
+ box_size[i] = box[i][i];
+ }
+
+ bSepDVDL = (fr->bSepDVDL && do_per_step(step, ir->nstlog));
+ debug_gmx();
+
+ /* do QMMM first if requested */
+ if (fr->bQMMM)
+ {
+ enerd->term[F_EQM] = calculate_QMMM(cr, x, f, fr, md);
+ }
+
+ if (bSepDVDL)
+ {
+ fprintf(fplog, "Step %s: non-bonded V and dVdl for node %d:\n",
+ gmx_step_str(step, buf), cr->nodeid);
+ }
+
+ /* Call the short range functions all in one go. */
+
+#ifdef GMX_MPI
+ /*#define TAKETIME ((cr->npmenodes) && (fr->timesteps < 12))*/
+#define TAKETIME FALSE
+ if (TAKETIME)
+ {
+ MPI_Barrier(cr->mpi_comm_mygroup);
+ t0 = MPI_Wtime();
+ }
+#endif
+
+ if (ir->nwall)
+ {
+ /* foreign lambda component for walls */
+ dvdl = do_walls(ir, fr, box, md, x, f, lambda[efptVDW],
+ enerd->grpp.ener[egLJSR], nrnb);
+ PRINT_SEPDVDL("Walls", 0.0, dvdl);
+ enerd->dvdl_lin[efptVDW] += dvdl;
+ }
+
+ /* If doing GB, reset dvda and calculate the Born radii */
+ if (ir->implicit_solvent)
+ {
+ wallcycle_sub_start(wcycle, ewcsNONBONDED);
+
+ for (i = 0; i < born->nr; i++)
+ {
+ fr->dvda[i] = 0;
+ }
+
+ if (bBornRadii)
+ {
+ calc_gb_rad(cr, fr, ir, top, atype, x, &(fr->gblist), born, md, nrnb);
+ }
+
+ wallcycle_sub_stop(wcycle, ewcsNONBONDED);
+ }
+
+ where();
+ /* We only do non-bonded calculation with group scheme here, the verlet
+ * calls are done from do_force_cutsVERLET(). */
+ if (fr->cutoff_scheme == ecutsGROUP && (flags & GMX_FORCE_NONBONDED))
+ {
+ donb_flags = 0;
+ /* Add short-range interactions */
+ donb_flags |= GMX_NONBONDED_DO_SR;
+
+ if (flags & GMX_FORCE_FORCES)
+ {
+ donb_flags |= GMX_NONBONDED_DO_FORCE;
+ }
+ if (flags & GMX_FORCE_ENERGY)
+ {
+ donb_flags |= GMX_NONBONDED_DO_POTENTIAL;
+ }
+ if (flags & GMX_FORCE_DO_LR)
+ {
+ donb_flags |= GMX_NONBONDED_DO_LR;
+ }
+
+ wallcycle_sub_start(wcycle, ewcsNONBONDED);
+ do_nonbonded(cr, fr, x, f, f_longrange, md, excl,
+ &enerd->grpp, box_size, nrnb,
+ lambda, dvdl_nb, -1, -1, donb_flags);
+
+ /* If we do foreign lambda and we have soft-core interactions
+ * we have to recalculate the (non-linear) energies contributions.
+ */
+ if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) && fepvals->sc_alpha != 0)
+ {
+ for (i = 0; i < enerd->n_lambda; i++)
+ {
+ for (j = 0; j < efptNR; j++)
+ {
+ lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
+ }
+ reset_foreign_enerdata(enerd);
+ do_nonbonded(cr, fr, x, f, f_longrange, md, excl,
+ &(enerd->foreign_grpp), box_size, nrnb,
+ lam_i, dvdl_dum, -1, -1,
+ (donb_flags & ~GMX_NONBONDED_DO_FORCE) | GMX_NONBONDED_DO_FOREIGNLAMBDA);
+ sum_epot(&ir->opts, &(enerd->foreign_grpp), enerd->foreign_term);
+ enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
+ }
+ }
+ wallcycle_sub_stop(wcycle, ewcsNONBONDED);
+ where();
+ }
+
+ /* If we are doing GB, calculate bonded forces and apply corrections
+ * to the solvation forces */
+ /* MRS: Eventually, many need to include free energy contribution here! */
+ if (ir->implicit_solvent)
+ {
+ wallcycle_sub_start(wcycle, ewcsBONDED);
+ calc_gb_forces(cr, md, born, top, atype, x, f, fr, idef,
+ ir->gb_algorithm, ir->sa_algorithm, nrnb, bBornRadii, &pbc, graph, enerd);
+ wallcycle_sub_stop(wcycle, ewcsBONDED);
+ }
+
+#ifdef GMX_MPI
+ if (TAKETIME)
+ {
+ t1 = MPI_Wtime();
+ fr->t_fnbf += t1-t0;
+ }
+#endif
+
+ if (fepvals->sc_alpha != 0)
+ {
+ enerd->dvdl_nonlin[efptVDW] += dvdl_nb[efptVDW];
+ }
+ else
+ {
+ enerd->dvdl_lin[efptVDW] += dvdl_nb[efptVDW];
+ }
+
+ if (fepvals->sc_alpha != 0)
+
+ /* even though coulomb part is linear, we already added it, beacuse we
+ need to go through the vdw calculation anyway */
+ {
+ enerd->dvdl_nonlin[efptCOUL] += dvdl_nb[efptCOUL];
+ }
+ else
+ {
+ enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
+ }
+
+ Vsr = 0;
+ if (bSepDVDL)
+ {
+ for (i = 0; i < enerd->grpp.nener; i++)
+ {
+ Vsr +=
+ (fr->bBHAM ?
+ enerd->grpp.ener[egBHAMSR][i] :
+ enerd->grpp.ener[egLJSR][i])
+ + enerd->grpp.ener[egCOULSR][i] + enerd->grpp.ener[egGB][i];
+ }
+ dvdlsum = dvdl_nb[efptVDW] + dvdl_nb[efptCOUL];
+ PRINT_SEPDVDL("VdW and Coulomb SR particle-p.", Vsr, dvdlsum);
+ }
+ debug_gmx();
+
+
+ if (debug)
+ {
+ pr_rvecs(debug, 0, "fshift after SR", fr->fshift, SHIFTS);
+ }
+
+ /* Shift the coordinates. Must be done before bonded forces and PPPM,
+ * but is also necessary for SHAKE and update, therefore it can NOT
+ * go when no bonded forces have to be evaluated.
+ */
+
+ /* Here sometimes we would not need to shift with NBFonly,
+ * but we do so anyhow for consistency of the returned coordinates.
+ */
+ if (graph)
+ {
+ shift_self(graph, box, x);
+ if (TRICLINIC(box))
+ {
+ inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes);
+ }
+ else
+ {
+ inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
+ }
+ }
+ /* Check whether we need to do bondeds or correct for exclusions */
+ if (fr->bMolPBC &&
+ ((flags & GMX_FORCE_BONDED)
+ || EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype)))
+ {
+ /* Since all atoms are in the rectangular or triclinic unit-cell,
+ * only single box vector shifts (2 in x) are required.
+ */
+ set_pbc_dd(&pbc, fr->ePBC, cr->dd, TRUE, box);
+ }
+ 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(&ir->opts, &(enerd->foreign_grpp), enerd->foreign_term);
+ enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
+ }
+ }
+ debug_gmx();
+
+ wallcycle_sub_stop(wcycle, ewcsBONDED);
+ }
+
+ where();
+
+ *cycles_pme = 0;
+ if (EEL_FULL(fr->eeltype))
+ {
+ bSB = (ir->nwall == 2);
+ if (bSB)
+ {
+ copy_mat(box, boxs);
+ svmul(ir->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
+ box_size[ZZ] *= ir->wall_ewald_zfac;
+ }
+
+ clear_mat(fr->vir_el_recip);
+
+ if (fr->bEwald)
+ {
+ Vcorr = 0;
+ dvdl = 0;
+
+ /* With the Verlet scheme exclusion forces are calculated
+ * in the non-bonded kernel.
+ */
+ /* The TPI molecule does not have exclusions with the rest
+ * of the system and no intra-molecular PME grid contributions
+ * will be calculated in gmx_pme_calc_energy.
+ */
+ if ((ir->cutoff_scheme == ecutsGROUP && fr->n_tpi == 0) ||
+ ir->ewald_geometry != eewg3D ||
+ ir->epsilon_surface != 0)
+ {
+ int nthreads, t;
+
+ wallcycle_sub_start(wcycle, ewcsEWALD_CORRECTION);
+
+ if (fr->n_tpi > 0)
+ {
+ gmx_fatal(FARGS, "TPI with PME currently only works in a 3D geometry with tin-foil boundary conditions");
+ }
+
+ nthreads = gmx_omp_nthreads_get(emntBonded);
+#pragma omp parallel for num_threads(nthreads) schedule(static)
+ for (t = 0; t < nthreads; t++)
+ {
+ int s, e, i;
+ rvec *fnv;
+ tensor *vir;
+ real *Vcorrt, *dvdlt;
+ if (t == 0)
+ {
+ fnv = fr->f_novirsum;
+ vir = &fr->vir_el_recip;
+ Vcorrt = &Vcorr;
+ dvdlt = &dvdl;
+ }
+ else
+ {
+ fnv = fr->f_t[t].f;
+ vir = &fr->f_t[t].vir;
+ Vcorrt = &fr->f_t[t].Vcorr;
+ dvdlt = &fr->f_t[t].dvdl[efptCOUL];
+ for (i = 0; i < fr->natoms_force; i++)
+ {
+ clear_rvec(fnv[i]);
+ }
+ clear_mat(*vir);
+ }
+ *dvdlt = 0;
+ *Vcorrt =
+ ewald_LRcorrection(fplog,
+ fr->excl_load[t], fr->excl_load[t+1],
+ cr, t, fr,
+ md->chargeA,
+ md->nChargePerturbed ? md->chargeB : NULL,
+ ir->cutoff_scheme != ecutsVERLET,
+ excl, x, bSB ? boxs : box, mu_tot,
+ ir->ewald_geometry,
+ ir->epsilon_surface,
+ fnv, *vir,
+ lambda[efptCOUL], dvdlt);
+ }
+ if (nthreads > 1)
+ {
+ reduce_thread_forces(fr->natoms_force, fr->f_novirsum,
+ fr->vir_el_recip,
+ &Vcorr, efptCOUL, &dvdl,
+ nthreads, fr->f_t);
+ }
+
+ wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
+ }
+
+ if (fr->n_tpi == 0)
+ {
+ Vcorr += ewald_charge_correction(cr, fr, lambda[efptCOUL], box,
+ &dvdl, fr->vir_el_recip);
+ }
+
+ PRINT_SEPDVDL("Ewald excl./charge/dip. corr.", Vcorr, dvdl);
+ enerd->dvdl_lin[efptCOUL] += dvdl;
+ }
+
+ status = 0;
+ Vlr = 0;
+ dvdl = 0;
+ switch (fr->eeltype)
+ {
+ case eelPME:
+ case eelPMESWITCH:
+ case eelPMEUSER:
+ case eelPMEUSERSWITCH:
+ case eelP3M_AD:
+ if (cr->duty & DUTY_PME)
+ {
+ assert(fr->n_tpi >= 0);
+ if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
+ {
+ pme_flags = GMX_PME_SPREAD_Q | GMX_PME_SOLVE;
+ if (flags & GMX_FORCE_FORCES)
+ {
+ pme_flags |= GMX_PME_CALC_F;
+ }
+ if (flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY))
+ {
+ pme_flags |= GMX_PME_CALC_ENER_VIR;
+ }
+ if (fr->n_tpi > 0)
+ {
+ /* We don't calculate f, but we do want the potential */
+ pme_flags |= GMX_PME_CALC_POT;
+ }
+ wallcycle_start(wcycle, ewcPMEMESH);
+ status = gmx_pme_do(fr->pmedata,
+ md->start, md->homenr - fr->n_tpi,
+ x, fr->f_novirsum,
+ md->chargeA, md->chargeB,
+ bSB ? boxs : box, cr,
+ DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
+ DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
+ nrnb, wcycle,
+ fr->vir_el_recip, fr->ewaldcoeff,
+ &Vlr, lambda[efptCOUL], &dvdl,
+ pme_flags);
+ *cycles_pme = wallcycle_stop(wcycle, ewcPMEMESH);
+
+ /* We should try to do as little computation after
+ * this as possible, because parallel PME synchronizes
+ * the nodes, so we want all load imbalance of the rest
+ * of the force calculation to be before the PME call.
+ * DD load balancing is done on the whole time of
+ * the force call (without PME).
+ */
+ }
+ if (fr->n_tpi > 0)
+ {
+ /* Determine the PME grid energy of the test molecule
+ * with the PME grid potential of the other charges.
+ */
+ gmx_pme_calc_energy(fr->pmedata, fr->n_tpi,
+ x + md->homenr - fr->n_tpi,
+ md->chargeA + md->homenr - fr->n_tpi,
+ &Vlr);
+ }
+ PRINT_SEPDVDL("PME mesh", Vlr, dvdl);
+ }
+ break;
+ case eelEWALD:
+ Vlr = do_ewald(fplog, FALSE, ir, x, fr->f_novirsum,
+ md->chargeA, md->chargeB,
+ box_size, cr, md->homenr,
+ fr->vir_el_recip, fr->ewaldcoeff,
+ lambda[efptCOUL], &dvdl, fr->ewald_table);
+ PRINT_SEPDVDL("Ewald long-range", Vlr, dvdl);
+ break;
+ default:
+ gmx_fatal(FARGS, "No such electrostatics method implemented %s",
+ eel_names[fr->eeltype]);
+ }
+ if (status != 0)
+ {
+ gmx_fatal(FARGS, "Error %d in long range electrostatics routine %s",
+ status, EELTYPE(fr->eeltype));
+ }
+ /* Note that with separate PME nodes we get the real energies later */
+ enerd->dvdl_lin[efptCOUL] += dvdl;
+ enerd->term[F_COUL_RECIP] = Vlr + Vcorr;
+ if (debug)
+ {
+ fprintf(debug, "Vlr = %g, Vcorr = %g, Vlr_corr = %g\n",
+ Vlr, Vcorr, enerd->term[F_COUL_RECIP]);
+ pr_rvecs(debug, 0, "vir_el_recip after corr", fr->vir_el_recip, DIM);
+ pr_rvecs(debug, 0, "fshift after LR Corrections", fr->fshift, SHIFTS);
+ }
+ }
+ else
+ {
+ if (EEL_RF(fr->eeltype))
+ {
+ /* With the Verlet scheme exclusion forces are calculated
+ * in the non-bonded kernel.
+ */
+ if (ir->cutoff_scheme != ecutsVERLET && fr->eeltype != eelRF_NEC)
+ {
+ dvdl = 0;
+ enerd->term[F_RF_EXCL] =
+ RF_excl_correction(fplog, fr, graph, md, excl, x, f,
+ fr->fshift, &pbc, lambda[efptCOUL], &dvdl);
+ }
+
+ enerd->dvdl_lin[efptCOUL] += dvdl;
+ PRINT_SEPDVDL("RF exclusion correction",
+ enerd->term[F_RF_EXCL], dvdl);
+ }
+ }
+ where();
+ debug_gmx();
+
+ if (debug)
+ {
+ print_nrnb(debug, nrnb);
+ }
+ debug_gmx();
+
+#ifdef GMX_MPI
+ if (TAKETIME)
+ {
+ t2 = MPI_Wtime();
+ MPI_Barrier(cr->mpi_comm_mygroup);
+ t3 = MPI_Wtime();
+ fr->t_wait += t3-t2;
+ if (fr->timesteps == 11)
+ {
+ fprintf(stderr, "* PP load balancing info: node %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),
+ (fr->t_fnbf+fr->t_wait)/fr->t_fnbf);
+ }
+ fr->timesteps++;
+ }
+#endif
+
+ if (debug)
+ {
+ pr_rvecs(debug, 0, "fshift after bondeds", fr->fshift, SHIFTS);
+ }
+
+}
+
+void init_enerdata(int ngener, int n_lambda, gmx_enerdata_t *enerd)
+{
+ int i, n2;
+
+ for (i = 0; i < F_NRE; i++)
+ {
+ enerd->term[i] = 0;
+ enerd->foreign_term[i] = 0;
+ }
+
+
+ for (i = 0; i < efptNR; i++)
+ {
+ enerd->dvdl_lin[i] = 0;
+ enerd->dvdl_nonlin[i] = 0;
+ }
+
+ n2 = ngener*ngener;
+ if (debug)
+ {
+ fprintf(debug, "Creating %d sized group matrix for energies\n", n2);
+ }
+ enerd->grpp.nener = n2;
+ enerd->foreign_grpp.nener = n2;
+ for (i = 0; (i < egNR); i++)
+ {
+ snew(enerd->grpp.ener[i], n2);
+ snew(enerd->foreign_grpp.ener[i], n2);
+ }
+
+ if (n_lambda)
+ {
+ enerd->n_lambda = 1 + n_lambda;
+ snew(enerd->enerpart_lambda, enerd->n_lambda);
+ }
+ else
+ {
+ enerd->n_lambda = 0;
+ }
+}
+
+void destroy_enerdata(gmx_enerdata_t *enerd)
+{
+ int i;
+
+ for (i = 0; (i < egNR); i++)
+ {
+ sfree(enerd->grpp.ener[i]);
+ }
+
+ for (i = 0; (i < egNR); i++)
+ {
+ sfree(enerd->foreign_grpp.ener[i]);
+ }
+
+ if (enerd->n_lambda)
+ {
+ sfree(enerd->enerpart_lambda);
+ }
+}
+
+static real sum_v(int n, real v[])
+{
+ real t;
+ int i;
+
+ t = 0.0;
+ for (i = 0; (i < n); i++)
+ {
+ t = t + v[i];
+ }
+
+ return t;
+}
+
+void sum_epot(t_grpopts *opts, gmx_grppairener_t *grpp, real *epot)
+{
+ int i;
+
+ /* Accumulate energies */
+ epot[F_COUL_SR] = sum_v(grpp->nener, grpp->ener[egCOULSR]);
+ epot[F_LJ] = sum_v(grpp->nener, grpp->ener[egLJSR]);
+ epot[F_LJ14] = sum_v(grpp->nener, grpp->ener[egLJ14]);
+ epot[F_COUL14] = sum_v(grpp->nener, grpp->ener[egCOUL14]);
+ epot[F_COUL_LR] = sum_v(grpp->nener, grpp->ener[egCOULLR]);
+ epot[F_LJ_LR] = sum_v(grpp->nener, grpp->ener[egLJLR]);
+ /* We have already added 1-2,1-3, and 1-4 terms to F_GBPOL */
+ epot[F_GBPOL] += sum_v(grpp->nener, grpp->ener[egGB]);
+
+/* lattice part of LR doesnt belong to any group
+ * and has been added earlier
+ */
+ epot[F_BHAM] = sum_v(grpp->nener, grpp->ener[egBHAMSR]);
+ epot[F_BHAM_LR] = sum_v(grpp->nener, grpp->ener[egBHAMLR]);
+
+ epot[F_EPOT] = 0;
+ for (i = 0; (i < F_EPOT); i++)
+ {
+ if (i != F_DISRESVIOL && i != F_ORIRESDEV)
+ {
+ epot[F_EPOT] += epot[i];
+ }
+ }
+}
+
+void sum_dhdl(gmx_enerdata_t *enerd, real *lambda, t_lambda *fepvals)
+{
+ int i, j, index;
+ double dlam;
+
+ enerd->dvdl_lin[efptVDW] += enerd->term[F_DVDL_VDW]; /* include dispersion correction */
+ enerd->term[F_DVDL] = 0.0;
+ for (i = 0; i < efptNR; i++)
+ {
+ if (fepvals->separate_dvdl[i])
+ {
+ /* could this be done more readably/compactly? */
+ switch (i)
+ {
+ case (efptMASS):
+ index = F_DKDL;
+ break;
+ case (efptCOUL):
+ index = F_DVDL_COUL;
+ break;
+ case (efptVDW):
+ index = F_DVDL_VDW;
+ break;
+ case (efptBONDED):
+ index = F_DVDL_BONDED;
+ break;
+ case (efptRESTRAINT):
+ index = F_DVDL_RESTRAINT;
+ break;
+ default:
+ index = F_DVDL;
+ break;
+ }
+ enerd->term[index] = enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
+ if (debug)
+ {
+ fprintf(debug, "dvdl-%s[%2d]: %f: non-linear %f + linear %f\n",
+ efpt_names[i], i, enerd->term[index], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
+ }
+ }
+ else
+ {
+ enerd->term[F_DVDL] += enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
+ if (debug)
+ {
+ fprintf(debug, "dvd-%sl[%2d]: %f: non-linear %f + linear %f\n",
+ efpt_names[0], i, enerd->term[F_DVDL], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
+ }
+ }
+ }
+
+ /* Notes on the foreign lambda free energy difference evaluation:
+ * Adding the potential and ekin terms that depend linearly on lambda
+ * as delta lam * dvdl to the energy differences is exact.
+ * For the constraints this is not exact, but we have no other option
+ * without literally changing the lengths and reevaluating the energies at each step.
+ * (try to remedy this post 4.6 - MRS)
+ * For the non-bonded LR term we assume that the soft-core (if present)
+ * no longer affects the energy beyond the short-range cut-off,
+ * which is a very good approximation (except for exotic settings).
+ * (investigate how to overcome this post 4.6 - MRS)
+ */
++ if (fepvals->separate_dvdl[efptBONDED])
++ {
++ enerd->term[F_DVDL_BONDED] += enerd->term[F_DVDL_CONSTR];
++ }
++ else
++ {
++ enerd->term[F_DVDL] += enerd->term[F_DVDL_CONSTR];
++ }
+ enerd->term[F_DVDL_CONSTR] = 0;
+
+ for (i = 0; i < fepvals->n_lambda; i++)
+ { /* note we are iterating over fepvals here!
+ For the current lam, dlam = 0 automatically,
+ so we don't need to add anything to the
+ enerd->enerpart_lambda[0] */
+
+ /* we don't need to worry about dvdl_lin contributions to dE at
+ current lambda, because the contributions to the current
+ lambda are automatically zeroed */
+
+ for (j = 0; j < efptNR; j++)
+ {
+ /* Note that this loop is over all dhdl components, not just the separated ones */
+ dlam = (fepvals->all_lambda[j][i]-lambda[j]);
+ enerd->enerpart_lambda[i+1] += dlam*enerd->dvdl_lin[j];
+ if (debug)
+ {
+ fprintf(debug, "enerdiff lam %g: (%15s), non-linear %f linear %f*%f\n",
+ fepvals->all_lambda[j][i], efpt_names[j],
+ (enerd->enerpart_lambda[i+1] - enerd->enerpart_lambda[0]),
+ dlam, enerd->dvdl_lin[j]);
+ }
+ }
+ }
+}
+
+
+void reset_foreign_enerdata(gmx_enerdata_t *enerd)
+{
+ int i, j;
+
+ /* First reset all foreign energy components. Foreign energies always called on
+ neighbor search steps */
+ for (i = 0; (i < egNR); i++)
+ {
+ for (j = 0; (j < enerd->grpp.nener); j++)
+ {
+ enerd->foreign_grpp.ener[i][j] = 0.0;
+ }
+ }
+
+ /* potential energy components */
+ for (i = 0; (i <= F_EPOT); i++)
+ {
+ enerd->foreign_term[i] = 0.0;
+ }
+}
+
+void reset_enerdata(t_grpopts *opts,
+ t_forcerec *fr, gmx_bool bNS,
+ gmx_enerdata_t *enerd,
+ gmx_bool bMaster)
+{
+ gmx_bool bKeepLR;
+ int i, j;
+
+ /* First reset all energy components, except for the long range terms
+ * on the master at non neighbor search steps, since the long range
+ * terms have already been summed at the last neighbor search step.
+ */
+ bKeepLR = (fr->bTwinRange && !bNS);
+ for (i = 0; (i < egNR); i++)
+ {
+ if (!(bKeepLR && bMaster && (i == egCOULLR || i == egLJLR)))
+ {
+ for (j = 0; (j < enerd->grpp.nener); j++)
+ {
+ enerd->grpp.ener[i][j] = 0.0;
+ }
+ }
+ }
+ for (i = 0; i < efptNR; i++)
+ {
+ enerd->dvdl_lin[i] = 0.0;
+ enerd->dvdl_nonlin[i] = 0.0;
+ }
+
+ /* Normal potential energy components */
+ for (i = 0; (i <= F_EPOT); i++)
+ {
+ enerd->term[i] = 0.0;
+ }
+ /* Initialize the dVdlambda term with the long range contribution */
+ /* Initialize the dvdl term with the long range contribution */
+ enerd->term[F_DVDL] = 0.0;
+ enerd->term[F_DVDL_COUL] = 0.0;
+ enerd->term[F_DVDL_VDW] = 0.0;
+ enerd->term[F_DVDL_BONDED] = 0.0;
+ enerd->term[F_DVDL_RESTRAINT] = 0.0;
+ enerd->term[F_DKDL] = 0.0;
+ if (enerd->n_lambda > 0)
+ {
+ for (i = 0; i < enerd->n_lambda; i++)
+ {
+ enerd->enerpart_lambda[i] = 0.0;
+ }
+ }
+ /* reset foreign energy data - separate function since we also call it elsewhere */
+ reset_foreign_enerdata(enerd);
+}
--- /dev/null
- nbnxn_cuda_init_const(fr->nbv->cu_nbv, ic, fr->nbv);
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * 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 the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * GROwing Monsters And Cloning Shrimps
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+#include <string.h>
+#include <assert.h>
+#include "sysstuff.h"
+#include "typedefs.h"
+#include "vec.h"
+#include "maths.h"
+#include "macros.h"
+#include "smalloc.h"
+#include "macros.h"
+#include "gmx_fatal.h"
+#include "gmx_fatal_collective.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 "partdec.h"
+#include "qmmm.h"
+#include "copyrite.h"
+#include "mtop_util.h"
+#include "nbnxn_search.h"
+#include "nbnxn_atomdata.h"
+#include "nbnxn_consts.h"
+#include "statutil.h"
+#include "gmx_omp_nthreads.h"
+#include "gmx_detect_hardware.h"
+
+#ifdef _MSC_VER
+/* MSVC definition for __cpuid() */
+#include <intrin.h>
+#endif
+
+#include "types/nbnxn_cuda_types_ext.h"
+#include "gpu_utils.h"
+#include "nbnxn_cuda_data_mgmt.h"
+#include "pmalloc_cuda.h"
+
+t_forcerec *mk_forcerec(void)
+{
+ t_forcerec *fr;
+
+ snew(fr, 1);
+
+ return fr;
+}
+
+#ifdef DEBUG
+static void pr_nbfp(FILE *fp, real *nbfp, gmx_bool bBHAM, int atnr)
+{
+ int i, j;
+
+ for (i = 0; (i < atnr); i++)
+ {
+ for (j = 0; (j < atnr); j++)
+ {
+ fprintf(fp, "%2d - %2d", i, j);
+ if (bBHAM)
+ {
+ fprintf(fp, " a=%10g, b=%10g, c=%10g\n", BHAMA(nbfp, atnr, i, j),
+ BHAMB(nbfp, atnr, i, j), BHAMC(nbfp, atnr, i, j)/6.0);
+ }
+ else
+ {
+ fprintf(fp, " c6=%10g, c12=%10g\n", C6(nbfp, atnr, i, j)/6.0,
+ C12(nbfp, atnr, i, j)/12.0);
+ }
+ }
+ }
+}
+#endif
+
+static real *mk_nbfp(const gmx_ffparams_t *idef, gmx_bool bBHAM)
+{
+ real *nbfp;
+ int i, j, k, atnr;
+
+ atnr = idef->atnr;
+ if (bBHAM)
+ {
+ snew(nbfp, 3*atnr*atnr);
+ for (i = k = 0; (i < atnr); i++)
+ {
+ for (j = 0; (j < atnr); j++, k++)
+ {
+ BHAMA(nbfp, atnr, i, j) = idef->iparams[k].bham.a;
+ BHAMB(nbfp, atnr, i, j) = idef->iparams[k].bham.b;
+ /* nbfp now includes the 6.0 derivative prefactor */
+ BHAMC(nbfp, atnr, i, j) = idef->iparams[k].bham.c*6.0;
+ }
+ }
+ }
+ else
+ {
+ snew(nbfp, 2*atnr*atnr);
+ for (i = k = 0; (i < atnr); i++)
+ {
+ for (j = 0; (j < atnr); j++, k++)
+ {
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ C6(nbfp, atnr, i, j) = idef->iparams[k].lj.c6*6.0;
+ C12(nbfp, atnr, i, j) = idef->iparams[k].lj.c12*12.0;
+ }
+ }
+ }
+
+ return nbfp;
+}
+
+/* This routine sets fr->solvent_opt to the most common solvent in the
+ * system, e.g. esolSPC or esolTIP4P. It will also mark each charge group in
+ * the fr->solvent_type array with the correct type (or esolNO).
+ *
+ * Charge groups that fulfill the conditions but are not identical to the
+ * most common one will be marked as esolNO in the solvent_type array.
+ *
+ * TIP3p is identical to SPC for these purposes, so we call it
+ * SPC in the arrays (Apologies to Bill Jorgensen ;-)
+ *
+ * NOTE: QM particle should not
+ * become an optimized solvent. Not even if there is only one charge
+ * group in the Qm
+ */
+
+typedef struct
+{
+ int model;
+ int count;
+ int vdwtype[4];
+ real charge[4];
+} solvent_parameters_t;
+
+static void
+check_solvent_cg(const gmx_moltype_t *molt,
+ int cg0,
+ int nmol,
+ const unsigned char *qm_grpnr,
+ const t_grps *qm_grps,
+ t_forcerec * fr,
+ int *n_solvent_parameters,
+ solvent_parameters_t **solvent_parameters_p,
+ int cginfo,
+ int *cg_sp)
+{
+ const t_blocka * excl;
+ t_atom *atom;
+ int j, k;
+ int j0, j1, nj;
+ gmx_bool perturbed;
+ gmx_bool has_vdw[4];
+ gmx_bool match;
+ real tmp_charge[4];
+ int tmp_vdwtype[4];
+ int tjA;
+ gmx_bool qm;
+ solvent_parameters_t *solvent_parameters;
+
+ /* We use a list with parameters for each solvent type.
+ * Every time we discover a new molecule that fulfills the basic
+ * conditions for a solvent we compare with the previous entries
+ * in these lists. If the parameters are the same we just increment
+ * the counter for that type, and otherwise we create a new type
+ * based on the current molecule.
+ *
+ * Once we've finished going through all molecules we check which
+ * solvent is most common, and mark all those molecules while we
+ * clear the flag on all others.
+ */
+
+ solvent_parameters = *solvent_parameters_p;
+
+ /* Mark the cg first as non optimized */
+ *cg_sp = -1;
+
+ /* Check if this cg has no exclusions with atoms in other charge groups
+ * and all atoms inside the charge group excluded.
+ * We only have 3 or 4 atom solvent loops.
+ */
+ if (GET_CGINFO_EXCL_INTER(cginfo) ||
+ !GET_CGINFO_EXCL_INTRA(cginfo))
+ {
+ return;
+ }
+
+ /* Get the indices of the first atom in this charge group */
+ j0 = molt->cgs.index[cg0];
+ j1 = molt->cgs.index[cg0+1];
+
+ /* Number of atoms in our molecule */
+ nj = j1 - j0;
+
+ if (debug)
+ {
+ fprintf(debug,
+ "Moltype '%s': there are %d atoms in this charge group\n",
+ *molt->name, nj);
+ }
+
+ /* Check if it could be an SPC (3 atoms) or TIP4p (4) water,
+ * otherwise skip it.
+ */
+ if (nj < 3 || nj > 4)
+ {
+ return;
+ }
+
+ /* Check if we are doing QM on this group */
+ qm = FALSE;
+ if (qm_grpnr != NULL)
+ {
+ for (j = j0; j < j1 && !qm; j++)
+ {
+ qm = (qm_grpnr[j] < qm_grps->nr - 1);
+ }
+ }
+ /* Cannot use solvent optimization with QM */
+ if (qm)
+ {
+ return;
+ }
+
+ atom = molt->atoms.atom;
+
+ /* Still looks like a solvent, time to check parameters */
+
+ /* If it is perturbed (free energy) we can't use the solvent loops,
+ * so then we just skip to the next molecule.
+ */
+ perturbed = FALSE;
+
+ for (j = j0; j < j1 && !perturbed; j++)
+ {
+ perturbed = PERTURBED(atom[j]);
+ }
+
+ if (perturbed)
+ {
+ return;
+ }
+
+ /* Now it's only a question if the VdW and charge parameters
+ * are OK. Before doing the check we compare and see if they are
+ * identical to a possible previous solvent type.
+ * First we assign the current types and charges.
+ */
+ for (j = 0; j < nj; j++)
+ {
+ tmp_vdwtype[j] = atom[j0+j].type;
+ tmp_charge[j] = atom[j0+j].q;
+ }
+
+ /* Does it match any previous solvent type? */
+ for (k = 0; k < *n_solvent_parameters; k++)
+ {
+ match = TRUE;
+
+
+ /* We can only match SPC with 3 atoms and TIP4p with 4 atoms */
+ if ( (solvent_parameters[k].model == esolSPC && nj != 3) ||
+ (solvent_parameters[k].model == esolTIP4P && nj != 4) )
+ {
+ match = FALSE;
+ }
+
+ /* Check that types & charges match for all atoms in molecule */
+ for (j = 0; j < nj && match == TRUE; j++)
+ {
+ if (tmp_vdwtype[j] != solvent_parameters[k].vdwtype[j])
+ {
+ match = FALSE;
+ }
+ if (tmp_charge[j] != solvent_parameters[k].charge[j])
+ {
+ match = FALSE;
+ }
+ }
+ if (match == TRUE)
+ {
+ /* Congratulations! We have a matched solvent.
+ * Flag it with this type for later processing.
+ */
+ *cg_sp = k;
+ solvent_parameters[k].count += nmol;
+
+ /* We are done with this charge group */
+ return;
+ }
+ }
+
+ /* If we get here, we have a tentative new solvent type.
+ * Before we add it we must check that it fulfills the requirements
+ * of the solvent optimized loops. First determine which atoms have
+ * VdW interactions.
+ */
+ for (j = 0; j < nj; j++)
+ {
+ has_vdw[j] = FALSE;
+ tjA = tmp_vdwtype[j];
+
+ /* Go through all other tpes and see if any have non-zero
+ * VdW parameters when combined with this one.
+ */
+ for (k = 0; k < fr->ntype && (has_vdw[j] == FALSE); k++)
+ {
+ /* We already checked that the atoms weren't perturbed,
+ * so we only need to check state A now.
+ */
+ if (fr->bBHAM)
+ {
+ has_vdw[j] = (has_vdw[j] ||
+ (BHAMA(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
+ (BHAMB(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
+ (BHAMC(fr->nbfp, fr->ntype, tjA, k) != 0.0));
+ }
+ else
+ {
+ /* Standard LJ */
+ has_vdw[j] = (has_vdw[j] ||
+ (C6(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
+ (C12(fr->nbfp, fr->ntype, tjA, k) != 0.0));
+ }
+ }
+ }
+
+ /* Now we know all we need to make the final check and assignment. */
+ if (nj == 3)
+ {
+ /* So, is it an SPC?
+ * For this we require thatn all atoms have charge,
+ * the charges on atom 2 & 3 should be the same, and only
+ * atom 1 might have VdW.
+ */
+ if (has_vdw[1] == FALSE &&
+ has_vdw[2] == FALSE &&
+ tmp_charge[0] != 0 &&
+ tmp_charge[1] != 0 &&
+ tmp_charge[2] == tmp_charge[1])
+ {
+ srenew(solvent_parameters, *n_solvent_parameters+1);
+ solvent_parameters[*n_solvent_parameters].model = esolSPC;
+ solvent_parameters[*n_solvent_parameters].count = nmol;
+ for (k = 0; k < 3; k++)
+ {
+ solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
+ solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
+ }
+
+ *cg_sp = *n_solvent_parameters;
+ (*n_solvent_parameters)++;
+ }
+ }
+ else if (nj == 4)
+ {
+ /* Or could it be a TIP4P?
+ * For this we require thatn atoms 2,3,4 have charge, but not atom 1.
+ * Only atom 1 mght have VdW.
+ */
+ if (has_vdw[1] == FALSE &&
+ has_vdw[2] == FALSE &&
+ has_vdw[3] == FALSE &&
+ tmp_charge[0] == 0 &&
+ tmp_charge[1] != 0 &&
+ tmp_charge[2] == tmp_charge[1] &&
+ tmp_charge[3] != 0)
+ {
+ srenew(solvent_parameters, *n_solvent_parameters+1);
+ solvent_parameters[*n_solvent_parameters].model = esolTIP4P;
+ solvent_parameters[*n_solvent_parameters].count = nmol;
+ for (k = 0; k < 4; k++)
+ {
+ solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
+ solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
+ }
+
+ *cg_sp = *n_solvent_parameters;
+ (*n_solvent_parameters)++;
+ }
+ }
+
+ *solvent_parameters_p = solvent_parameters;
+}
+
+static void
+check_solvent(FILE * fp,
+ const gmx_mtop_t * mtop,
+ t_forcerec * fr,
+ 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 n_solvent_parameters;
+ solvent_parameters_t *solvent_parameters;
+ int **cg_sp;
+ int bestsp, bestsol;
+
+ if (debug)
+ {
+ 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++)
+ {
+ molt = &mtop->moltype[mtop->molblock[mb].type];
+ cgs = &molt->cgs;
+ /* Here we have to loop over all individual molecules
+ * because we need to check for QMMM particles.
+ */
+ snew(cg_sp[mb], cginfo_mb[mb].cg_mod);
+ nmol_ch = cginfo_mb[mb].cg_mod/cgs->nr;
+ nmol = mtop->molblock[mb].nmol/nmol_ch;
+ for (mol = 0; mol < nmol_ch; mol++)
+ {
+ cgm = mol*cgs->nr;
+ am = mol*cgs->index[cgs->nr];
+ for (cg_mol = 0; cg_mol < cgs->nr; cg_mol++)
+ {
+ check_solvent_cg(molt, cg_mol, nmol,
+ mtop->groups.grpnr[egcQMMM] ?
+ mtop->groups.grpnr[egcQMMM]+at_offset+am : 0,
+ &mtop->groups.grps[egcQMMM],
+ fr,
+ &n_solvent_parameters, &solvent_parameters,
+ cginfo_mb[mb].cginfo[cgm+cg_mol],
+ &cg_sp[mb][cgm+cg_mol]);
+ }
+ }
+ cg_offset += cgs->nr;
+ at_offset += cgs->index[cgs->nr];
+ }
+
+ /* Puh! We finished going through all charge groups.
+ * Now find the most common solvent model.
+ */
+
+ /* Most common solvent this far */
+ bestsp = -2;
+ for (i = 0; i < n_solvent_parameters; i++)
+ {
+ if (bestsp == -2 ||
+ solvent_parameters[i].count > solvent_parameters[bestsp].count)
+ {
+ bestsp = i;
+ }
+ }
+
+ if (bestsp >= 0)
+ {
+ bestsol = solvent_parameters[bestsp].model;
+ }
+ else
+ {
+ bestsol = esolNO;
+ }
+
+#ifdef DISABLE_WATER_NLIST
+ bestsol = esolNO;
+#endif
+
+ fr->nWatMol = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ cgs = &mtop->moltype[mtop->molblock[mb].type].cgs;
+ nmol = (mtop->molblock[mb].nmol*cgs->nr)/cginfo_mb[mb].cg_mod;
+ for (i = 0; i < cginfo_mb[mb].cg_mod; i++)
+ {
+ if (cg_sp[mb][i] == bestsp)
+ {
+ SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], bestsol);
+ fr->nWatMol += nmol;
+ }
+ else
+ {
+ SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], esolNO);
+ }
+ }
+ sfree(cg_sp[mb]);
+ }
+ sfree(cg_sp);
+
+ if (bestsol != esolNO && fp != NULL)
+ {
+ fprintf(fp, "\nEnabling %s-like water optimization for %d molecules.\n\n",
+ esol_names[bestsol],
+ solvent_parameters[bestsp].count);
+ }
+
+ sfree(solvent_parameters);
+ fr->solvent_opt = bestsol;
+}
+
+enum {
+ acNONE = 0, acCONSTRAINT, acSETTLE
+};
+
+static cginfo_mb_t *init_cginfo_mb(FILE *fplog, const gmx_mtop_t *mtop,
+ t_forcerec *fr, gmx_bool bNoSolvOpt,
+ gmx_bool *bExcl_IntraCGAll_InterCGNone)
+{
+ const t_block *cgs;
+ const t_blocka *excl;
+ const gmx_moltype_t *molt;
+ const gmx_molblock_t *molb;
+ 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 *a_con;
+ int ftype;
+ int ia;
+ gmx_bool bId, *bExcl, bExclIntraAll, bExclInter, bHaveVDW, bHaveQ;
+
+ ncg_tot = ncg_mtop(mtop);
+ snew(cginfo_mb, mtop->nmolblock);
+
+ snew(type_VDW, fr->ntype);
+ for (ai = 0; ai < fr->ntype; ai++)
+ {
+ type_VDW[ai] = FALSE;
+ for (j = 0; j < fr->ntype; j++)
+ {
+ type_VDW[ai] = type_VDW[ai] ||
+ fr->bBHAM ||
+ C6(fr->nbfp, fr->ntype, ai, j) != 0 ||
+ C12(fr->nbfp, fr->ntype, ai, j) != 0;
+ }
+ }
+
+ *bExcl_IntraCGAll_InterCGNone = TRUE;
+
+ excl_nalloc = 10;
+ snew(bExcl, excl_nalloc);
+ cg_offset = 0;
+ a_offset = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molb = &mtop->molblock[mb];
+ molt = &mtop->moltype[molb->type];
+ cgs = &molt->cgs;
+ excl = &molt->excls;
+
+ /* Check if the cginfo is identical for all molecules in this block.
+ * If so, we only need an array of the size of one molecule.
+ * 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];
+ for (cg = 0; cg < cgs->nr; cg++)
+ {
+ a0 = cgs->index[cg];
+ a1 = cgs->index[cg+1];
+ if (ggrpnr(&mtop->groups, egcENER, a_offset+am+a0) !=
+ ggrpnr(&mtop->groups, egcENER, a_offset +a0))
+ {
+ bId = FALSE;
+ }
+ if (mtop->groups.grpnr[egcQMMM] != NULL)
+ {
+ for (ai = a0; ai < a1; ai++)
+ {
+ if (mtop->groups.grpnr[egcQMMM][a_offset+am+ai] !=
+ mtop->groups.grpnr[egcQMMM][a_offset +ai])
+ {
+ bId = FALSE;
+ }
+ }
+ }
+ }
+ }
+
+ cginfo_mb[mb].cg_start = cg_offset;
+ cginfo_mb[mb].cg_end = cg_offset + molb->nmol*cgs->nr;
+ cginfo_mb[mb].cg_mod = (bId ? 1 : molb->nmol)*cgs->nr;
+ snew(cginfo_mb[mb].cginfo, cginfo_mb[mb].cg_mod);
+ cginfo = cginfo_mb[mb].cginfo;
+
+ /* Set constraints flags for constrained atoms */
+ snew(a_con, molt->atoms.nr);
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (interaction_function[ftype].flags & IF_CONSTRAINT)
+ {
+ int nral;
+
+ nral = NRAL(ftype);
+ for (ia = 0; ia < molt->ilist[ftype].nr; ia += 1+nral)
+ {
+ int a;
+
+ for (a = 0; a < nral; a++)
+ {
+ a_con[molt->ilist[ftype].iatoms[ia+1+a]] =
+ (ftype == F_SETTLE ? acSETTLE : acCONSTRAINT);
+ }
+ }
+ }
+ }
+
+ for (m = 0; m < (bId ? 1 : molb->nmol); m++)
+ {
+ cgm = m*cgs->nr;
+ am = m*cgs->index[cgs->nr];
+ for (cg = 0; cg < cgs->nr; cg++)
+ {
+ a0 = cgs->index[cg];
+ a1 = cgs->index[cg+1];
+
+ /* Store the energy group in cginfo */
+ gid = ggrpnr(&mtop->groups, egcENER, a_offset+am+a0);
+ SET_CGINFO_GID(cginfo[cgm+cg], gid);
+
+ /* Check the intra/inter charge group exclusions */
+ if (a1-a0 > excl_nalloc)
+ {
+ excl_nalloc = a1 - a0;
+ srenew(bExcl, excl_nalloc);
+ }
+ /* bExclIntraAll: all intra cg interactions excluded
+ * bExclInter: any inter cg interactions excluded
+ */
+ bExclIntraAll = TRUE;
+ bExclInter = FALSE;
+ bHaveVDW = FALSE;
+ bHaveQ = FALSE;
+ for (ai = a0; ai < a1; ai++)
+ {
+ /* Check VDW and electrostatic interactions */
+ bHaveVDW = bHaveVDW || (type_VDW[molt->atoms.atom[ai].type] ||
+ type_VDW[molt->atoms.atom[ai].typeB]);
+ bHaveQ = bHaveQ || (molt->atoms.atom[ai].q != 0 ||
+ molt->atoms.atom[ai].qB != 0);
+
+ /* Clear the exclusion list for atom ai */
+ for (aj = a0; aj < a1; aj++)
+ {
+ bExcl[aj-a0] = FALSE;
+ }
+ /* Loop over all the exclusions of atom ai */
+ for (j = excl->index[ai]; j < excl->index[ai+1]; j++)
+ {
+ aj = excl->a[j];
+ if (aj < a0 || aj >= a1)
+ {
+ bExclInter = TRUE;
+ }
+ else
+ {
+ bExcl[aj-a0] = TRUE;
+ }
+ }
+ /* Check if ai excludes a0 to a1 */
+ for (aj = a0; aj < a1; aj++)
+ {
+ if (!bExcl[aj-a0])
+ {
+ bExclIntraAll = FALSE;
+ }
+ }
+
+ switch (a_con[ai])
+ {
+ case acCONSTRAINT:
+ SET_CGINFO_CONSTR(cginfo[cgm+cg]);
+ break;
+ case acSETTLE:
+ SET_CGINFO_SETTLE(cginfo[cgm+cg]);
+ break;
+ default:
+ break;
+ }
+ }
+ if (bExclIntraAll)
+ {
+ SET_CGINFO_EXCL_INTRA(cginfo[cgm+cg]);
+ }
+ if (bExclInter)
+ {
+ SET_CGINFO_EXCL_INTER(cginfo[cgm+cg]);
+ }
+ if (a1 - a0 > MAX_CHARGEGROUP_SIZE)
+ {
+ /* The size in cginfo is currently only read with DD */
+ gmx_fatal(FARGS, "A charge group has size %d which is larger than the limit of %d atoms", a1-a0, MAX_CHARGEGROUP_SIZE);
+ }
+ if (bHaveVDW)
+ {
+ SET_CGINFO_HAS_VDW(cginfo[cgm+cg]);
+ }
+ if (bHaveQ)
+ {
+ SET_CGINFO_HAS_Q(cginfo[cgm+cg]);
+ }
+ /* Store the charge group size */
+ SET_CGINFO_NATOMS(cginfo[cgm+cg], a1-a0);
+
+ if (!bExclIntraAll || bExclInter)
+ {
+ *bExcl_IntraCGAll_InterCGNone = FALSE;
+ }
+ }
+ }
+
+ sfree(a_con);
+
+ cg_offset += molb->nmol*cgs->nr;
+ a_offset += molb->nmol*cgs->index[cgs->nr];
+ }
+ sfree(bExcl);
+
+ /* the solvent optimizer is called after the QM is initialized,
+ * because we don't want to have the QM subsystemto become an
+ * optimized solvent
+ */
+
+ check_solvent(fplog, mtop, fr, cginfo_mb);
+
+ if (getenv("GMX_NO_SOLV_OPT"))
+ {
+ if (fplog)
+ {
+ fprintf(fplog, "Found environment variable GMX_NO_SOLV_OPT.\n"
+ "Disabling all solvent optimization\n");
+ }
+ fr->solvent_opt = esolNO;
+ }
+ if (bNoSolvOpt)
+ {
+ fr->solvent_opt = esolNO;
+ }
+ if (!fr->solvent_opt)
+ {
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ for (cg = 0; cg < cginfo_mb[mb].cg_mod; cg++)
+ {
+ SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[cg], esolNO);
+ }
+ }
+ }
+
+ return cginfo_mb;
+}
+
+static int *cginfo_expand(int nmb, cginfo_mb_t *cgi_mb)
+{
+ int ncg, mb, cg;
+ int *cginfo;
+
+ ncg = cgi_mb[nmb-1].cg_end;
+ snew(cginfo, ncg);
+ mb = 0;
+ for (cg = 0; cg < ncg; cg++)
+ {
+ while (cg >= cgi_mb[mb].cg_end)
+ {
+ mb++;
+ }
+ cginfo[cg] =
+ cgi_mb[mb].cginfo[(cg - cgi_mb[mb].cg_start) % cgi_mb[mb].cg_mod];
+ }
+
+ return cginfo;
+}
+
+static void set_chargesum(FILE *log, t_forcerec *fr, const gmx_mtop_t *mtop)
+{
+ double qsum, q2sum, q;
+ int mb, nmol, i;
+ const t_atoms *atoms;
+
+ qsum = 0;
+ q2sum = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ nmol = mtop->molblock[mb].nmol;
+ atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
+ for (i = 0; i < atoms->nr; i++)
+ {
+ q = atoms->atom[i].q;
+ qsum += nmol*q;
+ q2sum += nmol*q*q;
+ }
+ }
+ fr->qsum[0] = qsum;
+ fr->q2sum[0] = q2sum;
+ if (fr->efep != efepNO)
+ {
+ qsum = 0;
+ q2sum = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ nmol = mtop->molblock[mb].nmol;
+ atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
+ for (i = 0; i < atoms->nr; i++)
+ {
+ q = atoms->atom[i].qB;
+ qsum += nmol*q;
+ q2sum += nmol*q*q;
+ }
+ fr->qsum[1] = qsum;
+ fr->q2sum[1] = q2sum;
+ }
+ }
+ else
+ {
+ fr->qsum[1] = fr->qsum[0];
+ fr->q2sum[1] = fr->q2sum[0];
+ }
+ if (log)
+ {
+ if (fr->efep == efepNO)
+ {
+ fprintf(log, "System total charge: %.3f\n", fr->qsum[0]);
+ }
+ else
+ {
+ fprintf(log, "System total charge, top. A: %.3f top. B: %.3f\n",
+ fr->qsum[0], fr->qsum[1]);
+ }
+ }
+}
+
+void update_forcerec(FILE *log, t_forcerec *fr, matrix box)
+{
+ if (fr->eeltype == eelGRF)
+ {
+ calc_rffac(NULL, fr->eeltype, fr->epsilon_r, fr->epsilon_rf,
+ fr->rcoulomb, fr->temp, fr->zsquare, box,
+ &fr->kappa, &fr->k_rf, &fr->c_rf);
+ }
+}
+
+void set_avcsixtwelve(FILE *fplog, t_forcerec *fr, const gmx_mtop_t *mtop)
+{
+ const t_atoms *atoms, *atoms_tpi;
+ const t_blocka *excl;
+ int mb, nmol, nmolc, i, j, tpi, tpj, j1, j2, k, n, nexcl, q;
+#if (defined SIZEOF_LONG_LONG_INT) && (SIZEOF_LONG_LONG_INT >= 8)
+ long long int npair, npair_ij, tmpi, tmpj;
+#else
+ double npair, npair_ij, tmpi, tmpj;
+#endif
+ double csix, ctwelve;
+ int ntp, *typecount;
+ gmx_bool bBHAM;
+ real *nbfp;
+
+ ntp = fr->ntype;
+ bBHAM = fr->bBHAM;
+ nbfp = fr->nbfp;
+
+ for (q = 0; q < (fr->efep == efepNO ? 1 : 2); q++)
+ {
+ csix = 0;
+ ctwelve = 0;
+ npair = 0;
+ nexcl = 0;
+ if (!fr->n_tpi)
+ {
+ /* Count the types so we avoid natoms^2 operations */
+ snew(typecount, ntp);
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ nmol = mtop->molblock[mb].nmol;
+ atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
+ for (i = 0; i < atoms->nr; i++)
+ {
+ if (q == 0)
+ {
+ tpi = atoms->atom[i].type;
+ }
+ else
+ {
+ tpi = atoms->atom[i].typeB;
+ }
+ typecount[tpi] += nmol;
+ }
+ }
+ for (tpi = 0; tpi < ntp; tpi++)
+ {
+ for (tpj = tpi; tpj < ntp; tpj++)
+ {
+ tmpi = typecount[tpi];
+ tmpj = typecount[tpj];
+ if (tpi != tpj)
+ {
+ npair_ij = tmpi*tmpj;
+ }
+ else
+ {
+ npair_ij = tmpi*(tmpi - 1)/2;
+ }
+ if (bBHAM)
+ {
+ /* nbfp now includes the 6.0 derivative prefactor */
+ csix += npair_ij*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
+ }
+ else
+ {
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ csix += npair_ij* C6(nbfp, ntp, tpi, tpj)/6.0;
+ ctwelve += npair_ij* C12(nbfp, ntp, tpi, tpj)/12.0;
+ }
+ npair += npair_ij;
+ }
+ }
+ sfree(typecount);
+ /* Subtract the excluded pairs.
+ * The main reason for substracting exclusions is that in some cases
+ * some combinations might never occur and the parameters could have
+ * any value. These unused values should not influence the dispersion
+ * correction.
+ */
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ nmol = mtop->molblock[mb].nmol;
+ atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
+ excl = &mtop->moltype[mtop->molblock[mb].type].excls;
+ for (i = 0; (i < atoms->nr); i++)
+ {
+ if (q == 0)
+ {
+ tpi = atoms->atom[i].type;
+ }
+ else
+ {
+ tpi = atoms->atom[i].typeB;
+ }
+ j1 = excl->index[i];
+ j2 = excl->index[i+1];
+ for (j = j1; j < j2; j++)
+ {
+ k = excl->a[j];
+ if (k > i)
+ {
+ if (q == 0)
+ {
+ tpj = atoms->atom[k].type;
+ }
+ else
+ {
+ tpj = atoms->atom[k].typeB;
+ }
+ if (bBHAM)
+ {
+ /* nbfp now includes the 6.0 derivative prefactor */
+ csix -= nmol*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
+ }
+ else
+ {
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ csix -= nmol*C6 (nbfp, ntp, tpi, tpj)/6.0;
+ ctwelve -= nmol*C12(nbfp, ntp, tpi, tpj)/12.0;
+ }
+ nexcl += nmol;
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ /* Only correct for the interaction of the test particle
+ * with the rest of the system.
+ */
+ atoms_tpi =
+ &mtop->moltype[mtop->molblock[mtop->nmolblock-1].type].atoms;
+
+ npair = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ nmol = mtop->molblock[mb].nmol;
+ atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
+ for (j = 0; j < atoms->nr; j++)
+ {
+ nmolc = nmol;
+ /* Remove the interaction of the test charge group
+ * with itself.
+ */
+ if (mb == mtop->nmolblock-1)
+ {
+ nmolc--;
+
+ if (mb == 0 && nmol == 1)
+ {
+ gmx_fatal(FARGS, "Old format tpr with TPI, please generate a new tpr file");
+ }
+ }
+ if (q == 0)
+ {
+ tpj = atoms->atom[j].type;
+ }
+ else
+ {
+ tpj = atoms->atom[j].typeB;
+ }
+ for (i = 0; i < fr->n_tpi; i++)
+ {
+ if (q == 0)
+ {
+ tpi = atoms_tpi->atom[i].type;
+ }
+ else
+ {
+ tpi = atoms_tpi->atom[i].typeB;
+ }
+ if (bBHAM)
+ {
+ /* nbfp now includes the 6.0 derivative prefactor */
+ csix += nmolc*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
+ }
+ else
+ {
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ csix += nmolc*C6 (nbfp, ntp, tpi, tpj)/6.0;
+ ctwelve += nmolc*C12(nbfp, ntp, tpi, tpj)/12.0;
+ }
+ npair += nmolc;
+ }
+ }
+ }
+ }
+ if (npair - nexcl <= 0 && fplog)
+ {
+ fprintf(fplog, "\nWARNING: There are no atom pairs for dispersion correction\n\n");
+ csix = 0;
+ ctwelve = 0;
+ }
+ else
+ {
+ csix /= npair - nexcl;
+ ctwelve /= npair - nexcl;
+ }
+ if (debug)
+ {
+ fprintf(debug, "Counted %d exclusions\n", nexcl);
+ fprintf(debug, "Average C6 parameter is: %10g\n", (double)csix);
+ fprintf(debug, "Average C12 parameter is: %10g\n", (double)ctwelve);
+ }
+ fr->avcsix[q] = csix;
+ fr->avctwelve[q] = ctwelve;
+ }
+ if (fplog != NULL)
+ {
+ if (fr->eDispCorr == edispcAllEner ||
+ fr->eDispCorr == edispcAllEnerPres)
+ {
+ fprintf(fplog, "Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
+ fr->avcsix[0], fr->avctwelve[0]);
+ }
+ else
+ {
+ fprintf(fplog, "Long Range LJ corr.: <C6> %10.4e\n", fr->avcsix[0]);
+ }
+ }
+}
+
+
+static void set_bham_b_max(FILE *fplog, t_forcerec *fr,
+ const gmx_mtop_t *mtop)
+{
+ const t_atoms *at1, *at2;
+ int mt1, mt2, i, j, tpi, tpj, ntypes;
+ real b, bmin;
+ real *nbfp;
+
+ if (fplog)
+ {
+ fprintf(fplog, "Determining largest Buckingham b parameter for table\n");
+ }
+ nbfp = fr->nbfp;
+ ntypes = fr->ntype;
+
+ bmin = -1;
+ fr->bham_b_max = 0;
+ for (mt1 = 0; mt1 < mtop->nmoltype; mt1++)
+ {
+ at1 = &mtop->moltype[mt1].atoms;
+ for (i = 0; (i < at1->nr); i++)
+ {
+ tpi = at1->atom[i].type;
+ if (tpi >= ntypes)
+ {
+ gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", i, tpi, ntypes);
+ }
+
+ for (mt2 = mt1; mt2 < mtop->nmoltype; mt2++)
+ {
+ at2 = &mtop->moltype[mt2].atoms;
+ for (j = 0; (j < at2->nr); j++)
+ {
+ tpj = at2->atom[j].type;
+ if (tpj >= ntypes)
+ {
+ gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", j, tpj, ntypes);
+ }
+ b = BHAMB(nbfp, ntypes, tpi, tpj);
+ if (b > fr->bham_b_max)
+ {
+ fr->bham_b_max = b;
+ }
+ if ((b < bmin) || (bmin == -1))
+ {
+ bmin = b;
+ }
+ }
+ }
+ }
+ }
+ if (fplog)
+ {
+ fprintf(fplog, "Buckingham b parameters, min: %g, max: %g\n",
+ bmin, fr->bham_b_max);
+ }
+}
+
+static void make_nbf_tables(FILE *fp, const output_env_t oenv,
+ t_forcerec *fr, real rtab,
+ const t_commrec *cr,
+ const char *tabfn, char *eg1, char *eg2,
+ t_nblists *nbl)
+{
+ char buf[STRLEN];
+ int i, j;
+
+ if (tabfn == NULL)
+ {
+ if (debug)
+ {
+ fprintf(debug, "No table file name passed, can not read table, can not do non-bonded interactions\n");
+ }
+ return;
+ }
+
+ sprintf(buf, "%s", tabfn);
+ if (eg1 && eg2)
+ {
+ /* Append the two energy group names */
+ sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
+ eg1, eg2, ftp2ext(efXVG));
+ }
+ nbl->table_elec_vdw = make_tables(fp, oenv, fr, MASTER(cr), buf, rtab, 0);
+ /* Copy the contents of the table to separate coulomb and LJ tables too,
+ * to improve cache performance.
+ */
+ /* For performance reasons we want
+ * the table data to be aligned to 16-byte. The pointers could be freed
+ * but currently aren't.
+ */
+ nbl->table_elec.interaction = GMX_TABLE_INTERACTION_ELEC;
+ nbl->table_elec.format = nbl->table_elec_vdw.format;
+ nbl->table_elec.r = nbl->table_elec_vdw.r;
+ nbl->table_elec.n = nbl->table_elec_vdw.n;
+ nbl->table_elec.scale = nbl->table_elec_vdw.scale;
+ nbl->table_elec.scale_exp = nbl->table_elec_vdw.scale_exp;
+ nbl->table_elec.formatsize = nbl->table_elec_vdw.formatsize;
+ nbl->table_elec.ninteractions = 1;
+ nbl->table_elec.stride = nbl->table_elec.formatsize * nbl->table_elec.ninteractions;
+ snew_aligned(nbl->table_elec.data, nbl->table_elec.stride*(nbl->table_elec.n+1), 32);
+
+ nbl->table_vdw.interaction = GMX_TABLE_INTERACTION_VDWREP_VDWDISP;
+ nbl->table_vdw.format = nbl->table_elec_vdw.format;
+ nbl->table_vdw.r = nbl->table_elec_vdw.r;
+ nbl->table_vdw.n = nbl->table_elec_vdw.n;
+ nbl->table_vdw.scale = nbl->table_elec_vdw.scale;
+ nbl->table_vdw.scale_exp = nbl->table_elec_vdw.scale_exp;
+ nbl->table_vdw.formatsize = nbl->table_elec_vdw.formatsize;
+ nbl->table_vdw.ninteractions = 2;
+ nbl->table_vdw.stride = nbl->table_vdw.formatsize * nbl->table_vdw.ninteractions;
+ snew_aligned(nbl->table_vdw.data, nbl->table_vdw.stride*(nbl->table_vdw.n+1), 32);
+
+ for (i = 0; i <= nbl->table_elec_vdw.n; i++)
+ {
+ for (j = 0; j < 4; j++)
+ {
+ nbl->table_elec.data[4*i+j] = nbl->table_elec_vdw.data[12*i+j];
+ }
+ for (j = 0; j < 8; j++)
+ {
+ nbl->table_vdw.data[8*i+j] = nbl->table_elec_vdw.data[12*i+4+j];
+ }
+ }
+}
+
+static void count_tables(int ftype1, int ftype2, const gmx_mtop_t *mtop,
+ int *ncount, int **count)
+{
+ const gmx_moltype_t *molt;
+ const t_ilist *il;
+ int mt, ftype, stride, i, j, tabnr;
+
+ for (mt = 0; mt < mtop->nmoltype; mt++)
+ {
+ molt = &mtop->moltype[mt];
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (ftype == ftype1 || ftype == ftype2)
+ {
+ il = &molt->ilist[ftype];
+ stride = 1 + NRAL(ftype);
+ for (i = 0; i < il->nr; i += stride)
+ {
+ tabnr = mtop->ffparams.iparams[il->iatoms[i]].tab.table;
+ if (tabnr < 0)
+ {
+ gmx_fatal(FARGS, "A bonded table number is smaller than 0: %d\n", tabnr);
+ }
+ if (tabnr >= *ncount)
+ {
+ srenew(*count, tabnr+1);
+ for (j = *ncount; j < tabnr+1; j++)
+ {
+ (*count)[j] = 0;
+ }
+ *ncount = tabnr+1;
+ }
+ (*count)[tabnr]++;
+ }
+ }
+ }
+ }
+}
+
+static bondedtable_t *make_bonded_tables(FILE *fplog,
+ int ftype1, int ftype2,
+ const gmx_mtop_t *mtop,
+ const char *basefn, const char *tabext)
+{
+ int i, ncount, *count;
+ char tabfn[STRLEN];
+ bondedtable_t *tab;
+
+ tab = NULL;
+
+ ncount = 0;
+ count = NULL;
+ count_tables(ftype1, ftype2, mtop, &ncount, &count);
+
+ if (ncount > 0)
+ {
+ snew(tab, ncount);
+ for (i = 0; i < ncount; i++)
+ {
+ if (count[i] > 0)
+ {
+ sprintf(tabfn, "%s", basefn);
+ sprintf(tabfn + strlen(basefn) - strlen(ftp2ext(efXVG)) - 1, "_%s%d.%s",
+ tabext, i, ftp2ext(efXVG));
+ tab[i] = make_bonded_table(fplog, tabfn, NRAL(ftype1)-2);
+ }
+ }
+ sfree(count);
+ }
+
+ return tab;
+}
+
+void forcerec_set_ranges(t_forcerec *fr,
+ int ncg_home, int ncg_force,
+ int natoms_force,
+ int natoms_force_constr, int natoms_f_novirsum)
+{
+ fr->cg0 = 0;
+ fr->hcg = ncg_home;
+
+ /* fr->ncg_force is unused in the standard code,
+ * but it can be useful for modified code dealing with charge groups.
+ */
+ fr->ncg_force = ncg_force;
+ fr->natoms_force = natoms_force;
+ fr->natoms_force_constr = natoms_force_constr;
+
+ if (fr->natoms_force_constr > fr->nalloc_force)
+ {
+ fr->nalloc_force = over_alloc_dd(fr->natoms_force_constr);
+
+ if (fr->bTwinRange)
+ {
+ srenew(fr->f_twin, fr->nalloc_force);
+ }
+ }
+
+ if (fr->bF_NoVirSum)
+ {
+ fr->f_novirsum_n = natoms_f_novirsum;
+ if (fr->f_novirsum_n > fr->f_novirsum_nalloc)
+ {
+ fr->f_novirsum_nalloc = over_alloc_dd(fr->f_novirsum_n);
+ srenew(fr->f_novirsum_alloc, fr->f_novirsum_nalloc);
+ }
+ }
+ else
+ {
+ fr->f_novirsum_n = 0;
+ }
+}
+
+static real cutoff_inf(real cutoff)
+{
+ if (cutoff == 0)
+ {
+ cutoff = GMX_CUTOFF_INF;
+ }
+
+ return cutoff;
+}
+
+static void make_adress_tf_tables(FILE *fp, const output_env_t oenv,
+ t_forcerec *fr, const t_inputrec *ir,
+ const char *tabfn, const gmx_mtop_t *mtop,
+ matrix box)
+{
+ char buf[STRLEN];
+ int i, j;
+
+ if (tabfn == NULL)
+ {
+ gmx_fatal(FARGS, "No thermoforce table file given. Use -tabletf to specify a file\n");
+ return;
+ }
+
+ snew(fr->atf_tabs, ir->adress->n_tf_grps);
+
+ sprintf(buf, "%s", tabfn);
+ for (i = 0; i < ir->adress->n_tf_grps; i++)
+ {
+ j = ir->adress->tf_table_index[i]; /* get energy group index */
+ sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "tf_%s.%s",
+ *(mtop->groups.grpname[mtop->groups.grps[egcENER].nm_ind[j]]), ftp2ext(efXVG));
+ if (fp)
+ {
+ fprintf(fp, "loading tf table for energygrp index %d from %s\n", ir->adress->tf_table_index[i], buf);
+ }
+ fr->atf_tabs[i] = make_atf_table(fp, oenv, fr, buf, box);
+ }
+
+}
+
+gmx_bool can_use_allvsall(const t_inputrec *ir, const gmx_mtop_t *mtop,
+ gmx_bool bPrintNote, t_commrec *cr, FILE *fp)
+{
+ gmx_bool bAllvsAll;
+
+ bAllvsAll =
+ (
+ ir->rlist == 0 &&
+ ir->rcoulomb == 0 &&
+ ir->rvdw == 0 &&
+ ir->ePBC == epbcNONE &&
+ ir->vdwtype == evdwCUT &&
+ ir->coulombtype == eelCUT &&
+ ir->efep == efepNO &&
+ (ir->implicit_solvent == eisNO ||
+ (ir->implicit_solvent == eisGBSA && (ir->gb_algorithm == egbSTILL ||
+ ir->gb_algorithm == egbHCT ||
+ ir->gb_algorithm == egbOBC))) &&
+ getenv("GMX_NO_ALLVSALL") == NULL
+ );
+
+ if (bAllvsAll && ir->opts.ngener > 1)
+ {
+ const char *note = "NOTE: Can not use all-vs-all force loops, because there are multiple energy monitor groups; you might get significantly higher performance when using only a single energy monitor group.\n";
+
+ if (bPrintNote)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "\n%s\n", note);
+ }
+ if (fp != NULL)
+ {
+ fprintf(fp, "\n%s\n", note);
+ }
+ }
+ bAllvsAll = FALSE;
+ }
+
+ if (bAllvsAll && fp && MASTER(cr))
+ {
+ fprintf(fp, "\nUsing accelerated all-vs-all kernels.\n\n");
+ }
+
+ return bAllvsAll;
+}
+
+
+static void init_forcerec_f_threads(t_forcerec *fr, int nenergrp)
+{
+ int t, i;
+
+ /* These thread local data structures are used for bondeds only */
+ fr->nthreads = gmx_omp_nthreads_get(emntBonded);
+
+ if (fr->nthreads > 1)
+ {
+ snew(fr->f_t, fr->nthreads);
+ /* Thread 0 uses the global force and energy arrays */
+ for (t = 1; t < fr->nthreads; t++)
+ {
+ fr->f_t[t].f = NULL;
+ fr->f_t[t].f_nalloc = 0;
+ snew(fr->f_t[t].fshift, SHIFTS);
+ fr->f_t[t].grpp.nener = nenergrp*nenergrp;
+ for (i = 0; i < egNR; i++)
+ {
+ snew(fr->f_t[t].grpp.ener[i], fr->f_t[t].grpp.nener);
+ }
+ }
+ }
+}
+
+
+static void pick_nbnxn_kernel_cpu(FILE *fp,
+ const t_commrec *cr,
+ const gmx_cpuid_t cpuid_info,
+ const t_inputrec *ir,
+ int *kernel_type,
+ int *ewald_excl)
+{
+ *kernel_type = nbnxnk4x4_PlainC;
+ *ewald_excl = ewaldexclTable;
+
+#ifdef GMX_NBNXN_SIMD
+ {
+#ifdef GMX_NBNXN_SIMD_4XN
+ *kernel_type = nbnxnk4xN_SIMD_4xN;
+#endif
+#ifdef GMX_NBNXN_SIMD_2XNN
+ /* We expect the 2xNN kernels to be faster in most cases */
+ *kernel_type = nbnxnk4xN_SIMD_2xNN;
+#endif
+
+#if defined GMX_NBNXN_SIMD_4XN && defined GMX_X86_AVX_256
+ if (EEL_RF(ir->coulombtype) || ir->coulombtype == eelCUT)
+ {
+ /* The raw pair rate of the 4x8 kernel is higher than 2x(4+4),
+ * 10% with HT, 50% without HT, but extra zeros interactions
+ * can compensate. As we currently don't detect the actual use
+ * of HT, switch to 4x8 to avoid a potential performance hit.
+ */
+ *kernel_type = nbnxnk4xN_SIMD_4xN;
+ }
+#endif
+ if (getenv("GMX_NBNXN_SIMD_4XN") != NULL)
+ {
+#ifdef GMX_NBNXN_SIMD_4XN
+ *kernel_type = nbnxnk4xN_SIMD_4xN;
+#else
+ gmx_fatal(FARGS, "SIMD 4xN kernels requested, but Gromacs has been compiled without support for these kernels");
+#endif
+ }
+ if (getenv("GMX_NBNXN_SIMD_2XNN") != NULL)
+ {
+#ifdef GMX_NBNXN_SIMD_2XNN
+ *kernel_type = nbnxnk4xN_SIMD_2xNN;
+#else
+ gmx_fatal(FARGS, "SIMD 2x(N+N) kernels requested, but Gromacs has been compiled without support for these kernels");
+#endif
+ }
+
+ /* Analytical Ewald exclusion correction is only an option in the
+ * x86 SIMD kernel. This is faster in single precision
+ * on Bulldozer and slightly faster on Sandy Bridge.
+ */
+#if (defined GMX_X86_AVX_128_FMA || defined GMX_X86_AVX_256) && !defined GMX_DOUBLE
+ *ewald_excl = ewaldexclAnalytical;
+#endif
+ if (getenv("GMX_NBNXN_EWALD_TABLE") != NULL)
+ {
+ *ewald_excl = ewaldexclTable;
+ }
+ if (getenv("GMX_NBNXN_EWALD_ANALYTICAL") != NULL)
+ {
+ *ewald_excl = ewaldexclAnalytical;
+ }
+
+ }
+#endif /* GMX_X86_SSE2 */
+}
+
+
+const char *lookup_nbnxn_kernel_name(int kernel_type)
+{
+ const char *returnvalue = NULL;
+ switch (kernel_type)
+ {
+ case nbnxnkNotSet: returnvalue = "not set"; break;
+ case nbnxnk4x4_PlainC: returnvalue = "plain C"; break;
+#ifndef GMX_NBNXN_SIMD
+ case nbnxnk4xN_SIMD_4xN: returnvalue = "not available"; break;
+ case nbnxnk4xN_SIMD_2xNN: returnvalue = "not available"; break;
+#else
+#ifdef GMX_X86_SSE2
+#if GMX_NBNXN_SIMD_BITWIDTH == 128
+ /* x86 SIMD intrinsics can be converted to either SSE or AVX depending
+ * on compiler flags. As we use nearly identical intrinsics, using an AVX
+ * compiler flag without an AVX macro effectively results in AVX kernels.
+ * For gcc we check for __AVX__
+ * At least a check for icc should be added (if there is a macro)
+ */
+#if !(defined GMX_X86_AVX_128_FMA || defined __AVX__)
+#ifndef GMX_X86_SSE4_1
+ case nbnxnk4xN_SIMD_4xN: returnvalue = "SSE2"; break;
+ case nbnxnk4xN_SIMD_2xNN: returnvalue = "SSE2"; break;
+#else
+ case nbnxnk4xN_SIMD_4xN: returnvalue = "SSE4.1"; break;
+ case nbnxnk4xN_SIMD_2xNN: returnvalue = "SSE4.1"; break;
+#endif
+#else
+ case nbnxnk4xN_SIMD_4xN: returnvalue = "AVX-128"; break;
+ case nbnxnk4xN_SIMD_2xNN: returnvalue = "AVX-128"; break;
+#endif
+#endif
+#if GMX_NBNXN_SIMD_BITWIDTH == 256
+ case nbnxnk4xN_SIMD_4xN: returnvalue = "AVX-256"; break;
+ case nbnxnk4xN_SIMD_2xNN: returnvalue = "AVX-256"; break;
+#endif
+#else /* not GMX_X86_SSE2 */
+ case nbnxnk4xN_SIMD_4xN: returnvalue = "SIMD"; break;
+ case nbnxnk4xN_SIMD_2xNN: returnvalue = "SIMD"; break;
+#endif
+#endif
+ case nbnxnk8x8x8_CUDA: returnvalue = "CUDA"; break;
+ case nbnxnk8x8x8_PlainC: returnvalue = "plain C"; break;
+
+ case nbnxnkNR:
+ default:
+ gmx_fatal(FARGS, "Illegal kernel type selected");
+ returnvalue = NULL;
+ break;
+ }
+ return returnvalue;
+};
+
+static void pick_nbnxn_kernel(FILE *fp,
+ const t_commrec *cr,
+ const gmx_hw_info_t *hwinfo,
+ gmx_bool use_cpu_acceleration,
+ gmx_bool bUseGPU,
+ gmx_bool bEmulateGPU,
+ const t_inputrec *ir,
+ int *kernel_type,
+ int *ewald_excl,
+ gmx_bool bDoNonbonded)
+{
+ assert(kernel_type);
+
+ *kernel_type = nbnxnkNotSet;
+ *ewald_excl = ewaldexclTable;
+
+ if (bEmulateGPU)
+ {
+ *kernel_type = nbnxnk8x8x8_PlainC;
+
+ if (bDoNonbonded)
+ {
+ md_print_warn(cr, fp, "Emulating a GPU run on the CPU (slow)");
+ }
+ }
+ else if (bUseGPU)
+ {
+ *kernel_type = nbnxnk8x8x8_CUDA;
+ }
+
+ if (*kernel_type == nbnxnkNotSet)
+ {
+ if (use_cpu_acceleration)
+ {
+ pick_nbnxn_kernel_cpu(fp, cr, hwinfo->cpuid_info, ir,
+ kernel_type, ewald_excl);
+ }
+ else
+ {
+ *kernel_type = nbnxnk4x4_PlainC;
+ }
+ }
+
+ if (bDoNonbonded && fp != NULL)
+ {
+ fprintf(fp, "\nUsing %s %dx%d non-bonded kernels\n\n",
+ lookup_nbnxn_kernel_name(*kernel_type),
+ nbnxn_kernel_pairlist_simple(*kernel_type) ? NBNXN_CPU_CLUSTER_I_SIZE : NBNXN_GPU_CLUSTER_SIZE,
+ nbnxn_kernel_to_cj_size(*kernel_type));
+ }
+}
+
+static void pick_nbnxn_resources(FILE *fp,
+ const t_commrec *cr,
+ const gmx_hw_info_t *hwinfo,
+ gmx_bool bDoNonbonded,
+ gmx_bool *bUseGPU,
+ gmx_bool *bEmulateGPU)
+{
+ gmx_bool bEmulateGPUEnvVarSet;
+ char gpu_err_str[STRLEN];
+
+ *bUseGPU = FALSE;
+
+ bEmulateGPUEnvVarSet = (getenv("GMX_EMULATE_GPU") != NULL);
+
+ /* Run GPU emulation mode if GMX_EMULATE_GPU is defined. Because
+ * GPUs (currently) only handle non-bonded calculations, we will
+ * automatically switch to emulation if non-bonded calculations are
+ * turned off via GMX_NO_NONBONDED - this is the simple and elegant
+ * way to turn off GPU initialization, data movement, and cleanup.
+ *
+ * GPU emulation can be useful to assess the performance one can expect by
+ * adding GPU(s) to the machine. The conditional below allows this even
+ * if mdrun is compiled without GPU acceleration support.
+ * Note that you should freezing the system as otherwise it will explode.
+ */
+ *bEmulateGPU = (bEmulateGPUEnvVarSet ||
+ (!bDoNonbonded && hwinfo->bCanUseGPU));
+
+ /* Enable GPU mode when GPUs are available or no GPU emulation is requested.
+ */
+ if (hwinfo->bCanUseGPU && !(*bEmulateGPU))
+ {
+ /* 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, &hwinfo->gpu_info))
+ {
+ /* At this point the init should never fail as we made sure that
+ * we have all the GPUs we need. If it still does, we'll bail. */
+ gmx_fatal(FARGS, "On node %d failed to initialize GPU #%d: %s",
+ cr->nodeid,
+ get_gpu_device_id(&hwinfo->gpu_info, cr->rank_pp_intranode),
+ gpu_err_str);
+ }
+
+ /* Here we actually turn on hardware GPU acceleration */
+ *bUseGPU = TRUE;
+ }
+}
+
+gmx_bool uses_simple_tables(int cutoff_scheme,
+ nonbonded_verlet_t *nbv,
+ int group)
+{
+ gmx_bool bUsesSimpleTables = TRUE;
+ int grp_index;
+
+ switch (cutoff_scheme)
+ {
+ case ecutsGROUP:
+ bUsesSimpleTables = TRUE;
+ break;
+ case ecutsVERLET:
+ assert(NULL != nbv && NULL != nbv->grp);
+ grp_index = (group < 0) ? 0 : (nbv->ngrp - 1);
+ bUsesSimpleTables = nbnxn_kernel_pairlist_simple(nbv->grp[grp_index].kernel_type);
+ break;
+ default:
+ gmx_incons("unimplemented");
+ }
+ return bUsesSimpleTables;
+}
+
+static void init_ewald_f_table(interaction_const_t *ic,
+ gmx_bool bUsesSimpleTables,
+ real rtab)
+{
+ real maxr;
+
+ if (bUsesSimpleTables)
+ {
+ /* With a spacing of 0.0005 we are at the force summation accuracy
+ * for the SSE kernels for "normal" atomistic simulations.
+ */
+ ic->tabq_scale = ewald_spline3_table_scale(ic->ewaldcoeff,
+ ic->rcoulomb);
+
+ maxr = (rtab > ic->rcoulomb) ? rtab : ic->rcoulomb;
+ ic->tabq_size = (int)(maxr*ic->tabq_scale) + 2;
+ }
+ else
+ {
+ ic->tabq_size = GPU_EWALD_COULOMB_FORCE_TABLE_SIZE;
+ /* Subtract 2 iso 1 to avoid access out of range due to rounding */
+ ic->tabq_scale = (ic->tabq_size - 2)/ic->rcoulomb;
+ }
+
+ sfree_aligned(ic->tabq_coul_FDV0);
+ sfree_aligned(ic->tabq_coul_F);
+ sfree_aligned(ic->tabq_coul_V);
+
+ /* Create the original table data in FDV0 */
+ snew_aligned(ic->tabq_coul_FDV0, ic->tabq_size*4, 32);
+ snew_aligned(ic->tabq_coul_F, ic->tabq_size, 32);
+ snew_aligned(ic->tabq_coul_V, ic->tabq_size, 32);
+ table_spline3_fill_ewald_lr(ic->tabq_coul_F, ic->tabq_coul_V, ic->tabq_coul_FDV0,
+ ic->tabq_size, 1/ic->tabq_scale, ic->ewaldcoeff);
+}
+
+void init_interaction_const_tables(FILE *fp,
+ interaction_const_t *ic,
+ gmx_bool bUsesSimpleTables,
+ real rtab)
+{
+ real spacing;
+
+ if (ic->eeltype == eelEWALD || EEL_PME(ic->eeltype))
+ {
+ init_ewald_f_table(ic, bUsesSimpleTables, rtab);
+
+ if (fp != NULL)
+ {
+ fprintf(fp, "Initialized non-bonded Ewald correction tables, spacing: %.2e size: %d\n\n",
+ 1/ic->tabq_scale, ic->tabq_size);
+ }
+ }
+}
+
+void init_interaction_const(FILE *fp,
+ interaction_const_t **interaction_const,
+ const t_forcerec *fr,
+ real rtab)
+{
+ interaction_const_t *ic;
+ gmx_bool bUsesSimpleTables = TRUE;
+
+ snew(ic, 1);
+
+ /* Just allocate something so we can free it */
+ snew_aligned(ic->tabq_coul_FDV0, 16, 32);
+ snew_aligned(ic->tabq_coul_F, 16, 32);
+ snew_aligned(ic->tabq_coul_V, 16, 32);
+
+ ic->rlist = fr->rlist;
+ ic->rlistlong = fr->rlistlong;
+
+ /* Lennard-Jones */
+ ic->rvdw = fr->rvdw;
+ if (fr->vdw_modifier == eintmodPOTSHIFT)
+ {
+ ic->sh_invrc6 = pow(ic->rvdw, -6.0);
+ }
+ else
+ {
+ ic->sh_invrc6 = 0;
+ }
+
+ /* Electrostatics */
+ ic->eeltype = fr->eeltype;
+ ic->rcoulomb = fr->rcoulomb;
+ ic->epsilon_r = fr->epsilon_r;
+ ic->epsfac = fr->epsfac;
+
+ /* Ewald */
+ ic->ewaldcoeff = fr->ewaldcoeff;
+ if (fr->coulomb_modifier == eintmodPOTSHIFT)
+ {
+ ic->sh_ewald = gmx_erfc(ic->ewaldcoeff*ic->rcoulomb);
+ }
+ else
+ {
+ ic->sh_ewald = 0;
+ }
+
+ /* Reaction-field */
+ if (EEL_RF(ic->eeltype))
+ {
+ ic->epsilon_rf = fr->epsilon_rf;
+ ic->k_rf = fr->k_rf;
+ ic->c_rf = fr->c_rf;
+ }
+ else
+ {
+ /* For plain cut-off we might use the reaction-field kernels */
+ ic->epsilon_rf = ic->epsilon_r;
+ ic->k_rf = 0;
+ if (fr->coulomb_modifier == eintmodPOTSHIFT)
+ {
+ ic->c_rf = 1/ic->rcoulomb;
+ }
+ else
+ {
+ ic->c_rf = 0;
+ }
+ }
+
+ if (fp != NULL)
+ {
+ fprintf(fp, "Potential shift: LJ r^-12: %.3f r^-6 %.3f",
+ sqr(ic->sh_invrc6), ic->sh_invrc6);
+ if (ic->eeltype == eelCUT)
+ {
+ fprintf(fp, ", Coulomb %.3f", ic->c_rf);
+ }
+ else if (EEL_PME(ic->eeltype))
+ {
+ fprintf(fp, ", Ewald %.3e", ic->sh_ewald);
+ }
+ fprintf(fp, "\n");
+ }
+
+ *interaction_const = ic;
+
+ if (fr->nbv != NULL && fr->nbv->bUseGPU)
+ {
++ nbnxn_cuda_init_const(fr->nbv->cu_nbv, ic, fr->nbv->grp);
+ }
+
+ bUsesSimpleTables = uses_simple_tables(fr->cutoff_scheme, fr->nbv, -1);
+ init_interaction_const_tables(fp, ic, bUsesSimpleTables, rtab);
+}
+
+static void init_nb_verlet(FILE *fp,
+ nonbonded_verlet_t **nb_verlet,
+ const t_inputrec *ir,
+ const t_forcerec *fr,
+ const t_commrec *cr,
+ const char *nbpu_opt)
+{
+ nonbonded_verlet_t *nbv;
+ int i;
+ char *env;
+ gmx_bool bEmulateGPU, bHybridGPURun = FALSE;
+
+ nbnxn_alloc_t *nb_alloc;
+ nbnxn_free_t *nb_free;
+
+ snew(nbv, 1);
+
+ pick_nbnxn_resources(fp, cr, fr->hwinfo,
+ fr->bNonbonded,
+ &nbv->bUseGPU,
+ &bEmulateGPU);
+
+ nbv->nbs = NULL;
+
+ nbv->ngrp = (DOMAINDECOMP(cr) ? 2 : 1);
+ for (i = 0; i < nbv->ngrp; i++)
+ {
+ nbv->grp[i].nbl_lists.nnbl = 0;
+ nbv->grp[i].nbat = NULL;
+ nbv->grp[i].kernel_type = nbnxnkNotSet;
+
+ if (i == 0) /* local */
+ {
+ pick_nbnxn_kernel(fp, cr, fr->hwinfo, fr->use_cpu_acceleration,
+ nbv->bUseGPU, bEmulateGPU,
+ ir,
+ &nbv->grp[i].kernel_type,
+ &nbv->grp[i].ewald_excl,
+ fr->bNonbonded);
+ }
+ else /* non-local */
+ {
+ if (nbpu_opt != NULL && strcmp(nbpu_opt, "gpu_cpu") == 0)
+ {
+ /* Use GPU for local, select a CPU kernel for non-local */
+ pick_nbnxn_kernel(fp, cr, fr->hwinfo, fr->use_cpu_acceleration,
+ FALSE, FALSE,
+ ir,
+ &nbv->grp[i].kernel_type,
+ &nbv->grp[i].ewald_excl,
+ fr->bNonbonded);
+
+ bHybridGPURun = TRUE;
+ }
+ else
+ {
+ /* Use the same kernel for local and non-local interactions */
+ nbv->grp[i].kernel_type = nbv->grp[0].kernel_type;
+ nbv->grp[i].ewald_excl = nbv->grp[0].ewald_excl;
+ }
+ }
+ }
+
+ if (nbv->bUseGPU)
+ {
+ /* init the NxN GPU data; the last argument tells whether we'll have
+ * both local and non-local NB calculation on GPU */
+ nbnxn_cuda_init(fp, &nbv->cu_nbv,
+ &fr->hwinfo->gpu_info, cr->rank_pp_intranode,
+ (nbv->ngrp > 1) && !bHybridGPURun);
+
+ if ((env = getenv("GMX_NB_MIN_CI")) != NULL)
+ {
+ char *end;
+
+ nbv->min_ci_balanced = strtol(env, &end, 10);
+ if (!end || (*end != 0) || nbv->min_ci_balanced <= 0)
+ {
+ gmx_fatal(FARGS, "Invalid value passed in GMX_NB_MIN_CI=%s, positive integer required", env);
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "Neighbor-list balancing parameter: %d (passed as env. var.)\n",
+ nbv->min_ci_balanced);
+ }
+ }
+ else
+ {
+ nbv->min_ci_balanced = nbnxn_cuda_min_ci_balanced(nbv->cu_nbv);
+ if (debug)
+ {
+ fprintf(debug, "Neighbor-list balancing parameter: %d (auto-adjusted to the number of GPU multi-processors)\n",
+ nbv->min_ci_balanced);
+ }
+ }
+ }
+ else
+ {
+ nbv->min_ci_balanced = 0;
+ }
+
+ *nb_verlet = nbv;
+
+ nbnxn_init_search(&nbv->nbs,
+ DOMAINDECOMP(cr) ? &cr->dd->nc : NULL,
+ DOMAINDECOMP(cr) ? domdec_zones(cr->dd) : NULL,
+ gmx_omp_nthreads_get(emntNonbonded));
+
+ for (i = 0; i < nbv->ngrp; i++)
+ {
+ if (nbv->grp[0].kernel_type == nbnxnk8x8x8_CUDA)
+ {
+ nb_alloc = &pmalloc;
+ nb_free = &pfree;
+ }
+ else
+ {
+ nb_alloc = NULL;
+ nb_free = NULL;
+ }
+
+ nbnxn_init_pairlist_set(&nbv->grp[i].nbl_lists,
+ nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
+ /* 8x8x8 "non-simple" lists are ATM always combined */
+ !nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
+ nb_alloc, nb_free);
+
+ if (i == 0 ||
+ nbv->grp[0].kernel_type != nbv->grp[i].kernel_type)
+ {
+ snew(nbv->grp[i].nbat, 1);
+ nbnxn_atomdata_init(fp,
+ nbv->grp[i].nbat,
+ nbv->grp[i].kernel_type,
+ fr->ntype, fr->nbfp,
+ ir->opts.ngener,
+ nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type) ? gmx_omp_nthreads_get(emntNonbonded) : 1,
+ nb_alloc, nb_free);
+ }
+ else
+ {
+ nbv->grp[i].nbat = nbv->grp[0].nbat;
+ }
+ }
+}
+
+void init_forcerec(FILE *fp,
+ const output_env_t oenv,
+ t_forcerec *fr,
+ t_fcdata *fcd,
+ const t_inputrec *ir,
+ const gmx_mtop_t *mtop,
+ const t_commrec *cr,
+ matrix box,
+ gmx_bool bMolEpot,
+ const char *tabfn,
+ const char *tabafn,
+ const char *tabpfn,
+ const char *tabbfn,
+ const char *nbpu_opt,
+ gmx_bool bNoSolvOpt,
+ real print_force)
+{
+ int i, j, m, natoms, ngrp, negp_pp, negptable, egi, egj;
+ real rtab;
+ char *env;
+ double dbl;
+ rvec box_size;
+ const t_block *cgs;
+ gmx_bool bGenericKernelOnly;
+ gmx_bool bTab, bSep14tab, bNormalnblists;
+ t_nblists *nbl;
+ int *nm_ind, egp_flags;
+
+ if (fr->hwinfo == NULL)
+ {
+ /* Detect hardware, gather information.
+ * In mdrun, hwinfo has already been set before calling init_forcerec.
+ * Here we ignore GPUs, as tools will not use them anyhow.
+ */
+ snew(fr->hwinfo, 1);
+ gmx_detect_hardware(fp, fr->hwinfo, cr,
+ FALSE, FALSE, NULL);
+ }
+
+ /* By default we turn acceleration on, but it might be turned off further down... */
+ fr->use_cpu_acceleration = TRUE;
+
+ fr->bDomDec = DOMAINDECOMP(cr);
+
+ natoms = mtop->natoms;
+
+ if (check_box(ir->ePBC, box))
+ {
+ gmx_fatal(FARGS, check_box(ir->ePBC, box));
+ }
+
+ /* Test particle insertion ? */
+ if (EI_TPI(ir->eI))
+ {
+ /* Set to the size of the molecule to be inserted (the last one) */
+ /* Because of old style topologies, we have to use the last cg
+ * instead of the last molecule type.
+ */
+ cgs = &mtop->moltype[mtop->molblock[mtop->nmolblock-1].type].cgs;
+ fr->n_tpi = cgs->index[cgs->nr] - cgs->index[cgs->nr-1];
+ if (fr->n_tpi != mtop->mols.index[mtop->mols.nr] - mtop->mols.index[mtop->mols.nr-1])
+ {
+ gmx_fatal(FARGS, "The molecule to insert can not consist of multiple charge groups.\nMake it a single charge group.");
+ }
+ }
+ else
+ {
+ fr->n_tpi = 0;
+ }
+
+ /* Copy AdResS parameters */
+ if (ir->bAdress)
+ {
+ fr->adress_type = ir->adress->type;
+ fr->adress_const_wf = ir->adress->const_wf;
+ fr->adress_ex_width = ir->adress->ex_width;
+ fr->adress_hy_width = ir->adress->hy_width;
+ fr->adress_icor = ir->adress->icor;
+ fr->adress_site = ir->adress->site;
+ fr->adress_ex_forcecap = ir->adress->ex_forcecap;
+ fr->adress_do_hybridpairs = ir->adress->do_hybridpairs;
+
+
+ snew(fr->adress_group_explicit, ir->adress->n_energy_grps);
+ for (i = 0; i < ir->adress->n_energy_grps; i++)
+ {
+ fr->adress_group_explicit[i] = ir->adress->group_explicit[i];
+ }
+
+ fr->n_adress_tf_grps = ir->adress->n_tf_grps;
+ snew(fr->adress_tf_table_index, fr->n_adress_tf_grps);
+ for (i = 0; i < fr->n_adress_tf_grps; i++)
+ {
+ fr->adress_tf_table_index[i] = ir->adress->tf_table_index[i];
+ }
+ copy_rvec(ir->adress->refs, fr->adress_refs);
+ }
+ else
+ {
+ fr->adress_type = eAdressOff;
+ fr->adress_do_hybridpairs = FALSE;
+ }
+
+ /* Copy the user determined parameters */
+ fr->userint1 = ir->userint1;
+ fr->userint2 = ir->userint2;
+ fr->userint3 = ir->userint3;
+ fr->userint4 = ir->userint4;
+ fr->userreal1 = ir->userreal1;
+ fr->userreal2 = ir->userreal2;
+ fr->userreal3 = ir->userreal3;
+ fr->userreal4 = ir->userreal4;
+
+ /* Shell stuff */
+ fr->fc_stepsize = ir->fc_stepsize;
+
+ /* Free energy */
+ fr->efep = ir->efep;
+ fr->sc_alphavdw = ir->fepvals->sc_alpha;
+ if (ir->fepvals->bScCoul)
+ {
+ fr->sc_alphacoul = ir->fepvals->sc_alpha;
+ fr->sc_sigma6_min = pow(ir->fepvals->sc_sigma_min, 6);
+ }
+ else
+ {
+ fr->sc_alphacoul = 0;
+ fr->sc_sigma6_min = 0; /* only needed when bScCoul is on */
+ }
+ fr->sc_power = ir->fepvals->sc_power;
+ fr->sc_r_power = ir->fepvals->sc_r_power;
+ fr->sc_sigma6_def = pow(ir->fepvals->sc_sigma, 6);
+
+ env = getenv("GMX_SCSIGMA_MIN");
+ if (env != NULL)
+ {
+ dbl = 0;
+ sscanf(env, "%lf", &dbl);
+ fr->sc_sigma6_min = pow(dbl, 6);
+ if (fp)
+ {
+ fprintf(fp, "Setting the minimum soft core sigma to %g nm\n", dbl);
+ }
+ }
+
+ fr->bNonbonded = TRUE;
+ if (getenv("GMX_NO_NONBONDED") != NULL)
+ {
+ /* turn off non-bonded calculations */
+ fr->bNonbonded = FALSE;
+ md_print_warn(cr, fp,
+ "Found environment variable GMX_NO_NONBONDED.\n"
+ "Disabling nonbonded calculations.\n");
+ }
+
+ bGenericKernelOnly = FALSE;
+
+ /* We now check in the NS code whether a particular combination of interactions
+ * can be used with water optimization, and disable it if that is not the case.
+ */
+
+ if (getenv("GMX_NB_GENERIC") != NULL)
+ {
+ if (fp != NULL)
+ {
+ fprintf(fp,
+ "Found environment variable GMX_NB_GENERIC.\n"
+ "Disabling all interaction-specific nonbonded kernels, will only\n"
+ "use the slow generic ones in src/gmxlib/nonbonded/nb_generic.c\n\n");
+ }
+ bGenericKernelOnly = TRUE;
+ }
+
+ if (bGenericKernelOnly == TRUE)
+ {
+ bNoSolvOpt = TRUE;
+ }
+
+ if ( (getenv("GMX_DISABLE_CPU_ACCELERATION") != NULL) || (getenv("GMX_NOOPTIMIZEDKERNELS") != NULL) )
+ {
+ fr->use_cpu_acceleration = FALSE;
+ if (fp != NULL)
+ {
+ fprintf(fp,
+ "\nFound environment variable GMX_DISABLE_CPU_ACCELERATION.\n"
+ "Disabling all CPU architecture-specific (e.g. SSE2/SSE4/AVX) routines.\n\n");
+ }
+ }
+
+ fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
+
+ /* Check if we can/should do all-vs-all kernels */
+ fr->bAllvsAll = can_use_allvsall(ir, mtop, FALSE, NULL, NULL);
+ fr->AllvsAll_work = NULL;
+ fr->AllvsAll_workgb = NULL;
+
++ /* All-vs-all kernels have not been implemented in 4.6, and
++ * the SIMD group kernels are also buggy in this case. Non-accelerated
++ * group kernels are OK. See Redmine #1249. */
++ if (fr->bAllvsAll)
++ {
++ fr->bAllvsAll = FALSE;
++ fr->use_cpu_acceleration = FALSE;
++ if (fp != NULL)
++ {
++ fprintf(fp,
++ "\nYour simulation settings would have triggered the efficient all-vs-all\n"
++ "kernels in GROMACS 4.5, but these have not been implemented in GROMACS\n"
++ "4.6. Also, we can't use the accelerated SIMD kernels here because\n"
++ "of an unfixed bug. The reference C kernels are correct, though, so\n"
++ "we are proceeding by disabling all CPU architecture-specific\n"
++ "(e.g. SSE2/SSE4/AVX) routines. If performance is important, please\n"
++ "use GROMACS 4.5.7 or try cutoff-scheme = Verlet.\n\n");
++ }
++ }
+
+ /* Neighbour searching stuff */
+ fr->cutoff_scheme = ir->cutoff_scheme;
+ fr->bGrid = (ir->ns_type == ensGRID);
+ fr->ePBC = ir->ePBC;
+
+ /* Determine if we will do PBC for distances in bonded interactions */
+ if (fr->ePBC == epbcNONE)
+ {
+ fr->bMolPBC = FALSE;
+ }
+ else
+ {
+ if (!DOMAINDECOMP(cr))
+ {
+ /* The group cut-off scheme and SHAKE assume charge groups
+ * are whole, but not using molpbc is faster in most cases.
+ */
+ if (fr->cutoff_scheme == ecutsGROUP ||
+ (ir->eConstrAlg == econtSHAKE &&
+ (gmx_mtop_ftype_count(mtop, F_CONSTR) > 0 ||
+ gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0)))
+ {
+ fr->bMolPBC = ir->bPeriodicMols;
+ }
+ else
+ {
+ fr->bMolPBC = TRUE;
+ if (getenv("GMX_USE_GRAPH") != NULL)
+ {
+ fr->bMolPBC = FALSE;
+ if (fp)
+ {
+ fprintf(fp, "\nGMX_MOLPBC is set, using the graph for bonded interactions\n\n");
+ }
+ }
+ }
+ }
+ else
+ {
+ fr->bMolPBC = dd_bonded_molpbc(cr->dd, fr->ePBC);
+ }
+ }
+ fr->bGB = (ir->implicit_solvent == eisGBSA);
+
+ fr->rc_scaling = ir->refcoord_scaling;
+ copy_rvec(ir->posres_com, fr->posres_com);
+ copy_rvec(ir->posres_comB, fr->posres_comB);
+ fr->rlist = cutoff_inf(ir->rlist);
+ fr->rlistlong = cutoff_inf(ir->rlistlong);
+ fr->eeltype = ir->coulombtype;
+ fr->vdwtype = ir->vdwtype;
+
+ fr->coulomb_modifier = ir->coulomb_modifier;
+ fr->vdw_modifier = ir->vdw_modifier;
+
+ /* Electrostatics: Translate from interaction-setting-in-mdp-file to kernel interaction format */
+ switch (fr->eeltype)
+ {
+ case eelCUT:
+ fr->nbkernel_elec_interaction = (fr->bGB) ? GMX_NBKERNEL_ELEC_GENERALIZEDBORN : GMX_NBKERNEL_ELEC_COULOMB;
+ break;
+
+ case eelRF:
+ case eelGRF:
+ case eelRF_NEC:
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
+ break;
+
+ case eelRF_ZERO:
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
+ fr->coulomb_modifier = eintmodEXACTCUTOFF;
+ break;
+
+ case eelSWITCH:
+ case eelSHIFT:
+ case eelUSER:
+ case eelENCADSHIFT:
+ case eelPMESWITCH:
+ case eelPMEUSER:
+ case eelPMEUSERSWITCH:
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
+ break;
+
+ case eelPME:
+ case eelEWALD:
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_EWALD;
+ break;
+
+ default:
+ gmx_fatal(FARGS, "Unsupported electrostatic interaction: %s", eel_names[fr->eeltype]);
+ break;
+ }
+
+ /* Vdw: Translate from mdp settings to kernel format */
+ switch (fr->vdwtype)
+ {
+ case evdwCUT:
+ if (fr->bBHAM)
+ {
+ fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_BUCKINGHAM;
+ }
+ else
+ {
+ fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LENNARDJONES;
+ }
+ break;
+
+ case evdwSWITCH:
+ case evdwSHIFT:
+ case evdwUSER:
+ case evdwENCADSHIFT:
+ fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
+ break;
+
+ default:
+ gmx_fatal(FARGS, "Unsupported vdw interaction: %s", evdw_names[fr->vdwtype]);
+ break;
+ }
+
+ /* These start out identical to ir, but might be altered if we e.g. tabulate the interaction in the kernel */
+ fr->nbkernel_elec_modifier = fr->coulomb_modifier;
+ fr->nbkernel_vdw_modifier = fr->vdw_modifier;
+
+ fr->bTwinRange = fr->rlistlong > fr->rlist;
+ fr->bEwald = (EEL_PME(fr->eeltype) || fr->eeltype == eelEWALD);
+
+ fr->reppow = mtop->ffparams.reppow;
+
+ if (ir->cutoff_scheme == ecutsGROUP)
+ {
+ fr->bvdwtab = (fr->vdwtype != evdwCUT ||
+ !gmx_within_tol(fr->reppow, 12.0, 10*GMX_DOUBLE_EPS));
+ /* We have special kernels for standard Ewald and PME, but the pme-switch ones are tabulated above */
+ fr->bcoultab = !(fr->eeltype == eelCUT ||
+ fr->eeltype == eelEWALD ||
+ fr->eeltype == eelPME ||
+ fr->eeltype == eelRF ||
+ fr->eeltype == eelRF_ZERO);
+
+ /* If the user absolutely wants different switch/shift settings for coul/vdw, it is likely
+ * going to be faster to tabulate the interaction than calling the generic kernel.
+ */
+ if (fr->nbkernel_elec_modifier == eintmodPOTSWITCH && fr->nbkernel_vdw_modifier == eintmodPOTSWITCH)
+ {
+ if ((fr->rcoulomb_switch != fr->rvdw_switch) || (fr->rcoulomb != fr->rvdw))
+ {
+ fr->bcoultab = TRUE;
+ }
+ }
+ else if ((fr->nbkernel_elec_modifier == eintmodPOTSHIFT && fr->nbkernel_vdw_modifier == eintmodPOTSHIFT) ||
+ ((fr->nbkernel_elec_interaction == GMX_NBKERNEL_ELEC_REACTIONFIELD &&
+ fr->nbkernel_elec_modifier == eintmodEXACTCUTOFF &&
+ (fr->nbkernel_vdw_modifier == eintmodPOTSWITCH || fr->nbkernel_vdw_modifier == eintmodPOTSHIFT))))
+ {
+ if (fr->rcoulomb != fr->rvdw)
+ {
+ fr->bcoultab = TRUE;
+ }
+ }
+
+ if (getenv("GMX_REQUIRE_TABLES"))
+ {
+ fr->bvdwtab = TRUE;
+ fr->bcoultab = TRUE;
+ }
+
+ if (fp)
+ {
+ fprintf(fp, "Table routines are used for coulomb: %s\n", bool_names[fr->bcoultab]);
+ fprintf(fp, "Table routines are used for vdw: %s\n", bool_names[fr->bvdwtab ]);
+ }
+
+ if (fr->bvdwtab == TRUE)
+ {
+ fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
+ fr->nbkernel_vdw_modifier = eintmodNONE;
+ }
+ if (fr->bcoultab == TRUE)
+ {
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
+ fr->nbkernel_elec_modifier = eintmodNONE;
+ }
+ }
+
+ if (ir->cutoff_scheme == ecutsVERLET)
+ {
+ if (!gmx_within_tol(fr->reppow, 12.0, 10*GMX_DOUBLE_EPS))
+ {
+ gmx_fatal(FARGS, "Cut-off scheme %S only supports LJ repulsion power 12", ecutscheme_names[ir->cutoff_scheme]);
+ }
+ fr->bvdwtab = FALSE;
+ fr->bcoultab = FALSE;
+ }
+
+ /* Tables are used for direct ewald sum */
+ if (fr->bEwald)
+ {
+ if (EEL_PME(ir->coulombtype))
+ {
+ if (fp)
+ {
+ fprintf(fp, "Will do PME sum in reciprocal space.\n");
+ }
+ if (ir->coulombtype == eelP3M_AD)
+ {
+ please_cite(fp, "Hockney1988");
+ please_cite(fp, "Ballenegger2012");
+ }
+ else
+ {
+ please_cite(fp, "Essmann95a");
+ }
+
+ if (ir->ewald_geometry == eewg3DC)
+ {
+ if (fp)
+ {
+ fprintf(fp, "Using the Ewald3DC correction for systems with a slab geometry.\n");
+ }
+ please_cite(fp, "In-Chul99a");
+ }
+ }
+ fr->ewaldcoeff = calc_ewaldcoeff(ir->rcoulomb, ir->ewald_rtol);
+ init_ewald_tab(&(fr->ewald_table), cr, ir, fp);
+ if (fp)
+ {
+ fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for Ewald\n",
+ 1/fr->ewaldcoeff);
+ }
+ }
+
+ /* Electrostatics */
+ fr->epsilon_r = ir->epsilon_r;
+ fr->epsilon_rf = ir->epsilon_rf;
+ fr->fudgeQQ = mtop->ffparams.fudgeQQ;
+ fr->rcoulomb_switch = ir->rcoulomb_switch;
+ fr->rcoulomb = cutoff_inf(ir->rcoulomb);
+
+ /* Parameters for generalized RF */
+ fr->zsquare = 0.0;
+ fr->temp = 0.0;
+
+ if (fr->eeltype == eelGRF)
+ {
+ init_generalized_rf(fp, mtop, ir, fr);
+ }
+ else if (fr->eeltype == eelSHIFT)
+ {
+ for (m = 0; (m < DIM); m++)
+ {
+ box_size[m] = box[m][m];
+ }
+
+ if ((fr->eeltype == eelSHIFT && fr->rcoulomb > fr->rcoulomb_switch))
+ {
+ set_shift_consts(fp, fr->rcoulomb_switch, fr->rcoulomb, box_size, fr);
+ }
+ }
+
+ fr->bF_NoVirSum = (EEL_FULL(fr->eeltype) ||
+ gmx_mtop_ftype_count(mtop, F_POSRES) > 0 ||
+ gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0 ||
+ IR_ELEC_FIELD(*ir) ||
+ (fr->adress_icor != eAdressICOff)
+ );
+
+ if (fr->cutoff_scheme == ecutsGROUP &&
+ ncg_mtop(mtop) > fr->cg_nalloc && !DOMAINDECOMP(cr))
+ {
+ /* Count the total number of charge groups */
+ fr->cg_nalloc = ncg_mtop(mtop);
+ srenew(fr->cg_cm, fr->cg_nalloc);
+ }
+ if (fr->shift_vec == NULL)
+ {
+ snew(fr->shift_vec, SHIFTS);
+ }
+
+ if (fr->fshift == NULL)
+ {
+ snew(fr->fshift, SHIFTS);
+ }
+
+ if (fr->nbfp == NULL)
+ {
+ fr->ntype = mtop->ffparams.atnr;
+ fr->nbfp = mk_nbfp(&mtop->ffparams, fr->bBHAM);
+ }
+
+ /* Copy the energy group exclusions */
+ fr->egp_flags = ir->opts.egp_flags;
+
+ /* Van der Waals stuff */
+ fr->rvdw = cutoff_inf(ir->rvdw);
+ fr->rvdw_switch = ir->rvdw_switch;
+ if ((fr->vdwtype != evdwCUT) && (fr->vdwtype != evdwUSER) && !fr->bBHAM)
+ {
+ if (fr->rvdw_switch >= fr->rvdw)
+ {
+ gmx_fatal(FARGS, "rvdw_switch (%f) must be < rvdw (%f)",
+ fr->rvdw_switch, fr->rvdw);
+ }
+ if (fp)
+ {
+ fprintf(fp, "Using %s Lennard-Jones, switch between %g and %g nm\n",
+ (fr->eeltype == eelSWITCH) ? "switched" : "shifted",
+ fr->rvdw_switch, fr->rvdw);
+ }
+ }
+
+ if (fr->bBHAM && (fr->vdwtype == evdwSHIFT || fr->vdwtype == evdwSWITCH))
+ {
+ gmx_fatal(FARGS, "Switch/shift interaction not supported with Buckingham");
+ }
+
+ if (fp)
+ {
+ fprintf(fp, "Cut-off's: NS: %g Coulomb: %g %s: %g\n",
+ fr->rlist, fr->rcoulomb, fr->bBHAM ? "BHAM" : "LJ", fr->rvdw);
+ }
+
+ fr->eDispCorr = ir->eDispCorr;
+ if (ir->eDispCorr != edispcNO)
+ {
+ set_avcsixtwelve(fp, fr, mtop);
+ }
+
+ if (fr->bBHAM)
+ {
+ set_bham_b_max(fp, fr, mtop);
+ }
+
+ fr->gb_epsilon_solvent = ir->gb_epsilon_solvent;
+
+ /* Copy the GBSA data (radius, volume and surftens for each
+ * atomtype) from the topology atomtype section to forcerec.
+ */
+ snew(fr->atype_radius, fr->ntype);
+ snew(fr->atype_vol, fr->ntype);
+ snew(fr->atype_surftens, fr->ntype);
+ snew(fr->atype_gb_radius, fr->ntype);
+ snew(fr->atype_S_hct, fr->ntype);
+
+ if (mtop->atomtypes.nr > 0)
+ {
+ for (i = 0; i < fr->ntype; i++)
+ {
+ fr->atype_radius[i] = mtop->atomtypes.radius[i];
+ }
+ for (i = 0; i < fr->ntype; i++)
+ {
+ fr->atype_vol[i] = mtop->atomtypes.vol[i];
+ }
+ for (i = 0; i < fr->ntype; i++)
+ {
+ fr->atype_surftens[i] = mtop->atomtypes.surftens[i];
+ }
+ for (i = 0; i < fr->ntype; i++)
+ {
+ fr->atype_gb_radius[i] = mtop->atomtypes.gb_radius[i];
+ }
+ for (i = 0; i < fr->ntype; i++)
+ {
+ fr->atype_S_hct[i] = mtop->atomtypes.S_hct[i];
+ }
+ }
+
+ /* Generate the GB table if needed */
+ if (fr->bGB)
+ {
+#ifdef GMX_DOUBLE
+ fr->gbtabscale = 2000;
+#else
+ fr->gbtabscale = 500;
+#endif
+
+ fr->gbtabr = 100;
+ fr->gbtab = make_gb_table(fp, oenv, fr, tabpfn, fr->gbtabscale);
+
+ init_gb(&fr->born, cr, fr, ir, mtop, ir->rgbradii, ir->gb_algorithm);
+
+ /* Copy local gb data (for dd, this is done in dd_partition_system) */
+ if (!DOMAINDECOMP(cr))
+ {
+ make_local_gb(cr, fr->born, ir->gb_algorithm);
+ }
+ }
+
+ /* Set the charge scaling */
+ if (fr->epsilon_r != 0)
+ {
+ fr->epsfac = ONE_4PI_EPS0/fr->epsilon_r;
+ }
+ else
+ {
+ /* eps = 0 is infinite dieletric: no coulomb interactions */
+ fr->epsfac = 0;
+ }
+
+ /* Reaction field constants */
+ if (EEL_RF(fr->eeltype))
+ {
+ calc_rffac(fp, fr->eeltype, fr->epsilon_r, fr->epsilon_rf,
+ fr->rcoulomb, fr->temp, fr->zsquare, box,
+ &fr->kappa, &fr->k_rf, &fr->c_rf);
+ }
+
+ set_chargesum(fp, fr, mtop);
+
+ /* if we are using LR electrostatics, and they are tabulated,
+ * the tables will contain modified coulomb interactions.
+ * Since we want to use the non-shifted ones for 1-4
+ * coulombic interactions, we must have an extra set of tables.
+ */
+
+ /* Construct tables.
+ * A little unnecessary to make both vdw and coul tables sometimes,
+ * but what the heck... */
+
+ bTab = fr->bcoultab || fr->bvdwtab || fr->bEwald;
+
+ bSep14tab = ((!bTab || fr->eeltype != eelCUT || fr->vdwtype != evdwCUT ||
+ fr->bBHAM || fr->bEwald) &&
+ (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 ||
+ gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0 ||
+ gmx_mtop_ftype_count(mtop, F_LJC_PAIRS_NB) > 0));
+
+ negp_pp = ir->opts.ngener - ir->nwall;
+ negptable = 0;
+ if (!bTab)
+ {
+ bNormalnblists = TRUE;
+ fr->nnblists = 1;
+ }
+ else
+ {
+ bNormalnblists = (ir->eDispCorr != edispcNO);
+ for (egi = 0; egi < negp_pp; egi++)
+ {
+ for (egj = egi; egj < negp_pp; egj++)
+ {
+ egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
+ if (!(egp_flags & EGP_EXCL))
+ {
+ if (egp_flags & EGP_TABLE)
+ {
+ negptable++;
+ }
+ else
+ {
+ bNormalnblists = TRUE;
+ }
+ }
+ }
+ }
+ if (bNormalnblists)
+ {
+ fr->nnblists = negptable + 1;
+ }
+ else
+ {
+ fr->nnblists = negptable;
+ }
+ if (fr->nnblists > 1)
+ {
+ snew(fr->gid2nblists, ir->opts.ngener*ir->opts.ngener);
+ }
+ }
+
+ if (ir->adress)
+ {
+ fr->nnblists *= 2;
+ }
+
+ snew(fr->nblists, fr->nnblists);
+
+ /* This code automatically gives table length tabext without cut-off's,
+ * in that case grompp should already have checked that we do not need
+ * normal tables and we only generate tables for 1-4 interactions.
+ */
+ rtab = ir->rlistlong + ir->tabext;
+
+ if (bTab)
+ {
+ /* make tables for ordinary interactions */
+ if (bNormalnblists)
+ {
+ make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn, NULL, NULL, &fr->nblists[0]);
+ if (ir->adress)
+ {
+ make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn, NULL, NULL, &fr->nblists[fr->nnblists/2]);
+ }
+ if (!bSep14tab)
+ {
+ fr->tab14 = fr->nblists[0].table_elec_vdw;
+ }
+ m = 1;
+ }
+ else
+ {
+ m = 0;
+ }
+ if (negptable > 0)
+ {
+ /* Read the special tables for certain energy group pairs */
+ nm_ind = mtop->groups.grps[egcENER].nm_ind;
+ for (egi = 0; egi < negp_pp; egi++)
+ {
+ for (egj = egi; egj < negp_pp; egj++)
+ {
+ 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;
+ }
+ /* Read the table file with the two energy groups names appended */
+ make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn,
+ *mtop->groups.grpname[nm_ind[egi]],
+ *mtop->groups.grpname[nm_ind[egj]],
+ &fr->nblists[m]);
+ if (ir->adress)
+ {
+ make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn,
+ *mtop->groups.grpname[nm_ind[egi]],
+ *mtop->groups.grpname[nm_ind[egj]],
+ &fr->nblists[fr->nnblists/2+m]);
+ }
+ m++;
+ }
+ else if (fr->nnblists > 1)
+ {
+ fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = 0;
+ }
+ }
+ }
+ }
+ }
+ if (bSep14tab)
+ {
+ /* generate extra tables with plain Coulomb for 1-4 interactions only */
+ fr->tab14 = make_tables(fp, oenv, fr, MASTER(cr), tabpfn, rtab,
+ GMX_MAKETABLES_14ONLY);
+ }
+
+ /* Read AdResS Thermo Force table if needed */
+ if (fr->adress_icor == eAdressICThermoForce)
+ {
+ /* old todo replace */
+
+ if (ir->adress->n_tf_grps > 0)
+ {
+ make_adress_tf_tables(fp, oenv, fr, ir, tabfn, mtop, box);
+
+ }
+ else
+ {
+ /* load the default table */
+ snew(fr->atf_tabs, 1);
+ fr->atf_tabs[DEFAULT_TF_TABLE] = make_atf_table(fp, oenv, fr, tabafn, box);
+ }
+ }
+
+ /* Wall stuff */
+ fr->nwall = ir->nwall;
+ if (ir->nwall && ir->wall_type == ewtTABLE)
+ {
+ make_wall_tables(fp, oenv, ir, tabfn, &mtop->groups, fr);
+ }
+
+ if (fcd && tabbfn)
+ {
+ fcd->bondtab = make_bonded_tables(fp,
+ F_TABBONDS, F_TABBONDSNC,
+ mtop, tabbfn, "b");
+ fcd->angletab = make_bonded_tables(fp,
+ F_TABANGLES, -1,
+ mtop, tabbfn, "a");
+ fcd->dihtab = make_bonded_tables(fp,
+ F_TABDIHS, -1,
+ mtop, tabbfn, "d");
+ }
+ else
+ {
+ if (debug)
+ {
+ fprintf(debug, "No fcdata or table file name passed, can not read table, can not do bonded interactions\n");
+ }
+ }
+
+ /* QM/MM initialization if requested
+ */
+ if (ir->bQMMM)
+ {
+ fprintf(stderr, "QM/MM calculation requested.\n");
+ }
+
+ fr->bQMMM = ir->bQMMM;
+ fr->qr = mk_QMMMrec();
+
+ /* Set all the static charge group info */
+ fr->cginfo_mb = init_cginfo_mb(fp, mtop, fr, bNoSolvOpt,
+ &fr->bExcl_IntraCGAll_InterCGNone);
+ if (DOMAINDECOMP(cr))
+ {
+ fr->cginfo = NULL;
+ }
+ else
+ {
+ fr->cginfo = cginfo_expand(mtop->nmolblock, fr->cginfo_mb);
+ }
+
+ if (!DOMAINDECOMP(cr))
+ {
+ /* When using particle decomposition, the effect of the second argument,
+ * which sets fr->hcg, is corrected later in do_md and init_em.
+ */
+ forcerec_set_ranges(fr, ncg_mtop(mtop), ncg_mtop(mtop),
+ mtop->natoms, mtop->natoms, mtop->natoms);
+ }
+
+ fr->print_force = print_force;
+
+
+ /* coarse load balancing vars */
+ fr->t_fnbf = 0.;
+ fr->t_wait = 0.;
+ fr->timesteps = 0;
+
+ /* Initialize neighbor search */
+ init_ns(fp, cr, &fr->ns, fr, mtop, box);
+
+ if (cr->duty & DUTY_PP)
+ {
+ gmx_nonbonded_setup(fp, fr, bGenericKernelOnly);
+ /*
+ if (ir->bAdress)
+ {
+ gmx_setup_adress_kernels(fp,bGenericKernelOnly);
+ }
+ */
+ }
+
+ /* Initialize the thread working data for bonded interactions */
+ init_forcerec_f_threads(fr, mtop->groups.grps[egcENER].nr);
+
+ snew(fr->excl_load, fr->nthreads+1);
+
+ if (fr->cutoff_scheme == ecutsVERLET)
+ {
+ if (ir->rcoulomb != ir->rvdw)
+ {
+ gmx_fatal(FARGS, "With Verlet lists rcoulomb and rvdw should be identical");
+ }
+
+ init_nb_verlet(fp, &fr->nbv, ir, fr, cr, nbpu_opt);
+ }
+
+ /* fr->ic is used both by verlet and group kernels (to some extent) now */
+ init_interaction_const(fp, &fr->ic, fr, rtab);
+ if (ir->eDispCorr != edispcNO)
+ {
+ calc_enervirdiff(fp, ir->eDispCorr, fr);
+ }
+}
+
+#define pr_real(fp, r) fprintf(fp, "%s: %e\n",#r, r)
+#define pr_int(fp, i) fprintf((fp), "%s: %d\n",#i, i)
+#define pr_bool(fp, b) fprintf((fp), "%s: %s\n",#b, bool_names[b])
+
+void pr_forcerec(FILE *fp, t_forcerec *fr, t_commrec *cr)
+{
+ int i;
+
+ pr_real(fp, fr->rlist);
+ pr_real(fp, fr->rcoulomb);
+ pr_real(fp, fr->fudgeQQ);
+ pr_bool(fp, fr->bGrid);
+ pr_bool(fp, fr->bTwinRange);
+ /*pr_int(fp,fr->cg0);
+ pr_int(fp,fr->hcg);*/
+ for (i = 0; i < fr->nnblists; i++)
+ {
+ pr_int(fp, fr->nblists[i].table_elec_vdw.n);
+ }
+ pr_real(fp, fr->rcoulomb_switch);
+ pr_real(fp, fr->rcoulomb);
+
+ fflush(fp);
+}
+
+void forcerec_set_excl_load(t_forcerec *fr,
+ const gmx_localtop_t *top, const t_commrec *cr)
+{
+ const int *ind, *a;
+ int t, i, j, ntot, n, ntarget;
+
+ if (cr != NULL && PARTDECOMP(cr))
+ {
+ /* No OpenMP with particle decomposition */
+ pd_at_range(cr,
+ &fr->excl_load[0],
+ &fr->excl_load[1]);
+
+ return;
+ }
+
+ ind = top->excls.index;
+ a = top->excls.a;
+
+ ntot = 0;
+ for (i = 0; i < top->excls.nr; i++)
+ {
+ for (j = ind[i]; j < ind[i+1]; j++)
+ {
+ if (a[j] > i)
+ {
+ ntot++;
+ }
+ }
+ }
+
+ fr->excl_load[0] = 0;
+ n = 0;
+ i = 0;
+ for (t = 1; t <= fr->nthreads; t++)
+ {
+ ntarget = (ntot*t)/fr->nthreads;
+ while (i < top->excls.nr && n < ntarget)
+ {
+ for (j = ind[i]; j < ind[i+1]; j++)
+ {
+ if (a[j] > i)
+ {
+ n++;
+ }
+ }
+ i++;
+ }
+ fr->excl_load[t] = i;
+ }
+}
--- /dev/null
- const nonbonded_verlet_t *nbv,
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2012, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+ *
+ * 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 the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <assert.h>
+
+#include <cuda.h>
+
+#include "gmx_fatal.h"
+#include "smalloc.h"
+#include "tables.h"
+#include "typedefs.h"
+#include "types/nb_verlet.h"
+#include "types/interaction_const.h"
+#include "types/force_flags.h"
+#include "../nbnxn_consts.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"
+
+static bool bUseCudaEventBlockingSync = false; /* makes the CPU thread block */
+
+/* This is a heuristically determined parameter for the Fermi architecture for
+ * the minimum size of ci lists by multiplying this constant with the # of
+ * multiprocessors on the current device.
+ */
+static unsigned int gpu_min_ci_balanced_factor = 40;
+
+/* Functions from nbnxn_cuda.cu */
+extern void nbnxn_cuda_set_cacheconfig(cuda_dev_info_t *devinfo);
+extern const struct texture<float, 1, cudaReadModeElementType>& nbnxn_cuda_get_nbfp_texref();
+extern const struct texture<float, 1, cudaReadModeElementType>& nbnxn_cuda_get_coulomb_tab_texref();
+
+/* We should actually be using md_print_warn in md_logging.c,
+ * but we can't include mpi.h in CUDA code.
+ */
+static void md_print_warn(FILE *fplog,
+ const char *fmt, ...)
+{
+ va_list ap;
+
+ if (fplog != NULL)
+ {
+ /* 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);
+ }
+}
+
+
+/* Fw. decl. */
+static void nbnxn_cuda_clear_e_fshift(nbnxn_cuda_ptr_t cu_nb);
+
+
+/*! Tabulates the Ewald Coulomb force and initializes the size/scale
+ and the table GPU array. If called with an already allocated table,
+ it just re-uploads the table.
+ */
+static void init_ewald_coulomb_force_table(cu_nbparam_t *nbp)
+{
+ float *ftmp, *coul_tab;
+ int tabsize;
+ double tabscale;
+ cudaError_t stat;
+
+ tabsize = GPU_EWALD_COULOMB_FORCE_TABLE_SIZE;
+ /* Subtract 2 iso 1 to avoid access out of range due to rounding */
+ tabscale = (tabsize - 2) / sqrt(nbp->rcoulomb_sq);
+
+ pmalloc((void**)&ftmp, tabsize*sizeof(*ftmp));
+
+ table_spline3_fill_ewald_lr(ftmp, NULL, NULL, tabsize,
+ 1/tabscale, nbp->ewald_beta);
+
+ /* If the table pointer == NULL the table is generated the first time =>
+ the array pointer will be saved to nbparam and the texture is bound.
+ */
+ coul_tab = nbp->coulomb_tab;
+ if (coul_tab == NULL)
+ {
+ stat = cudaMalloc((void **)&coul_tab, tabsize*sizeof(*coul_tab));
+ CU_RET_ERR(stat, "cudaMalloc failed on coul_tab");
+
+ nbp->coulomb_tab = coul_tab;
+
+ cudaChannelFormatDesc cd = cudaCreateChannelDesc<float>();
+ stat = cudaBindTexture(NULL, &nbnxn_cuda_get_coulomb_tab_texref(),
+ coul_tab, &cd, tabsize*sizeof(*coul_tab));
+ CU_RET_ERR(stat, "cudaBindTexture on coul_tab failed");
+ }
+
+ cu_copy_H2D(coul_tab, ftmp, tabsize*sizeof(*coul_tab));
+
+ nbp->coulomb_tab_size = tabsize;
+ nbp->coulomb_tab_scale = tabscale;
+
+ pfree(ftmp);
+}
+
+
+/*! Initializes the atomdata structure first time, it only gets filled at
+ pair-search. */
+static void init_atomdata_first(cu_atomdata_t *ad, int ntypes)
+{
+ cudaError_t stat;
+
+ ad->ntypes = ntypes;
+ stat = cudaMalloc((void**)&ad->shift_vec, SHIFTS*sizeof(*ad->shift_vec));
+ CU_RET_ERR(stat, "cudaMalloc failed on ad->shift_vec");
+ ad->bShiftVecUploaded = false;
+
+ stat = cudaMalloc((void**)&ad->fshift, SHIFTS*sizeof(*ad->fshift));
+ CU_RET_ERR(stat, "cudaMalloc failed on ad->fshift");
+
+ stat = cudaMalloc((void**)&ad->e_lj, sizeof(*ad->e_lj));
+ CU_RET_ERR(stat, "cudaMalloc failed on ad->e_lj");
+ stat = cudaMalloc((void**)&ad->e_el, sizeof(*ad->e_el));
+ CU_RET_ERR(stat, "cudaMalloc failed on ad->e_el");
+
+ /* initialize to NULL poiters to data that is not allocated here and will
+ need reallocation in nbnxn_cuda_init_atomdata */
+ ad->xq = NULL;
+ ad->f = NULL;
+
+ /* size -1 indicates that the respective array hasn't been initialized yet */
+ ad->natoms = -1;
+ ad->nalloc = -1;
+}
+
+/*! Selects the Ewald kernel type, analytical on SM 3.0 and later, tabulated on
+ earlier GPUs, single or twin cut-off. */
+static int pick_ewald_kernel_type(bool bTwinCut,
+ const cuda_dev_info_t *dev_info)
+{
+ bool bUseAnalyticalEwald, bForceAnalyticalEwald, bForceTabulatedEwald;
+ int kernel_type;
+
+ /* Benchmarking/development environment variables to force the use of
+ analytical or tabulated Ewald kernel. */
+ bForceAnalyticalEwald = (getenv("GMX_CUDA_NB_ANA_EWALD") != NULL);
+ bForceTabulatedEwald = (getenv("GMX_CUDA_NB_TAB_EWALD") != NULL);
+
+ if (bForceAnalyticalEwald && bForceTabulatedEwald)
+ {
+ gmx_incons("Both analytical and tabulated Ewald CUDA non-bonded kernels "
+ "requested through environment variables.");
+ }
+
+ /* By default, on SM 3.0 and later use analytical Ewald, on earlier tabulated. */
+ if ((dev_info->prop.major >= 3 || bForceAnalyticalEwald) && !bForceTabulatedEwald)
+ {
+ bUseAnalyticalEwald = true;
+
+ if (debug)
+ {
+ fprintf(debug, "Using analytical Ewald CUDA kernels\n");
+ }
+ }
+ else
+ {
+ bUseAnalyticalEwald = false;
+
+ if (debug)
+ {
+ fprintf(debug, "Using tabulated Ewald CUDA kernels\n");
+ }
+ }
+
+ /* Use twin cut-off kernels if requested by bTwinCut or the env. var.
+ forces it (use it for debugging/benchmarking only). */
+ if (!bTwinCut && (getenv("GMX_CUDA_NB_EWALD_TWINCUT") == NULL))
+ {
+ kernel_type = bUseAnalyticalEwald ? eelCuEWALD_ANA : eelCuEWALD_TAB;
+ }
+ else
+ {
+ kernel_type = bUseAnalyticalEwald ? eelCuEWALD_ANA_TWIN : eelCuEWALD_TAB_TWIN;
+ }
+
+ return kernel_type;
+}
+
+
+/*! Initializes the nonbonded parameter data structure. */
+static void init_nbparam(cu_nbparam_t *nbp,
+ const interaction_const_t *ic,
- ntypes = nbv->grp[0].nbat->ntype;
++ const nbnxn_atomdata_t *nbat,
+ const cuda_dev_info_t *dev_info)
+{
+ cudaError_t stat;
+ int ntypes, nnbfp;
+
- cu_copy_H2D(nbp->nbfp, nbv->grp[0].nbat->nbfp, nnbfp*sizeof(*nbp->nbfp));
++ ntypes = nbat->ntype;
+
+ nbp->ewald_beta = ic->ewaldcoeff;
+ nbp->sh_ewald = ic->sh_ewald;
+ nbp->epsfac = ic->epsfac;
+ nbp->two_k_rf = 2.0 * ic->k_rf;
+ nbp->c_rf = ic->c_rf;
+ nbp->rvdw_sq = ic->rvdw * ic->rvdw;
+ nbp->rcoulomb_sq= ic->rcoulomb * ic->rcoulomb;
+ nbp->rlist_sq = ic->rlist * ic->rlist;
+ nbp->sh_invrc6 = ic->sh_invrc6;
+
+ if (ic->eeltype == eelCUT)
+ {
+ nbp->eeltype = eelCuCUT;
+ }
+ else if (EEL_RF(ic->eeltype))
+ {
+ nbp->eeltype = eelCuRF;
+ }
+ else if ((EEL_PME(ic->eeltype) || ic->eeltype==eelEWALD))
+ {
+ /* Initially rcoulomb == rvdw, so it's surely not twin cut-off. */
+ nbp->eeltype = pick_ewald_kernel_type(false, dev_info);
+ }
+ else
+ {
+ /* Shouldn't happen, as this is checked when choosing Verlet-scheme */
+ gmx_incons("The requested electrostatics type is not implemented in the CUDA GPU accelerated kernels!");
+ }
+
+ /* generate table for PME */
+ nbp->coulomb_tab = NULL;
+ if (nbp->eeltype == eelCuEWALD_TAB || nbp->eeltype == eelCuEWALD_TAB_TWIN)
+ {
+ init_ewald_coulomb_force_table(nbp);
+ }
+
+ nnbfp = 2*ntypes*ntypes;
+ stat = cudaMalloc((void **)&nbp->nbfp, nnbfp*sizeof(*nbp->nbfp));
+ CU_RET_ERR(stat, "cudaMalloc failed on nbp->nbfp");
- if (nb->dev_info->prop.ECCEnabled == 1)
++ cu_copy_H2D(nbp->nbfp, nbat->nbfp, nnbfp*sizeof(*nbp->nbfp));
+
+ cudaChannelFormatDesc cd = cudaCreateChannelDesc<float>();
+ stat = cudaBindTexture(NULL, &nbnxn_cuda_get_nbfp_texref(),
+ nbp->nbfp, &cd, nnbfp*sizeof(*nbp->nbfp));
+ CU_RET_ERR(stat, "cudaBindTexture on nbfp failed");
+}
+
+/*! 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)
+{
+ cu_nbparam_t *nbp = cu_nb->nbparam;
+
+ nbp->rlist_sq = ic->rlist * ic->rlist;
+ nbp->rcoulomb_sq = ic->rcoulomb * ic->rcoulomb;
+ nbp->ewald_beta = ic->ewaldcoeff;
+
+ nbp->eeltype = pick_ewald_kernel_type(ic->rcoulomb != ic->rvdw,
+ cu_nb->dev_info);
+
+ init_ewald_coulomb_force_table(cu_nb->nbparam);
+}
+
+/*! Initializes the pair list data structure. */
+static void init_plist(cu_plist_t *pl)
+{
+ /* initialize to NULL pointers to data that is not allocated here and will
+ need reallocation in nbnxn_cuda_init_pairlist */
+ pl->sci = NULL;
+ pl->cj4 = NULL;
+ pl->excl = NULL;
+
+ /* size -1 indicates that the respective array hasn't been initialized yet */
+ pl->na_c = -1;
+ pl->nsci = -1;
+ pl->sci_nalloc = -1;
+ pl->ncj4 = -1;
+ pl->cj4_nalloc = -1;
+ pl->nexcl = -1;
+ pl->excl_nalloc = -1;
+ pl->bDoPrune = false;
+}
+
+/*! Initializes the timer data structure. */
+static void init_timers(cu_timers_t *t, bool bUseTwoStreams)
+{
+ cudaError_t stat;
+ int eventflags = ( bUseCudaEventBlockingSync ? cudaEventBlockingSync: cudaEventDefault );
+
+ stat = cudaEventCreateWithFlags(&(t->start_atdat), eventflags);
+ CU_RET_ERR(stat, "cudaEventCreate on start_atdat failed");
+ stat = cudaEventCreateWithFlags(&(t->stop_atdat), eventflags);
+ CU_RET_ERR(stat, "cudaEventCreate on stop_atdat failed");
+
+ /* The non-local counters/stream (second in the array) are needed only with DD. */
+ for (int i = 0; i <= (bUseTwoStreams ? 1 : 0); i++)
+ {
+ stat = cudaEventCreateWithFlags(&(t->start_nb_k[i]), eventflags);
+ CU_RET_ERR(stat, "cudaEventCreate on start_nb_k failed");
+ stat = cudaEventCreateWithFlags(&(t->stop_nb_k[i]), eventflags);
+ CU_RET_ERR(stat, "cudaEventCreate on stop_nb_k failed");
+
+
+ stat = cudaEventCreateWithFlags(&(t->start_pl_h2d[i]), eventflags);
+ CU_RET_ERR(stat, "cudaEventCreate on start_pl_h2d failed");
+ stat = cudaEventCreateWithFlags(&(t->stop_pl_h2d[i]), eventflags);
+ CU_RET_ERR(stat, "cudaEventCreate on stop_pl_h2d failed");
+
+ stat = cudaEventCreateWithFlags(&(t->start_nb_h2d[i]), eventflags);
+ CU_RET_ERR(stat, "cudaEventCreate on start_nb_h2d failed");
+ stat = cudaEventCreateWithFlags(&(t->stop_nb_h2d[i]), eventflags);
+ CU_RET_ERR(stat, "cudaEventCreate on stop_nb_h2d failed");
+
+ stat = cudaEventCreateWithFlags(&(t->start_nb_d2h[i]), eventflags);
+ CU_RET_ERR(stat, "cudaEventCreate on start_nb_d2h failed");
+ stat = cudaEventCreateWithFlags(&(t->stop_nb_d2h[i]), eventflags);
+ CU_RET_ERR(stat, "cudaEventCreate on stop_nb_d2h failed");
+ }
+}
+
+/*! Initializes the timings data structure. */
+static void init_timings(wallclock_gpu_t *t)
+{
+ int i, j;
+
+ t->nb_h2d_t = 0.0;
+ t->nb_d2h_t = 0.0;
+ t->nb_c = 0;
+ t->pl_h2d_t = 0.0;
+ t->pl_h2d_c = 0;
+ for (i = 0; i < 2; i++)
+ {
+ for(j = 0; j < 2; j++)
+ {
+ t->ktime[i][j].t = 0.0;
+ t->ktime[i][j].c = 0;
+ }
+ }
+}
+
+/* Decide which kernel version to use (default or legacy) based on:
+ * - CUDA version used for compilation
+ * - non-bonded kernel selector environment variables
+ * - GPU architecture version
+ */
+static int pick_nbnxn_kernel_version(FILE *fplog,
+ cuda_dev_info_t *devinfo)
+{
+ bool bForceLegacyKernel, bForceDefaultKernel, bCUDA40, bCUDA32;
+ char sbuf[STRLEN];
+ int kver;
+
+ /* Legacy kernel (former k2), kept for backward compatibility as it is
+ faster than the default with CUDA 3.2/4.0 on Fermi (not on Kepler). */
+ bForceLegacyKernel = (getenv("GMX_CUDA_NB_LEGACY") != NULL);
+ /* default kernel (former k3). */
+ bForceDefaultKernel = (getenv("GMX_CUDA_NB_DEFAULT") != NULL);
+
+ if ((unsigned)(bForceLegacyKernel + bForceDefaultKernel) > 1)
+ {
+ gmx_fatal(FARGS, "Multiple CUDA non-bonded kernels requested; to manually pick a kernel set only one \n"
+ "of the following environment variables: \n"
+ "GMX_CUDA_NB_DEFAULT, GMX_CUDA_NB_LEGACY");
+ }
+
+ bCUDA32 = bCUDA40 = false;
+#if CUDA_VERSION == 3200
+ bCUDA32 = true;
+ sprintf(sbuf, "3.2");
+#elif CUDA_VERSION == 4000
+ bCUDA40 = true;
+ sprintf(sbuf, "4.0");
+#endif
+
+ /* default is default ;) */
+ kver = eNbnxnCuKDefault;
+
+ /* Consider switching to legacy kernels only on Fermi */
+ if (devinfo->prop.major < 3 && (bCUDA32 || bCUDA40))
+ {
+ /* use legacy kernel unless something else is forced by an env. var */
+ if (bForceDefaultKernel)
+ {
+ md_print_warn(fplog,
+ "NOTE: CUDA %s compilation detected; with this compiler version the legacy\n"
+ " non-bonded kernels perform best. However, the default kernels were\n"
+ " selected by the GMX_CUDA_NB_DEFAULT environment variable.\n"
+ " For best performance upgrade your CUDA toolkit.\n",
+ sbuf);
+ }
+ else
+ {
+ kver = eNbnxnCuKLegacy;
+ }
+ }
+ else
+ {
+ /* issue note if the non-default kernel is forced by an env. var */
+ if (bForceLegacyKernel)
+ {
+ md_print_warn(fplog,
+ "NOTE: Legacy non-bonded CUDA kernels selected by the GMX_CUDA_NB_LEGACY\n"
+ " env. var. Consider using using the default kernels which should be faster!\n");
+
+ kver = eNbnxnCuKLegacy;
+ }
+ }
+
+ return kver;
+}
+
+void nbnxn_cuda_init(FILE *fplog,
+ nbnxn_cuda_ptr_t *p_cu_nb,
+ gmx_gpu_info_t *gpu_info, int my_gpu_index,
+ gmx_bool bLocalAndNonlocal)
+{
+ cudaError_t stat;
+ nbnxn_cuda_ptr_t nb;
+ char sbuf[STRLEN];
+ bool bStreamSync, bNoStreamSync, bTMPIAtomics, bX86, bOldDriver;
+ int cuda_drv_ver;
+
+ assert(gpu_info);
+
+ if (p_cu_nb == NULL) return;
+
+ snew(nb, 1);
+ snew(nb->atdat, 1);
+ snew(nb->nbparam, 1);
+ snew(nb->plist[eintLocal], 1);
+ if (bLocalAndNonlocal)
+ {
+ snew(nb->plist[eintNonlocal], 1);
+ }
+
+ nb->bUseTwoStreams = bLocalAndNonlocal;
+
+ snew(nb->timers, 1);
+ snew(nb->timings, 1);
+
+ /* init nbst */
+ pmalloc((void**)&nb->nbst.e_lj, sizeof(*nb->nbst.e_lj));
+ pmalloc((void**)&nb->nbst.e_el, sizeof(*nb->nbst.e_el));
+ pmalloc((void**)&nb->nbst.fshift, SHIFTS * sizeof(*nb->nbst.fshift));
+
+ init_plist(nb->plist[eintLocal]);
+
+ /* local/non-local GPU streams */
+ stat = cudaStreamCreate(&nb->stream[eintLocal]);
+ CU_RET_ERR(stat, "cudaStreamCreate on stream[eintLocal] failed");
+ if (nb->bUseTwoStreams)
+ {
+ init_plist(nb->plist[eintNonlocal]);
+ stat = cudaStreamCreate(&nb->stream[eintNonlocal]);
+ CU_RET_ERR(stat, "cudaStreamCreate on stream[eintNonlocal] failed");
+ }
+
+ /* init events for sychronization (timing disabled for performance reasons!) */
+ stat = cudaEventCreateWithFlags(&nb->nonlocal_done, cudaEventDisableTiming);
+ CU_RET_ERR(stat, "cudaEventCreate on nonlocal_done failed");
+ stat = cudaEventCreateWithFlags(&nb->misc_ops_done, cudaEventDisableTiming);
+ CU_RET_ERR(stat, "cudaEventCreate on misc_ops_one failed");
+
+ /* set device info, just point it to the right GPU among the detected ones */
+ nb->dev_info = &gpu_info->cuda_dev[get_gpu_device_id(gpu_info, my_gpu_index)];
+
+ /* On GPUs with ECC enabled, cudaStreamSynchronize shows a large overhead
+ * (which increases with shorter time/step) caused by a known CUDA driver bug.
+ * To work around the issue we'll use an (admittedly fragile) memory polling
+ * waiting to preserve performance. This requires support for atomic
+ * operations and only works on x86/x86_64.
+ * With polling wait event-timing also needs to be disabled.
+ *
+ * The overhead is greatly reduced in API v5.0 drivers and the improvement
+ $ is independent of runtime version. Hence, with API v5.0 drivers and later
+ * we won't switch to polling.
+ *
+ * NOTE: Unfortunately, this is known to fail when GPUs are shared by (t)MPI,
+ * ranks so we will also disable it in that case.
+ */
+
+ bStreamSync = getenv("GMX_CUDA_STREAMSYNC") != NULL;
+ bNoStreamSync = getenv("GMX_NO_CUDA_STREAMSYNC") != NULL;
+
+#ifdef TMPI_ATOMICS
+ bTMPIAtomics = true;
+#else
+ bTMPIAtomics = false;
+#endif
+
+#if defined(i386) || defined(__x86_64__)
+ bX86 = true;
+#else
+ bX86 = false;
+#endif
+
+ if (bStreamSync && bNoStreamSync)
+ {
+ gmx_fatal(FARGS, "Conflicting environment variables: both GMX_CUDA_STREAMSYNC and GMX_NO_CUDA_STREAMSYNC defined");
+ }
+
+ stat = cudaDriverGetVersion(&cuda_drv_ver);
+ CU_RET_ERR(stat, "cudaDriverGetVersion failed");
++
+ bOldDriver = (cuda_drv_ver < 5000);
+
- if (bOldDriver && !gpu_info->bDevShare)
++ if ((nb->dev_info->prop.ECCEnabled == 1) && bOldDriver)
+ {
++ /* Polling wait should be used instead of cudaStreamSynchronize only if:
++ * - ECC is ON & driver is old (checked above),
++ * - we're on x86/x86_64,
++ * - atomics are available, and
++ * - GPUs are not being shared.
++ */
++ bool bShouldUsePollSync = (bX86 && bTMPIAtomics && !gpu_info->bDevShare);
++
+ if (bStreamSync)
+ {
+ nb->bUseStreamSync = true;
+
+ /* only warn if polling should be used */
- /* Can/should turn of cudaStreamSynchronize wait only if
- * - we're on x86/x86_64
- * - atomics are available
- * - GPUs are not being shared
- * - and driver is old. */
- nb->bUseStreamSync =
- (bX86 && bTMPIAtomics && !gpu_info->bDevShare && bOldDriver) ?
- true : false;
-
- if (nb->bUseStreamSync)
++ if (bShouldUsePollSync)
+ {
+ md_print_warn(fplog,
+ "NOTE: Using a GPU with ECC enabled and CUDA driver API version <5.0, but\n"
+ " cudaStreamSynchronize waiting is forced by the GMX_CUDA_STREAMSYNC env. var.\n");
+ }
+ }
+ else
+ {
- " cause performance loss. Switching to the alternative polling GPU waiting.\n"
++ nb->bUseStreamSync = !bShouldUsePollSync;
++
++ if (bShouldUsePollSync)
+ {
+ md_print_warn(fplog,
+ "NOTE: Using a GPU with ECC enabled and CUDA driver API version <5.0, known to\n"
- else if (bOldDriver)
++ " cause performance loss. Switching to the alternative polling GPU wait.\n"
+ " If you encounter issues, switch back to standard GPU waiting by setting\n"
+ " the GMX_CUDA_STREAMSYNC environment variable.\n");
+ }
- "NOTE: Using a GPU with ECC enabled and CUDA driver API version <5.0. A bug in this\n"
- " driver can cause performance loss.\n"
- " However, the polling waiting workaround can not be used because\n%s\n"
++ else
+ {
+ /* Tell the user that the ECC+old driver combination can be bad */
+ sprintf(sbuf,
- (!bX86 || !bTMPIAtomics) ?
- " atomic operations are not supported by the platform/CPU+compiler." :
- " GPU(s) are being oversubscribed.");
++ "NOTE: Using a GPU with ECC enabled and CUDA driver API version <5.0.\n"
++ " A known bug in this driver version can cause performance loss.\n"
++ " However, the polling wait workaround can not be used because\n%s\n"
+ " Consider updating the driver or turning ECC off.",
- void nbnxn_cuda_init_const(nbnxn_cuda_ptr_t cu_nb,
- const interaction_const_t *ic,
- const nonbonded_verlet_t *nbv)
++ (bX86 && bTMPIAtomics) ?
++ " GPU(s) are being oversubscribed." :
++ " atomic operations are not supported by the platform/CPU+compiler.");
+ md_print_warn(fplog, sbuf);
+ }
+ }
+ }
+ else
+ {
+ if (bNoStreamSync)
+ {
+ nb->bUseStreamSync = false;
+
+ md_print_warn(fplog,
+ "NOTE: Polling wait for GPU synchronization requested by GMX_NO_CUDA_STREAMSYNC\n");
+ }
+ else
+ {
+ /* no/off ECC, cudaStreamSynchronize not turned off by env. var. */
+ nb->bUseStreamSync = true;
+ }
+ }
+
+ /* CUDA timing disabled as event timers don't work:
+ - with multiple streams = domain-decomposition;
+ - with the polling waiting hack (without cudaStreamSynchronize);
+ - when turned off by GMX_DISABLE_CUDA_TIMING.
+ */
+ nb->bDoTime = (!nb->bUseTwoStreams && nb->bUseStreamSync &&
+ (getenv("GMX_DISABLE_CUDA_TIMING") == NULL));
+
+ if (nb->bDoTime)
+ {
+ init_timers(nb->timers, nb->bUseTwoStreams);
+ init_timings(nb->timings);
+ }
+
+ /* set the kernel type for the current GPU */
+ nb->kernel_ver = pick_nbnxn_kernel_version(fplog, nb->dev_info);
+ /* pick L1 cache configuration */
+ nbnxn_cuda_set_cacheconfig(nb->dev_info);
+
+ *p_cu_nb = nb;
+
+ if (debug)
+ {
+ fprintf(debug, "Initialized CUDA data structures.\n");
+ }
+}
+
- init_atomdata_first(cu_nb->atdat, nbv->grp[0].nbat->ntype);
- init_nbparam(cu_nb->nbparam, ic, nbv, cu_nb->dev_info);
++void nbnxn_cuda_init_const(nbnxn_cuda_ptr_t cu_nb,
++ const interaction_const_t *ic,
++ const nonbonded_verlet_group_t *nbv_group)
+{
++ init_atomdata_first(cu_nb->atdat, nbv_group[0].nbat->ntype);
++ init_nbparam(cu_nb->nbparam, ic, nbv_group[0].nbat, cu_nb->dev_info);
+
+ /* clear energy and shift force outputs */
+ nbnxn_cuda_clear_e_fshift(cu_nb);
+}
+
+void nbnxn_cuda_init_pairlist(nbnxn_cuda_ptr_t cu_nb,
+ const nbnxn_pairlist_t *h_plist,
+ int iloc)
+{
+ char sbuf[STRLEN];
+ cudaError_t stat;
+ bool bDoTime = cu_nb->bDoTime;
+ cudaStream_t stream = cu_nb->stream[iloc];
+ cu_plist_t *d_plist = cu_nb->plist[iloc];
+
+ if (d_plist->na_c < 0)
+ {
+ d_plist->na_c = h_plist->na_ci;
+ }
+ else
+ {
+ if (d_plist->na_c != h_plist->na_ci)
+ {
+ sprintf(sbuf, "In cu_init_plist: the #atoms per cell has changed (from %d to %d)",
+ d_plist->na_c, h_plist->na_ci);
+ gmx_incons(sbuf);
+ }
+ }
+
+ if (bDoTime)
+ {
+ stat = cudaEventRecord(cu_nb->timers->start_pl_h2d[iloc], stream);
+ CU_RET_ERR(stat, "cudaEventRecord failed");
+ }
+
+ cu_realloc_buffered((void **)&d_plist->sci, h_plist->sci, sizeof(*d_plist->sci),
+ &d_plist->nsci, &d_plist->sci_nalloc,
+ h_plist->nsci,
+ stream, true);
+
+ cu_realloc_buffered((void **)&d_plist->cj4, h_plist->cj4, sizeof(*d_plist->cj4),
+ &d_plist->ncj4, &d_plist->cj4_nalloc,
+ h_plist->ncj4,
+ stream, true);
+
+ cu_realloc_buffered((void **)&d_plist->excl, h_plist->excl, sizeof(*d_plist->excl),
+ &d_plist->nexcl, &d_plist->excl_nalloc,
+ h_plist->nexcl,
+ stream, true);
+
+ if (bDoTime)
+ {
+ stat = cudaEventRecord(cu_nb->timers->stop_pl_h2d[iloc], stream);
+ CU_RET_ERR(stat, "cudaEventRecord failed");
+ }
+
+ /* need to prune the pair list during the next step */
+ d_plist->bDoPrune = true;
+}
+
+void nbnxn_cuda_upload_shiftvec(nbnxn_cuda_ptr_t cu_nb,
+ const nbnxn_atomdata_t *nbatom)
+{
+ cu_atomdata_t *adat = cu_nb->atdat;
+ cudaStream_t ls = cu_nb->stream[eintLocal];
+
+ /* only if we have a dynamic box */
+ if (nbatom->bDynamicBox || !adat->bShiftVecUploaded)
+ {
+ cu_copy_H2D_async(adat->shift_vec, nbatom->shift_vec,
+ SHIFTS * sizeof(*adat->shift_vec), ls);
+ adat->bShiftVecUploaded = true;
+ }
+}
+
+/*! Clears the first natoms_clear elements of the GPU nonbonded force output array. */
+static void nbnxn_cuda_clear_f(nbnxn_cuda_ptr_t cu_nb, int natoms_clear)
+{
+ cudaError_t stat;
+ cu_atomdata_t *adat = cu_nb->atdat;
+ cudaStream_t ls = cu_nb->stream[eintLocal];
+
+ stat = cudaMemsetAsync(adat->f, 0, natoms_clear * sizeof(*adat->f), ls);
+ CU_RET_ERR(stat, "cudaMemsetAsync on f falied");
+}
+
+/*! Clears nonbonded shift force output array and energy outputs on the GPU. */
+static void nbnxn_cuda_clear_e_fshift(nbnxn_cuda_ptr_t cu_nb)
+{
+ cudaError_t stat;
+ cu_atomdata_t *adat = cu_nb->atdat;
+ cudaStream_t ls = cu_nb->stream[eintLocal];
+
+ stat = cudaMemsetAsync(adat->fshift, 0, SHIFTS * sizeof(*adat->fshift), ls);
+ CU_RET_ERR(stat, "cudaMemsetAsync on fshift falied");
+ stat = cudaMemsetAsync(adat->e_lj, 0, sizeof(*adat->e_lj), ls);
+ CU_RET_ERR(stat, "cudaMemsetAsync on e_lj falied");
+ stat = cudaMemsetAsync(adat->e_el, 0, sizeof(*adat->e_el), ls);
+ CU_RET_ERR(stat, "cudaMemsetAsync on e_el falied");
+}
+
+void nbnxn_cuda_clear_outputs(nbnxn_cuda_ptr_t cu_nb, int flags)
+{
+ nbnxn_cuda_clear_f(cu_nb, cu_nb->atdat->natoms);
+ /* clear shift force array and energies if the outputs were
+ used in the current step */
+ if (flags & GMX_FORCE_VIRIAL)
+ {
+ nbnxn_cuda_clear_e_fshift(cu_nb);
+ }
+}
+
+void nbnxn_cuda_init_atomdata(nbnxn_cuda_ptr_t cu_nb,
+ const nbnxn_atomdata_t *nbat)
+{
+ cudaError_t stat;
+ int nalloc, natoms;
+ bool realloced;
+ bool bDoTime = cu_nb->bDoTime;
+ cu_timers_t *timers = cu_nb->timers;
+ cu_atomdata_t *d_atdat = cu_nb->atdat;
+ cudaStream_t ls = cu_nb->stream[eintLocal];
+
+ natoms = nbat->natoms;
+ realloced = false;
+
+ if (bDoTime)
+ {
+ /* time async copy */
+ stat = cudaEventRecord(timers->start_atdat, ls);
+ CU_RET_ERR(stat, "cudaEventRecord failed");
+ }
+
+ /* need to reallocate if we have to copy more atoms than the amount of space
+ available and only allocate if we haven't initialized yet, i.e d_atdat->natoms == -1 */
+ if (natoms > d_atdat->nalloc)
+ {
+ nalloc = over_alloc_small(natoms);
+
+ /* free up first if the arrays have already been initialized */
+ if (d_atdat->nalloc != -1)
+ {
+ cu_free_buffered(d_atdat->f, &d_atdat->natoms, &d_atdat->nalloc);
+ cu_free_buffered(d_atdat->xq);
+ cu_free_buffered(d_atdat->atom_types);
+ }
+
+ stat = cudaMalloc((void **)&d_atdat->f, nalloc*sizeof(*d_atdat->f));
+ CU_RET_ERR(stat, "cudaMalloc failed on d_atdat->f");
+ stat = cudaMalloc((void **)&d_atdat->xq, nalloc*sizeof(*d_atdat->xq));
+ CU_RET_ERR(stat, "cudaMalloc failed on d_atdat->xq");
+
+ stat = cudaMalloc((void **)&d_atdat->atom_types, nalloc*sizeof(*d_atdat->atom_types));
+ CU_RET_ERR(stat, "cudaMalloc failed on d_atdat->atom_types");
+
+ d_atdat->nalloc = nalloc;
+ realloced = true;
+ }
+
+ d_atdat->natoms = natoms;
+ d_atdat->natoms_local = nbat->natoms_local;
+
+ /* need to clear GPU f output if realloc happened */
+ if (realloced)
+ {
+ nbnxn_cuda_clear_f(cu_nb, nalloc);
+ }
+
+ cu_copy_H2D_async(d_atdat->atom_types, nbat->type,
+ natoms*sizeof(*d_atdat->atom_types), ls);
+
+ if (bDoTime)
+ {
+ stat = cudaEventRecord(timers->stop_atdat, ls);
+ CU_RET_ERR(stat, "cudaEventRecord failed");
+ }
+}
+
+void nbnxn_cuda_free(FILE *fplog, nbnxn_cuda_ptr_t cu_nb)
+{
+ cudaError_t stat;
+ cu_atomdata_t *atdat;
+ cu_nbparam_t *nbparam;
+ cu_plist_t *plist, *plist_nl;
+ cu_timers_t *timers;
+
+ if (cu_nb == NULL) return;
+
+ atdat = cu_nb->atdat;
+ nbparam = cu_nb->nbparam;
+ plist = cu_nb->plist[eintLocal];
+ plist_nl = cu_nb->plist[eintNonlocal];
+ timers = cu_nb->timers;
+
+ if (nbparam->eeltype == eelCuEWALD_TAB || nbparam->eeltype == eelCuEWALD_TAB_TWIN)
+ {
+ stat = cudaUnbindTexture(nbnxn_cuda_get_coulomb_tab_texref());
+ CU_RET_ERR(stat, "cudaUnbindTexture on coulomb_tab failed");
+ cu_free_buffered(nbparam->coulomb_tab, &nbparam->coulomb_tab_size);
+ }
+
+ stat = cudaEventDestroy(cu_nb->nonlocal_done);
+ CU_RET_ERR(stat, "cudaEventDestroy failed on timers->nonlocal_done");
+ stat = cudaEventDestroy(cu_nb->misc_ops_done);
+ CU_RET_ERR(stat, "cudaEventDestroy failed on timers->misc_ops_done");
+
+ if (cu_nb->bDoTime)
+ {
+ stat = cudaEventDestroy(timers->start_atdat);
+ CU_RET_ERR(stat, "cudaEventDestroy failed on timers->start_atdat");
+ stat = cudaEventDestroy(timers->stop_atdat);
+ CU_RET_ERR(stat, "cudaEventDestroy failed on timers->stop_atdat");
+
+ /* The non-local counters/stream (second in the array) are needed only with DD. */
+ for (int i = 0; i <= (cu_nb->bUseTwoStreams ? 1 : 0); i++)
+ {
+ stat = cudaEventDestroy(timers->start_nb_k[i]);
+ CU_RET_ERR(stat, "cudaEventDestroy failed on timers->start_nb_k");
+ stat = cudaEventDestroy(timers->stop_nb_k[i]);
+ CU_RET_ERR(stat, "cudaEventDestroy failed on timers->stop_nb_k");
+
+ stat = cudaEventDestroy(timers->start_pl_h2d[i]);
+ CU_RET_ERR(stat, "cudaEventDestroy failed on timers->start_pl_h2d");
+ stat = cudaEventDestroy(timers->stop_pl_h2d[i]);
+ CU_RET_ERR(stat, "cudaEventDestroy failed on timers->stop_pl_h2d");
+
+ stat = cudaStreamDestroy(cu_nb->stream[i]);
+ CU_RET_ERR(stat, "cudaStreamDestroy failed on stream");
+
+ stat = cudaEventDestroy(timers->start_nb_h2d[i]);
+ CU_RET_ERR(stat, "cudaEventDestroy failed on timers->start_nb_h2d");
+ stat = cudaEventDestroy(timers->stop_nb_h2d[i]);
+ CU_RET_ERR(stat, "cudaEventDestroy failed on timers->stop_nb_h2d");
+
+ stat = cudaEventDestroy(timers->start_nb_d2h[i]);
+ CU_RET_ERR(stat, "cudaEventDestroy failed on timers->start_nb_d2h");
+ stat = cudaEventDestroy(timers->stop_nb_d2h[i]);
+ CU_RET_ERR(stat, "cudaEventDestroy failed on timers->stop_nb_d2h");
+ }
+ }
+
+ stat = cudaUnbindTexture(nbnxn_cuda_get_nbfp_texref());
+ CU_RET_ERR(stat, "cudaUnbindTexture on coulomb_tab failed");
+ cu_free_buffered(nbparam->nbfp);
+
+ stat = cudaFree(atdat->shift_vec);
+ CU_RET_ERR(stat, "cudaFree failed on atdat->shift_vec");
+ stat = cudaFree(atdat->fshift);
+ CU_RET_ERR(stat, "cudaFree failed on atdat->fshift");
+
+ stat = cudaFree(atdat->e_lj);
+ CU_RET_ERR(stat, "cudaFree failed on atdat->e_lj");
+ stat = cudaFree(atdat->e_el);
+ CU_RET_ERR(stat, "cudaFree failed on atdat->e_el");
+
+ cu_free_buffered(atdat->f, &atdat->natoms, &atdat->nalloc);
+ cu_free_buffered(atdat->xq);
+ cu_free_buffered(atdat->atom_types, &atdat->ntypes);
+
+ cu_free_buffered(plist->sci, &plist->nsci, &plist->sci_nalloc);
+ cu_free_buffered(plist->cj4, &plist->ncj4, &plist->cj4_nalloc);
+ cu_free_buffered(plist->excl, &plist->nexcl, &plist->excl_nalloc);
+ if (cu_nb->bUseTwoStreams)
+ {
+ cu_free_buffered(plist_nl->sci, &plist_nl->nsci, &plist_nl->sci_nalloc);
+ cu_free_buffered(plist_nl->cj4, &plist_nl->ncj4, &plist_nl->cj4_nalloc);
+ cu_free_buffered(plist_nl->excl, &plist_nl->nexcl, &plist->excl_nalloc);
+ }
+
+ sfree(atdat);
+ sfree(nbparam);
+ sfree(plist);
+ if (cu_nb->bUseTwoStreams)
+ {
+ sfree(plist_nl);
+ }
+ sfree(timers);
+ sfree(cu_nb->timings);
+ sfree(cu_nb);
+
+ if (debug)
+ {
+ fprintf(debug, "Cleaned up CUDA data structures.\n");
+ }
+}
+
+void cu_synchstream_atdat(nbnxn_cuda_ptr_t cu_nb, int iloc)
+{
+ cudaError_t stat;
+ cudaStream_t stream = cu_nb->stream[iloc];
+
+ stat = cudaStreamWaitEvent(stream, cu_nb->timers->stop_atdat, 0);
+ CU_RET_ERR(stat, "cudaStreamWaitEvent failed");
+}
+
+wallclock_gpu_t * nbnxn_cuda_get_timings(nbnxn_cuda_ptr_t cu_nb)
+{
+ return (cu_nb != NULL && cu_nb->bDoTime) ? cu_nb->timings : NULL;
+}
+
+void nbnxn_cuda_reset_timings(nbnxn_cuda_ptr_t cu_nb)
+{
+ if (cu_nb->bDoTime)
+ {
+ init_timings(cu_nb->timings);
+ }
+}
+
+int nbnxn_cuda_min_ci_balanced(nbnxn_cuda_ptr_t cu_nb)
+{
+ return cu_nb != NULL ?
+ gpu_min_ci_balanced_factor*cu_nb->dev_info->prop.multiProcessorCount : 0;
+
+}
--- /dev/null
- static FILE *open_slab_out(const char *fn, t_rot *rot, const output_env_t oenv)
+/*
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * 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 the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "domdec.h"
+#include "gmx_wallcycle.h"
+#include "gmx_cyclecounter.h"
+#include "trnio.h"
+#include "smalloc.h"
+#include "network.h"
+#include "pbc.h"
+#include "futil.h"
+#include "mdrun.h"
+#include "txtdump.h"
+#include "names.h"
+#include "mtop_util.h"
+#include "names.h"
+#include "nrjac.h"
+#include "vec.h"
+#include "gmx_ga2la.h"
+#include "xvgr.h"
+#include "gmxfio.h"
+#include "groupcoord.h"
+#include "pull_rotation.h"
+#include "gmx_sort.h"
+#include "copyrite.h"
+#include "macros.h"
+
+
+static char *RotStr = {"Enforced rotation:"};
+
+
+/* Set the minimum weight for the determination of the slab centers */
+#define WEIGHT_MIN (10*GMX_FLOAT_MIN)
+
+/* Helper structure for sorting positions along rotation vector */
+typedef struct {
+ real xcproj; /* Projection of xc on the rotation vector */
+ int ind; /* Index of xc */
+ real m; /* Mass */
+ rvec x; /* Position */
+ rvec x_ref; /* Reference position */
+} sort_along_vec_t;
+
+
+/* Enforced rotation / flexible: determine the angle of each slab */
+typedef struct gmx_slabdata
+{
+ int nat; /* Number of atoms belonging to this slab */
+ rvec *x; /* The positions belonging to this slab. In
+ general, this should be all positions of the
+ whole rotation group, but we leave those away
+ that have a small enough weight */
+ rvec *ref; /* Same for reference */
+ real *weight; /* The weight for each atom */
+} t_gmx_slabdata;
+
+
+/* Helper structure for potential fitting */
+typedef struct gmx_potfit
+{
+ real *degangle; /* Set of angles for which the potential is
+ calculated. The optimum fit is determined as
+ the angle for with the potential is minimal */
+ real *V; /* Potential for the different angles */
+ matrix *rotmat; /* Rotation matrix corresponding to the angles */
+} t_gmx_potfit;
+
+
+/* Enforced rotation data for all groups */
+typedef struct gmx_enfrot
+{
+ FILE *out_rot; /* Output file for rotation data */
+ FILE *out_torque; /* Output file for torque data */
+ FILE *out_angles; /* Output file for slab angles for flexible type */
+ FILE *out_slabs; /* Output file for slab centers */
+ int bufsize; /* Allocation size of buf */
+ rvec *xbuf; /* Coordinate buffer variable for sorting */
+ real *mbuf; /* Masses buffer variable for sorting */
+ sort_along_vec_t *data; /* Buffer variable needed for position sorting */
+ real *mpi_inbuf; /* MPI buffer */
+ real *mpi_outbuf; /* MPI buffer */
+ int mpi_bufsize; /* Allocation size of in & outbuf */
+ unsigned long Flags; /* mdrun flags */
+ gmx_bool bOut; /* Used to skip first output when appending to
+ * avoid duplicate entries in rotation outfiles */
+} t_gmx_enfrot;
+
+
+/* Global enforced rotation data for a single rotation group */
+typedef struct gmx_enfrotgrp
+{
+ real degangle; /* Rotation angle in degrees */
+ matrix rotmat; /* Rotation matrix */
+ atom_id *ind_loc; /* Local rotation indices */
+ int nat_loc; /* Number of local group atoms */
+ int nalloc_loc; /* Allocation size for ind_loc and weight_loc */
+
+ real V; /* Rotation potential for this rotation group */
+ rvec *f_rot_loc; /* Array to store the forces on the local atoms
+ resulting from enforced rotation potential */
+
+ /* Collective coordinates for the whole rotation group */
+ real *xc_ref_length; /* Length of each x_rotref vector after x_rotref
+ has been put into origin */
+ int *xc_ref_ind; /* Position of each local atom in the collective
+ array */
+ rvec xc_center; /* Center of the rotation group positions, may
+ be mass weighted */
+ rvec xc_ref_center; /* dito, for the reference positions */
+ rvec *xc; /* Current (collective) positions */
+ ivec *xc_shifts; /* Current (collective) shifts */
+ ivec *xc_eshifts; /* Extra shifts since last DD step */
+ rvec *xc_old; /* Old (collective) positions */
+ rvec *xc_norm; /* Normalized form of the current positions */
+ rvec *xc_ref_sorted; /* Reference positions (sorted in the same order
+ as xc when sorted) */
+ int *xc_sortind; /* Where is a position found after sorting? */
+ real *mc; /* Collective masses */
+ real *mc_sorted;
+ real invmass; /* one over the total mass of the rotation group */
+
+ real torque_v; /* Torque in the direction of rotation vector */
+ real angle_v; /* Actual angle of the whole rotation group */
+ /* Fixed rotation only */
+ real weight_v; /* Weights for angle determination */
+ rvec *xr_loc; /* Local reference coords, correctly rotated */
+ rvec *x_loc_pbc; /* Local current coords, correct PBC image */
+ real *m_loc; /* Masses of the current local atoms */
+
+ /* Flexible rotation only */
+ int nslabs_alloc; /* For this many slabs memory is allocated */
+ int slab_first; /* Lowermost slab for that the calculation needs
+ to be performed at a given time step */
+ int slab_last; /* Uppermost slab ... */
+ int slab_first_ref; /* First slab for which ref. center is stored */
+ int slab_last_ref; /* Last ... */
+ int slab_buffer; /* Slab buffer region around reference slabs */
+ int *firstatom; /* First relevant atom for a slab */
+ int *lastatom; /* Last relevant atom for a slab */
+ rvec *slab_center; /* Gaussian-weighted slab center */
+ rvec *slab_center_ref; /* Gaussian-weighted slab center for the
+ reference positions */
+ real *slab_weights; /* Sum of gaussian weights in a slab */
+ real *slab_torque_v; /* Torque T = r x f for each slab. */
+ /* torque_v = m.v = angular momentum in the
+ direction of v */
+ real max_beta; /* min_gaussian from inputrec->rotgrp is the
+ minimum value the gaussian must have so that
+ the force is actually evaluated max_beta is
+ just another way to put it */
+ real *gn_atom; /* Precalculated gaussians for a single atom */
+ int *gn_slabind; /* Tells to which slab each precalculated gaussian
+ belongs */
+ rvec *slab_innersumvec; /* Inner sum of the flexible2 potential per slab;
+ this is precalculated for optimization reasons */
+ t_gmx_slabdata *slab_data; /* Holds atom positions and gaussian weights
+ of atoms belonging to a slab */
+
+ /* For potential fits with varying angle: */
+ t_gmx_potfit *PotAngleFit; /* Used for fit type 'potential' */
+} t_gmx_enfrotgrp;
+
+
+/* Activate output of forces for correctness checks */
+/* #define PRINT_FORCES */
+#ifdef PRINT_FORCES
+#define PRINT_FORCE_J fprintf(stderr, "f%d = %15.8f %15.8f %15.8f\n", erg->xc_ref_ind[j], erg->f_rot_loc[j][XX], erg->f_rot_loc[j][YY], erg->f_rot_loc[j][ZZ]);
+#define PRINT_POT_TAU if (MASTER(cr)) { \
+ fprintf(stderr, "potential = %15.8f\n" "torque = %15.8f\n", erg->V, erg->torque_v); \
+}
+#else
+#define PRINT_FORCE_J
+#define PRINT_POT_TAU
+#endif
+
+/* Shortcuts for often used queries */
+#define ISFLEX(rg) ( (rg->eType == erotgFLEX) || (rg->eType == erotgFLEXT) || (rg->eType == erotgFLEX2) || (rg->eType == erotgFLEX2T) )
+#define ISCOLL(rg) ( (rg->eType == erotgFLEX) || (rg->eType == erotgFLEXT) || (rg->eType == erotgFLEX2) || (rg->eType == erotgFLEX2T) || (rg->eType == erotgRMPF) || (rg->eType == erotgRM2PF) )
+
+
+/* Does any of the rotation groups use slab decomposition? */
+static gmx_bool HaveFlexibleGroups(t_rot *rot)
+{
+ int g;
+ t_rotgrp *rotg;
+
+
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ if (ISFLEX(rotg))
+ {
+ return TRUE;
+ }
+ }
+
+ return FALSE;
+}
+
+
+/* Is for any group the fit angle determined by finding the minimum of the
+ * rotation potential? */
+static gmx_bool HavePotFitGroups(t_rot *rot)
+{
+ int g;
+ t_rotgrp *rotg;
+
+
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ if (erotgFitPOT == rotg->eFittype)
+ {
+ return TRUE;
+ }
+ }
+
+ return FALSE;
+}
+
+
+static double** allocate_square_matrix(int dim)
+{
+ int i;
+ double** mat = NULL;
+
+
+ snew(mat, dim);
+ for (i = 0; i < dim; i++)
+ {
+ snew(mat[i], dim);
+ }
+
+ return mat;
+}
+
+
+static void free_square_matrix(double** mat, int dim)
+{
+ int i;
+
+
+ for (i = 0; i < dim; i++)
+ {
+ sfree(mat[i]);
+ }
+ sfree(mat);
+}
+
+
+/* Return the angle for which the potential is minimal */
+static real get_fitangle(t_rotgrp *rotg, gmx_enfrotgrp_t erg)
+{
+ int i;
+ real fitangle = -999.9;
+ real pot_min = GMX_FLOAT_MAX;
+ t_gmx_potfit *fit;
+
+
+ fit = erg->PotAngleFit;
+
+ for (i = 0; i < rotg->PotAngle_nstep; i++)
+ {
+ if (fit->V[i] < pot_min)
+ {
+ pot_min = fit->V[i];
+ fitangle = fit->degangle[i];
+ }
+ }
+
+ return fitangle;
+}
+
+
+/* Reduce potential angle fit data for this group at this time step? */
+static gmx_inline gmx_bool bPotAngle(t_rot *rot, t_rotgrp *rotg, gmx_large_int_t step)
+{
+ return ( (erotgFitPOT == rotg->eFittype) && (do_per_step(step, rot->nstsout) || do_per_step(step, rot->nstrout)) );
+}
+
+/* Reduce slab torqe data for this group at this time step? */
+static gmx_inline gmx_bool bSlabTau(t_rot *rot, t_rotgrp *rotg, gmx_large_int_t step)
+{
+ return ( (ISFLEX(rotg)) && do_per_step(step, rot->nstsout) );
+}
+
+/* Output rotation energy, torques, etc. for each rotation group */
+static void reduce_output(t_commrec *cr, t_rot *rot, real t, gmx_large_int_t step)
+{
+ int g, i, islab, nslabs = 0;
+ int count; /* MPI element counter */
+ t_rotgrp *rotg;
+ gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ real fitangle;
+ gmx_bool bFlex;
+
+
+ er = rot->enfrot;
+
+ /* Fill the MPI buffer with stuff to reduce. If items are added for reduction
+ * here, the MPI buffer size has to be enlarged also in calc_mpi_bufsize() */
+ if (PAR(cr))
+ {
+ count = 0;
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg = rotg->enfrotgrp;
+ nslabs = erg->slab_last - erg->slab_first + 1;
+ er->mpi_inbuf[count++] = erg->V;
+ er->mpi_inbuf[count++] = erg->torque_v;
+ er->mpi_inbuf[count++] = erg->angle_v;
+ er->mpi_inbuf[count++] = erg->weight_v; /* weights are not needed for flex types, but this is just a single value */
+
+ if (bPotAngle(rot, rotg, step))
+ {
+ for (i = 0; i < rotg->PotAngle_nstep; i++)
+ {
+ er->mpi_inbuf[count++] = erg->PotAngleFit->V[i];
+ }
+ }
+ if (bSlabTau(rot, rotg, step))
+ {
+ for (i = 0; i < nslabs; i++)
+ {
+ er->mpi_inbuf[count++] = erg->slab_torque_v[i];
+ }
+ }
+ }
+ if (count > er->mpi_bufsize)
+ {
+ gmx_fatal(FARGS, "%s MPI buffer overflow, please report this error.", RotStr);
+ }
+
+#ifdef GMX_MPI
+ MPI_Reduce(er->mpi_inbuf, er->mpi_outbuf, count, GMX_MPI_REAL, MPI_SUM, MASTERRANK(cr), cr->mpi_comm_mygroup);
+#endif
+
+ /* Copy back the reduced data from the buffer on the master */
+ if (MASTER(cr))
+ {
+ count = 0;
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg = rotg->enfrotgrp;
+ nslabs = erg->slab_last - erg->slab_first + 1;
+ erg->V = er->mpi_outbuf[count++];
+ erg->torque_v = er->mpi_outbuf[count++];
+ erg->angle_v = er->mpi_outbuf[count++];
+ erg->weight_v = er->mpi_outbuf[count++];
+
+ if (bPotAngle(rot, rotg, step))
+ {
+ for (i = 0; i < rotg->PotAngle_nstep; i++)
+ {
+ erg->PotAngleFit->V[i] = er->mpi_outbuf[count++];
+ }
+ }
+ if (bSlabTau(rot, rotg, step))
+ {
+ for (i = 0; i < nslabs; i++)
+ {
+ erg->slab_torque_v[i] = er->mpi_outbuf[count++];
+ }
+ }
+ }
+ }
+ }
+
+ /* Output */
+ if (MASTER(cr))
+ {
+ /* Angle and torque for each rotation group */
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ bFlex = ISFLEX(rotg);
+
+ erg = rotg->enfrotgrp;
+
+ /* Output to main rotation output file: */
+ if (do_per_step(step, rot->nstrout) )
+ {
+ if (erotgFitPOT == rotg->eFittype)
+ {
+ fitangle = get_fitangle(rotg, erg);
+ }
+ else
+ {
+ if (bFlex)
+ {
+ fitangle = erg->angle_v; /* RMSD fit angle */
+ }
+ else
+ {
+ fitangle = (erg->angle_v/erg->weight_v)*180.0*M_1_PI;
+ }
+ }
+ fprintf(er->out_rot, "%12.4f", fitangle);
+ fprintf(er->out_rot, "%12.3e", erg->torque_v);
+ fprintf(er->out_rot, "%12.3e", erg->V);
+ }
+
+ if (do_per_step(step, rot->nstsout) )
+ {
+ /* Output to torque log file: */
+ if (bFlex)
+ {
+ fprintf(er->out_torque, "%12.3e%6d", t, g);
+ for (i = erg->slab_first; i <= erg->slab_last; i++)
+ {
+ islab = i - erg->slab_first; /* slab index */
+ /* Only output if enough weight is in slab */
+ if (erg->slab_weights[islab] > rotg->min_gaussian)
+ {
+ fprintf(er->out_torque, "%6d%12.3e", i, erg->slab_torque_v[islab]);
+ }
+ }
+ fprintf(er->out_torque, "\n");
+ }
+
+ /* Output to angles log file: */
+ if (erotgFitPOT == rotg->eFittype)
+ {
+ fprintf(er->out_angles, "%12.3e%6d%12.4f", t, g, erg->degangle);
+ /* Output energies at a set of angles around the reference angle */
+ for (i = 0; i < rotg->PotAngle_nstep; i++)
+ {
+ fprintf(er->out_angles, "%12.3e", erg->PotAngleFit->V[i]);
+ }
+ fprintf(er->out_angles, "\n");
+ }
+ }
+ }
+ if (do_per_step(step, rot->nstrout) )
+ {
+ fprintf(er->out_rot, "\n");
+ }
+ }
+}
+
+
+/* Add the forces from enforced rotation potential to the local forces.
+ * Should be called after the SR forces have been evaluated */
+extern real add_rot_forces(t_rot *rot, rvec f[], t_commrec *cr, gmx_large_int_t step, real t)
+{
+ int g, l, ii;
+ t_rotgrp *rotg;
+ gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ real Vrot = 0.0; /* If more than one rotation group is present, Vrot
+ assembles the local parts from all groups */
+
+
+ er = rot->enfrot;
+
+ /* Loop over enforced rotation groups (usually 1, though)
+ * Apply the forces from rotation potentials */
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg = rotg->enfrotgrp;
+ Vrot += erg->V; /* add the local parts from the nodes */
+ for (l = 0; l < erg->nat_loc; l++)
+ {
+ /* Get the right index of the local force */
+ ii = erg->ind_loc[l];
+ /* Add */
+ rvec_inc(f[ii], erg->f_rot_loc[l]);
+ }
+ }
+
+ /* Reduce energy,torque, angles etc. to get the sum values (per rotation group)
+ * on the master and output these values to file. */
+ if ( (do_per_step(step, rot->nstrout) || do_per_step(step, rot->nstsout)) && er->bOut)
+ {
+ reduce_output(cr, rot, t, step);
+ }
+
+ /* When appending, er->bOut is FALSE the first time to avoid duplicate entries */
+ er->bOut = TRUE;
+
+ PRINT_POT_TAU
+
+ return Vrot;
+}
+
+
+/* The Gaussian norm is chosen such that the sum of the gaussian functions
+ * over the slabs is approximately 1.0 everywhere */
+#define GAUSS_NORM 0.569917543430618
+
+
+/* Calculate the maximum beta that leads to a gaussian larger min_gaussian,
+ * also does some checks
+ */
+static double calc_beta_max(real min_gaussian, real slab_dist)
+{
+ double sigma;
+ double arg;
+
+
+ /* Actually the next two checks are already made in grompp */
+ if (slab_dist <= 0)
+ {
+ gmx_fatal(FARGS, "Slab distance of flexible rotation groups must be >=0 !");
+ }
+ if (min_gaussian <= 0)
+ {
+ gmx_fatal(FARGS, "Cutoff value for Gaussian must be > 0. (You requested %f)");
+ }
+
+ /* Define the sigma value */
+ sigma = 0.7*slab_dist;
+
+ /* Calculate the argument for the logarithm and check that the log() result is negative or 0 */
+ arg = min_gaussian/GAUSS_NORM;
+ if (arg > 1.0)
+ {
+ gmx_fatal(FARGS, "min_gaussian of flexible rotation groups must be <%g", GAUSS_NORM);
+ }
+
+ return sqrt(-2.0*sigma*sigma*log(min_gaussian/GAUSS_NORM));
+}
+
+
+static gmx_inline real calc_beta(rvec curr_x, t_rotgrp *rotg, int n)
+{
+ return iprod(curr_x, rotg->vec) - rotg->slab_dist * n;
+}
+
+
+static gmx_inline real gaussian_weight(rvec curr_x, t_rotgrp *rotg, int n)
+{
+ const real norm = GAUSS_NORM;
+ real sigma;
+
+
+ /* Define the sigma value */
+ sigma = 0.7*rotg->slab_dist;
+ /* Calculate the Gaussian value of slab n for position curr_x */
+ return norm * exp( -0.5 * sqr( calc_beta(curr_x, rotg, n)/sigma ) );
+}
+
+
+/* Returns the weight in a single slab, also calculates the Gaussian- and mass-
+ * weighted sum of positions for that slab */
+static real get_slab_weight(int j, t_rotgrp *rotg, rvec xc[], real mc[], rvec *x_weighted_sum)
+{
+ rvec curr_x; /* The position of an atom */
+ rvec curr_x_weighted; /* The gaussian-weighted position */
+ real gaussian; /* A single gaussian weight */
+ real wgauss; /* gaussian times current mass */
+ real slabweight = 0.0; /* The sum of weights in the slab */
+ int i, islab;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg = rotg->enfrotgrp;
+ clear_rvec(*x_weighted_sum);
+
+ /* Slab index */
+ islab = j - erg->slab_first;
+
+ /* Loop over all atoms in the rotation group */
+ for (i = 0; i < rotg->nat; i++)
+ {
+ copy_rvec(xc[i], curr_x);
+ gaussian = gaussian_weight(curr_x, rotg, j);
+ wgauss = gaussian * mc[i];
+ svmul(wgauss, curr_x, curr_x_weighted);
+ rvec_add(*x_weighted_sum, curr_x_weighted, *x_weighted_sum);
+ slabweight += wgauss;
+ } /* END of loop over rotation group atoms */
+
+ return slabweight;
+}
+
+
+static void get_slab_centers(
+ t_rotgrp *rotg, /* The rotation group information */
+ rvec *xc, /* The rotation group positions; will
+ typically be enfrotgrp->xc, but at first call
+ it is enfrotgrp->xc_ref */
+ real *mc, /* The masses of the rotation group atoms */
+ int g, /* The number of the rotation group */
+ real time, /* Used for output only */
+ FILE *out_slabs, /* For outputting center per slab information */
+ gmx_bool bOutStep, /* Is this an output step? */
+ gmx_bool bReference) /* If this routine is called from
+ init_rot_group we need to store
+ the reference slab centers */
+{
+ int j, islab;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg = rotg->enfrotgrp;
+
+ /* Loop over slabs */
+ for (j = erg->slab_first; j <= erg->slab_last; j++)
+ {
+ islab = j - erg->slab_first;
+ erg->slab_weights[islab] = get_slab_weight(j, rotg, xc, mc, &erg->slab_center[islab]);
+
+ /* We can do the calculations ONLY if there is weight in the slab! */
+ if (erg->slab_weights[islab] > WEIGHT_MIN)
+ {
+ svmul(1.0/erg->slab_weights[islab], erg->slab_center[islab], erg->slab_center[islab]);
+ }
+ else
+ {
+ /* We need to check this here, since we divide through slab_weights
+ * in the flexible low-level routines! */
+ gmx_fatal(FARGS, "Not enough weight in slab %d. Slab center cannot be determined!", j);
+ }
+
+ /* At first time step: save the centers of the reference structure */
+ if (bReference)
+ {
+ copy_rvec(erg->slab_center[islab], erg->slab_center_ref[islab]);
+ }
+ } /* END of loop over slabs */
+
+ /* Output on the master */
+ if ( (NULL != out_slabs) && bOutStep)
+ {
+ fprintf(out_slabs, "%12.3e%6d", time, g);
+ for (j = erg->slab_first; j <= erg->slab_last; j++)
+ {
+ islab = j - erg->slab_first;
+ fprintf(out_slabs, "%6d%12.3e%12.3e%12.3e",
+ j, erg->slab_center[islab][XX], erg->slab_center[islab][YY], erg->slab_center[islab][ZZ]);
+ }
+ fprintf(out_slabs, "\n");
+ }
+}
+
+
+static void calc_rotmat(
+ rvec vec,
+ real degangle, /* Angle alpha of rotation at time t in degrees */
+ matrix rotmat) /* Rotation matrix */
+{
+ real radangle; /* Rotation angle in radians */
+ real cosa; /* cosine alpha */
+ real sina; /* sine alpha */
+ real OMcosa; /* 1 - cos(alpha) */
+ real dumxy, dumxz, dumyz; /* save computations */
+ rvec rot_vec; /* Rotate around rot_vec ... */
+
+
+ radangle = degangle * M_PI/180.0;
+ copy_rvec(vec, rot_vec );
+
+ /* Precompute some variables: */
+ cosa = cos(radangle);
+ sina = sin(radangle);
+ OMcosa = 1.0 - cosa;
+ dumxy = rot_vec[XX]*rot_vec[YY]*OMcosa;
+ dumxz = rot_vec[XX]*rot_vec[ZZ]*OMcosa;
+ dumyz = rot_vec[YY]*rot_vec[ZZ]*OMcosa;
+
+ /* Construct the rotation matrix for this rotation group: */
+ /* 1st column: */
+ rotmat[XX][XX] = cosa + rot_vec[XX]*rot_vec[XX]*OMcosa;
+ rotmat[YY][XX] = dumxy + rot_vec[ZZ]*sina;
+ rotmat[ZZ][XX] = dumxz - rot_vec[YY]*sina;
+ /* 2nd column: */
+ rotmat[XX][YY] = dumxy - rot_vec[ZZ]*sina;
+ rotmat[YY][YY] = cosa + rot_vec[YY]*rot_vec[YY]*OMcosa;
+ rotmat[ZZ][YY] = dumyz + rot_vec[XX]*sina;
+ /* 3rd column: */
+ rotmat[XX][ZZ] = dumxz + rot_vec[YY]*sina;
+ rotmat[YY][ZZ] = dumyz - rot_vec[XX]*sina;
+ rotmat[ZZ][ZZ] = cosa + rot_vec[ZZ]*rot_vec[ZZ]*OMcosa;
+
+#ifdef PRINTMATRIX
+ int iii, jjj;
+
+ for (iii = 0; iii < 3; iii++)
+ {
+ for (jjj = 0; jjj < 3; jjj++)
+ {
+ fprintf(stderr, " %10.8f ", rotmat[iii][jjj]);
+ }
+ fprintf(stderr, "\n");
+ }
+#endif
+}
+
+
+/* Calculates torque on the rotation axis tau = position x force */
+static gmx_inline real torque(
+ rvec rotvec, /* rotation vector; MUST be normalized! */
+ rvec force, /* force */
+ rvec x, /* position of atom on which the force acts */
+ rvec pivot) /* pivot point of rotation axis */
+{
+ rvec vectmp, tau;
+
+
+ /* Subtract offset */
+ rvec_sub(x, pivot, vectmp);
+
+ /* position x force */
+ cprod(vectmp, force, tau);
+
+ /* Return the part of the torque which is parallel to the rotation vector */
+ return iprod(tau, rotvec);
+}
+
+
+/* Right-aligned output of value with standard width */
+static void print_aligned(FILE *fp, char *str)
+{
+ fprintf(fp, "%12s", str);
+}
+
+
+/* Right-aligned output of value with standard short width */
+static void print_aligned_short(FILE *fp, char *str)
+{
+ fprintf(fp, "%6s", str);
+}
+
+
+static FILE *open_output_file(const char *fn, int steps, const char what[])
+{
+ FILE *fp;
+
+
+ fp = ffopen(fn, "w");
+
+ fprintf(fp, "# Output of %s is written in intervals of %d time step%s.\n#\n",
+ what, steps, steps > 1 ? "s" : "");
+
+ return fp;
+}
+
+
+/* Open output file for slab center data. Call on master only */
- static FILE *open_angles_out(const char *fn, t_rot *rot, const output_env_t oenv)
++static FILE *open_slab_out(const char *fn, t_rot *rot)
+{
+ FILE *fp;
+ int g, i;
+ t_rotgrp *rotg;
+
+
+ if (rot->enfrot->Flags & MD_APPENDFILES)
+ {
+ fp = gmx_fio_fopen(fn, "a");
+ }
+ else
+ {
+ fp = open_output_file(fn, rot->nstsout, "gaussian weighted slab centers");
+
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ if (ISFLEX(rotg))
+ {
+ fprintf(fp, "# Rotation group %d (%s), slab distance %f nm, %s.\n",
+ g, erotg_names[rotg->eType], rotg->slab_dist,
+ rotg->bMassW ? "centers of mass" : "geometrical centers");
+ }
+ }
+
+ fprintf(fp, "# Reference centers are listed first (t=-1).\n");
+ fprintf(fp, "# The following columns have the syntax:\n");
+ fprintf(fp, "# ");
+ print_aligned_short(fp, "t");
+ print_aligned_short(fp, "grp");
+ /* Print legend for the first two entries only ... */
+ for (i = 0; i < 2; i++)
+ {
+ print_aligned_short(fp, "slab");
+ print_aligned(fp, "X center");
+ print_aligned(fp, "Y center");
+ print_aligned(fp, "Z center");
+ }
+ fprintf(fp, " ...\n");
+ fflush(fp);
+ }
+
+ return fp;
+}
+
+
+/* Adds 'buf' to 'str' */
+static void add_to_string(char **str, char *buf)
+{
+ int len;
+
+
+ len = strlen(*str) + strlen(buf) + 1;
+ srenew(*str, len);
+ strcat(*str, buf);
+}
+
+
+static void add_to_string_aligned(char **str, char *buf)
+{
+ char buf_aligned[STRLEN];
+
+ sprintf(buf_aligned, "%12s", buf);
+ add_to_string(str, buf_aligned);
+}
+
+
+/* Open output file and print some general information about the rotation groups.
+ * Call on master only */
+static FILE *open_rot_out(const char *fn, t_rot *rot, const output_env_t oenv)
+{
+ FILE *fp;
+ int g, nsets;
+ t_rotgrp *rotg;
+ const char **setname;
+ char buf[50], buf2[75];
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ gmx_bool bFlex;
+ char *LegendStr = NULL;
+
+
+ if (rot->enfrot->Flags & MD_APPENDFILES)
+ {
+ fp = gmx_fio_fopen(fn, "a");
+ }
+ else
+ {
+ fp = xvgropen(fn, "Rotation angles and energy", "Time (ps)", "angles (degrees) and energies (kJ/mol)", oenv);
+ fprintf(fp, "# Output of enforced rotation data is written in intervals of %d time step%s.\n#\n", rot->nstrout, rot->nstrout > 1 ? "s" : "");
+ fprintf(fp, "# The scalar tau is the torque (kJ/mol) in the direction of the rotation vector v.\n");
+ fprintf(fp, "# To obtain the vectorial torque, multiply tau with the group's rot_vec.\n");
+ fprintf(fp, "# For flexible groups, tau(t,n) from all slabs n have been summed in a single value tau(t) here.\n");
+ fprintf(fp, "# The torques tau(t,n) are found in the rottorque.log (-rt) output file\n");
+
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg = rotg->enfrotgrp;
+ bFlex = ISFLEX(rotg);
+
+ fprintf(fp, "#\n");
+ fprintf(fp, "# ROTATION GROUP %d, potential type '%s':\n", g, erotg_names[rotg->eType]);
+ fprintf(fp, "# rot_massw%d %s\n", g, yesno_names[rotg->bMassW]);
+ fprintf(fp, "# rot_vec%d %12.5e %12.5e %12.5e\n", g, rotg->vec[XX], rotg->vec[YY], rotg->vec[ZZ]);
+ fprintf(fp, "# rot_rate%d %12.5e degrees/ps\n", g, rotg->rate);
+ fprintf(fp, "# rot_k%d %12.5e kJ/(mol*nm^2)\n", g, rotg->k);
+ if (rotg->eType == erotgISO || rotg->eType == erotgPM || rotg->eType == erotgRM || rotg->eType == erotgRM2)
+ {
+ fprintf(fp, "# rot_pivot%d %12.5e %12.5e %12.5e nm\n", g, rotg->pivot[XX], rotg->pivot[YY], rotg->pivot[ZZ]);
+ }
+
+ if (bFlex)
+ {
+ fprintf(fp, "# rot_slab_distance%d %f nm\n", g, rotg->slab_dist);
+ fprintf(fp, "# rot_min_gaussian%d %12.5e\n", g, rotg->min_gaussian);
+ }
+
+ /* Output the centers of the rotation groups for the pivot-free potentials */
+ if ((rotg->eType == erotgISOPF) || (rotg->eType == erotgPMPF) || (rotg->eType == erotgRMPF) || (rotg->eType == erotgRM2PF
+ || (rotg->eType == erotgFLEXT) || (rotg->eType == erotgFLEX2T)) )
+ {
+ fprintf(fp, "# ref. grp. %d center %12.5e %12.5e %12.5e\n", g,
+ erg->xc_ref_center[XX], erg->xc_ref_center[YY], erg->xc_ref_center[ZZ]);
+
+ fprintf(fp, "# grp. %d init.center %12.5e %12.5e %12.5e\n", g,
+ erg->xc_center[XX], erg->xc_center[YY], erg->xc_center[ZZ]);
+ }
+
+ if ( (rotg->eType == erotgRM2) || (rotg->eType == erotgFLEX2) || (rotg->eType == erotgFLEX2T) )
+ {
+ fprintf(fp, "# rot_eps%d %12.5e nm^2\n", g, rotg->eps);
+ }
+ if (erotgFitPOT == rotg->eFittype)
+ {
+ fprintf(fp, "#\n");
+ fprintf(fp, "# theta_fit%d is determined by first evaluating the potential for %d angles around theta_ref%d.\n",
+ g, rotg->PotAngle_nstep, g);
+ fprintf(fp, "# The fit angle is the one with the smallest potential. It is given as the deviation\n");
+ fprintf(fp, "# from the reference angle, i.e. if theta_ref=X and theta_fit=Y, then the angle with\n");
+ fprintf(fp, "# minimal value of the potential is X+Y. Angular resolution is %g degrees.\n", rotg->PotAngle_step);
+ }
+ }
+
+ /* Print a nice legend */
+ snew(LegendStr, 1);
+ LegendStr[0] = '\0';
+ sprintf(buf, "# %6s", "time");
+ add_to_string_aligned(&LegendStr, buf);
+
+ nsets = 0;
+ snew(setname, 4*rot->ngrp);
+
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ sprintf(buf, "theta_ref%d", g);
+ add_to_string_aligned(&LegendStr, buf);
+
+ sprintf(buf2, "%s (degrees)", buf);
+ setname[nsets] = strdup(buf2);
+ nsets++;
+ }
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ bFlex = ISFLEX(rotg);
+
+ /* For flexible axis rotation we use RMSD fitting to determine the
+ * actual angle of the rotation group */
+ if (bFlex || erotgFitPOT == rotg->eFittype)
+ {
+ sprintf(buf, "theta_fit%d", g);
+ }
+ else
+ {
+ sprintf(buf, "theta_av%d", g);
+ }
+ add_to_string_aligned(&LegendStr, buf);
+ sprintf(buf2, "%s (degrees)", buf);
+ setname[nsets] = strdup(buf2);
+ nsets++;
+
+ sprintf(buf, "tau%d", g);
+ add_to_string_aligned(&LegendStr, buf);
+ sprintf(buf2, "%s (kJ/mol)", buf);
+ setname[nsets] = strdup(buf2);
+ nsets++;
+
+ sprintf(buf, "energy%d", g);
+ add_to_string_aligned(&LegendStr, buf);
+ sprintf(buf2, "%s (kJ/mol)", buf);
+ setname[nsets] = strdup(buf2);
+ nsets++;
+ }
+ fprintf(fp, "#\n");
+
+ if (nsets > 1)
+ {
+ xvgr_legend(fp, nsets, setname, oenv);
+ }
+ sfree(setname);
+
+ fprintf(fp, "#\n# Legend for the following data columns:\n");
+ fprintf(fp, "%s\n", LegendStr);
+ sfree(LegendStr);
+
+ fflush(fp);
+ }
+
+ return fp;
+}
+
+
+/* Call on master only */
- static FILE *open_torque_out(const char *fn, t_rot *rot, const output_env_t oenv)
++static FILE *open_angles_out(const char *fn, t_rot *rot)
+{
+ int g, i;
+ FILE *fp;
+ t_rotgrp *rotg;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ char buf[100];
+
+
+ if (rot->enfrot->Flags & MD_APPENDFILES)
+ {
+ fp = gmx_fio_fopen(fn, "a");
+ }
+ else
+ {
+ /* Open output file and write some information about it's structure: */
+ fp = open_output_file(fn, rot->nstsout, "rotation group angles");
+ fprintf(fp, "# All angles given in degrees, time in ps.\n");
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg = rotg->enfrotgrp;
+
+ /* Output for this group happens only if potential type is flexible or
+ * if fit type is potential! */
+ if (ISFLEX(rotg) || (erotgFitPOT == rotg->eFittype) )
+ {
+ if (ISFLEX(rotg))
+ {
+ sprintf(buf, " slab distance %f nm, ", rotg->slab_dist);
+ }
+ else
+ {
+ buf[0] = '\0';
+ }
+
+ fprintf(fp, "#\n# ROTATION GROUP %d '%s',%s fit type '%s'.\n",
+ g, erotg_names[rotg->eType], buf, erotg_fitnames[rotg->eFittype]);
+
+ /* Special type of fitting using the potential minimum. This is
+ * done for the whole group only, not for the individual slabs. */
+ if (erotgFitPOT == rotg->eFittype)
+ {
+ fprintf(fp, "# To obtain theta_fit%d, the potential is evaluated for %d angles around theta_ref%d\n", g, rotg->PotAngle_nstep, g);
+ fprintf(fp, "# The fit angle in the rotation standard outfile is the one with minimal energy E(theta_fit) [kJ/mol].\n");
+ fprintf(fp, "#\n");
+ }
+
+ fprintf(fp, "# Legend for the group %d data columns:\n", g);
+ fprintf(fp, "# ");
+ print_aligned_short(fp, "time");
+ print_aligned_short(fp, "grp");
+ print_aligned(fp, "theta_ref");
+
+ if (erotgFitPOT == rotg->eFittype)
+ {
+ /* Output the set of angles around the reference angle */
+ for (i = 0; i < rotg->PotAngle_nstep; i++)
+ {
+ sprintf(buf, "E(%g)", erg->PotAngleFit->degangle[i]);
+ print_aligned(fp, buf);
+ }
+ }
+ else
+ {
+ /* Output fit angle for each slab */
+ print_aligned_short(fp, "slab");
+ print_aligned_short(fp, "atoms");
+ print_aligned(fp, "theta_fit");
+ print_aligned_short(fp, "slab");
+ print_aligned_short(fp, "atoms");
+ print_aligned(fp, "theta_fit");
+ fprintf(fp, " ...");
+ }
+ fprintf(fp, "\n");
+ }
+ }
+ fflush(fp);
+ }
+
+ return fp;
+}
+
+
+/* Open torque output file and write some information about it's structure.
+ * Call on master only */
- /* Determine the max slab */
++static FILE *open_torque_out(const char *fn, t_rot *rot)
+{
+ FILE *fp;
+ int g;
+ t_rotgrp *rotg;
+
+
+ if (rot->enfrot->Flags & MD_APPENDFILES)
+ {
+ fp = gmx_fio_fopen(fn, "a");
+ }
+ else
+ {
+ fp = open_output_file(fn, rot->nstsout, "torques");
+
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ if (ISFLEX(rotg))
+ {
+ fprintf(fp, "# Rotation group %d (%s), slab distance %f nm.\n", g, erotg_names[rotg->eType], rotg->slab_dist);
+ fprintf(fp, "# The scalar tau is the torque (kJ/mol) in the direction of the rotation vector.\n");
+ fprintf(fp, "# To obtain the vectorial torque, multiply tau with\n");
+ fprintf(fp, "# rot_vec%d %10.3e %10.3e %10.3e\n", g, rotg->vec[XX], rotg->vec[YY], rotg->vec[ZZ]);
+ fprintf(fp, "#\n");
+ }
+ }
+ fprintf(fp, "# Legend for the following data columns: (tau=torque for that slab):\n");
+ fprintf(fp, "# ");
+ print_aligned_short(fp, "t");
+ print_aligned_short(fp, "grp");
+ print_aligned_short(fp, "slab");
+ print_aligned(fp, "tau");
+ print_aligned_short(fp, "slab");
+ print_aligned(fp, "tau");
+ fprintf(fp, " ...\n");
+ fflush(fp);
+ }
+
+ return fp;
+}
+
+
+static void swap_val(double* vec, int i, int j)
+{
+ double tmp = vec[j];
+
+
+ vec[j] = vec[i];
+ vec[i] = tmp;
+}
+
+
+static void swap_col(double **mat, int i, int j)
+{
+ double tmp[3] = {mat[0][j], mat[1][j], mat[2][j]};
+
+
+ mat[0][j] = mat[0][i];
+ mat[1][j] = mat[1][i];
+ mat[2][j] = mat[2][i];
+
+ mat[0][i] = tmp[0];
+ mat[1][i] = tmp[1];
+ mat[2][i] = tmp[2];
+}
+
+
+/* Eigenvectors are stored in columns of eigen_vec */
+static void diagonalize_symmetric(
+ double **matrix,
+ double **eigen_vec,
+ double eigenval[3])
+{
+ int n_rot;
+
+
+ jacobi(matrix, 3, eigenval, eigen_vec, &n_rot);
+
+ /* sort in ascending order */
+ if (eigenval[0] > eigenval[1])
+ {
+ swap_val(eigenval, 0, 1);
+ swap_col(eigen_vec, 0, 1);
+ }
+ if (eigenval[1] > eigenval[2])
+ {
+ swap_val(eigenval, 1, 2);
+ swap_col(eigen_vec, 1, 2);
+ }
+ if (eigenval[0] > eigenval[1])
+ {
+ swap_val(eigenval, 0, 1);
+ swap_col(eigen_vec, 0, 1);
+ }
+}
+
+
+static void align_with_z(
+ rvec* s, /* Structure to align */
+ int natoms,
+ rvec axis)
+{
+ int i, j, k;
+ rvec zet = {0.0, 0.0, 1.0};
+ rvec rot_axis = {0.0, 0.0, 0.0};
+ rvec *rotated_str = NULL;
+ real ooanorm;
+ real angle;
+ matrix rotmat;
+
+
+ snew(rotated_str, natoms);
+
+ /* Normalize the axis */
+ ooanorm = 1.0/norm(axis);
+ svmul(ooanorm, axis, axis);
+
+ /* Calculate the angle for the fitting procedure */
+ cprod(axis, zet, rot_axis);
+ angle = acos(axis[2]);
+ if (angle < 0.0)
+ {
+ angle += M_PI;
+ }
+
+ /* Calculate the rotation matrix */
+ calc_rotmat(rot_axis, angle*180.0/M_PI, rotmat);
+
+ /* Apply the rotation matrix to s */
+ for (i = 0; i < natoms; i++)
+ {
+ for (j = 0; j < 3; j++)
+ {
+ for (k = 0; k < 3; k++)
+ {
+ rotated_str[i][j] += rotmat[j][k]*s[i][k];
+ }
+ }
+ }
+
+ /* Rewrite the rotated structure to s */
+ for (i = 0; i < natoms; i++)
+ {
+ for (j = 0; j < 3; j++)
+ {
+ s[i][j] = rotated_str[i][j];
+ }
+ }
+
+ sfree(rotated_str);
+}
+
+
+static void calc_correl_matrix(rvec* Xstr, rvec* Ystr, double** Rmat, int natoms)
+{
+ int i, j, k;
+
+
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j < 3; j++)
+ {
+ Rmat[i][j] = 0.0;
+ }
+ }
+
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j < 3; j++)
+ {
+ for (k = 0; k < natoms; k++)
+ {
+ Rmat[i][j] += Ystr[k][i] * Xstr[k][j];
+ }
+ }
+ }
+}
+
+
+static void weigh_coords(rvec* str, real* weight, int natoms)
+{
+ int i, j;
+
+
+ for (i = 0; i < natoms; i++)
+ {
+ for (j = 0; j < 3; j++)
+ {
+ str[i][j] *= sqrt(weight[i]);
+ }
+ }
+}
+
+
+static real opt_angle_analytic(
+ rvec* ref_s,
+ rvec* act_s,
+ real* weight,
+ int natoms,
+ rvec ref_com,
+ rvec act_com,
+ rvec axis)
+{
+ int i, j, k;
+ rvec *ref_s_1 = NULL;
+ rvec *act_s_1 = NULL;
+ rvec shift;
+ double **Rmat, **RtR, **eigvec;
+ double eigval[3];
+ double V[3][3], WS[3][3];
+ double rot_matrix[3][3];
+ double opt_angle;
+
+
+ /* Do not change the original coordinates */
+ snew(ref_s_1, natoms);
+ snew(act_s_1, natoms);
+ for (i = 0; i < natoms; i++)
+ {
+ copy_rvec(ref_s[i], ref_s_1[i]);
+ copy_rvec(act_s[i], act_s_1[i]);
+ }
+
+ /* Translate the structures to the origin */
+ shift[XX] = -ref_com[XX];
+ shift[YY] = -ref_com[YY];
+ shift[ZZ] = -ref_com[ZZ];
+ translate_x(ref_s_1, natoms, shift);
+
+ shift[XX] = -act_com[XX];
+ shift[YY] = -act_com[YY];
+ shift[ZZ] = -act_com[ZZ];
+ translate_x(act_s_1, natoms, shift);
+
+ /* Align rotation axis with z */
+ align_with_z(ref_s_1, natoms, axis);
+ align_with_z(act_s_1, natoms, axis);
+
+ /* Correlation matrix */
+ Rmat = allocate_square_matrix(3);
+
+ for (i = 0; i < natoms; i++)
+ {
+ ref_s_1[i][2] = 0.0;
+ act_s_1[i][2] = 0.0;
+ }
+
+ /* Weight positions with sqrt(weight) */
+ if (NULL != weight)
+ {
+ weigh_coords(ref_s_1, weight, natoms);
+ weigh_coords(act_s_1, weight, natoms);
+ }
+
+ /* Calculate correlation matrices R=YXt (X=ref_s; Y=act_s) */
+ calc_correl_matrix(ref_s_1, act_s_1, Rmat, natoms);
+
+ /* Calculate RtR */
+ RtR = allocate_square_matrix(3);
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j < 3; j++)
+ {
+ for (k = 0; k < 3; k++)
+ {
+ RtR[i][j] += Rmat[k][i] * Rmat[k][j];
+ }
+ }
+ }
+ /* Diagonalize RtR */
+ snew(eigvec, 3);
+ for (i = 0; i < 3; i++)
+ {
+ snew(eigvec[i], 3);
+ }
+
+ diagonalize_symmetric(RtR, eigvec, eigval);
+ swap_col(eigvec, 0, 1);
+ swap_col(eigvec, 1, 2);
+ swap_val(eigval, 0, 1);
+ swap_val(eigval, 1, 2);
+
+ /* Calculate V */
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j < 3; j++)
+ {
+ V[i][j] = 0.0;
+ WS[i][j] = 0.0;
+ }
+ }
+
+ for (i = 0; i < 2; i++)
+ {
+ for (j = 0; j < 2; j++)
+ {
+ WS[i][j] = eigvec[i][j] / sqrt(eigval[j]);
+ }
+ }
+
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j < 3; j++)
+ {
+ for (k = 0; k < 3; k++)
+ {
+ V[i][j] += Rmat[i][k]*WS[k][j];
+ }
+ }
+ }
+ free_square_matrix(Rmat, 3);
+
+ /* Calculate optimal rotation matrix */
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j < 3; j++)
+ {
+ rot_matrix[i][j] = 0.0;
+ }
+ }
+
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j < 3; j++)
+ {
+ for (k = 0; k < 3; k++)
+ {
+ rot_matrix[i][j] += eigvec[i][k]*V[j][k];
+ }
+ }
+ }
+ rot_matrix[2][2] = 1.0;
+
+ /* In some cases abs(rot_matrix[0][0]) can be slighly larger
+ * than unity due to numerical inacurracies. To be able to calculate
+ * the acos function, we put these values back in range. */
+ if (rot_matrix[0][0] > 1.0)
+ {
+ rot_matrix[0][0] = 1.0;
+ }
+ else if (rot_matrix[0][0] < -1.0)
+ {
+ rot_matrix[0][0] = -1.0;
+ }
+
+ /* Determine the optimal rotation angle: */
+ opt_angle = (-1.0)*acos(rot_matrix[0][0])*180.0/M_PI;
+ if (rot_matrix[0][1] < 0.0)
+ {
+ opt_angle = (-1.0)*opt_angle;
+ }
+
+ /* Give back some memory */
+ free_square_matrix(RtR, 3);
+ sfree(ref_s_1);
+ sfree(act_s_1);
+ for (i = 0; i < 3; i++)
+ {
+ sfree(eigvec[i]);
+ }
+ sfree(eigvec);
+
+ return (real) opt_angle;
+}
+
+
+/* Determine angle of the group by RMSD fit to the reference */
+/* Not parallelized, call this routine only on the master */
+static real flex_fit_angle(t_rotgrp *rotg)
+{
+ int i;
+ rvec *fitcoords = NULL;
+ rvec center; /* Center of positions passed to the fit routine */
+ real fitangle; /* Angle of the rotation group derived by fitting */
+ rvec coord;
+ real scal;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg = rotg->enfrotgrp;
+
+ /* Get the center of the rotation group.
+ * Note, again, erg->xc has been sorted in do_flexible */
+ get_center(erg->xc, erg->mc_sorted, rotg->nat, center);
+
+ /* === Determine the optimal fit angle for the rotation group === */
+ if (rotg->eFittype == erotgFitNORM)
+ {
+ /* Normalize every position to it's reference length */
+ for (i = 0; i < rotg->nat; i++)
+ {
+ /* Put the center of the positions into the origin */
+ rvec_sub(erg->xc[i], center, coord);
+ /* Determine the scaling factor for the length: */
+ scal = erg->xc_ref_length[erg->xc_sortind[i]] / norm(coord);
+ /* Get position, multiply with the scaling factor and save */
+ svmul(scal, coord, erg->xc_norm[i]);
+ }
+ fitcoords = erg->xc_norm;
+ }
+ else
+ {
+ fitcoords = erg->xc;
+ }
+ /* From the point of view of the current positions, the reference has rotated
+ * backwards. Since we output the angle relative to the fixed reference,
+ * we need the minus sign. */
+ fitangle = -opt_angle_analytic(erg->xc_ref_sorted, fitcoords, erg->mc_sorted,
+ rotg->nat, erg->xc_ref_center, center, rotg->vec);
+
+ return fitangle;
+}
+
+
+/* Determine actual angle of each slab by RMSD fit to the reference */
+/* Not parallelized, call this routine only on the master */
+static void flex_fit_angle_perslab(
+ int g,
+ t_rotgrp *rotg,
+ double t,
+ real degangle,
+ FILE *fp)
+{
+ int i, l, n, islab, ind;
+ rvec curr_x, ref_x;
+ rvec act_center; /* Center of actual positions that are passed to the fit routine */
+ rvec ref_center; /* Same for the reference positions */
+ real fitangle; /* Angle of a slab derived from an RMSD fit to
+ * the reference structure at t=0 */
+ t_gmx_slabdata *sd;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ real OOm_av; /* 1/average_mass of a rotation group atom */
+ real m_rel; /* Relative mass of a rotation group atom */
+
+
+ erg = rotg->enfrotgrp;
+
+ /* Average mass of a rotation group atom: */
+ OOm_av = erg->invmass*rotg->nat;
+
+ /**********************************/
+ /* First collect the data we need */
+ /**********************************/
+
+ /* Collect the data for the individual slabs */
+ for (n = erg->slab_first; n <= erg->slab_last; n++)
+ {
+ islab = n - erg->slab_first; /* slab index */
+ sd = &(rotg->enfrotgrp->slab_data[islab]);
+ sd->nat = erg->lastatom[islab]-erg->firstatom[islab]+1;
+ ind = 0;
+
+ /* Loop over the relevant atoms in the slab */
+ for (l = erg->firstatom[islab]; l <= erg->lastatom[islab]; l++)
+ {
+ /* Current position of this atom: x[ii][XX/YY/ZZ] */
+ copy_rvec(erg->xc[l], curr_x);
+
+ /* The (unrotated) reference position of this atom is copied to ref_x.
+ * Beware, the xc coords have been sorted in do_flexible */
+ copy_rvec(erg->xc_ref_sorted[l], ref_x);
+
+ /* Save data for doing angular RMSD fit later */
+ /* Save the current atom position */
+ copy_rvec(curr_x, sd->x[ind]);
+ /* Save the corresponding reference position */
+ copy_rvec(ref_x, sd->ref[ind]);
+
+ /* Maybe also mass-weighting was requested. If yes, additionally
+ * multiply the weights with the relative mass of the atom. If not,
+ * multiply with unity. */
+ m_rel = erg->mc_sorted[l]*OOm_av;
+
+ /* Save the weight for this atom in this slab */
+ sd->weight[ind] = gaussian_weight(curr_x, rotg, n) * m_rel;
+
+ /* Next atom in this slab */
+ ind++;
+ }
+ }
+
+ /******************************/
+ /* Now do the fit calculation */
+ /******************************/
+
+ fprintf(fp, "%12.3e%6d%12.3f", t, g, degangle);
+
+ /* === Now do RMSD fitting for each slab === */
+ /* We require at least SLAB_MIN_ATOMS in a slab, such that the fit makes sense. */
+#define SLAB_MIN_ATOMS 4
+
+ for (n = erg->slab_first; n <= erg->slab_last; n++)
+ {
+ islab = n - erg->slab_first; /* slab index */
+ sd = &(rotg->enfrotgrp->slab_data[islab]);
+ if (sd->nat >= SLAB_MIN_ATOMS)
+ {
+ /* Get the center of the slabs reference and current positions */
+ get_center(sd->ref, sd->weight, sd->nat, ref_center);
+ get_center(sd->x, sd->weight, sd->nat, act_center);
+ if (rotg->eFittype == erotgFitNORM)
+ {
+ /* Normalize every position to it's reference length
+ * prior to performing the fit */
+ for (i = 0; i < sd->nat; i++) /* Center */
+ {
+ rvec_dec(sd->ref[i], ref_center);
+ rvec_dec(sd->x[i], act_center);
+ /* Normalize x_i such that it gets the same length as ref_i */
+ svmul( norm(sd->ref[i])/norm(sd->x[i]), sd->x[i], sd->x[i] );
+ }
+ /* We already subtracted the centers */
+ clear_rvec(ref_center);
+ clear_rvec(act_center);
+ }
+ fitangle = -opt_angle_analytic(sd->ref, sd->x, sd->weight, sd->nat,
+ ref_center, act_center, rotg->vec);
+ fprintf(fp, "%6d%6d%12.3f", n, sd->nat, fitangle);
+ }
+ }
+ fprintf(fp, "\n");
+
+#undef SLAB_MIN_ATOMS
+}
+
+
+/* Shift x with is */
+static gmx_inline void shift_single_coord(matrix box, rvec x, const ivec is)
+{
+ int tx, ty, tz;
+
+
+ tx = is[XX];
+ ty = is[YY];
+ tz = is[ZZ];
+
+ if (TRICLINIC(box))
+ {
+ x[XX] += tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
+ x[YY] += ty*box[YY][YY]+tz*box[ZZ][YY];
+ x[ZZ] += tz*box[ZZ][ZZ];
+ }
+ else
+ {
+ x[XX] += tx*box[XX][XX];
+ x[YY] += ty*box[YY][YY];
+ x[ZZ] += tz*box[ZZ][ZZ];
+ }
+}
+
+
+/* Determine the 'home' slab of this atom which is the
+ * slab with the highest Gaussian weight of all */
+#define round(a) (int)(a+0.5)
+static gmx_inline int get_homeslab(
+ rvec curr_x, /* The position for which the home slab shall be determined */
+ rvec rotvec, /* The rotation vector */
+ real slabdist) /* The slab distance */
+{
+ real dist;
+
+
+ /* The distance of the atom to the coordinate center (where the
+ * slab with index 0) is */
+ dist = iprod(rotvec, curr_x);
+
+ return round(dist / slabdist);
+}
+
+
+/* For a local atom determine the relevant slabs, i.e. slabs in
+ * which the gaussian is larger than min_gaussian
+ */
+static int get_single_atom_gaussians(
+ rvec curr_x,
+ t_rotgrp *rotg)
+{
+ int slab, homeslab;
+ real g;
+ int count = 0;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg = rotg->enfrotgrp;
+
+ /* Determine the 'home' slab of this atom: */
+ homeslab = get_homeslab(curr_x, rotg->vec, rotg->slab_dist);
+
+ /* First determine the weight in the atoms home slab: */
+ g = gaussian_weight(curr_x, rotg, homeslab);
+
+ erg->gn_atom[count] = g;
+ erg->gn_slabind[count] = homeslab;
+ count++;
+
+
+ /* Determine the max slab */
+ slab = homeslab;
+ while (g > rotg->min_gaussian)
+ {
+ slab++;
+ g = gaussian_weight(curr_x, rotg, slab);
+ erg->gn_slabind[count] = slab;
+ erg->gn_atom[count] = g;
+ count++;
+ }
+ count--;
+
- rvec lastatom, /* Last atom along v */
- int g) /* The rotation group number */
++ /* Determine the min slab */
+ slab = homeslab;
+ do
+ {
+ slab--;
+ g = gaussian_weight(curr_x, rotg, slab);
+ erg->gn_slabind[count] = slab;
+ erg->gn_atom[count] = g;
+ count++;
+ }
+ while (g > rotg->min_gaussian);
+ count--;
+
+ return count;
+}
+
+
+static void flex2_precalc_inner_sum(t_rotgrp *rotg)
+{
+ int i, n, islab;
+ rvec xi; /* positions in the i-sum */
+ rvec xcn, ycn; /* the current and the reference slab centers */
+ real gaussian_xi;
+ rvec yi0;
+ rvec rin; /* Helper variables */
+ real fac, fac2;
+ rvec innersumvec;
+ real OOpsii, OOpsiistar;
+ real sin_rin; /* s_ii.r_ii */
+ rvec s_in, tmpvec, tmpvec2;
+ real mi, wi; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg = rotg->enfrotgrp;
+ N_M = rotg->nat * erg->invmass;
+
+ /* Loop over all slabs that contain something */
+ for (n = erg->slab_first; n <= erg->slab_last; n++)
+ {
+ islab = n - erg->slab_first; /* slab index */
+
+ /* The current center of this slab is saved in xcn: */
+ copy_rvec(erg->slab_center[islab], xcn);
+ /* ... and the reference center in ycn: */
+ copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
+
+ /*** D. Calculate the whole inner sum used for second and third sum */
+ /* For slab n, we need to loop over all atoms i again. Since we sorted
+ * the atoms with respect to the rotation vector, we know that it is sufficient
+ * to calculate from firstatom to lastatom only. All other contributions will
+ * be very small. */
+ clear_rvec(innersumvec);
+ for (i = erg->firstatom[islab]; i <= erg->lastatom[islab]; i++)
+ {
+ /* Coordinate xi of this atom */
+ copy_rvec(erg->xc[i], xi);
+
+ /* The i-weights */
+ gaussian_xi = gaussian_weight(xi, rotg, n);
+ mi = erg->mc_sorted[i]; /* need the sorted mass here */
+ wi = N_M*mi;
+
+ /* Calculate rin */
+ copy_rvec(erg->xc_ref_sorted[i], yi0); /* Reference position yi0 */
+ rvec_sub(yi0, ycn, tmpvec2); /* tmpvec2 = yi0 - ycn */
+ mvmul(erg->rotmat, tmpvec2, rin); /* rin = Omega.(yi0 - ycn) */
+
+ /* Calculate psi_i* and sin */
+ rvec_sub(xi, xcn, tmpvec2); /* tmpvec2 = xi - xcn */
+ cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x (xi - xcn) */
+ OOpsiistar = norm2(tmpvec)+rotg->eps; /* OOpsii* = 1/psii* = |v x (xi-xcn)|^2 + eps */
+ OOpsii = norm(tmpvec); /* OOpsii = 1 / psii = |v x (xi - xcn)| */
+
+ /* * v x (xi - xcn) */
+ unitv(tmpvec, s_in); /* sin = ---------------- */
+ /* |v x (xi - xcn)| */
+
+ sin_rin = iprod(s_in, rin); /* sin_rin = sin . rin */
+
+ /* Now the whole sum */
+ fac = OOpsii/OOpsiistar;
+ svmul(fac, rin, tmpvec);
+ fac2 = fac*fac*OOpsii;
+ svmul(fac2*sin_rin, s_in, tmpvec2);
+ rvec_dec(tmpvec, tmpvec2);
+
+ svmul(wi*gaussian_xi*sin_rin, tmpvec, tmpvec2);
+
+ rvec_inc(innersumvec, tmpvec2);
+ } /* now we have the inner sum, used both for sum2 and sum3 */
+
+ /* Save it to be used in do_flex2_lowlevel */
+ copy_rvec(innersumvec, erg->slab_innersumvec[islab]);
+ } /* END of loop over slabs */
+}
+
+
+static void flex_precalc_inner_sum(t_rotgrp *rotg)
+{
+ int i, n, islab;
+ rvec xi; /* position */
+ rvec xcn, ycn; /* the current and the reference slab centers */
+ rvec qin, rin; /* q_i^n and r_i^n */
+ real bin;
+ rvec tmpvec;
+ rvec innersumvec; /* Inner part of sum_n2 */
+ real gaussian_xi; /* Gaussian weight gn(xi) */
+ real mi, wi; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg = rotg->enfrotgrp;
+ N_M = rotg->nat * erg->invmass;
+
+ /* Loop over all slabs that contain something */
+ for (n = erg->slab_first; n <= erg->slab_last; n++)
+ {
+ islab = n - erg->slab_first; /* slab index */
+
+ /* The current center of this slab is saved in xcn: */
+ copy_rvec(erg->slab_center[islab], xcn);
+ /* ... and the reference center in ycn: */
+ copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
+
+ /* For slab n, we need to loop over all atoms i again. Since we sorted
+ * the atoms with respect to the rotation vector, we know that it is sufficient
+ * to calculate from firstatom to lastatom only. All other contributions will
+ * be very small. */
+ clear_rvec(innersumvec);
+ for (i = erg->firstatom[islab]; i <= erg->lastatom[islab]; i++)
+ {
+ /* Coordinate xi of this atom */
+ copy_rvec(erg->xc[i], xi);
+
+ /* The i-weights */
+ gaussian_xi = gaussian_weight(xi, rotg, n);
+ mi = erg->mc_sorted[i]; /* need the sorted mass here */
+ wi = N_M*mi;
+
+ /* Calculate rin and qin */
+ rvec_sub(erg->xc_ref_sorted[i], ycn, tmpvec); /* tmpvec = yi0-ycn */
+ mvmul(erg->rotmat, tmpvec, rin); /* rin = Omega.(yi0 - ycn) */
+ cprod(rotg->vec, rin, tmpvec); /* tmpvec = v x Omega*(yi0-ycn) */
+
+ /* * v x Omega*(yi0-ycn) */
+ unitv(tmpvec, qin); /* qin = --------------------- */
+ /* |v x Omega*(yi0-ycn)| */
+
+ /* Calculate bin */
+ rvec_sub(xi, xcn, tmpvec); /* tmpvec = xi-xcn */
+ bin = iprod(qin, tmpvec); /* bin = qin*(xi-xcn) */
+
+ svmul(wi*gaussian_xi*bin, qin, tmpvec);
+
+ /* Add this contribution to the inner sum: */
+ rvec_add(innersumvec, tmpvec, innersumvec);
+ } /* now we have the inner sum vector S^n for this slab */
+ /* Save it to be used in do_flex_lowlevel */
+ copy_rvec(innersumvec, erg->slab_innersumvec[islab]);
+ }
+}
+
+
+static real do_flex2_lowlevel(
+ t_rotgrp *rotg,
+ real sigma, /* The Gaussian width sigma */
+ rvec x[],
+ gmx_bool bOutstepRot,
+ gmx_bool bOutstepSlab,
+ matrix box)
+{
+ int count, ic, ii, j, m, n, islab, iigrp, ifit;
+ rvec xj; /* position in the i-sum */
+ rvec yj0; /* the reference position in the j-sum */
+ rvec xcn, ycn; /* the current and the reference slab centers */
+ real V; /* This node's part of the rotation pot. energy */
+ real gaussian_xj; /* Gaussian weight */
+ real beta;
+
+ real numerator, fit_numerator;
+ rvec rjn, fit_rjn; /* Helper variables */
+ real fac, fac2;
+
+ real OOpsij, OOpsijstar;
+ real OOsigma2; /* 1/(sigma^2) */
+ real sjn_rjn;
+ real betasigpsi;
+ rvec sjn, tmpvec, tmpvec2, yj0_ycn;
+ rvec sum1vec_part, sum1vec, sum2vec_part, sum2vec, sum3vec, sum4vec, innersumvec;
+ real sum3, sum4;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ real mj, wj; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+ real Wjn; /* g_n(x_j) m_j / Mjn */
+ gmx_bool bCalcPotFit;
+
+ /* To calculate the torque per slab */
+ rvec slab_force; /* Single force from slab n on one atom */
+ rvec slab_sum1vec_part;
+ real slab_sum3part, slab_sum4part;
+ rvec slab_sum1vec, slab_sum2vec, slab_sum3vec, slab_sum4vec;
+
+
+ erg = rotg->enfrotgrp;
+
+ /* Pre-calculate the inner sums, so that we do not have to calculate
+ * them again for every atom */
+ flex2_precalc_inner_sum(rotg);
+
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
+
+ /********************************************************/
+ /* Main loop over all local atoms of the rotation group */
+ /********************************************************/
+ N_M = rotg->nat * erg->invmass;
+ V = 0.0;
+ OOsigma2 = 1.0 / (sigma*sigma);
+ for (j = 0; j < erg->nat_loc; j++)
+ {
+ /* Local index of a rotation group atom */
+ ii = erg->ind_loc[j];
+ /* Position of this atom in the collective array */
+ iigrp = erg->xc_ref_ind[j];
+ /* Mass-weighting */
+ mj = erg->mc[iigrp]; /* need the unsorted mass here */
+ wj = N_M*mj;
+
+ /* Current position of this atom: x[ii][XX/YY/ZZ]
+ * Note that erg->xc_center contains the center of mass in case the flex2-t
+ * potential was chosen. For the flex2 potential erg->xc_center must be
+ * zero. */
+ rvec_sub(x[ii], erg->xc_center, xj);
+
+ /* Shift this atom such that it is near its reference */
+ shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
+
+ /* Determine the slabs to loop over, i.e. the ones with contributions
+ * larger than min_gaussian */
+ count = get_single_atom_gaussians(xj, rotg);
+
+ clear_rvec(sum1vec_part);
+ clear_rvec(sum2vec_part);
+ sum3 = 0.0;
+ sum4 = 0.0;
+ /* Loop over the relevant slabs for this atom */
+ for (ic = 0; ic < count; ic++)
+ {
+ n = erg->gn_slabind[ic];
+
+ /* Get the precomputed Gaussian value of curr_slab for curr_x */
+ gaussian_xj = erg->gn_atom[ic];
+
+ islab = n - erg->slab_first; /* slab index */
+
+ /* The (unrotated) reference position of this atom is copied to yj0: */
+ copy_rvec(rotg->x_ref[iigrp], yj0);
+
+ beta = calc_beta(xj, rotg, n);
+
+ /* The current center of this slab is saved in xcn: */
+ copy_rvec(erg->slab_center[islab], xcn);
+ /* ... and the reference center in ycn: */
+ copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
+
+ rvec_sub(yj0, ycn, yj0_ycn); /* yj0_ycn = yj0 - ycn */
+
+ /* Rotate: */
+ mvmul(erg->rotmat, yj0_ycn, rjn); /* rjn = Omega.(yj0 - ycn) */
+
+ /* Subtract the slab center from xj */
+ rvec_sub(xj, xcn, tmpvec2); /* tmpvec2 = xj - xcn */
++
++ /* In rare cases, when an atom position coincides with a slab center
++ * (tmpvec2 == 0) we cannot compute the vector product for sjn.
++ * However, since the atom is located directly on the pivot, this
++ * slab's contribution to the force on that atom will be zero
++ * anyway. Therefore, we directly move on to the next slab. */
++ if ( 0 == norm(tmpvec2) )
++ {
++ continue;
++ }
+
+ /* Calculate sjn */
+ cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x (xj - xcn) */
+
+ OOpsijstar = norm2(tmpvec)+rotg->eps; /* OOpsij* = 1/psij* = |v x (xj-xcn)|^2 + eps */
+
+ numerator = sqr(iprod(tmpvec, rjn));
+
+ /*********************************/
+ /* Add to the rotation potential */
+ /*********************************/
+ V += 0.5*rotg->k*wj*gaussian_xj*numerator/OOpsijstar;
+
+ /* If requested, also calculate the potential for a set of angles
+ * near the current reference angle */
+ if (bCalcPotFit)
+ {
+ for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
+ {
+ mvmul(erg->PotAngleFit->rotmat[ifit], yj0_ycn, fit_rjn);
+ fit_numerator = sqr(iprod(tmpvec, fit_rjn));
+ erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*gaussian_xj*fit_numerator/OOpsijstar;
+ }
+ }
+
+ /*************************************/
+ /* Now calculate the force on atom j */
+ /*************************************/
+
+ OOpsij = norm(tmpvec); /* OOpsij = 1 / psij = |v x (xj - xcn)| */
+
+ /* * v x (xj - xcn) */
+ unitv(tmpvec, sjn); /* sjn = ---------------- */
+ /* |v x (xj - xcn)| */
+
+ sjn_rjn = iprod(sjn, rjn); /* sjn_rjn = sjn . rjn */
+
+
+ /*** A. Calculate the first of the four sum terms: ****************/
+ fac = OOpsij/OOpsijstar;
+ svmul(fac, rjn, tmpvec);
+ fac2 = fac*fac*OOpsij;
+ svmul(fac2*sjn_rjn, sjn, tmpvec2);
+ rvec_dec(tmpvec, tmpvec2);
+ fac2 = wj*gaussian_xj; /* also needed for sum4 */
+ svmul(fac2*sjn_rjn, tmpvec, slab_sum1vec_part);
+ /********************/
+ /*** Add to sum1: ***/
+ /********************/
+ rvec_inc(sum1vec_part, slab_sum1vec_part); /* sum1 still needs to vector multiplied with v */
+
+ /*** B. Calculate the forth of the four sum terms: ****************/
+ betasigpsi = beta*OOsigma2*OOpsij; /* this is also needed for sum3 */
+ /********************/
+ /*** Add to sum4: ***/
+ /********************/
+ slab_sum4part = fac2*betasigpsi*fac*sjn_rjn*sjn_rjn; /* Note that fac is still valid from above */
+ sum4 += slab_sum4part;
+
+ /*** C. Calculate Wjn for second and third sum */
+ /* Note that we can safely divide by slab_weights since we check in
+ * get_slab_centers that it is non-zero. */
+ Wjn = gaussian_xj*mj/erg->slab_weights[islab];
+
+ /* We already have precalculated the inner sum for slab n */
+ copy_rvec(erg->slab_innersumvec[islab], innersumvec);
+
+ /* Weigh the inner sum vector with Wjn */
+ svmul(Wjn, innersumvec, innersumvec);
+
+ /*** E. Calculate the second of the four sum terms: */
+ /********************/
+ /*** Add to sum2: ***/
+ /********************/
+ rvec_inc(sum2vec_part, innersumvec); /* sum2 still needs to be vector crossproduct'ed with v */
+
+ /*** F. Calculate the third of the four sum terms: */
+ slab_sum3part = betasigpsi * iprod(sjn, innersumvec);
+ sum3 += slab_sum3part; /* still needs to be multiplied with v */
+
+ /*** G. Calculate the torque on the local slab's axis: */
+ if (bOutstepRot)
+ {
+ /* Sum1 */
+ cprod(slab_sum1vec_part, rotg->vec, slab_sum1vec);
+ /* Sum2 */
+ cprod(innersumvec, rotg->vec, slab_sum2vec);
+ /* Sum3 */
+ svmul(slab_sum3part, rotg->vec, slab_sum3vec);
+ /* Sum4 */
+ svmul(slab_sum4part, rotg->vec, slab_sum4vec);
+
+ /* The force on atom ii from slab n only: */
+ for (m = 0; m < DIM; m++)
+ {
+ slab_force[m] = rotg->k * (-slab_sum1vec[m] + slab_sum2vec[m] - slab_sum3vec[m] + 0.5*slab_sum4vec[m]);
+ }
+
+ erg->slab_torque_v[islab] += torque(rotg->vec, slab_force, xj, xcn);
+ }
+ } /* END of loop over slabs */
+
+ /* Construct the four individual parts of the vector sum: */
+ cprod(sum1vec_part, rotg->vec, sum1vec); /* sum1vec = { } x v */
+ cprod(sum2vec_part, rotg->vec, sum2vec); /* sum2vec = { } x v */
+ svmul(sum3, rotg->vec, sum3vec); /* sum3vec = { } . v */
+ svmul(sum4, rotg->vec, sum4vec); /* sum4vec = { } . v */
+
+ /* Store the additional force so that it can be added to the force
+ * array after the normal forces have been evaluated */
+ for (m = 0; m < DIM; m++)
+ {
+ erg->f_rot_loc[j][m] = rotg->k * (-sum1vec[m] + sum2vec[m] - sum3vec[m] + 0.5*sum4vec[m]);
+ }
+
+#ifdef SUM_PARTS
+ fprintf(stderr, "sum1: %15.8f %15.8f %15.8f\n", -rotg->k*sum1vec[XX], -rotg->k*sum1vec[YY], -rotg->k*sum1vec[ZZ]);
+ fprintf(stderr, "sum2: %15.8f %15.8f %15.8f\n", rotg->k*sum2vec[XX], rotg->k*sum2vec[YY], rotg->k*sum2vec[ZZ]);
+ fprintf(stderr, "sum3: %15.8f %15.8f %15.8f\n", -rotg->k*sum3vec[XX], -rotg->k*sum3vec[YY], -rotg->k*sum3vec[ZZ]);
+ fprintf(stderr, "sum4: %15.8f %15.8f %15.8f\n", 0.5*rotg->k*sum4vec[XX], 0.5*rotg->k*sum4vec[YY], 0.5*rotg->k*sum4vec[ZZ]);
+#endif
+
+ PRINT_FORCE_J
+
+ } /* END of loop over local atoms */
+
+ return V;
+}
+
+
+static real do_flex_lowlevel(
+ t_rotgrp *rotg,
+ real sigma, /* The Gaussian width sigma */
+ rvec x[],
+ gmx_bool bOutstepRot,
+ gmx_bool bOutstepSlab,
+ matrix box)
+{
+ int count, ic, ifit, ii, j, m, n, islab, iigrp;
+ rvec xj, yj0; /* current and reference position */
+ rvec xcn, ycn; /* the current and the reference slab centers */
+ rvec yj0_ycn; /* yj0 - ycn */
+ rvec xj_xcn; /* xj - xcn */
+ rvec qjn, fit_qjn; /* q_i^n */
+ rvec sum_n1, sum_n2; /* Two contributions to the rotation force */
+ rvec innersumvec; /* Inner part of sum_n2 */
+ rvec s_n;
+ rvec force_n; /* Single force from slab n on one atom */
+ rvec force_n1, force_n2; /* First and second part of force_n */
+ rvec tmpvec, tmpvec2, tmp_f; /* Helper variables */
+ real V; /* The rotation potential energy */
+ real OOsigma2; /* 1/(sigma^2) */
+ real beta; /* beta_n(xj) */
+ real bjn, fit_bjn; /* b_j^n */
+ real gaussian_xj; /* Gaussian weight gn(xj) */
+ real betan_xj_sigma2;
+ real mj, wj; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ gmx_bool bCalcPotFit;
+
+
+ erg = rotg->enfrotgrp;
+
+ /* Pre-calculate the inner sums, so that we do not have to calculate
+ * them again for every atom */
+ flex_precalc_inner_sum(rotg);
+
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
+
+ /********************************************************/
+ /* Main loop over all local atoms of the rotation group */
+ /********************************************************/
+ OOsigma2 = 1.0/(sigma*sigma);
+ N_M = rotg->nat * erg->invmass;
+ V = 0.0;
+ for (j = 0; j < erg->nat_loc; j++)
+ {
+ /* Local index of a rotation group atom */
+ ii = erg->ind_loc[j];
+ /* Position of this atom in the collective array */
+ iigrp = erg->xc_ref_ind[j];
+ /* Mass-weighting */
+ mj = erg->mc[iigrp]; /* need the unsorted mass here */
+ wj = N_M*mj;
+
+ /* Current position of this atom: x[ii][XX/YY/ZZ]
+ * Note that erg->xc_center contains the center of mass in case the flex-t
+ * potential was chosen. For the flex potential erg->xc_center must be
+ * zero. */
+ rvec_sub(x[ii], erg->xc_center, xj);
+
+ /* Shift this atom such that it is near its reference */
+ shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
+
+ /* Determine the slabs to loop over, i.e. the ones with contributions
+ * larger than min_gaussian */
+ count = get_single_atom_gaussians(xj, rotg);
+
+ clear_rvec(sum_n1);
+ clear_rvec(sum_n2);
+
+ /* Loop over the relevant slabs for this atom */
+ for (ic = 0; ic < count; ic++)
+ {
+ n = erg->gn_slabind[ic];
+
+ /* Get the precomputed Gaussian for xj in slab n */
+ gaussian_xj = erg->gn_atom[ic];
+
+ islab = n - erg->slab_first; /* slab index */
+
+ /* The (unrotated) reference position of this atom is saved in yj0: */
+ copy_rvec(rotg->x_ref[iigrp], yj0);
+
+ beta = calc_beta(xj, rotg, n);
+
+ /* The current center of this slab is saved in xcn: */
+ copy_rvec(erg->slab_center[islab], xcn);
+ /* ... and the reference center in ycn: */
+ copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
+
+ rvec_sub(yj0, ycn, yj0_ycn); /* yj0_ycn = yj0 - ycn */
+
+ /* Rotate: */
+ mvmul(erg->rotmat, yj0_ycn, tmpvec2); /* tmpvec2= Omega.(yj0-ycn) */
+
+ /* Subtract the slab center from xj */
+ rvec_sub(xj, xcn, xj_xcn); /* xj_xcn = xj - xcn */
+
++ /* In rare cases, when an atom position coincides with a slab center
++ * (xj_xcn == 0) we cannot compute the vector product for qjn.
++ * However, since the atom is located directly on the pivot, this
++ * slab's contribution to the force on that atom will be zero
++ * anyway. Therefore, we directly move on to the next slab. */
++ if ( 0 == norm(xj_xcn) )
++ {
++ continue;
++ }
++
+ /* Calculate qjn */
+ cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec= v x Omega.(yj0-ycn) */
+
+ /* * v x Omega.(yj0-ycn) */
+ unitv(tmpvec, qjn); /* qjn = --------------------- */
+ /* |v x Omega.(yj0-ycn)| */
+
+ bjn = iprod(qjn, xj_xcn); /* bjn = qjn * (xj - xcn) */
+
+ /*********************************/
+ /* Add to the rotation potential */
+ /*********************************/
+ V += 0.5*rotg->k*wj*gaussian_xj*sqr(bjn);
+
+ /* If requested, also calculate the potential for a set of angles
+ * near the current reference angle */
+ if (bCalcPotFit)
+ {
+ for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
+ {
+ /* As above calculate Omega.(yj0-ycn), now for the other angles */
+ mvmul(erg->PotAngleFit->rotmat[ifit], yj0_ycn, tmpvec2); /* tmpvec2= Omega.(yj0-ycn) */
+ /* As above calculate qjn */
+ cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec= v x Omega.(yj0-ycn) */
+ /* * v x Omega.(yj0-ycn) */
+ unitv(tmpvec, fit_qjn); /* fit_qjn = --------------------- */
+ /* |v x Omega.(yj0-ycn)| */
+ fit_bjn = iprod(fit_qjn, xj_xcn); /* fit_bjn = fit_qjn * (xj - xcn) */
+ /* Add to the rotation potential for this angle */
+ erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*gaussian_xj*sqr(fit_bjn);
+ }
+ }
+
+ /****************************************************************/
+ /* sum_n1 will typically be the main contribution to the force: */
+ /****************************************************************/
+ betan_xj_sigma2 = beta*OOsigma2; /* beta_n(xj)/sigma^2 */
+
+ /* The next lines calculate
+ * qjn - (bjn*beta(xj)/(2sigma^2))v */
+ svmul(bjn*0.5*betan_xj_sigma2, rotg->vec, tmpvec2);
+ rvec_sub(qjn, tmpvec2, tmpvec);
+
+ /* Multiply with gn(xj)*bjn: */
+ svmul(gaussian_xj*bjn, tmpvec, tmpvec2);
+
+ /* Sum over n: */
+ rvec_inc(sum_n1, tmpvec2);
+
+ /* We already have precalculated the Sn term for slab n */
+ copy_rvec(erg->slab_innersumvec[islab], s_n);
+ /* * beta_n(xj) */
+ svmul(betan_xj_sigma2*iprod(s_n, xj_xcn), rotg->vec, tmpvec); /* tmpvec = ---------- s_n (xj-xcn) */
+ /* sigma^2 */
+
+ rvec_sub(s_n, tmpvec, innersumvec);
+
+ /* We can safely divide by slab_weights since we check in get_slab_centers
+ * that it is non-zero. */
+ svmul(gaussian_xj/erg->slab_weights[islab], innersumvec, innersumvec);
+
+ rvec_add(sum_n2, innersumvec, sum_n2);
+
+ /* Calculate the torque: */
+ if (bOutstepRot)
+ {
+ /* The force on atom ii from slab n only: */
+ svmul(-rotg->k*wj, tmpvec2, force_n1); /* part 1 */
+ svmul( rotg->k*mj, innersumvec, force_n2); /* part 2 */
+ rvec_add(force_n1, force_n2, force_n);
+ erg->slab_torque_v[islab] += torque(rotg->vec, force_n, xj, xcn);
+ }
+ } /* END of loop over slabs */
+
+ /* Put both contributions together: */
+ svmul(wj, sum_n1, sum_n1);
+ svmul(mj, sum_n2, sum_n2);
+ rvec_sub(sum_n2, sum_n1, tmp_f); /* F = -grad V */
+
+ /* Store the additional force so that it can be added to the force
+ * array after the normal forces have been evaluated */
+ for (m = 0; m < DIM; m++)
+ {
+ erg->f_rot_loc[j][m] = rotg->k*tmp_f[m];
+ }
+
+ PRINT_FORCE_J
+
+ } /* END of loop over local atoms */
+
+ return V;
+}
+
+#ifdef PRINT_COORDS
+static void print_coordinates(t_rotgrp *rotg, rvec x[], matrix box, int step)
+{
+ int i;
+ static FILE *fp;
+ static char buf[STRLEN];
+ static gmx_bool bFirst = 1;
+
+
+ if (bFirst)
+ {
+ sprintf(buf, "coords%d.txt", cr->nodeid);
+ fp = fopen(buf, "w");
+ bFirst = 0;
+ }
+
+ fprintf(fp, "\nStep %d\n", step);
+ fprintf(fp, "box: %f %f %f %f %f %f %f %f %f\n",
+ box[XX][XX], box[XX][YY], box[XX][ZZ],
+ box[YY][XX], box[YY][YY], box[YY][ZZ],
+ box[ZZ][XX], box[ZZ][ZZ], box[ZZ][ZZ]);
+ for (i = 0; i < rotg->nat; i++)
+ {
+ fprintf(fp, "%4d %f %f %f\n", i,
+ erg->xc[i][XX], erg->xc[i][YY], erg->xc[i][ZZ]);
+ }
+ fflush(fp);
+
+}
+#endif
+
+
+static int projection_compare(const void *a, const void *b)
+{
+ sort_along_vec_t *xca, *xcb;
+
+
+ xca = (sort_along_vec_t *)a;
+ xcb = (sort_along_vec_t *)b;
+
+ if (xca->xcproj < xcb->xcproj)
+ {
+ return -1;
+ }
+ else if (xca->xcproj > xcb->xcproj)
+ {
+ return 1;
+ }
+ else
+ {
+ return 0;
+ }
+}
+
+
+static void sort_collective_coordinates(
+ t_rotgrp *rotg, /* Rotation group */
+ sort_along_vec_t *data) /* Buffer for sorting the positions */
+{
+ int i;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg = rotg->enfrotgrp;
+
+ /* The projection of the position vector on the rotation vector is
+ * the relevant value for sorting. Fill the 'data' structure */
+ for (i = 0; i < rotg->nat; i++)
+ {
+ data[i].xcproj = iprod(erg->xc[i], rotg->vec); /* sort criterium */
+ data[i].m = erg->mc[i];
+ data[i].ind = i;
+ copy_rvec(erg->xc[i], data[i].x );
+ copy_rvec(rotg->x_ref[i], data[i].x_ref);
+ }
+ /* Sort the 'data' structure */
+ gmx_qsort(data, rotg->nat, sizeof(sort_along_vec_t), projection_compare);
+
+ /* Copy back the sorted values */
+ for (i = 0; i < rotg->nat; i++)
+ {
+ copy_rvec(data[i].x, erg->xc[i] );
+ copy_rvec(data[i].x_ref, erg->xc_ref_sorted[i]);
+ erg->mc_sorted[i] = data[i].m;
+ erg->xc_sortind[i] = data[i].ind;
+ }
+}
+
+
+/* For each slab, get the first and the last index of the sorted atom
+ * indices */
+static void get_firstlast_atom_per_slab(t_rotgrp *rotg)
+{
+ int i, islab, n;
+ real beta;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg = rotg->enfrotgrp;
+
+ /* Find the first atom that needs to enter the calculation for each slab */
+ n = erg->slab_first; /* slab */
+ i = 0; /* start with the first atom */
+ do
+ {
+ /* Find the first atom that significantly contributes to this slab */
+ do /* move forward in position until a large enough beta is found */
+ {
+ beta = calc_beta(erg->xc[i], rotg, n);
+ i++;
+ }
+ while ((beta < -erg->max_beta) && (i < rotg->nat));
+ i--;
+ islab = n - erg->slab_first; /* slab index */
+ erg->firstatom[islab] = i;
+ /* Proceed to the next slab */
+ n++;
+ }
+ while (n <= erg->slab_last);
+
+ /* Find the last atom for each slab */
+ n = erg->slab_last; /* start with last slab */
+ i = rotg->nat-1; /* start with the last atom */
+ do
+ {
+ do /* move backward in position until a large enough beta is found */
+ {
+ beta = calc_beta(erg->xc[i], rotg, n);
+ i--;
+ }
+ while ((beta > erg->max_beta) && (i > -1));
+ i++;
+ islab = n - erg->slab_first; /* slab index */
+ erg->lastatom[islab] = i;
+ /* Proceed to the next slab */
+ n--;
+ }
+ while (n >= erg->slab_first);
+}
+
+
+/* Determine the very first and very last slab that needs to be considered
+ * For the first slab that needs to be considered, we have to find the smallest
+ * n that obeys:
+ *
+ * x_first * v - n*Delta_x <= beta_max
+ *
+ * slab index n, slab distance Delta_x, rotation vector v. For the last slab we
+ * have to find the largest n that obeys
+ *
+ * x_last * v - n*Delta_x >= -beta_max
+ *
+ */
+static gmx_inline int get_first_slab(
+ t_rotgrp *rotg, /* The rotation group (inputrec data) */
+ real max_beta, /* The max_beta value, instead of min_gaussian */
+ rvec firstatom) /* First atom after sorting along the rotation vector v */
+{
+ /* Find the first slab for the first atom */
+ return ceil((iprod(firstatom, rotg->vec) - max_beta)/rotg->slab_dist);
+}
+
+
+static gmx_inline int get_last_slab(
+ t_rotgrp *rotg, /* The rotation group (inputrec data) */
+ real max_beta, /* The max_beta value, instead of min_gaussian */
+ rvec lastatom) /* Last atom along v */
+{
+ /* Find the last slab for the last atom */
+ return floor((iprod(lastatom, rotg->vec) + max_beta)/rotg->slab_dist);
+}
+
+
+static void get_firstlast_slab_check(
+ t_rotgrp *rotg, /* The rotation group (inputrec data) */
+ t_gmx_enfrotgrp *erg, /* The rotation group (data only accessible in this file) */
+ rvec firstatom, /* First atom after sorting along the rotation vector v */
- gmx_large_int_t step, /* The time step */
++ rvec lastatom) /* Last atom along v */
+{
+ erg->slab_first = get_first_slab(rotg, erg->max_beta, firstatom);
+ erg->slab_last = get_last_slab(rotg, erg->max_beta, lastatom);
+
++ /* Calculate the slab buffer size, which changes when slab_first changes */
++ erg->slab_buffer = erg->slab_first - erg->slab_first_ref;
++
+ /* Check whether we have reference data to compare against */
+ if (erg->slab_first < erg->slab_first_ref)
+ {
+ gmx_fatal(FARGS, "%s No reference data for first slab (n=%d), unable to proceed.",
+ RotStr, erg->slab_first);
+ }
+
+ /* Check whether we have reference data to compare against */
+ if (erg->slab_last > erg->slab_last_ref)
+ {
+ gmx_fatal(FARGS, "%s No reference data for last slab (n=%d), unable to proceed.",
+ RotStr, erg->slab_last);
+ }
+}
+
+
+/* Enforced rotation with a flexible axis */
+static void do_flexible(
+ gmx_bool bMaster,
+ gmx_enfrot_t enfrot, /* Other rotation data */
+ t_rotgrp *rotg, /* The rotation group */
+ int g, /* Group number */
+ rvec x[], /* The local positions */
+ matrix box,
+ double t, /* Time in picoseconds */
- get_firstlast_slab_check(rotg, erg, erg->xc[0], erg->xc[rotg->nat-1], g);
+ gmx_bool bOutstepRot, /* Output to main rotation output file */
+ gmx_bool bOutstepSlab) /* Output per-slab data */
+{
+ int l, nslabs;
+ real sigma; /* The Gaussian width sigma */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg = rotg->enfrotgrp;
+
+ /* Define the sigma value */
+ sigma = 0.7*rotg->slab_dist;
+
+ /* Sort the collective coordinates erg->xc along the rotation vector. This is
+ * an optimization for the inner loop. */
+ sort_collective_coordinates(rotg, enfrot->data);
+
+ /* Determine the first relevant slab for the first atom and the last
+ * relevant slab for the last atom */
- rvec x[], /* The positions */
- matrix box, /* The simulation box */
- double t, /* Time in picoseconds */
- gmx_large_int_t step, /* The time step */
++ get_firstlast_slab_check(rotg, erg, erg->xc[0], erg->xc[rotg->nat-1]);
+
+ /* Determine for each slab depending on the min_gaussian cutoff criterium,
+ * a first and a last atom index inbetween stuff needs to be calculated */
+ get_firstlast_atom_per_slab(rotg);
+
+ /* Determine the gaussian-weighted center of positions for all slabs */
+ get_slab_centers(rotg, erg->xc, erg->mc_sorted, g, t, enfrot->out_slabs, bOutstepSlab, FALSE);
+
+ /* Clear the torque per slab from last time step: */
+ nslabs = erg->slab_last - erg->slab_first + 1;
+ for (l = 0; l < nslabs; l++)
+ {
+ erg->slab_torque_v[l] = 0.0;
+ }
+
+ /* Call the rotational forces kernel */
+ if (rotg->eType == erotgFLEX || rotg->eType == erotgFLEXT)
+ {
+ erg->V = do_flex_lowlevel(rotg, sigma, x, bOutstepRot, bOutstepSlab, box);
+ }
+ else if (rotg->eType == erotgFLEX2 || rotg->eType == erotgFLEX2T)
+ {
+ erg->V = do_flex2_lowlevel(rotg, sigma, x, bOutstepRot, bOutstepSlab, box);
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Unknown flexible rotation type");
+ }
+
+ /* Determine angle by RMSD fit to the reference - Let's hope this */
+ /* only happens once in a while, since this is not parallelized! */
+ if (bMaster && (erotgFitPOT != rotg->eFittype) )
+ {
+ if (bOutstepRot)
+ {
+ /* Fit angle of the whole rotation group */
+ erg->angle_v = flex_fit_angle(rotg);
+ }
+ if (bOutstepSlab)
+ {
+ /* Fit angle of each slab */
+ flex_fit_angle_perslab(g, rotg, t, erg->degangle, enfrot->out_angles);
+ }
+ }
+
+ /* Lump together the torques from all slabs: */
+ erg->torque_v = 0.0;
+ for (l = 0; l < nslabs; l++)
+ {
+ erg->torque_v += erg->slab_torque_v[l];
+ }
+}
+
+
+/* Calculate the angle between reference and actual rotation group atom,
+ * both projected into a plane perpendicular to the rotation vector: */
+static void angle(t_rotgrp *rotg,
+ rvec x_act,
+ rvec x_ref,
+ real *alpha,
+ real *weight) /* atoms near the rotation axis should count less than atoms far away */
+{
+ rvec xp, xrp; /* current and reference positions projected on a plane perpendicular to pg->vec */
+ rvec dum;
+
+
+ /* Project x_ref and x into a plane through the origin perpendicular to rot_vec: */
+ /* Project x_ref: xrp = x_ref - (vec * x_ref) * vec */
+ svmul(iprod(rotg->vec, x_ref), rotg->vec, dum);
+ rvec_sub(x_ref, dum, xrp);
+ /* Project x_act: */
+ svmul(iprod(rotg->vec, x_act), rotg->vec, dum);
+ rvec_sub(x_act, dum, xp);
+
+ /* Retrieve information about which vector precedes. gmx_angle always
+ * returns a positive angle. */
+ cprod(xp, xrp, dum); /* if reference precedes, this is pointing into the same direction as vec */
+
+ if (iprod(rotg->vec, dum) >= 0)
+ {
+ *alpha = -gmx_angle(xrp, xp);
+ }
+ else
+ {
+ *alpha = +gmx_angle(xrp, xp);
+ }
+
+ /* Also return the weight */
+ *weight = norm(xp);
+}
+
+
+/* Project first vector onto a plane perpendicular to the second vector
+ * dr = dr - (dr.v)v
+ * Note that v must be of unit length.
+ */
+static gmx_inline void project_onto_plane(rvec dr, const rvec v)
+{
+ rvec tmp;
+
+
+ svmul(iprod(dr, v), v, tmp); /* tmp = (dr.v)v */
+ rvec_dec(dr, tmp); /* dr = dr - (dr.v)v */
+}
+
+
+/* Fixed rotation: The rotation reference group rotates around the v axis. */
+/* The atoms of the actual rotation group are attached with imaginary */
+/* springs to the reference atoms. */
+static void do_fixed(
+ t_rotgrp *rotg, /* The rotation group */
- rvec x[], /* The positions */
- matrix box, /* The simulation box */
- double t, /* Time in picoseconds */
- gmx_large_int_t step, /* The time step */
+ gmx_bool bOutstepRot, /* Output to main rotation output file */
+ gmx_bool bOutstepSlab) /* Output per-slab data */
+{
+ int ifit, j, jj, m;
+ rvec dr;
+ rvec tmp_f; /* Force */
+ real alpha; /* a single angle between an actual and a reference position */
+ real weight; /* single weight for a single angle */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ rvec xi_xc; /* xi - xc */
+ gmx_bool bCalcPotFit;
+ rvec fit_xr_loc;
+
+ /* for mass weighting: */
+ real wi; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+ real k_wi; /* k times wi */
+
+ gmx_bool bProject;
+
+
+ erg = rotg->enfrotgrp;
+ bProject = (rotg->eType == erotgPM) || (rotg->eType == erotgPMPF);
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
+
+ N_M = rotg->nat * erg->invmass;
+
+ /* Each process calculates the forces on its local atoms */
+ for (j = 0; j < erg->nat_loc; j++)
+ {
+ /* Calculate (x_i-x_c) resp. (x_i-u) */
+ rvec_sub(erg->x_loc_pbc[j], erg->xc_center, xi_xc);
+
+ /* Calculate Omega*(y_i-y_c)-(x_i-x_c) */
+ rvec_sub(erg->xr_loc[j], xi_xc, dr);
+
+ if (bProject)
+ {
+ project_onto_plane(dr, rotg->vec);
+ }
+
+ /* Mass-weighting */
+ wi = N_M*erg->m_loc[j];
+
+ /* Store the additional force so that it can be added to the force
+ * array after the normal forces have been evaluated */
+ k_wi = rotg->k*wi;
+ for (m = 0; m < DIM; m++)
+ {
+ tmp_f[m] = k_wi*dr[m];
+ erg->f_rot_loc[j][m] = tmp_f[m];
+ erg->V += 0.5*k_wi*sqr(dr[m]);
+ }
+
+ /* If requested, also calculate the potential for a set of angles
+ * near the current reference angle */
+ if (bCalcPotFit)
+ {
+ for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
+ {
+ /* Index of this rotation group atom with respect to the whole rotation group */
+ jj = erg->xc_ref_ind[j];
+
+ /* Rotate with the alternative angle. Like rotate_local_reference(),
+ * just for a single local atom */
+ mvmul(erg->PotAngleFit->rotmat[ifit], rotg->x_ref[jj], fit_xr_loc); /* fit_xr_loc = Omega*(y_i-y_c) */
+
+ /* Calculate Omega*(y_i-y_c)-(x_i-x_c) */
+ rvec_sub(fit_xr_loc, xi_xc, dr);
+
+ if (bProject)
+ {
+ project_onto_plane(dr, rotg->vec);
+ }
+
+ /* Add to the rotation potential for this angle: */
+ erg->PotAngleFit->V[ifit] += 0.5*k_wi*norm2(dr);
+ }
+ }
+
+ if (bOutstepRot)
+ {
+ /* Add to the torque of this rotation group */
+ erg->torque_v += torque(rotg->vec, tmp_f, erg->x_loc_pbc[j], erg->xc_center);
+
+ /* Calculate the angle between reference and actual rotation group atom. */
+ angle(rotg, xi_xc, erg->xr_loc[j], &alpha, &weight); /* angle in rad, weighted */
+ erg->angle_v += alpha * weight;
+ erg->weight_v += weight;
+ }
+ /* If you want enforced rotation to contribute to the virial,
+ * activate the following lines:
+ if (MASTER(cr))
+ {
+ Add the rotation contribution to the virial
+ for(j=0; j<DIM; j++)
+ for(m=0;m<DIM;m++)
+ vir[j][m] += 0.5*f[ii][j]*dr[m];
+ }
+ */
+
+ PRINT_FORCE_J
+
+ } /* end of loop over local rotation group atoms */
+}
+
+
+/* Calculate the radial motion potential and forces */
+static void do_radial_motion(
+ t_rotgrp *rotg, /* The rotation group */
- double t, /* Time in picoseconds */
- gmx_large_int_t step, /* The time step */
+ gmx_bool bOutstepRot, /* Output to main rotation output file */
+ gmx_bool bOutstepSlab) /* Output per-slab data */
+{
+ int j, jj, ifit;
+ rvec tmp_f; /* Force */
+ real alpha; /* a single angle between an actual and a reference position */
+ real weight; /* single weight for a single angle */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ rvec xj_u; /* xj - u */
+ rvec tmpvec, fit_tmpvec;
+ real fac, fac2, sum = 0.0;
+ rvec pj;
+ gmx_bool bCalcPotFit;
+
+ /* For mass weighting: */
+ real wj; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+
+
+ erg = rotg->enfrotgrp;
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
+
+ N_M = rotg->nat * erg->invmass;
+
+ /* Each process calculates the forces on its local atoms */
+ for (j = 0; j < erg->nat_loc; j++)
+ {
+ /* Calculate (xj-u) */
+ rvec_sub(erg->x_loc_pbc[j], erg->xc_center, xj_u); /* xj_u = xj-u */
+
+ /* Calculate Omega.(yj0-u) */
+ cprod(rotg->vec, erg->xr_loc[j], tmpvec); /* tmpvec = v x Omega.(yj0-u) */
+
+ /* * v x Omega.(yj0-u) */
+ unitv(tmpvec, pj); /* pj = --------------------- */
+ /* | v x Omega.(yj0-u) | */
+
+ fac = iprod(pj, xj_u); /* fac = pj.(xj-u) */
+ fac2 = fac*fac;
+
+ /* Mass-weighting */
+ wj = N_M*erg->m_loc[j];
+
+ /* Store the additional force so that it can be added to the force
+ * array after the normal forces have been evaluated */
+ svmul(-rotg->k*wj*fac, pj, tmp_f);
+ copy_rvec(tmp_f, erg->f_rot_loc[j]);
+ sum += wj*fac2;
+
+ /* If requested, also calculate the potential for a set of angles
+ * near the current reference angle */
+ if (bCalcPotFit)
+ {
+ for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
+ {
+ /* Index of this rotation group atom with respect to the whole rotation group */
+ jj = erg->xc_ref_ind[j];
+
+ /* Rotate with the alternative angle. Like rotate_local_reference(),
+ * just for a single local atom */
+ mvmul(erg->PotAngleFit->rotmat[ifit], rotg->x_ref[jj], fit_tmpvec); /* fit_tmpvec = Omega*(yj0-u) */
+
+ /* Calculate Omega.(yj0-u) */
+ cprod(rotg->vec, fit_tmpvec, tmpvec); /* tmpvec = v x Omega.(yj0-u) */
+ /* * v x Omega.(yj0-u) */
+ unitv(tmpvec, pj); /* pj = --------------------- */
+ /* | v x Omega.(yj0-u) | */
+
+ fac = iprod(pj, xj_u); /* fac = pj.(xj-u) */
+ fac2 = fac*fac;
+
+ /* Add to the rotation potential for this angle: */
+ erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*fac2;
+ }
+ }
+
+ if (bOutstepRot)
+ {
+ /* Add to the torque of this rotation group */
+ erg->torque_v += torque(rotg->vec, tmp_f, erg->x_loc_pbc[j], erg->xc_center);
+
+ /* Calculate the angle between reference and actual rotation group atom. */
+ angle(rotg, xj_u, erg->xr_loc[j], &alpha, &weight); /* angle in rad, weighted */
+ erg->angle_v += alpha * weight;
+ erg->weight_v += weight;
+ }
+
+ PRINT_FORCE_J
+
+ } /* end of loop over local rotation group atoms */
+ erg->V = 0.5*rotg->k*sum;
+}
+
+
+/* Calculate the radial motion pivot-free potential and forces */
+static void do_radial_motion_pf(
+ t_rotgrp *rotg, /* The rotation group */
+ rvec x[], /* The positions */
+ matrix box, /* The simulation box */
- double t, /* Time in picoseconds */
- gmx_large_int_t step, /* The time step */
+ gmx_bool bOutstepRot, /* Output to main rotation output file */
+ gmx_bool bOutstepSlab) /* Output per-slab data */
+{
+ int i, ii, iigrp, ifit, j;
+ rvec xj; /* Current position */
+ rvec xj_xc; /* xj - xc */
+ rvec yj0_yc0; /* yj0 - yc0 */
+ rvec tmp_f; /* Force */
+ real alpha; /* a single angle between an actual and a reference position */
+ real weight; /* single weight for a single angle */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ rvec tmpvec, tmpvec2;
+ rvec innersumvec; /* Precalculation of the inner sum */
+ rvec innersumveckM;
+ real fac, fac2, V = 0.0;
+ rvec qi, qj;
+ gmx_bool bCalcPotFit;
+
+ /* For mass weighting: */
+ real mj, wi, wj; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+
+
+ erg = rotg->enfrotgrp;
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
+
+ N_M = rotg->nat * erg->invmass;
+
+ /* Get the current center of the rotation group: */
+ get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
+
+ /* Precalculate Sum_i [ wi qi.(xi-xc) qi ] which is needed for every single j */
+ clear_rvec(innersumvec);
+ for (i = 0; i < rotg->nat; i++)
+ {
+ /* Mass-weighting */
+ wi = N_M*erg->mc[i];
+
+ /* Calculate qi. Note that xc_ref_center has already been subtracted from
+ * x_ref in init_rot_group.*/
+ mvmul(erg->rotmat, rotg->x_ref[i], tmpvec); /* tmpvec = Omega.(yi0-yc0) */
+
+ cprod(rotg->vec, tmpvec, tmpvec2); /* tmpvec2 = v x Omega.(yi0-yc0) */
+
+ /* * v x Omega.(yi0-yc0) */
+ unitv(tmpvec2, qi); /* qi = ----------------------- */
+ /* | v x Omega.(yi0-yc0) | */
+
+ rvec_sub(erg->xc[i], erg->xc_center, tmpvec); /* tmpvec = xi-xc */
+
+ svmul(wi*iprod(qi, tmpvec), qi, tmpvec2);
+
+ rvec_inc(innersumvec, tmpvec2);
+ }
+ svmul(rotg->k*erg->invmass, innersumvec, innersumveckM);
+
+ /* Each process calculates the forces on its local atoms */
+ for (j = 0; j < erg->nat_loc; j++)
+ {
+ /* Local index of a rotation group atom */
+ ii = erg->ind_loc[j];
+ /* Position of this atom in the collective array */
+ iigrp = erg->xc_ref_ind[j];
+ /* Mass-weighting */
+ mj = erg->mc[iigrp]; /* need the unsorted mass here */
+ wj = N_M*mj;
+
+ /* Current position of this atom: x[ii][XX/YY/ZZ] */
+ copy_rvec(x[ii], xj);
+
+ /* Shift this atom such that it is near its reference */
+ shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
+
+ /* The (unrotated) reference position is yj0. yc0 has already
+ * been subtracted in init_rot_group */
+ copy_rvec(rotg->x_ref[iigrp], yj0_yc0); /* yj0_yc0 = yj0 - yc0 */
+
+ /* Calculate Omega.(yj0-yc0) */
+ mvmul(erg->rotmat, yj0_yc0, tmpvec2); /* tmpvec2 = Omega.(yj0 - yc0) */
+
+ cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x Omega.(yj0-yc0) */
+
+ /* * v x Omega.(yj0-yc0) */
+ unitv(tmpvec, qj); /* qj = ----------------------- */
+ /* | v x Omega.(yj0-yc0) | */
+
+ /* Calculate (xj-xc) */
+ rvec_sub(xj, erg->xc_center, xj_xc); /* xj_xc = xj-xc */
+
+ fac = iprod(qj, xj_xc); /* fac = qj.(xj-xc) */
+ fac2 = fac*fac;
+
+ /* Store the additional force so that it can be added to the force
+ * array after the normal forces have been evaluated */
+ svmul(-rotg->k*wj*fac, qj, tmp_f); /* part 1 of force */
+ svmul(mj, innersumveckM, tmpvec); /* part 2 of force */
+ rvec_inc(tmp_f, tmpvec);
+ copy_rvec(tmp_f, erg->f_rot_loc[j]);
+ V += wj*fac2;
+
+ /* If requested, also calculate the potential for a set of angles
+ * near the current reference angle */
+ if (bCalcPotFit)
+ {
+ for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
+ {
+ /* Rotate with the alternative angle. Like rotate_local_reference(),
+ * just for a single local atom */
+ mvmul(erg->PotAngleFit->rotmat[ifit], yj0_yc0, tmpvec2); /* tmpvec2 = Omega*(yj0-yc0) */
+
+ /* Calculate Omega.(yj0-u) */
+ cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x Omega.(yj0-yc0) */
+ /* * v x Omega.(yj0-yc0) */
+ unitv(tmpvec, qj); /* qj = ----------------------- */
+ /* | v x Omega.(yj0-yc0) | */
+
+ fac = iprod(qj, xj_xc); /* fac = qj.(xj-xc) */
+ fac2 = fac*fac;
+
+ /* Add to the rotation potential for this angle: */
+ erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*fac2;
+ }
+ }
+
+ if (bOutstepRot)
+ {
+ /* Add to the torque of this rotation group */
+ erg->torque_v += torque(rotg->vec, tmp_f, xj, erg->xc_center);
+
+ /* Calculate the angle between reference and actual rotation group atom. */
+ angle(rotg, xj_xc, yj0_yc0, &alpha, &weight); /* angle in rad, weighted */
+ erg->angle_v += alpha * weight;
+ erg->weight_v += weight;
+ }
+
+ PRINT_FORCE_J
+
+ } /* end of loop over local rotation group atoms */
+ erg->V = 0.5*rotg->k*V;
+}
+
+
+/* Precalculate the inner sum for the radial motion 2 forces */
+static void radial_motion2_precalc_inner_sum(t_rotgrp *rotg, rvec innersumvec)
+{
+ int i;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ rvec xi_xc; /* xj - xc */
+ rvec tmpvec, tmpvec2;
+ real fac, fac2;
+ rvec ri, si;
+ real siri;
+ rvec v_xi_xc; /* v x (xj - u) */
+ real psii, psiistar;
+ real wi; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+ rvec sumvec;
+
+ erg = rotg->enfrotgrp;
+ N_M = rotg->nat * erg->invmass;
+
+ /* Loop over the collective set of positions */
+ clear_rvec(sumvec);
+ for (i = 0; i < rotg->nat; i++)
+ {
+ /* Mass-weighting */
+ wi = N_M*erg->mc[i];
+
+ rvec_sub(erg->xc[i], erg->xc_center, xi_xc); /* xi_xc = xi-xc */
+
+ /* Calculate ri. Note that xc_ref_center has already been subtracted from
+ * x_ref in init_rot_group.*/
+ mvmul(erg->rotmat, rotg->x_ref[i], ri); /* ri = Omega.(yi0-yc0) */
+
+ cprod(rotg->vec, xi_xc, v_xi_xc); /* v_xi_xc = v x (xi-u) */
+
+ fac = norm2(v_xi_xc);
+ /* * 1 */
+ psiistar = 1.0/(fac + rotg->eps); /* psiistar = --------------------- */
+ /* |v x (xi-xc)|^2 + eps */
+
+ psii = gmx_invsqrt(fac); /* 1 */
+ /* psii = ------------- */
+ /* |v x (xi-xc)| */
+
+ svmul(psii, v_xi_xc, si); /* si = psii * (v x (xi-xc) ) */
+
+ fac = iprod(v_xi_xc, ri); /* fac = (v x (xi-xc)).ri */
+ fac2 = fac*fac;
+
+ siri = iprod(si, ri); /* siri = si.ri */
+
+ svmul(psiistar/psii, ri, tmpvec);
+ svmul(psiistar*psiistar/(psii*psii*psii) * siri, si, tmpvec2);
+ rvec_dec(tmpvec, tmpvec2);
+ cprod(tmpvec, rotg->vec, tmpvec2);
+
+ svmul(wi*siri, tmpvec2, tmpvec);
+
+ rvec_inc(sumvec, tmpvec);
+ }
+ svmul(rotg->k*erg->invmass, sumvec, innersumvec);
+}
+
+
+/* Calculate the radial motion 2 potential and forces */
+static void do_radial_motion2(
+ t_rotgrp *rotg, /* The rotation group */
+ rvec x[], /* The positions */
+ matrix box, /* The simulation box */
- /* From the extreme coordinates of the reference group, determine the first
+ gmx_bool bOutstepRot, /* Output to main rotation output file */
+ gmx_bool bOutstepSlab) /* Output per-slab data */
+{
+ int ii, iigrp, ifit, j;
+ rvec xj; /* Position */
+ real alpha; /* a single angle between an actual and a reference position */
+ real weight; /* single weight for a single angle */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ rvec xj_u; /* xj - u */
+ rvec yj0_yc0; /* yj0 -yc0 */
+ rvec tmpvec, tmpvec2;
+ real fac, fit_fac, fac2, Vpart = 0.0;
+ rvec rj, fit_rj, sj;
+ real sjrj;
+ rvec v_xj_u; /* v x (xj - u) */
+ real psij, psijstar;
+ real mj, wj; /* For mass-weighting of the positions */
+ real N_M; /* N/M */
+ gmx_bool bPF;
+ rvec innersumvec;
+ gmx_bool bCalcPotFit;
+
+
+ erg = rotg->enfrotgrp;
+
+ bPF = rotg->eType == erotgRM2PF;
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
+
+
+ clear_rvec(yj0_yc0); /* Make the compiler happy */
+
+ clear_rvec(innersumvec);
+ if (bPF)
+ {
+ /* For the pivot-free variant we have to use the current center of
+ * mass of the rotation group instead of the pivot u */
+ get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
+
+ /* Also, we precalculate the second term of the forces that is identical
+ * (up to the weight factor mj) for all forces */
+ radial_motion2_precalc_inner_sum(rotg, innersumvec);
+ }
+
+ N_M = rotg->nat * erg->invmass;
+
+ /* Each process calculates the forces on its local atoms */
+ for (j = 0; j < erg->nat_loc; j++)
+ {
+ if (bPF)
+ {
+ /* Local index of a rotation group atom */
+ ii = erg->ind_loc[j];
+ /* Position of this atom in the collective array */
+ iigrp = erg->xc_ref_ind[j];
+ /* Mass-weighting */
+ mj = erg->mc[iigrp];
+
+ /* Current position of this atom: x[ii] */
+ copy_rvec(x[ii], xj);
+
+ /* Shift this atom such that it is near its reference */
+ shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
+
+ /* The (unrotated) reference position is yj0. yc0 has already
+ * been subtracted in init_rot_group */
+ copy_rvec(rotg->x_ref[iigrp], yj0_yc0); /* yj0_yc0 = yj0 - yc0 */
+
+ /* Calculate Omega.(yj0-yc0) */
+ mvmul(erg->rotmat, yj0_yc0, rj); /* rj = Omega.(yj0-yc0) */
+ }
+ else
+ {
+ mj = erg->m_loc[j];
+ copy_rvec(erg->x_loc_pbc[j], xj);
+ copy_rvec(erg->xr_loc[j], rj); /* rj = Omega.(yj0-u) */
+ }
+ /* Mass-weighting */
+ wj = N_M*mj;
+
+ /* Calculate (xj-u) resp. (xj-xc) */
+ rvec_sub(xj, erg->xc_center, xj_u); /* xj_u = xj-u */
+
+ cprod(rotg->vec, xj_u, v_xj_u); /* v_xj_u = v x (xj-u) */
+
+ fac = norm2(v_xj_u);
+ /* * 1 */
+ psijstar = 1.0/(fac + rotg->eps); /* psistar = -------------------- */
+ /* |v x (xj-u)|^2 + eps */
+
+ psij = gmx_invsqrt(fac); /* 1 */
+ /* psij = ------------ */
+ /* |v x (xj-u)| */
+
+ svmul(psij, v_xj_u, sj); /* sj = psij * (v x (xj-u) ) */
+
+ fac = iprod(v_xj_u, rj); /* fac = (v x (xj-u)).rj */
+ fac2 = fac*fac;
+
+ sjrj = iprod(sj, rj); /* sjrj = sj.rj */
+
+ svmul(psijstar/psij, rj, tmpvec);
+ svmul(psijstar*psijstar/(psij*psij*psij) * sjrj, sj, tmpvec2);
+ rvec_dec(tmpvec, tmpvec2);
+ cprod(tmpvec, rotg->vec, tmpvec2);
+
+ /* Store the additional force so that it can be added to the force
+ * array after the normal forces have been evaluated */
+ svmul(-rotg->k*wj*sjrj, tmpvec2, tmpvec);
+ svmul(mj, innersumvec, tmpvec2); /* This is != 0 only for the pivot-free variant */
+
+ rvec_add(tmpvec2, tmpvec, erg->f_rot_loc[j]);
+ Vpart += wj*psijstar*fac2;
+
+ /* If requested, also calculate the potential for a set of angles
+ * near the current reference angle */
+ if (bCalcPotFit)
+ {
+ for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
+ {
+ if (bPF)
+ {
+ mvmul(erg->PotAngleFit->rotmat[ifit], yj0_yc0, fit_rj); /* fit_rj = Omega.(yj0-yc0) */
+ }
+ else
+ {
+ /* Position of this atom in the collective array */
+ iigrp = erg->xc_ref_ind[j];
+ /* Rotate with the alternative angle. Like rotate_local_reference(),
+ * just for a single local atom */
+ mvmul(erg->PotAngleFit->rotmat[ifit], rotg->x_ref[iigrp], fit_rj); /* fit_rj = Omega*(yj0-u) */
+ }
+ fit_fac = iprod(v_xj_u, fit_rj); /* fac = (v x (xj-u)).fit_rj */
+ /* Add to the rotation potential for this angle: */
+ erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*psijstar*fit_fac*fit_fac;
+ }
+ }
+
+ if (bOutstepRot)
+ {
+ /* Add to the torque of this rotation group */
+ erg->torque_v += torque(rotg->vec, erg->f_rot_loc[j], xj, erg->xc_center);
+
+ /* Calculate the angle between reference and actual rotation group atom. */
+ angle(rotg, xj_u, rj, &alpha, &weight); /* angle in rad, weighted */
+ erg->angle_v += alpha * weight;
+ erg->weight_v += weight;
+ }
+
+ PRINT_FORCE_J
+
+ } /* end of loop over local rotation group atoms */
+ erg->V = 0.5*rotg->k*Vpart;
+}
+
+
+/* Determine the smallest and largest position vector (with respect to the
+ * rotation vector) for the reference group */
+static void get_firstlast_atom_ref(
+ t_rotgrp *rotg,
+ int *firstindex,
+ int *lastindex)
+{
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ int i;
+ real xcproj; /* The projection of a reference position on the
+ rotation vector */
+ real minproj, maxproj; /* Smallest and largest projection on v */
+
+
+
+ erg = rotg->enfrotgrp;
+
+ /* Start with some value */
+ minproj = iprod(rotg->x_ref[0], rotg->vec);
+ maxproj = minproj;
+
+ /* This is just to ensure that it still works if all the atoms of the
+ * reference structure are situated in a plane perpendicular to the rotation
+ * vector */
+ *firstindex = 0;
+ *lastindex = rotg->nat-1;
+
+ /* Loop over all atoms of the reference group,
+ * project them on the rotation vector to find the extremes */
+ for (i = 0; i < rotg->nat; i++)
+ {
+ xcproj = iprod(rotg->x_ref[i], rotg->vec);
+ if (xcproj < minproj)
+ {
+ minproj = xcproj;
+ *firstindex = i;
+ }
+ if (xcproj > maxproj)
+ {
+ maxproj = xcproj;
+ *lastindex = i;
+ }
+ }
+}
+
+
+/* Allocate memory for the slabs */
+static void allocate_slabs(
+ t_rotgrp *rotg,
+ FILE *fplog,
+ int g,
+ gmx_bool bVerbose)
+{
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ int i, nslabs;
+
+
+ erg = rotg->enfrotgrp;
+
+ /* More slabs than are defined for the reference are never needed */
+ nslabs = erg->slab_last_ref - erg->slab_first_ref + 1;
+
+ /* Remember how many we allocated */
+ erg->nslabs_alloc = nslabs;
+
+ if ( (NULL != fplog) && bVerbose)
+ {
+ fprintf(fplog, "%s allocating memory to store data for %d slabs (rotation group %d).\n",
+ RotStr, nslabs, g);
+ }
+ snew(erg->slab_center, nslabs);
+ snew(erg->slab_center_ref, nslabs);
+ snew(erg->slab_weights, nslabs);
+ snew(erg->slab_torque_v, nslabs);
+ snew(erg->slab_data, nslabs);
+ snew(erg->gn_atom, nslabs);
+ snew(erg->gn_slabind, nslabs);
+ snew(erg->slab_innersumvec, nslabs);
+ for (i = 0; i < nslabs; i++)
+ {
+ snew(erg->slab_data[i].x, rotg->nat);
+ snew(erg->slab_data[i].ref, rotg->nat);
+ snew(erg->slab_data[i].weight, rotg->nat);
+ }
+ snew(erg->xc_ref_sorted, rotg->nat);
+ snew(erg->xc_sortind, rotg->nat);
+ snew(erg->firstatom, nslabs);
+ snew(erg->lastatom, nslabs);
+}
+
+
- int first, last, firststart;
++/* From the extreme positions of the reference group, determine the first
+ * and last slab of the reference. We can never have more slabs in the real
+ * simulation than calculated here for the reference.
+ */
+static void get_firstlast_slab_ref(t_rotgrp *rotg, real mc[], int ref_firstindex, int ref_lastindex)
+{
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
- firststart = first;
++ int first, last;
+ rvec dummy;
+
+
+ erg = rotg->enfrotgrp;
+ first = get_first_slab(rotg, erg->max_beta, rotg->x_ref[ref_firstindex]);
+ last = get_last_slab( rotg, erg->max_beta, rotg->x_ref[ref_lastindex ]);
-
- erg->slab_buffer = firststart - erg->slab_first_ref;
+
+ while (get_slab_weight(first, rotg, rotg->x_ref, mc, &dummy) > WEIGHT_MIN)
+ {
+ first--;
+ }
+ erg->slab_first_ref = first+1;
+ while (get_slab_weight(last, rotg, rotg->x_ref, mc, &dummy) > WEIGHT_MIN)
+ {
+ last++;
+ }
+ erg->slab_last_ref = last-1;
- /* From the extreme coordinates of the reference group, determine the first
+}
+
+
+/* Special version of copy_rvec:
+ * During the copy procedure of xcurr to b, the correct PBC image is chosen
+ * such that the copied vector ends up near its reference position xref */
+static inline void copy_correct_pbc_image(
+ const rvec xcurr, /* copy vector xcurr ... */
+ rvec b, /* ... to b ... */
+ const rvec xref, /* choosing the PBC image such that b ends up near xref */
+ matrix box,
+ int npbcdim)
+{
+ rvec dx;
+ int d, m;
+ ivec shift;
+
+
+ /* Shortest PBC distance between the atom and its reference */
+ rvec_sub(xcurr, xref, dx);
+
+ /* Determine the shift for this atom */
+ clear_ivec(shift);
+ for (m = npbcdim-1; m >= 0; m--)
+ {
+ while (dx[m] < -0.5*box[m][m])
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ dx[d] += box[m][d];
+ }
+ shift[m]++;
+ }
+ while (dx[m] >= 0.5*box[m][m])
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ dx[d] -= box[m][d];
+ }
+ shift[m]--;
+ }
+ }
+
+ /* Apply the shift to the position */
+ copy_rvec(xcurr, b);
+ shift_single_coord(box, b, shift);
+}
+
+
+static void init_rot_group(FILE *fplog, t_commrec *cr, int g, t_rotgrp *rotg,
+ rvec *x, gmx_mtop_t *mtop, gmx_bool bVerbose, FILE *out_slabs, matrix box,
+ t_inputrec *ir, gmx_bool bOutputCenters)
+{
+ int i, ii;
+ rvec coord, xref, *xdum;
+ gmx_bool bFlex, bColl;
+ t_atom *atom;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ int ref_firstindex, ref_lastindex;
+ gmx_mtop_atomlookup_t alook = NULL;
+ real mass, totalmass;
+ real start = 0.0;
+ double t_start;
+
+
+ /* Do we have a flexible axis? */
+ bFlex = ISFLEX(rotg);
+ /* Do we use a global set of coordinates? */
+ bColl = ISCOLL(rotg);
+
+ erg = rotg->enfrotgrp;
+
+ /* Allocate space for collective coordinates if needed */
+ if (bColl)
+ {
+ snew(erg->xc, rotg->nat);
+ snew(erg->xc_shifts, rotg->nat);
+ snew(erg->xc_eshifts, rotg->nat);
+ snew(erg->xc_old, rotg->nat);
+
+ if (rotg->eFittype == erotgFitNORM)
+ {
+ snew(erg->xc_ref_length, rotg->nat); /* in case fit type NORM is chosen */
+ snew(erg->xc_norm, rotg->nat);
+ }
+ }
+ else
+ {
+ snew(erg->xr_loc, rotg->nat);
+ snew(erg->x_loc_pbc, rotg->nat);
+ }
+
+ snew(erg->f_rot_loc, rotg->nat);
+ snew(erg->xc_ref_ind, rotg->nat);
+
+ /* Make space for the calculation of the potential at other angles (used
+ * for fitting only) */
+ if (erotgFitPOT == rotg->eFittype)
+ {
+ snew(erg->PotAngleFit, 1);
+ snew(erg->PotAngleFit->degangle, rotg->PotAngle_nstep);
+ snew(erg->PotAngleFit->V, rotg->PotAngle_nstep);
+ snew(erg->PotAngleFit->rotmat, rotg->PotAngle_nstep);
+
+ /* Get the set of angles around the reference angle */
+ start = -0.5 * (rotg->PotAngle_nstep - 1)*rotg->PotAngle_step;
+ for (i = 0; i < rotg->PotAngle_nstep; i++)
+ {
+ erg->PotAngleFit->degangle[i] = start + i*rotg->PotAngle_step;
+ }
+ }
+ else
+ {
+ erg->PotAngleFit = NULL;
+ }
+
+ /* xc_ref_ind needs to be set to identity in the serial case */
+ if (!PAR(cr))
+ {
+ for (i = 0; i < rotg->nat; i++)
+ {
+ erg->xc_ref_ind[i] = i;
+ }
+ }
+
+ /* Copy the masses so that the center can be determined. For all types of
+ * enforced rotation, we store the masses in the erg->mc array. */
+ if (rotg->bMassW)
+ {
+ alook = gmx_mtop_atomlookup_init(mtop);
+ }
+ snew(erg->mc, rotg->nat);
+ if (bFlex)
+ {
+ snew(erg->mc_sorted, rotg->nat);
+ }
+ if (!bColl)
+ {
+ snew(erg->m_loc, rotg->nat);
+ }
+ totalmass = 0.0;
+ for (i = 0; i < rotg->nat; i++)
+ {
+ if (rotg->bMassW)
+ {
+ gmx_mtop_atomnr_to_atom(alook, rotg->ind[i], &atom);
+ mass = atom->m;
+ }
+ else
+ {
+ mass = 1.0;
+ }
+ erg->mc[i] = mass;
+ totalmass += mass;
+ }
+ erg->invmass = 1.0/totalmass;
+
+ if (rotg->bMassW)
+ {
+ gmx_mtop_atomlookup_destroy(alook);
+ }
+
+ /* Set xc_ref_center for any rotation potential */
+ if ((rotg->eType == erotgISO) || (rotg->eType == erotgPM) || (rotg->eType == erotgRM) || (rotg->eType == erotgRM2))
+ {
+ /* Set the pivot point for the fixed, stationary-axis potentials. This
+ * won't change during the simulation */
+ copy_rvec(rotg->pivot, erg->xc_ref_center);
+ copy_rvec(rotg->pivot, erg->xc_center );
+ }
+ else
+ {
+ /* Center of the reference positions */
+ get_center(rotg->x_ref, erg->mc, rotg->nat, erg->xc_ref_center);
+
+ /* Center of the actual positions */
+ if (MASTER(cr))
+ {
+ snew(xdum, rotg->nat);
+ for (i = 0; i < rotg->nat; i++)
+ {
+ ii = rotg->ind[i];
+ copy_rvec(x[ii], xdum[i]);
+ }
+ get_center(xdum, erg->mc, rotg->nat, erg->xc_center);
+ sfree(xdum);
+ }
+#ifdef GMX_MPI
+ if (PAR(cr))
+ {
+ gmx_bcast(sizeof(erg->xc_center), erg->xc_center, cr);
+ }
+#endif
+ }
+
+ if (bColl)
+ {
+ /* Save the original (whole) set of positions in xc_old such that at later
+ * steps the rotation group can always be made whole again. If the simulation is
+ * restarted, we compute the starting reference positions (given the time)
+ * and assume that the correct PBC image of each position is the one nearest
+ * to the current reference */
+ if (MASTER(cr))
+ {
+ /* Calculate the rotation matrix for this angle: */
+ t_start = ir->init_t + ir->init_step*ir->delta_t;
+ erg->degangle = rotg->rate * t_start;
+ calc_rotmat(rotg->vec, erg->degangle, erg->rotmat);
+
+ for (i = 0; i < rotg->nat; i++)
+ {
+ ii = rotg->ind[i];
+
+ /* Subtract pivot, rotate, and add pivot again. This will yield the
+ * reference position for time t */
+ rvec_sub(rotg->x_ref[i], erg->xc_ref_center, coord);
+ mvmul(erg->rotmat, coord, xref);
+ rvec_inc(xref, erg->xc_ref_center);
+
+ copy_correct_pbc_image(x[ii], erg->xc_old[i], xref, box, 3);
+ }
+ }
+#ifdef GMX_MPI
+ if (PAR(cr))
+ {
+ gmx_bcast(rotg->nat*sizeof(erg->xc_old[0]), erg->xc_old, cr);
+ }
+#endif
+ }
+
+ if ( (rotg->eType != erotgFLEX) && (rotg->eType != erotgFLEX2) )
+ {
+ /* Put the reference positions into origin: */
+ for (i = 0; i < rotg->nat; i++)
+ {
+ rvec_dec(rotg->x_ref[i], erg->xc_ref_center);
+ }
+ }
+
+ /* Enforced rotation with flexible axis */
+ if (bFlex)
+ {
+ /* Calculate maximum beta value from minimum gaussian (performance opt.) */
+ erg->max_beta = calc_beta_max(rotg->min_gaussian, rotg->slab_dist);
+
+ /* Determine the smallest and largest coordinate with respect to the rotation vector */
+ get_firstlast_atom_ref(rotg, &ref_firstindex, &ref_lastindex);
+
- er->out_slabs = open_slab_out(opt2fn("-rs", nfile, fnm), rot, oenv);
++ /* From the extreme positions of the reference group, determine the first
+ * and last slab of the reference. */
+ get_firstlast_slab_ref(rotg, erg->mc, ref_firstindex, ref_lastindex);
+
+ /* Allocate memory for the slabs */
+ allocate_slabs(rotg, fplog, g, bVerbose);
+
+ /* Flexible rotation: determine the reference centers for the rest of the simulation */
+ erg->slab_first = erg->slab_first_ref;
+ erg->slab_last = erg->slab_last_ref;
+ get_slab_centers(rotg, rotg->x_ref, erg->mc, g, -1, out_slabs, bOutputCenters, TRUE);
+
+ /* Length of each x_rotref vector from center (needed if fit routine NORM is chosen): */
+ if (rotg->eFittype == erotgFitNORM)
+ {
+ for (i = 0; i < rotg->nat; i++)
+ {
+ rvec_sub(rotg->x_ref[i], erg->xc_ref_center, coord);
+ erg->xc_ref_length[i] = norm(coord);
+ }
+ }
+ }
+}
+
+
+extern void dd_make_local_rotation_groups(gmx_domdec_t *dd, t_rot *rot)
+{
+ gmx_ga2la_t ga2la;
+ int g;
+ t_rotgrp *rotg;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+ ga2la = dd->ga2la;
+
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg = rotg->enfrotgrp;
+
+
+ dd_make_local_group_indices(ga2la, rotg->nat, rotg->ind,
+ &erg->nat_loc, &erg->ind_loc, &erg->nalloc_loc, erg->xc_ref_ind);
+ }
+}
+
+
+/* Calculate the size of the MPI buffer needed in reduce_output() */
+static int calc_mpi_bufsize(t_rot *rot)
+{
+ int g;
+ int count_group, count_total;
+ t_rotgrp *rotg;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ count_total = 0;
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg = rotg->enfrotgrp;
+
+ /* Count the items that are transferred for this group: */
+ count_group = 4; /* V, torque, angle, weight */
+
+ /* Add the maximum number of slabs for flexible groups */
+ if (ISFLEX(rotg))
+ {
+ count_group += erg->slab_last_ref - erg->slab_first_ref + 1;
+ }
+
+ /* Add space for the potentials at different angles: */
+ if (erotgFitPOT == rotg->eFittype)
+ {
+ count_group += rotg->PotAngle_nstep;
+ }
+
+ /* Add to the total number: */
+ count_total += count_group;
+ }
+
+ return count_total;
+}
+
+
+extern void init_rot(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
+ t_commrec *cr, rvec *x, matrix box, gmx_mtop_t *mtop, const output_env_t oenv,
+ gmx_bool bVerbose, unsigned long Flags)
+{
+ t_rot *rot;
+ t_rotgrp *rotg;
+ int g;
+ int nat_max = 0; /* Size of biggest rotation group */
+ gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ rvec *x_pbc = NULL; /* Space for the pbc-correct atom positions */
+
+
+ if ( (PAR(cr)) && !DOMAINDECOMP(cr) )
+ {
+ gmx_fatal(FARGS, "Enforced rotation is only implemented for domain decomposition!");
+ }
+
+ if (MASTER(cr) && bVerbose)
+ {
+ fprintf(stdout, "%s Initializing ...\n", RotStr);
+ }
+
+ rot = ir->rot;
+ snew(rot->enfrot, 1);
+ er = rot->enfrot;
+ er->Flags = Flags;
+
+ /* When appending, skip first output to avoid duplicate entries in the data files */
+ if (er->Flags & MD_APPENDFILES)
+ {
+ er->bOut = FALSE;
+ }
+ else
+ {
+ er->bOut = TRUE;
+ }
+
+ if (MASTER(cr) && er->bOut)
+ {
+ please_cite(fplog, "Kutzner2011");
+ }
+
+ /* Output every step for reruns */
+ if (er->Flags & MD_RERUN)
+ {
+ if (NULL != fplog)
+ {
+ fprintf(fplog, "%s rerun - will write rotation output every available step.\n", RotStr);
+ }
+ rot->nstrout = 1;
+ rot->nstsout = 1;
+ }
+
+ er->out_slabs = NULL;
+ if (MASTER(cr) && HaveFlexibleGroups(rot) )
+ {
- er->out_angles = open_angles_out(opt2fn("-ra", nfile, fnm), rot, oenv);
++ er->out_slabs = open_slab_out(opt2fn("-rs", nfile, fnm), rot);
+ }
+
+ if (MASTER(cr))
+ {
+ /* Remove pbc, make molecule whole.
+ * When ir->bContinuation=TRUE this has already been done, but ok. */
+ snew(x_pbc, mtop->natoms);
+ m_rveccopy(mtop->natoms, x, x_pbc);
+ do_pbc_first_mtop(NULL, ir->ePBC, box, mtop, x_pbc);
+ /* All molecules will be whole now, but not necessarily in the home box.
+ * Additionally, if a rotation group consists of more than one molecule
+ * (e.g. two strands of DNA), each one of them can end up in a different
+ * periodic box. This is taken care of in init_rot_group. */
+ }
+
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+
+ if (NULL != fplog)
+ {
+ fprintf(fplog, "%s group %d type '%s'\n", RotStr, g, erotg_names[rotg->eType]);
+ }
+
+ if (rotg->nat > 0)
+ {
+ /* Allocate space for the rotation group's data: */
+ snew(rotg->enfrotgrp, 1);
+ erg = rotg->enfrotgrp;
+
+ nat_max = max(nat_max, rotg->nat);
+
+ if (PAR(cr))
+ {
+ erg->nat_loc = 0;
+ erg->nalloc_loc = 0;
+ erg->ind_loc = NULL;
+ }
+ else
+ {
+ erg->nat_loc = rotg->nat;
+ erg->ind_loc = rotg->ind;
+ }
+ init_rot_group(fplog, cr, g, rotg, x_pbc, mtop, bVerbose, er->out_slabs, box, ir,
+ !(er->Flags & MD_APPENDFILES) ); /* Do not output the reference centers
+ * again if we are appending */
+ }
+ }
+
+ /* Allocate space for enforced rotation buffer variables */
+ er->bufsize = nat_max;
+ snew(er->data, nat_max);
+ snew(er->xbuf, nat_max);
+ snew(er->mbuf, nat_max);
+
+ /* Buffers for MPI reducing torques, angles, weights (for each group), and V */
+ if (PAR(cr))
+ {
+ er->mpi_bufsize = calc_mpi_bufsize(rot) + 100; /* larger to catch errors */
+ snew(er->mpi_inbuf, er->mpi_bufsize);
+ snew(er->mpi_outbuf, er->mpi_bufsize);
+ }
+ else
+ {
+ er->mpi_bufsize = 0;
+ er->mpi_inbuf = NULL;
+ er->mpi_outbuf = NULL;
+ }
+
+ /* Only do I/O on the MASTER */
+ er->out_angles = NULL;
+ er->out_rot = NULL;
+ er->out_torque = NULL;
+ if (MASTER(cr))
+ {
+ er->out_rot = open_rot_out(opt2fn("-ro", nfile, fnm), rot, oenv);
+
+ if (rot->nstsout > 0)
+ {
+ if (HaveFlexibleGroups(rot) || HavePotFitGroups(rot) )
+ {
- er->out_torque = open_torque_out(opt2fn("-rt", nfile, fnm), rot, oenv);
++ er->out_angles = open_angles_out(opt2fn("-ra", nfile, fnm), rot);
+ }
+ if (HaveFlexibleGroups(rot) )
+ {
- extern void finish_rot(FILE *fplog, t_rot *rot)
++ er->out_torque = open_torque_out(opt2fn("-rt", nfile, fnm), rot);
+ }
+ }
+
+ sfree(x_pbc);
+ }
+}
+
+
- do_fixed(rotg, x, box, t, step, outstep_rot, outstep_slab);
++extern void finish_rot(t_rot *rot)
+{
+ gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
+
+
+ er = rot->enfrot;
+ if (er->out_rot)
+ {
+ gmx_fio_fclose(er->out_rot);
+ }
+ if (er->out_slabs)
+ {
+ gmx_fio_fclose(er->out_slabs);
+ }
+ if (er->out_angles)
+ {
+ gmx_fio_fclose(er->out_angles);
+ }
+ if (er->out_torque)
+ {
+ gmx_fio_fclose(er->out_torque);
+ }
+}
+
+
+/* Rotate the local reference positions and store them in
+ * erg->xr_loc[0...(nat_loc-1)]
+ *
+ * Note that we already subtracted u or y_c from the reference positions
+ * in init_rot_group().
+ */
+static void rotate_local_reference(t_rotgrp *rotg)
+{
+ gmx_enfrotgrp_t erg;
+ int i, ii;
+
+
+ erg = rotg->enfrotgrp;
+
+ for (i = 0; i < erg->nat_loc; i++)
+ {
+ /* Index of this rotation group atom with respect to the whole rotation group */
+ ii = erg->xc_ref_ind[i];
+ /* Rotate */
+ mvmul(erg->rotmat, rotg->x_ref[ii], erg->xr_loc[i]);
+ }
+}
+
+
+/* Select the PBC representation for each local x position and store that
+ * for later usage. We assume the right PBC image of an x is the one nearest to
+ * its rotated reference */
+static void choose_pbc_image(rvec x[], t_rotgrp *rotg, matrix box, int npbcdim)
+{
+ int i, ii;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ rvec xref;
+
+
+ erg = rotg->enfrotgrp;
+
+ for (i = 0; i < erg->nat_loc; i++)
+ {
+ /* Index of a rotation group atom */
+ ii = erg->ind_loc[i];
+
+ /* Get the correctly rotated reference position. The pivot was already
+ * subtracted in init_rot_group() from the reference positions. Also,
+ * the reference positions have already been rotated in
+ * rotate_local_reference(). For the current reference position we thus
+ * only need to add the pivot again. */
+ copy_rvec(erg->xr_loc[i], xref);
+ rvec_inc(xref, erg->xc_ref_center);
+
+ copy_correct_pbc_image(x[ii], erg->x_loc_pbc[i], xref, box, npbcdim);
+ }
+}
+
+
+extern void do_rotation(
+ t_commrec *cr,
+ t_inputrec *ir,
+ matrix box,
+ rvec x[],
+ real t,
+ gmx_large_int_t step,
+ gmx_wallcycle_t wcycle,
+ gmx_bool bNS)
+{
+ int g, i, ii;
+ t_rot *rot;
+ t_rotgrp *rotg;
+ gmx_bool outstep_slab, outstep_rot;
+ gmx_bool bFlex, bColl;
+ gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ rvec transvec;
+ t_gmx_potfit *fit = NULL; /* For fit type 'potential' determine the fit
+ angle via the potential minimum */
+
+ /* Enforced rotation cycle counting: */
+ gmx_cycles_t cycles_comp; /* Cycles for the enf. rotation computation
+ only, does not count communication. This
+ counter is used for load-balancing */
+
+#ifdef TAKETIME
+ double t0;
+#endif
+
+ rot = ir->rot;
+ er = rot->enfrot;
+
+ /* When to output in main rotation output file */
+ outstep_rot = do_per_step(step, rot->nstrout) && er->bOut;
+ /* When to output per-slab data */
+ outstep_slab = do_per_step(step, rot->nstsout) && er->bOut;
+
+ /* Output time into rotation output file */
+ if (outstep_rot && MASTER(cr))
+ {
+ fprintf(er->out_rot, "%12.3e", t);
+ }
+
+ /**************************************************************************/
+ /* First do ALL the communication! */
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg = rotg->enfrotgrp;
+
+ /* Do we have a flexible axis? */
+ bFlex = ISFLEX(rotg);
+ /* Do we use a collective (global) set of coordinates? */
+ bColl = ISCOLL(rotg);
+
+ /* Calculate the rotation matrix for this angle: */
+ erg->degangle = rotg->rate * t;
+ calc_rotmat(rotg->vec, erg->degangle, erg->rotmat);
+
+ if (bColl)
+ {
+ /* Transfer the rotation group's positions such that every node has
+ * all of them. Every node contributes its local positions x and stores
+ * it in the collective erg->xc array. */
+ communicate_group_positions(cr, erg->xc, erg->xc_shifts, erg->xc_eshifts, bNS,
+ x, rotg->nat, erg->nat_loc, erg->ind_loc, erg->xc_ref_ind, erg->xc_old, box);
+ }
+ else
+ {
+ /* Fill the local masses array;
+ * this array changes in DD/neighborsearching steps */
+ if (bNS)
+ {
+ for (i = 0; i < erg->nat_loc; i++)
+ {
+ /* Index of local atom w.r.t. the collective rotation group */
+ ii = erg->xc_ref_ind[i];
+ erg->m_loc[i] = erg->mc[ii];
+ }
+ }
+
+ /* Calculate Omega*(y_i-y_c) for the local positions */
+ rotate_local_reference(rotg);
+
+ /* Choose the nearest PBC images of the group atoms with respect
+ * to the rotated reference positions */
+ choose_pbc_image(x, rotg, box, 3);
+
+ /* Get the center of the rotation group */
+ if ( (rotg->eType == erotgISOPF) || (rotg->eType == erotgPMPF) )
+ {
+ get_center_comm(cr, erg->x_loc_pbc, erg->m_loc, erg->nat_loc, rotg->nat, erg->xc_center);
+ }
+ }
+
+ } /* End of loop over rotation groups */
+
+ /**************************************************************************/
+ /* Done communicating, we can start to count cycles for the load balancing now ... */
+ cycles_comp = gmx_cycles_read();
+
+
+#ifdef TAKETIME
+ t0 = MPI_Wtime();
+#endif
+
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg = rotg->enfrotgrp;
+
+ bFlex = ISFLEX(rotg);
+ bColl = ISCOLL(rotg);
+
+ if (outstep_rot && MASTER(cr))
+ {
+ fprintf(er->out_rot, "%12.4f", erg->degangle);
+ }
+
+ /* Calculate angles and rotation matrices for potential fitting: */
+ if ( (outstep_rot || outstep_slab) && (erotgFitPOT == rotg->eFittype) )
+ {
+ fit = erg->PotAngleFit;
+ for (i = 0; i < rotg->PotAngle_nstep; i++)
+ {
+ calc_rotmat(rotg->vec, erg->degangle + fit->degangle[i], fit->rotmat[i]);
+
+ /* Clear value from last step */
+ erg->PotAngleFit->V[i] = 0.0;
+ }
+ }
+
+ /* Clear values from last time step */
+ erg->V = 0.0;
+ erg->torque_v = 0.0;
+ erg->angle_v = 0.0;
+ erg->weight_v = 0.0;
+
+ switch (rotg->eType)
+ {
+ case erotgISO:
+ case erotgISOPF:
+ case erotgPM:
+ case erotgPMPF:
- do_radial_motion(rotg, x, box, t, step, outstep_rot, outstep_slab);
++ do_fixed(rotg, outstep_rot, outstep_slab);
+ break;
+ case erotgRM:
- do_radial_motion_pf(rotg, x, box, t, step, outstep_rot, outstep_slab);
++ do_radial_motion(rotg, outstep_rot, outstep_slab);
+ break;
+ case erotgRMPF:
- do_radial_motion2(rotg, x, box, t, step, outstep_rot, outstep_slab);
++ do_radial_motion_pf(rotg, x, box, outstep_rot, outstep_slab);
+ break;
+ case erotgRM2:
+ case erotgRM2PF:
- do_flexible(MASTER(cr), er, rotg, g, x, box, t, step, outstep_rot, outstep_slab);
++ do_radial_motion2(rotg, x, box, outstep_rot, outstep_slab);
+ break;
+ case erotgFLEXT:
+ case erotgFLEX2T:
+ /* Subtract the center of the rotation group from the collective positions array
+ * Also store the center in erg->xc_center since it needs to be subtracted
+ * in the low level routines from the local coordinates as well */
+ get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
+ svmul(-1.0, erg->xc_center, transvec);
+ translate_x(erg->xc, rotg->nat, transvec);
- do_flexible(MASTER(cr), er, rotg, g, x, box, t, step, outstep_rot, outstep_slab);
++ do_flexible(MASTER(cr), er, rotg, g, x, box, t, outstep_rot, outstep_slab);
+ break;
+ case erotgFLEX:
+ case erotgFLEX2:
+ /* Do NOT subtract the center of mass in the low level routines! */
+ clear_rvec(erg->xc_center);
++ do_flexible(MASTER(cr), er, rotg, g, x, box, t, outstep_rot, outstep_slab);
+ break;
+ default:
+ gmx_fatal(FARGS, "No such rotation potential.");
+ break;
+ }
+ }
+
+#ifdef TAKETIME
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "%s calculation (step %d) took %g seconds.\n", RotStr, step, MPI_Wtime()-t0);
+ }
+#endif
+
+ /* Stop the enforced rotation cycle counter and add the computation-only
+ * cycles to the force cycles for load balancing */
+ cycles_comp = gmx_cycles_read() - cycles_comp;
+
+ if (DOMAINDECOMP(cr) && wcycle)
+ {
+ dd_cycles_add(cr->dd, cycles_comp, ddCyclF);
+ }
+}
--- /dev/null
- dvdl += lagr[i]*dt_2*
- (idef->iparams[type].constr.dB-idef->iparams[type].constr.dA);
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * 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 the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * GROwing Monsters And Cloning Shrimps
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+#include "sysstuff.h"
+#include "typedefs.h"
+#include "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,
+ int natoms, 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,
+ int natoms, 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, natoms, 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
- " not within 1 of (1.2, 3.1, 2.4)",
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2009,2010,2011,2012, by the GROMACS development team, led by
+ * David van der Spoel, Berk Hess, 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 selhelp.h.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_selection
+ */
+#include <string>
+#include <vector>
+#include <utility>
+
+#include <boost/scoped_ptr.hpp>
+
+#include "gromacs/onlinehelp/helptopic.h"
+#include "gromacs/onlinehelp/helpwritercontext.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/file.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "selhelp.h"
+#include "selmethod.h"
+#include "symrec.h"
+
+namespace
+{
+
+struct CommonHelpText
+{
+ static const char name[];
+ static const char title[];
+ static const char *const text[];
+};
+
+const char CommonHelpText::name[] = "selections";
+const char CommonHelpText::title[] =
+ "Selection syntax and usage";
+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]",
+
+ "Each analysis tool requires a different number of selections and the",
+ "selections are interpreted differently. The general idea is still the",
+ "same: each selection evaluates to a set of positions, where a position",
+ "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.",
+};
+
+struct ArithmeticHelpText
+{
+ static const char name[];
+ static const char title[];
+ static const char *const text[];
+};
+
+const char ArithmeticHelpText::name[] = "arithmetic";
+const char ArithmeticHelpText::title[] =
+ "Arithmetic expressions in selections";
+const char *const ArithmeticHelpText::text[] = {
+ "Basic arithmetic evaluation is supported for numeric expressions.",
+ "Supported operations are addition, subtraction, negation, multiplication,",
+ "division, and exponentiation (using ^).",
+ "Result of a division by zero or other illegal operations is undefined.",
+};
+
+struct CmdLineHelpText
+{
+ static const char name[];
+ static const char title[];
+ static const char *const text[];
+};
+
+const char CmdLineHelpText::name[] = "cmdline";
+const char CmdLineHelpText::title[] =
+ "Specifying selections from command line";
+const char *const CmdLineHelpText::text[] = {
+ "If no selections are provided on the command line, you are prompted to",
+ "type the selections interactively (a pipe can also be used to provide",
+ "the selections in this case for most tools). While this works well for",
+ "testing, it is easier to provide the selections from the command line",
+ "if they are complex or for scripting.[PAR]",
+
+ "Each tool has different command-line arguments for specifying selections",
+ "(listed by [TT][PROGRAM] help <tool>[tt]).",
+ "You can either pass a single string containing all selections (separated",
+ "by semicolons), or multiple strings, each containing one selection.",
+ "Note that you need to quote the selections to protect them from the",
+ "shell.[PAR]",
+
+ "If you set a selection command-line argument, but do not provide any",
+ "selections, you are prompted to type the selections for that argument",
+ "interactively. This is useful if that selection argument is optional,",
+ "in which case it is not normally prompted for.[PAR]",
+
+ "To provide selections from a file, use [TT]-sf file.dat[tt] in the place",
+ "of the selection for a selection argument (e.g.,",
+ "[TT]-select -sf file.dat[tt]). In general, the [TT]-sf[tt] argument reads",
+ "selections from the provided file and assigns them to selection arguments",
+ "that have been specified up to that point, but for which no selections",
+ "have been provided.",
+ "As a special case, [TT]-sf[tt] provided on its own, without preceding",
+ "selection arguments, assigns the selections to all (yet unset) required",
+ "selections (i.e., those that would be promted interactively if no",
+ "selections are provided on the command line).[PAR]",
+
+ "To use groups from a traditional index file, use argument [TT]-n[tt]",
+ "to provide a file. See the \"syntax\" subtopic for how to use them.",
+ "If this option is not provided, default groups are generated.",
+ "The default groups are generated by reading selections from a file",
+ "[TT]defselection.dat[tt]. If such a file is found in the current",
+ "directory, it is used instead of the one provided by default.[PAR]",
+
+ "Depending on the tool, two additional command-line arguments may be",
+ "available to control the behavior:[BR]",
+ "1. [TT]-seltype[tt] can be used to specify the default type of",
+ "positions to calculate for each selection.[BR]",
+ "2. [TT]-selrpos[tt] can be used to specify the default type of",
+ "positions used in selecting atoms by coordinates.[BR]",
+ "See the \"positions\" subtopic for more information on these options.",
+};
+
+struct EvaluationHelpText
+{
+ static const char name[];
+ static const char title[];
+ static const char *const text[];
+};
+
+const char EvaluationHelpText::name[] = "evaluation";
+const char EvaluationHelpText::title[] =
+ "Selection evaluation and optimization";
+const char *const EvaluationHelpText::text[] = {
+ "Boolean evaluation proceeds from left to right and is short-circuiting",
+ "i.e., as soon as it is known whether an atom will be selected, the",
+ "remaining expressions are not evaluated at all.",
+ "This can be used to optimize the selections: you should write the",
+ "most restrictive and/or the most inexpensive expressions first in",
+ "boolean expressions.",
+ "The relative ordering between dynamic and static expressions does not",
+ "matter: all static expressions are evaluated only once, before the first",
+ "frame, and the result becomes the leftmost expression.[PAR]",
+
+ "Another point for optimization is in common subexpressions: they are not",
+ "automatically recognized, but can be manually optimized by the use of",
+ "variables. This can have a big impact on the performance of complex",
+ "selections, in particular if you define several index groups like this:",
+ " [TT]rdist = distance from com of resnr 1 to 5;[tt][BR]",
+ " [TT]resname RES and rdist < 2;[tt][BR]",
+ " [TT]resname RES and rdist < 4;[tt][BR]",
+ " [TT]resname RES and rdist < 6;[tt][BR]",
+ "Without the variable assignment, the distances would be evaluated three",
+ "times, although they are exactly the same within each selection.",
+ "Anything assigned into a variable becomes a common subexpression that",
+ "is evaluated only once during a frame.",
+ "Currently, in some cases the use of variables can actually lead to a small",
+ "performance loss because of the checks necessary to determine for which",
+ "atoms the expression has already been evaluated, but this should not be",
+ "a major problem.",
+};
+
+struct ExamplesHelpText
+{
+ static const char name[];
+ static const char title[];
+ static const char *const text[];
+};
+
+const char ExamplesHelpText::name[] = "examples";
+const char ExamplesHelpText::title[] =
+ "Selection examples";
+const char *const ExamplesHelpText::text[] = {
+ // TODO: Once there are more tools available, use examples that invoke
+ // tools and explain what the selections do in those tools.
+ "Below, examples of increasingly complex selections are given.[PAR]",
+
+ "Selection of all water oxygens:[BR]",
+ " resname SOL and name OW",
+ "[PAR]",
+
+ "Centers of mass of residues 1 to 5 and 10:[BR]",
+ " res_com of resnr 1 to 5 10",
+ "[PAR]",
+
+ "All atoms farther than 1 nm of a fixed position:[BR]",
++ " not within 1 of [1.2, 3.1, 2.4]",
+ "[PAR]",
+
+ "All atoms of a residue LIG within 0.5 nm of a protein (with a custom name):[BR]",
+ " \"Close to protein\" resname LIG and within 0.5 of group \"Protein\"",
+ "[PAR]",
+
+ "All protein residues that have at least one atom within 0.5 nm of a residue LIG:[BR]",
+ " group \"Protein\" and same residue as within 0.5 of resname LIG",
+ "[PAR]",
+
+ "All RES residues whose COM is between 2 and 4 nm from the COM of all of them:[BR]",
+ " rdist = res_com distance from com of resname RES[BR]",
+ " resname RES and rdist >= 2 and rdist <= 4",
+ "[PAR]",
+
+ "Selection like C1 C2 C2 C3 C3 C4 ... C8 C9 (e.g., for g_bond):[BR]",
+ " name \"C[1-8]\" merge name \"C[2-9]\"",
+};
+
+struct KeywordsHelpText
+{
+ static const char name[];
+ static const char title[];
+ static const char *const text[];
+};
+
+const char KeywordsHelpText::name[] = "keywords";
+const char KeywordsHelpText::title[] =
+ "Selection keywords";
+const char *const KeywordsHelpText::text[] = {
+ "The following selection keywords are currently available.",
+ "For keywords marked with a star, additional help is available through",
+ "a subtopic KEYWORD, where KEYWORD is the name of the keyword.",
+};
+
+struct LimitationsHelpText
+{
+ static const char name[];
+ static const char title[];
+ static const char *const text[];
+};
+
+const char LimitationsHelpText::name[] = "limitations";
+const char LimitationsHelpText::title[] =
+ "Selection limitations";
+const char *const LimitationsHelpText::text[] = {
+ "Some analysis programs may require a special structure for the input",
+ "selections (e.g., [TT]g_angle[tt] requires the index group to be made",
+ "of groups of three or four atoms).",
+ "For such programs, it is up to the user to provide a proper selection",
+ "expression that always returns such positions.",
+ "[PAR]",
+
+ "Due to technical reasons, having a negative value as the first value in",
+ "expressions like[BR]",
+ "[TT]charge -1 to -0.7[tt][BR]",
+ "result in a syntax error. A workaround is to write[BR]",
+ "[TT]charge {-1 to -0.7}[tt][BR]",
+ "instead.[PAR]",
+
+ "When [TT]name[tt] selection keyword is used together with PDB input",
+ "files, the behavior may be unintuitive. When Gromacs reads in a PDB",
+ "file, 4 character atom names that start with a digit are transformed",
+ "such that, e.g., 1HG2 becomes HG21, and the latter is what is matched",
+ "by the [TT]name[tt] keyword. Use [TT]pdbname[tt] to match the atom name",
+ "as it appears in the input PDB file.",
+};
+
+struct PositionsHelpText
+{
+ static const char name[];
+ static const char title[];
+ static const char *const text[];
+};
+
+const char PositionsHelpText::name[] = "positions";
+const char PositionsHelpText::title[] =
+ "Specifying positions in selections";
+const char *const PositionsHelpText::text[] = {
+ "Possible ways of specifying positions in selections are:[PAR]",
+
+ "1. A constant position can be defined as [TT][XX, YY, ZZ][tt], where",
+ "[TT]XX[tt], [TT]YY[tt] and [TT]ZZ[tt] are real numbers.[PAR]",
+
+ "2. [TT]com of ATOM_EXPR [pbc][tt] or [TT]cog of ATOM_EXPR [pbc][tt]",
+ "calculate the center of mass/geometry of [TT]ATOM_EXPR[tt]. If",
+ "[TT]pbc[tt] is specified, the center is calculated iteratively to try",
+ "to deal with cases where [TT]ATOM_EXPR[tt] wraps around periodic",
+ "boundary conditions.[PAR]",
+
+ "3. [TT]POSTYPE of ATOM_EXPR[tt] calculates the specified positions for",
+ "the atoms in [TT]ATOM_EXPR[tt].",
+ "[TT]POSTYPE[tt] can be [TT]atom[tt], [TT]res_com[tt], [TT]res_cog[tt],",
+ "[TT]mol_com[tt] or [TT]mol_cog[tt], with an optional prefix [TT]whole_[tt]",
+ "[TT]part_[tt] or [TT]dyn_[tt].",
+ "[TT]whole_[tt] calculates the centers for the whole residue/molecule,",
+ "even if only part of it is selected.",
+ "[TT]part_[tt] prefix calculates the centers for the selected atoms, but",
+ "uses always the same atoms for the same residue/molecule. The used atoms",
+ "are determined from the the largest group allowed by the selection.",
+ "[TT]dyn_[tt] calculates the centers strictly only for the selected atoms.",
+ "If no prefix is specified, whole selections default to [TT]part_[tt] and",
+ "other places default to [TT]whole_[tt].",
+ "The latter is often desirable to select the same molecules in different",
+ "tools, while the first is a compromise between speed ([TT]dyn_[tt]",
+ "positions can be slower to evaluate than [TT]part_[tt]) and intuitive",
+ "behavior.[PAR]",
+
+ "4. [TT]ATOM_EXPR[tt], when given for whole selections, is handled as 3.",
+ "above, using the position type from the command-line argument",
+ "[TT]-seltype[tt].[PAR]",
+
+ "Selection keywords that select atoms based on their positions, such as",
+ "[TT]dist from[tt], use by default the positions defined by the",
+ "[TT]-selrpos[tt] command-line option.",
+ "This can be overridden by prepending a [TT]POSTYPE[tt] specifier to the",
+ "keyword. For example, [TT]res_com dist from POS[tt] evaluates the",
+ "residue center of mass distances. In the example, all atoms of a residue",
+ "are either selected or not, based on the single distance calculated.",
+};
+
+struct SyntaxHelpText
+{
+ static const char name[];
+ static const char title[];
+ static const char *const text[];
+};
+
+const char SyntaxHelpText::name[] = "syntax";
+const char SyntaxHelpText::title[] =
+ "Selection syntax";
+const char *const SyntaxHelpText::text[] = {
+ "A set of selections consists of one or more selections, separated by",
+ "semicolons. Each selection defines a set of positions for the analysis.",
+ "Each selection can also be preceded by a string that gives a name for",
+ "the selection for use in, e.g., graph legends.",
+ "If no name is provided, the string used for the selection is used",
+ "automatically as the name.[PAR]",
+
+ "For interactive input, the syntax is slightly altered: line breaks can",
+ "also be used to separate selections. \\ followed by a line break can",
+ "be used to continue a line if necessary.",
+ "Notice that the above only applies to real interactive input,",
+ "not if you provide the selections, e.g., from a pipe.[PAR]",
+
+ "It is possible to use variables to store selection expressions.",
+ "A variable is defined with the following syntax:[BR]",
+ "[TT]VARNAME = EXPR ;[tt][BR]",
+ "where [TT]EXPR[tt] is any valid selection expression.",
+ "After this, [TT]VARNAME[tt] can be used anywhere where [TT]EXPR[tt]",
+ "would be valid.[PAR]",
+
+ "Selections are composed of three main types of expressions, those that",
+ "define atoms ([TT]ATOM_EXPR[tt]s), those that define positions",
+ "([TT]POS_EXPR[tt]s), and those that evaluate to numeric values",
+ "([TT]NUM_EXPR[tt]s). Each selection should be a [TT]POS_EXPR[tt]",
+ "or a [TT]ATOM_EXPR[tt] (the latter is automatically converted to",
+ "positions). The basic rules are as follows:[BR]",
+ "1. An expression like [TT]NUM_EXPR1 < NUM_EXPR2[tt] evaluates to an",
+ "[TT]ATOM_EXPR[tt] that selects all the atoms for which the comparison",
+ "is true.[BR]",
+ "2. Atom expressions can be combined with boolean operations such as",
+ "[TT]not ATOM_EXPR[tt], [TT]ATOM_EXPR and ATOM_EXPR[tt], or",
+ "[TT]ATOM_EXPR or ATOM_EXPR[tt]. Parentheses can be used to alter the",
+ "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]",
+
+ "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])",
+ "or regular expressions (e.g., [TT]resname \"R[AB]\"[tt]).",
+ "The match type is automatically guessed from the string: if it contains",
+ "other characters than letters, numbers, '*', or '?', it is interpreted",
+ "as a regular expression.",
+ "To force the matching to use literal string matching, use",
+ "[TT]name = \"C*\"[tt] to match a literal C*.",
+ "To force other type of matching, use '?' or '~' in place of '=' to force",
+ "wildcard or regular expression matching, respectively.[PAR]",
+
+ "Strings that contain non-alphanumeric characters should be enclosed in",
+ "double quotes as in the examples. For other strings, the quotes are",
+ "optional, but if the value conflicts with a reserved keyword, a syntax",
+ "error will occur. If your strings contain uppercase letters, this should",
+ "not happen.[PAR]",
+
+ "Index groups provided with the [TT]-n[tt] command-line option or",
+ "generated by default can be accessed with [TT]group NR[tt] or",
+ "[TT]group NAME[tt], where [TT]NR[tt] is a zero-based index of the group",
+ "and [TT]NAME[tt] is part of the name of the desired group.",
+ "The keyword [TT]group[tt] is optional if the whole selection is",
+ "provided from an index group.",
+ "To see a list of available groups in the interactive mode, press enter",
+ "in the beginning of a line.",
+};
+
+} // namespace
+
+namespace gmx
+{
+
+namespace
+{
+
+/*! \internal \brief
+ * Help topic implementation for an individual selection method.
+ *
+ * \ingroup module_selection
+ */
+class KeywordDetailsHelpTopic : public AbstractSimpleHelpTopic
+{
+ public:
+ //! Initialize help topic for the given selection method.
+ KeywordDetailsHelpTopic(const std::string &name,
+ const gmx_ana_selmethod_t &method)
+ : name_(name), method_(method)
+ {
+ }
+
+ virtual const char *name() const
+ {
+ return name_.c_str();
+ }
+ virtual const char *title() const
+ {
+ return NULL;
+ }
+
+ protected:
+ virtual std::string helpText() const
+ {
+ return concatenateStrings(method_.help.help, method_.help.nlhelp);
+ }
+
+ private:
+ std::string name_;
+ const gmx_ana_selmethod_t &method_;
+
+ GMX_DISALLOW_COPY_AND_ASSIGN(KeywordDetailsHelpTopic);
+};
+
+/*! \internal \brief
+ * Custom help topic for printing a list of selection keywords.
+ *
+ * \ingroup module_selection
+ */
+class KeywordsHelpTopic : public CompositeHelpTopic<KeywordsHelpText>
+{
+ public:
+ KeywordsHelpTopic();
+
+ virtual void writeHelp(const HelpWriterContext &context) const;
+
+ private:
+ /*! \brief
+ * Container for known selection methods.
+ *
+ * The first item in the pair is the name of the selection method, and
+ * the second points to the static data structure that describes the
+ * method.
+ * The name in the first item may differ from the name of the static
+ * data structure if an alias is defined for that method.
+ */
+ typedef std::vector<std::pair<std::string,
+ const gmx_ana_selmethod_t *> >
+ MethodList;
+
+ /*! \brief
+ * Prints a brief list of keywords (selection methods) available.
+ *
+ * \param[in] context Context for printing the help.
+ * \param[in] type Only methods that return this type are printed.
+ * \param[in] bModifiers If false, \ref SMETH_MODIFIER methods are
+ * excluded, otherwise only them are printed.
+ */
+ void printKeywordList(const HelpWriterContext &context,
+ e_selvalue_t type, bool bModifiers) const;
+
+ MethodList methods_;
+};
+
+KeywordsHelpTopic::KeywordsHelpTopic()
+{
+ // TODO: This is not a very elegant way of getting the list of selection
+ // methods, but this needs to be rewritten in any case if/when #652 is
+ // implemented.
+ boost::scoped_ptr<SelectionParserSymbolTable> symtab(
+ new SelectionParserSymbolTable);
+ gmx_ana_selmethod_register_defaults(symtab.get());
+
+ SelectionParserSymbolIterator symbol
+ = symtab->beginIterator(SelectionParserSymbol::MethodSymbol);
+ while (symbol != symtab->endIterator())
+ {
+ const std::string &symname = symbol->name();
+ const gmx_ana_selmethod_t *method = symbol->methodValue();
+ methods_.push_back(std::make_pair(std::string(symname), method));
+ if (method->help.nlhelp > 0 && method->help.help != NULL)
+ {
+ addSubTopic(HelpTopicPointer(
+ new KeywordDetailsHelpTopic(symname, *method)));
+ }
+ ++symbol;
+ }
+}
+
+void KeywordsHelpTopic::writeHelp(const HelpWriterContext &context) const
+{
+ if (context.outputFormat() != eHelpOutputFormat_Console)
+ {
+ GMX_THROW(NotImplementedError(
+ "Selection help is not implemented for this output format"));
+ }
+ // TODO: The markup here is not really appropriate, and printKeywordList()
+ // still prints raw text, but these are waiting for discussion of the
+ // markup format in #969.
+ writeBasicHelpTopic(context, *this, helpText());
+ context.writeTextBlock("[BR]");
+
+ // Print the list of keywords
+ context.writeTextBlock(
+ "Keywords that select atoms by an integer property:[BR]"
+ "(use in expressions or like \"atomnr 1 to 5 7 9\")[BR]");
+ printKeywordList(context, INT_VALUE, false);
+ context.writeTextBlock("[BR]");
+
+ context.writeTextBlock(
+ "Keywords that select atoms by a numeric property:[BR]"
+ "(use in expressions or like \"occupancy 0.5 to 1\")[BR]");
+ printKeywordList(context, REAL_VALUE, false);
+ context.writeTextBlock("[BR]");
+
+ context.writeTextBlock(
+ "Keywords that select atoms by a string property:[BR]"
+ "(use like \"name PATTERN [PATTERN] ...\")[BR]");
+ printKeywordList(context, STR_VALUE, false);
+ context.writeTextBlock("[BR]");
+
+ context.writeTextBlock(
+ "Additional keywords that directly select atoms:[BR]");
+ printKeywordList(context, GROUP_VALUE, false);
+ context.writeTextBlock("[BR]");
+
+ context.writeTextBlock(
+ "Keywords that directly evaluate to positions:[BR]"
+ "(see also \"positions\" subtopic)[BR]");
+ printKeywordList(context, POS_VALUE, false);
+ context.writeTextBlock("[BR]");
+
+ context.writeTextBlock("Additional keywords:[BR]");
+ printKeywordList(context, POS_VALUE, true);
+ printKeywordList(context, NO_VALUE, true);
+}
+
+void KeywordsHelpTopic::printKeywordList(const HelpWriterContext &context,
+ e_selvalue_t type,
+ bool bModifiers) const
+{
+ File &file = context.outputFile();
+ MethodList::const_iterator iter;
+ for (iter = methods_.begin(); iter != methods_.end(); ++iter)
+ {
+ const gmx_ana_selmethod_t &method = *iter->second;
+ bool bIsModifier = (method.flags & SMETH_MODIFIER) != 0;
+ if (method.type == type && bModifiers == bIsModifier)
+ {
+ bool bHasHelp = (method.help.nlhelp > 0 && method.help.help != NULL);
+ file.writeString(formatString(" %c ", bHasHelp ? '*' : ' '));
+ if (method.help.syntax != NULL)
+ {
+ file.writeLine(method.help.syntax);
+ }
+ else
+ {
+ std::string symname = iter->first;
+ if (symname != method.name)
+ {
+ symname.append(formatString(" (synonym for %s)", method.name));
+ }
+ file.writeLine(symname);
+ }
+ }
+ }
+}
+
+} // namespace
+
+/*! \cond internal */
+HelpTopicPointer createSelectionHelpTopic()
+{
+ CompositeHelpTopicPointer root(new CompositeHelpTopic<CommonHelpText>);
+ root->registerSubTopic<SimpleHelpTopic<ArithmeticHelpText> >();
+ root->registerSubTopic<SimpleHelpTopic<CmdLineHelpText> >();
+ root->registerSubTopic<SimpleHelpTopic<EvaluationHelpText> >();
+ root->registerSubTopic<SimpleHelpTopic<ExamplesHelpText> >();
+ root->registerSubTopic<KeywordsHelpTopic>();
+ root->registerSubTopic<SimpleHelpTopic<LimitationsHelpText> >();
+ root->registerSubTopic<SimpleHelpTopic<PositionsHelpText> >();
+ root->registerSubTopic<SimpleHelpTopic<SyntaxHelpText> >();
+ return move(root);
+}
+//! \endcond
+
+} // namespace gmx
--- /dev/null
- enerd->term[F_DVDL_CONSTR] += dvdl_constr;
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * 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 the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "typedefs.h"
+#include "smalloc.h"
+#include "sysstuff.h"
+#include "vec.h"
+#include "statutil.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 "trnio.h"
+#include "xtcio.h"
+#include "mdrun.h"
+#include "md_support.h"
+#include "md_logging.h"
+#include "confio.h"
+#include "network.h"
+#include "pull.h"
+#include "xvgr.h"
+#include "physics.h"
+#include "names.h"
+#include "xmdrun.h"
+#include "ionize.h"
+#include "disre.h"
+#include "orires.h"
+#include "pme.h"
+#include "mdatoms.h"
+#include "repl_ex.h"
+#include "qmmm.h"
+#include "domdec.h"
+#include "domdec_network.h"
+#include "partdec.h"
+#include "topsort.h"
+#include "coulomb.h"
+#include "constr.h"
+#include "shellfc.h"
+#include "compute_io.h"
+#include "mvdata.h"
+#include "checkpoint.h"
+#include "mtop_util.h"
+#include "sighandler.h"
+#include "txtdump.h"
+#include "string2.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 "gromacs/utility/gmxmpi.h"
+
+#ifdef GMX_FAHCORE
+#include "corewrap.h"
+#endif
+
+static void reset_all_counters(FILE *fplog, t_commrec *cr,
+ gmx_large_int_t step,
+ gmx_large_int_t *step_rel, t_inputrec *ir,
+ gmx_wallcycle_t wcycle, t_nrnb *nrnb,
+ gmx_runtime_t *runtime,
+ nbnxn_cuda_ptr_t cu_nbv)
+{
+ char sbuf[STEPSTRSIZE];
+
+ /* Reset all the counters related to performance over the run */
+ 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);
+ }
+
+ wallcycle_stop(wcycle, ewcRUN);
+ wallcycle_reset_all(wcycle);
+ if (DOMAINDECOMP(cr))
+ {
+ reset_dd_statistics_counters(cr->dd);
+ }
+ init_nrnb(nrnb);
+ ir->init_step += *step_rel;
+ ir->nsteps -= *step_rel;
+ *step_rel = 0;
+ wallcycle_start(wcycle, ewcRUN);
+ runtime_start(runtime);
+ print_date_and_time(fplog, cr->nodeid, "Restarted time", runtime);
+}
+
+double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
+ const output_env_t oenv, gmx_bool bVerbose, gmx_bool bCompact,
+ int nstglobalcomm,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ int stepout, t_inputrec *ir,
+ gmx_mtop_t *top_global,
+ t_fcdata *fcd,
+ t_state *state_global,
+ t_mdatoms *mdatoms,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_edsam_t ed, t_forcerec *fr,
+ int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t membed,
+ real cpt_period, real max_hours,
+ const char *deviceOptions,
+ unsigned long Flags,
+ gmx_runtime_t *runtime)
+{
+ gmx_mdoutf_t *outf;
+ gmx_large_int_t step, step_rel;
+ double run_time;
+ double t, t0, lam0[efptNR];
+ gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEner;
+ gmx_bool bNS, bNStList, bSimAnn, bStopCM, bRerunMD, bNotLastFrame = FALSE,
+ bFirstStep, bStateFromCP, bStateFromTPX, bInitStep, bLastStep,
+ bBornRadii, bStartingFromCpt;
+ gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
+ gmx_bool do_ene, do_log, do_verbose, bRerunWarnNoV = TRUE,
+ bForceUpdate = FALSE, bCPT;
+ int mdof_flags;
+ gmx_bool bMasterState;
+ int force_flags, cglo_flags;
+ tensor force_vir, shake_vir, total_vir, tmp_vir, pres;
+ int i, m;
+ t_trxstatus *status;
+ rvec mu_tot;
+ t_vcm *vcm;
+ t_state *bufstate = NULL;
+ matrix *scale_tot, pcoupl_mu, M, ebox;
+ gmx_nlheur_t nlh;
+ t_trxframe rerun_fr;
+ gmx_repl_ex_t repl_ex = NULL;
+ int nchkpt = 1;
+ gmx_localtop_t *top;
+ t_mdebin *mdebin = NULL;
+ df_history_t df_history;
+ t_state *state = NULL;
+ rvec *f_global = NULL;
+ int n_xtc = -1;
+ rvec *x_xtc = NULL;
+ gmx_enerdata_t *enerd;
+ rvec *f = NULL;
+ gmx_global_stat_t gstat;
+ gmx_update_t upd = NULL;
+ t_graph *graph = NULL;
+ globsig_t gs;
+ gmx_rng_t mcrng = NULL;
+ gmx_bool bFFscan;
+ gmx_groups_t *groups;
+ gmx_ekindata_t *ekind, *ekind_save;
+ gmx_shellfc_t shellfc;
+ int count, nconverged = 0;
+ real timestep = 0;
+ double tcount = 0;
+ gmx_bool bIonize = FALSE;
+ gmx_bool bTCR = FALSE, bConverged = TRUE, bOK, bSumEkinhOld, bExchanged;
+ gmx_bool bAppend;
+ gmx_bool bResetCountersHalfMaxH = FALSE;
+ gmx_bool bVV, bIterativeCase, bFirstIterate, bTemp, bPres, bTrotter;
+ gmx_bool bUpdateDoLR;
+ real mu_aver = 0, dvdl_constr;
+ int a0, a1, gnx = 0, ii;
+ atom_id *grpindex = NULL;
+ char *grpname;
+ t_coupl_rec *tcr = NULL;
+ rvec *xcopy = NULL, *vcopy = NULL, *cbuf = NULL;
+ matrix boxcopy = {{0}}, lastbox;
+ tensor tmpvir;
+ real fom, oldfom, veta_save, pcurr, scalevir, tracevir;
+ real vetanew = 0;
+ int lamnew = 0;
+ /* for FEP */
+ int nstfep;
+ real rate;
+ 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_large_int_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 */
+ pme_load_balancing_t pme_loadbal = NULL;
+ double cycles_pmes;
+ gmx_bool bPMETuneTry = FALSE, bPMETuneRunning = FALSE;
+
+#ifdef GMX_FAHCORE
+ /* Temporary addition for FAHCORE checkpointing */
+ int chkpt_ret;
+#endif
+
+ /* Check for special mdrun options */
+ bRerunMD = (Flags & MD_RERUN);
+ bIonize = (Flags & MD_IONIZE);
+ bFFscan = (Flags & MD_FFSCAN);
+ bAppend = (Flags & MD_APPENDFILES);
+ if (Flags & MD_RESETCOUNTERSHALFWAY)
+ {
+ if (ir->nsteps > 0)
+ {
+ /* Signal to reset the counters half the simulation steps. */
+ wcycle_set_reset_counters(wcycle, ir->nsteps/2);
+ }
+ /* Signal to reset the counters halfway the simulation time. */
+ bResetCountersHalfMaxH = (max_hours > 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);
+ if (bVV) /* to store the initial velocities while computing virial */
+ {
+ snew(cbuf, top_global->natoms);
+ }
+ /* 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.*/
+ bTrotter = (bVV && (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir) || IR_NVT_TROTTER(ir)));
+
+ if (bRerunMD)
+ {
+ /* Since we don't know if the frames read are related in any way,
+ * rebuild the neighborlist at every step.
+ */
+ ir->nstlist = 1;
+ ir->nstcalcenergy = 1;
+ nstglobalcomm = 1;
+ }
+
+ check_ir_old_tpx_versions(cr, fplog, ir, top_global);
+
+ nstglobalcomm = check_nstglobalcomm(fplog, cr, nstglobalcomm, ir);
+ bGStatEveryStep = (nstglobalcomm == 1);
+
+ if (!bGStatEveryStep && ir->nstlist == -1 && fplog != NULL)
+ {
+ fprintf(fplog,
+ "To reduce the energy communication with nstlist = -1\n"
+ "the neighbor list validity should not be checked at every step,\n"
+ "this means that exact integration is not guaranteed.\n"
+ "The neighbor list validity is checked after:\n"
+ " <n.list life time> - 2*std.dev.(n.list life time) steps.\n"
+ "In most cases this will result in exact integration.\n"
+ "This reduces the energy communication by a factor of 2 to 3.\n"
+ "If you want less energy communication, set nstlist > 3.\n\n");
+ }
+
+ if (bRerunMD || bFFscan)
+ {
+ ir->nstxtcout = 0;
+ }
+ groups = &top_global->groups;
+
+ /* Initial values */
+ init_md(fplog, cr, ir, oenv, &t, &t0, state_global->lambda,
+ &(state_global->fep_state), lam0,
+ nrnb, top_global, &upd,
+ nfile, fnm, &outf, &mdebin,
+ force_vir, shake_vir, mu_tot, &bSimAnn, &vcm, state_global, Flags);
+
+ clear_mat(total_vir);
+ clear_mat(pres);
+ /* Energy terms and groups */
+ snew(enerd, 1);
+ init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
+ enerd);
+ if (DOMAINDECOMP(cr))
+ {
+ f = NULL;
+ }
+ else
+ {
+ snew(f, top_global->natoms);
+ }
+
+ /* lambda Monte carlo random number generator */
+ if (ir->bExpanded)
+ {
+ mcrng = gmx_rng_init(ir->expandedvals->lmc_seed);
+ }
+ /* copy the state into df_history */
+ copy_df_history(&df_history, &state_global->dfhist);
+
+ /* Kinetic energy data */
+ snew(ekind, 1);
+ init_ekindata(fplog, top_global, &(ir->opts), ekind);
+ /* needed for iteration of constraints */
+ snew(ekind_save, 1);
+ init_ekindata(fplog, top_global, &(ir->opts), ekind_save);
+ /* Copy the cos acceleration to the groups struct */
+ ekind->cosacc.cos_accel = ir->cos_accel;
+
+ gstat = global_stat_init(ir);
+ debug_gmx();
+
+ /* Check for polarizable models and flexible constraints */
+ shellfc = init_shell_flexcon(fplog,
+ top_global, n_flexible_constraints(constr),
+ (ir->bContinuation ||
+ (DOMAINDECOMP(cr) && !MASTER(cr))) ?
+ NULL : state_global->x);
+
+ if (DEFORM(*ir))
+ {
+#ifdef GMX_THREAD_MPI
+ tMPI_Thread_mutex_lock(&deform_init_box_mutex);
+#endif
+ set_deform_reference_box(upd,
+ deform_init_init_step_tpx,
+ deform_init_box_tpx);
+#ifdef GMX_THREAD_MPI
+ tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
+#endif
+ }
+
+ {
+ double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
+ if ((io > 2000) && MASTER(cr))
+ {
+ fprintf(stderr,
+ "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
+ io);
+ }
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ top = dd_init_local_top(top_global);
+
+ snew(state, 1);
+ dd_init_local_state(cr->dd, state_global, state);
+
+ if (DDMASTER(cr->dd) && ir->nstfout)
+ {
+ snew(f_global, state_global->natoms);
+ }
+ }
+ else
+ {
+ if (PAR(cr))
+ {
+ /* Initialize the particle decomposition and split the topology */
+ top = split_system(fplog, top_global, ir, cr);
+
+ pd_cg_range(cr, &fr->cg0, &fr->hcg);
+ pd_at_range(cr, &a0, &a1);
+ }
+ else
+ {
+ top = gmx_mtop_generate_local_top(top_global, ir);
+
+ a0 = 0;
+ a1 = top_global->natoms;
+ }
+
+ forcerec_set_excl_load(fr, top, cr);
+
+ state = partdec_init_local_state(cr, state_global);
+ f_global = f;
+
+ atoms2md(top_global, ir, 0, NULL, a0, a1-a0, mdatoms);
+
+ if (vsite)
+ {
+ set_vsite_top(vsite, top, mdatoms, cr);
+ }
+
+ if (ir->ePBC != epbcNONE && !fr->bMolPBC)
+ {
+ graph = mk_graph(fplog, &(top->idef), 0, top_global->natoms, FALSE, FALSE);
+ }
+
+ if (shellfc)
+ {
+ make_local_shells(cr, mdatoms, shellfc);
+ }
+
+ init_bonded_thread_force_reduction(fr, &top->idef);
+
+ if (ir->pull && PAR(cr))
+ {
+ dd_make_local_pull_groups(NULL, ir->pull, mdatoms);
+ }
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ /* Distribute the charge groups over the nodes from the master node */
+ dd_partition_system(fplog, ir->init_step, cr, TRUE, 1,
+ state_global, top_global, ir,
+ state, &f, mdatoms, top, fr,
+ vsite, shellfc, constr,
+ nrnb, wcycle, FALSE);
+
+ }
+
+ update_mdatoms(mdatoms, state->lambda[efptMASS]);
+
+ if (opt2bSet("-cpi", nfile, fnm))
+ {
+ bStateFromCP = gmx_fexist_master(opt2fn_master("-cpi", nfile, fnm, cr), cr);
+ }
+ else
+ {
+ bStateFromCP = FALSE;
+ }
+
+ if (MASTER(cr))
+ {
+ if (bStateFromCP)
+ {
+ /* Update mdebin with energy history if appending to output files */
+ if (Flags & MD_APPENDFILES)
+ {
+ restore_energyhistory_from_state(mdebin, &state_global->enerhist);
+ }
+ else
+ {
+ /* We might have read an energy history from checkpoint,
+ * free the allocated memory and reset the counts.
+ */
+ done_energyhistory(&state_global->enerhist);
+ init_energyhistory(&state_global->enerhist);
+ }
+ }
+ /* Set the initial energy history in state by updating once */
+ update_energyhistory(&state_global->enerhist, mdebin);
+ }
+
+ if ((state->flags & (1<<estLD_RNG)) && (Flags & MD_READ_RNG))
+ {
+ /* Set the random state if we read a checkpoint file */
+ set_stochd_state(upd, state);
+ }
+
+ if (state->flags & (1<<estMC_RNG))
+ {
+ set_mc_state(mcrng, state);
+ }
+
+ /* Initialize constraints */
+ if (constr)
+ {
+ if (!DOMAINDECOMP(cr))
+ {
+ set_constraints(constr, top, ir, mdatoms, cr);
+ }
+ }
+
+ /* Check whether we have to GCT stuff */
+ bTCR = ftp2bSet(efGCT, nfile, fnm);
+ if (bTCR)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "Will do General Coupling Theory!\n");
+ }
+ gnx = top_global->mols.nr;
+ snew(grpindex, gnx);
+ for (i = 0; (i < gnx); i++)
+ {
+ grpindex[i] = i;
+ }
+ }
+
+ if (repl_ex_nst > 0)
+ {
+ /* We need to be sure replica exchange can only occur
+ * when the energies are current */
+ check_nst_param(fplog, cr, "nstcalcenergy", ir->nstcalcenergy,
+ "repl_ex_nst", &repl_ex_nst);
+ /* This check needs to happen before inter-simulation
+ * signals are initialized, too */
+ }
+ if (repl_ex_nst > 0 && MASTER(cr))
+ {
+ repl_ex = init_replica_exchange(fplog, cr->ms, state_global, ir,
+ repl_ex_nst, repl_ex_nex, repl_ex_seed);
+ }
+
+ /* PME tuning is only supported with GPUs or PME nodes and not with rerun.
+ * With perturbed charges with soft-core we should not change the cut-off.
+ */
+ if ((Flags & MD_TUNEPME) &&
+ EEL_PME(fr->eeltype) &&
+ ( (fr->cutoff_scheme == ecutsVERLET && fr->nbv->bUseGPU) || !(cr->duty & DUTY_PME)) &&
+ !(ir->efep != efepNO && mdatoms->nChargePerturbed > 0 && ir->fepvals->bScCoul) &&
+ !bRerunMD)
+ {
+ pme_loadbal_init(&pme_loadbal, ir, state->box, fr->ic, fr->pmedata);
+ cycles_pmes = 0;
+ if (cr->duty & DUTY_PME)
+ {
+ /* Start tuning right away, as we can't measure the load */
+ bPMETuneRunning = TRUE;
+ }
+ else
+ {
+ /* Separate PME nodes, we can measure the PP/PME load balance */
+ bPMETuneTry = TRUE;
+ }
+ }
+
+ if (!ir->bContinuation && !bRerunMD)
+ {
+ if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
+ {
+ /* Set the velocities of frozen particles to zero */
+ for (i = mdatoms->start; i < mdatoms->start+mdatoms->homenr; i++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
+ {
+ state->v[i][m] = 0;
+ }
+ }
+ }
+ }
+
+ if (constr)
+ {
+ /* Constrain the initial coordinates and velocities */
+ do_constrain_first(fplog, constr, ir, mdatoms, state, f,
+ graph, cr, nrnb, fr, top, shake_vir);
+ }
+ if (vsite)
+ {
+ /* Construct the virtual sites for the initial configuration */
+ construct_vsites(fplog, vsite, state->x, nrnb, ir->delta_t, NULL,
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, graph, cr, state->box);
+ }
+ }
+
+ debug_gmx();
+
+ /* set free energy calculation frequency as the minimum of nstdhdl, nstexpanded, and nstrepl_ex_nst*/
+ nstfep = ir->fepvals->nstdhdl;
+ if (ir->bExpanded && (nstfep > ir->expandedvals->nstexpanded))
+ {
+ nstfep = ir->expandedvals->nstexpanded;
+ }
+ if (repl_ex_nst > 0 && nstfep > repl_ex_nst)
+ {
+ nstfep = repl_ex_nst;
+ }
+
+ /* I'm assuming we need global communication the first time! MRS */
+ cglo_flags = (CGLO_TEMPERATURE | CGLO_GSTAT
+ | ((ir->comm_mode != ecmNO) ? CGLO_STOPCM : 0)
+ | (bVV ? CGLO_PRESSURE : 0)
+ | (bVV ? CGLO_CONSTRAINT : 0)
+ | (bRerunMD ? CGLO_RERUNMD : 0)
+ | ((Flags & MD_READ_EKIN) ? CGLO_READEKIN : 0));
+
+ bSumEkinhOld = FALSE;
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld, cglo_flags);
+ if (ir->eI == eiVVAK)
+ {
+ /* a second call to get the half step temperature initialized as well */
+ /* we do the same call as above, but turn the pressure off -- internally to
+ compute_globals, this is recognized as a velocity verlet half-step
+ kinetic energy calculation. This minimized excess variables, but
+ perhaps loses some logic?*/
+
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ cglo_flags &~(CGLO_STOPCM | CGLO_PRESSURE));
+ }
+
+ /* Calculate the initial half step temperature, and save the ekinh_old */
+ if (!(Flags & MD_STARTFROMCPT))
+ {
+ for (i = 0; (i < ir->opts.ngtc); i++)
+ {
+ copy_mat(ekind->tcstat[i].ekinh, ekind->tcstat[i].ekinh_old);
+ }
+ }
+ if (ir->eI != eiVV)
+ {
+ enerd->term[F_TEMP] *= 2; /* result of averages being done over previous and current step,
+ 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);
+ }
+ if (bFFscan)
+ {
+ snew(xcopy, state->natoms);
+ snew(vcopy, state->natoms);
+ copy_rvecn(state->x, xcopy, 0, state->natoms);
+ copy_rvecn(state->v, vcopy, 0, state->natoms);
+ copy_mat(state->box, boxcopy);
+ }
+
+ /* 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);
+
+ if (MASTER(cr))
+ {
+ if (constr && !ir->bContinuation && ir->eConstrAlg == econtLINCS)
+ {
+ fprintf(fplog,
+ "RMS relative constraint deviation after constraining: %.2e\n",
+ constr_rmsd(constr, FALSE));
+ }
+ if (EI_STATE_VELOCITY(ir->eI))
+ {
+ fprintf(fplog, "Initial temperature: %g K\n", enerd->term[F_TEMP]);
+ }
+ if (bRerunMD)
+ {
+ fprintf(stderr, "starting md rerun '%s', reading coordinates from"
+ " input trajectory '%s'\n\n",
+ *(top_global->name), opt2fn("-rerun", nfile, fnm));
+ if (bVerbose)
+ {
+ fprintf(stderr, "Calculated time to finish depends on nsteps from "
+ "run input file,\nwhich may not correspond to the time "
+ "needed to process input trajectory.\n\n");
+ }
+ }
+ else
+ {
+ char tbuf[20];
+ fprintf(stderr, "starting mdrun '%s'\n",
+ *(top_global->name));
+ if (ir->nsteps >= 0)
+ {
+ sprintf(tbuf, "%8.1f", (ir->init_step+ir->nsteps)*ir->delta_t);
+ }
+ else
+ {
+ sprintf(tbuf, "%s", "infinite");
+ }
+ if (ir->init_step > 0)
+ {
+ fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
+ gmx_step_str(ir->init_step+ir->nsteps, sbuf), tbuf,
+ gmx_step_str(ir->init_step, sbuf2),
+ ir->init_step*ir->delta_t);
+ }
+ else
+ {
+ fprintf(stderr, "%s steps, %s ps.\n",
+ gmx_step_str(ir->nsteps, sbuf), tbuf);
+ }
+ }
+ fprintf(fplog, "\n");
+ }
+
+ /* Set and write start time */
+ runtime_start(runtime);
+ print_date_and_time(fplog, cr->nodeid, "Started mdrun", runtime);
+ wallcycle_start(wcycle, ewcRUN);
+ if (fplog)
+ {
+ fprintf(fplog, "\n");
+ }
+
+ /* safest point to do file checkpointing is here. More general point would be immediately before integrator call */
+#ifdef GMX_FAHCORE
+ chkpt_ret = fcCheckPointParallel( cr->nodeid,
+ NULL, 0);
+ if (chkpt_ret == 0)
+ {
+ gmx_fatal( 3, __FILE__, __LINE__, "Checkpoint error on step %d\n", 0 );
+ }
+#endif
+
+ debug_gmx();
+ /***********************************************************
+ *
+ * Loop over MD steps
+ *
+ ************************************************************/
+
+ /* if rerunMD then read coordinates and velocities from input trajectory */
+ if (bRerunMD)
+ {
+ if (getenv("GMX_FORCE_UPDATE"))
+ {
+ bForceUpdate = TRUE;
+ }
+
+ rerun_fr.natoms = 0;
+ if (MASTER(cr))
+ {
+ bNotLastFrame = read_first_frame(oenv, &status,
+ opt2fn("-rerun", nfile, fnm),
+ &rerun_fr, TRX_NEED_X | TRX_READ_V);
+ if (rerun_fr.natoms != top_global->natoms)
+ {
+ gmx_fatal(FARGS,
+ "Number of atoms in trajectory (%d) does not match the "
+ "run input file (%d)\n",
+ rerun_fr.natoms, top_global->natoms);
+ }
+ if (ir->ePBC != epbcNONE)
+ {
+ if (!rerun_fr.bBox)
+ {
+ gmx_fatal(FARGS, "Rerun trajectory frame step %d time %f does not contain a box, while pbc is used", rerun_fr.step, rerun_fr.time);
+ }
+ if (max_cutoff2(ir->ePBC, rerun_fr.box) < sqr(fr->rlistlong))
+ {
+ gmx_fatal(FARGS, "Rerun trajectory frame step %d time %f has too small box dimensions", rerun_fr.step, rerun_fr.time);
+ }
+ }
+ }
+
+ if (PAR(cr))
+ {
+ rerun_parallel_comm(cr, &rerun_fr, &bNotLastFrame);
+ }
+
+ if (ir->ePBC != epbcNONE)
+ {
+ /* Set the shift vectors.
+ * Necessary here when have a static box different from the tpr box.
+ */
+ calc_shifts(rerun_fr.box, fr->shift_vec);
+ }
+ }
+
+ /* loop over MD steps or if rerunMD to end of input trajectory */
+ bFirstStep = TRUE;
+ /* Skip the first Nose-Hoover integration when we get the state from tpx */
+ bStateFromTPX = !bStateFromCP;
+ bInitStep = bFirstStep && (bStateFromTPX || bVV);
+ bStartingFromCpt = (Flags & MD_STARTFROMCPT) && bInitStep;
+ bLastStep = FALSE;
+ bSumEkinhOld = FALSE;
+ bExchanged = FALSE;
+
+ init_global_signals(&gs, cr, ir, repl_ex_nst);
+
+ 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 */
+ multisim_nsteps = get_multisim_nsteps(cr, ir->nsteps);
+ }
+
+
+ /* and stop now if we should */
+ bLastStep = (bRerunMD || (ir->nsteps >= 0 && step_rel > ir->nsteps) ||
+ ((multisim_nsteps >= 0) && (step_rel >= multisim_nsteps )));
+ while (!bLastStep || (bRerunMD && bNotLastFrame))
+ {
+
+ wallcycle_start(wcycle, ewcSTEP);
+
+ if (bRerunMD)
+ {
+ if (rerun_fr.bStep)
+ {
+ step = rerun_fr.step;
+ step_rel = step - ir->init_step;
+ }
+ if (rerun_fr.bTime)
+ {
+ t = rerun_fr.time;
+ }
+ else
+ {
+ t = step;
+ }
+ }
+ else
+ {
+ bLastStep = (step_rel == ir->nsteps);
+ t = t0 + step*ir->delta_t;
+ }
+
+ if (ir->efep != efepNO || ir->bSimTemp)
+ {
+ /* find and set the current lambdas. If rerunning, we either read in a state, or a lambda value,
+ requiring different logic. */
+
+ set_current_lambdas(step, ir->fepvals, bRerunMD, &rerun_fr, state_global, state, lam0);
+ bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
+ bDoFEP = (do_per_step(step, nstfep) && (ir->efep != efepNO));
+ bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded) && (ir->bExpanded) && (step > 0));
+ }
+
+ if (bSimAnn)
+ {
+ update_annealing_target_temp(&(ir->opts), t);
+ }
+
+ if (bRerunMD)
+ {
+ if (!(DOMAINDECOMP(cr) && !MASTER(cr)))
+ {
+ for (i = 0; i < state_global->natoms; i++)
+ {
+ copy_rvec(rerun_fr.x[i], state_global->x[i]);
+ }
+ if (rerun_fr.bV)
+ {
+ for (i = 0; i < state_global->natoms; i++)
+ {
+ copy_rvec(rerun_fr.v[i], state_global->v[i]);
+ }
+ }
+ else
+ {
+ for (i = 0; i < state_global->natoms; i++)
+ {
+ clear_rvec(state_global->v[i]);
+ }
+ if (bRerunWarnNoV)
+ {
+ fprintf(stderr, "\nWARNING: Some frames do not contain velocities.\n"
+ " Ekin, temperature and pressure are incorrect,\n"
+ " the virial will be incorrect when constraints are present.\n"
+ "\n");
+ bRerunWarnNoV = FALSE;
+ }
+ }
+ }
+ copy_mat(rerun_fr.box, state_global->box);
+ copy_mat(state_global->box, state->box);
+
+ if (vsite && (Flags & MD_RERUN_VSITE))
+ {
+ if (DOMAINDECOMP(cr))
+ {
+ gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented for domain decomposition, use particle decomposition");
+ }
+ if (graph)
+ {
+ /* Following is necessary because the graph may get out of sync
+ * with the coordinates if we only have every N'th coordinate set
+ */
+ mk_mshift(fplog, graph, fr->ePBC, state->box, state->x);
+ shift_self(graph, state->box, state->x);
+ }
+ construct_vsites(fplog, vsite, state->x, nrnb, ir->delta_t, state->v,
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, graph, cr, state->box);
+ if (graph)
+ {
+ unshift_self(graph, state->box, state->x);
+ }
+ }
+ }
+
+ /* Stop Center of Mass motion */
+ bStopCM = (ir->comm_mode != ecmNO && do_per_step(step, ir->nstcomm));
+
+ /* Copy back starting coordinates in case we're doing a forcefield scan */
+ if (bFFscan)
+ {
+ for (ii = 0; (ii < state->natoms); ii++)
+ {
+ copy_rvec(xcopy[ii], state->x[ii]);
+ copy_rvec(vcopy[ii], state->v[ii]);
+ }
+ copy_mat(boxcopy, state->box);
+ }
+
+ if (bRerunMD)
+ {
+ /* for rerun MD always do Neighbour Searching */
+ bNS = (bFirstStep || ir->nstlist != 0);
+ bNStList = bNS;
+ }
+ else
+ {
+ /* Determine whether or not to do Neighbour Searching and LR */
+ bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
+
+ bNS = (bFirstStep || bExchanged || bNStList || bDoFEP ||
+ (ir->nstlist == -1 && nlh.nabnsb > 0));
+
+ if (bNS && ir->nstlist == -1)
+ {
+ set_nlistheuristics(&nlh, bFirstStep || bExchanged || bDoFEP, step);
+ }
+ }
+
+ /* check whether we should stop because another simulation has
+ stopped. */
+ if (MULTISIM(cr))
+ {
+ if ( (multisim_nsteps >= 0) && (step_rel >= multisim_nsteps) &&
+ (multisim_nsteps != ir->nsteps) )
+ {
+ if (bNS)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr,
+ "Stopping simulation %d because another one has finished\n",
+ cr->ms->sim);
+ }
+ bLastStep = TRUE;
+ gs.sig[eglsCHKPT] = 1;
+ }
+ }
+ }
+
+ /* < 0 means stop at next step, > 0 means stop at next NS step */
+ if ( (gs.set[eglsSTOPCOND] < 0 ) ||
+ ( (gs.set[eglsSTOPCOND] > 0 ) && ( bNS || ir->nstlist == 0)) )
+ {
+ bLastStep = TRUE;
+ }
+
+ /* Determine whether or not to update the Born radii if doing GB */
+ bBornRadii = bFirstStep;
+ if (ir->implicit_solvent && (step % ir->nstgbradii == 0))
+ {
+ bBornRadii = TRUE;
+ }
+
+ do_log = do_per_step(step, ir->nstlog) || bFirstStep || bLastStep;
+ do_verbose = bVerbose &&
+ (step % stepout == 0 || bFirstStep || bLastStep);
+
+ if (bNS && !(bFirstStep && ir->bContinuation && !bRerunMD))
+ {
+ if (bRerunMD)
+ {
+ bMasterState = TRUE;
+ }
+ else
+ {
+ bMasterState = FALSE;
+ /* Correct the new box if it is too skewed */
+ if (DYNAMIC_BOX(*ir))
+ {
+ if (correct_box(fplog, step, state->box, graph))
+ {
+ bMasterState = TRUE;
+ }
+ }
+ if (DOMAINDECOMP(cr) && bMasterState)
+ {
+ dd_collect_state(cr->dd, state, state_global);
+ }
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ /* Repartition the domain decomposition */
+ wallcycle_start(wcycle, ewcDOMDEC);
+ dd_partition_system(fplog, step, cr,
+ bMasterState, nstglobalcomm,
+ state_global, top_global, ir,
+ state, &f, mdatoms, top, fr,
+ vsite, shellfc, constr,
+ nrnb, wcycle,
+ do_verbose && !bPMETuneRunning);
+ wallcycle_stop(wcycle, ewcDOMDEC);
+ /* If using an iterative integrator, reallocate space to match the decomposition */
+ }
+ }
+
+ if (MASTER(cr) && do_log && !bFFscan)
+ {
+ print_ebin_header(fplog, step, t, state->lambda[efptFEP]); /* can we improve the information printed here? */
+ }
+
+ if (ir->efep != efepNO)
+ {
+ update_mdatoms(mdatoms, state->lambda[efptMASS]);
+ }
+
+ if ((bRerunMD && rerun_fr.bV) || bExchanged)
+ {
+
+ /* We need the kinetic energy at minus the half step for determining
+ * the full step kinetic energy and possibly for T-coupling.*/
+ /* This may not be quite working correctly yet . . . . */
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
+ }
+ clear_mat(force_vir);
+
+ /* Ionize the atoms if necessary */
+ if (bIonize)
+ {
+ ionize(fplog, oenv, mdatoms, top_global, t, ir, state->x, state->v,
+ mdatoms->start, mdatoms->start+mdatoms->homenr, state->box, cr);
+ }
+
+ /* Update force field in ffscan program */
+ if (bFFscan)
+ {
+ if (update_forcefield(fplog,
+ nfile, fnm, fr,
+ mdatoms->nr, state->x, state->box))
+ {
+ gmx_finalize_par();
+
+ exit(0);
+ }
+ }
+
+ /* We write a checkpoint at this MD step when:
+ * either at an NS step when we signalled through gs,
+ * or at the last step (but not when we do not want confout),
+ * but never at the first step or with rerun.
+ */
+ bCPT = (((gs.set[eglsCHKPT] && (bNS || ir->nstlist == 0)) ||
+ (bLastStep && (Flags & MD_CONFOUT))) &&
+ step > ir->init_step && !bRerunMD);
+ if (bCPT)
+ {
+ gs.set[eglsCHKPT] = 0;
+ }
+
+ /* Determine the energy and pressure:
+ * at nstcalcenergy steps and at energy output steps (set below).
+ */
+ if (EI_VV(ir->eI) && (!bInitStep))
+ {
+ /* for vv, the first half of the integration actually corresponds
+ to the previous step. bCalcEner is only required to be evaluated on the 'next' step,
+ but the virial needs to be calculated on both the current step and the 'next' step. Future
+ reorganization may be able to get rid of one of the bCalcVir=TRUE steps. */
+
+ bCalcEner = do_per_step(step-1, ir->nstcalcenergy);
+ bCalcVir = bCalcEner ||
+ (ir->epc != epcNO && (do_per_step(step, ir->nstpcouple) || do_per_step(step-1, ir->nstpcouple)));
+ }
+ else
+ {
+ bCalcEner = do_per_step(step, ir->nstcalcenergy);
+ bCalcVir = bCalcEner ||
+ (ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
+ }
+
+ /* 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_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
+
+ if (do_ene || do_log)
+ {
+ bCalcVir = TRUE;
+ bCalcEner = TRUE;
+ bGStat = TRUE;
+ }
+
+ /* these CGLO_ options remain the same throughout the iteration */
+ cglo_flags = ((bRerunMD ? CGLO_RERUNMD : 0) |
+ (bGStat ? CGLO_GSTAT : 0)
+ );
+
+ force_flags = (GMX_FORCE_STATECHANGED |
+ ((DYNAMIC_BOX(*ir) || bRerunMD) ? GMX_FORCE_DYNAMICBOX : 0) |
+ GMX_FORCE_ALLFORCES |
+ GMX_FORCE_SEPLRF |
+ (bCalcVir ? GMX_FORCE_VIRIAL : 0) |
+ (bCalcEner ? GMX_FORCE_ENERGY : 0) |
+ (bDoFEP ? GMX_FORCE_DHDL : 0)
+ );
+
+ if (fr->bTwinRange)
+ {
+ if (do_per_step(step, ir->nstcalclr))
+ {
+ force_flags |= GMX_FORCE_DO_LR;
+ }
+ }
+
+ if (shellfc)
+ {
+ /* Now is the time to relax the shells */
+ count = relax_shell_flexcon(fplog, cr, bVerbose, bFFscan ? step+1 : step,
+ ir, bNS, force_flags,
+ bStopCM, top, top_global,
+ constr, enerd, fcd,
+ state, f, force_vir, mdatoms,
+ nrnb, wcycle, graph, groups,
+ shellfc, fr, bBornRadii, t, mu_tot,
+ state->natoms, &bConverged, vsite,
+ outf->fp_field);
+ tcount += count;
+
+ if (bConverged)
+ {
+ nconverged++;
+ }
+ }
+ else
+ {
+ /* The coordinates (x) are shifted (to get whole molecules)
+ * in do_force.
+ * This is parallellized as well, and does communication too.
+ * Check comments in sim_util.c
+ */
+ do_force(fplog, cr, ir, step, nrnb, wcycle, top, top_global, groups,
+ state->box, state->x, &state->hist,
+ f, force_vir, mdatoms, enerd, fcd,
+ state->lambda, graph,
+ fr, vsite, mu_tot, t, outf->fp_field, ed, bBornRadii,
+ (bNS ? GMX_FORCE_NS : 0) | force_flags);
+ }
+
+ if (bTCR)
+ {
+ mu_aver = calc_mu_aver(cr, state->x, mdatoms->chargeA,
+ mu_tot, &top_global->mols, mdatoms, gnx, grpindex);
+ }
+
+ if (bTCR && bFirstStep)
+ {
+ tcr = init_coupling(fplog, nfile, fnm, cr, fr, mdatoms, &(top->idef));
+ fprintf(fplog, "Done init_coupling\n");
+ fflush(fplog);
+ }
+
+ if (bVV && !bStartingFromCpt && !bRerunMD)
+ /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
+ {
+ if (ir->eI == eiVV && bInitStep)
+ {
+ /* if using velocity verlet with full time step Ekin,
+ * take the first half step only to compute the
+ * virial for the first step. From there,
+ * revert back to the initial coordinates
+ * so that the input is actually the initial step.
+ */
+ copy_rvecn(state->v, cbuf, 0, state->natoms); /* should make this better for parallelizing? */
+ }
+ else
+ {
+ /* this is for NHC in the Ekin(t+dt/2) version of vv */
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ1);
+ }
+
+ /* If we are using twin-range interactions where the long-range component
+ * is only evaluated every nstcalclr>1 steps, we should do a special update
+ * step to combine the long-range forces on these steps.
+ * For nstcalclr=1 this is not done, since the forces would have been added
+ * directly to the short-range forces already.
+ */
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+ update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC,
+ f, bUpdateDoLR, fr->f_twin, fcd,
+ ekind, M, wcycle, 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)
+ {
+ 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. */
+ {
+ update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+ state, fr->bMolPBC, graph, f,
+ &top->idef, shake_vir, NULL,
+ cr, nrnb, wcycle, upd, constr,
+ bInitStep, TRUE, bCalcVir, vetanew);
+
+ if (!bOK && !bFFscan)
+ {
+ gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
+ }
+
+ }
+ else if (graph)
+ {
+ /* Need to unshift here if a do_force has been
+ 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
+ * printed out.
+ * Think about ways around this in the future?
+ * For now, keep this choice in comments.
+ */
+ /*bPres = (ir->eI==eiVV || IR_NPT_TROTTER(ir)); */
+ /*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?*/
+ {
+ bSumEkinhOld = TRUE;
+ }
+ /* for vv, the first half of the integration actually corresponds to the previous step.
+ So we need information from the last step in the first half of the integration */
+ if (bGStat || do_per_step(step-1, nstglobalcomm))
+ {
+ 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, NULL, FALSE, state->box,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ cglo_flags
+ | CGLO_ENERGY
+ | (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:
+ a) We compute Ekin at the full time step
+ if 1) we are using the AveVel Ekin, and it's not the
+ initial step, or 2) if we are using AveEkin, but need the full
+ time step kinetic energy for the pressure (always true now, since we want accurate statistics).
+ b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
+ EkinAveVel because it's needed for the pressure */
+ }
+ /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
+ if (!bInitStep)
+ {
+ if (bTrotter)
+ {
+ m_add(force_vir, shake_vir, total_vir); /* we need the un-dispersion corrected total vir here */
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ2);
+ }
+ else
+ {
+ if (bExchanged)
+ {
+
+ /* We need the kinetic energy at minus the half step for determining
+ * the full step kinetic energy and possibly for T-coupling.*/
+ /* This may not be quite working correctly yet . . . . */
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
+ }
+ }
+ }
+
+ if (iterate.bIterationActive &&
+ done_iterating(cr, fplog, step, &iterate, bFirstIterate,
+ state->veta, &vetanew))
+ {
+ break;
+ }
+ bFirstIterate = FALSE;
+ }
+
+ if (bTrotter && !bInitStep)
+ {
+ copy_mat(shake_vir, state->svir_prev);
+ copy_mat(force_vir, state->fvir_prev);
+ if (IR_NVT_TROTTER(ir) && ir->eI == eiVV)
+ {
+ /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
+ enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, NULL, (ir->eI == eiVV), FALSE, FALSE);
+ enerd->term[F_EKIN] = trace(ekind->ekin);
+ }
+ }
+ /* if it's the initial step, we performed this first step just to get the constraint virial */
+ if (bInitStep && ir->eI == eiVV)
+ {
+ copy_rvecn(cbuf, state->v, 0, state->natoms);
+ }
+ }
+
+ /* MRS -- now done iterating -- compute the conserved quantity */
+ if (bVV)
+ {
+ saved_conserved_quantity = compute_conserved_from_auxiliary(ir, state, &MassQ);
+ if (ir->eI == eiVV)
+ {
+ last_ekin = enerd->term[F_EKIN];
+ }
+ if ((ir->eDispCorr != edispcEnerPres) && (ir->eDispCorr != edispcAllEnerPres))
+ {
+ saved_conserved_quantity -= enerd->term[F_DISPCORR];
+ }
+ /* sum up the foreign energy and dhdl terms for vv. currently done every step so that dhdl is correct in the .edr */
+ if (!bRerunMD)
+ {
+ sum_dhdl(enerd, state->lambda, ir->fepvals);
+ }
+ }
+
+ /* ######## END FIRST UPDATE STEP ############## */
+ /* ######## If doing VV, we now have v(dt) ###### */
+ if (bDoExpanded)
+ {
+ /* perform extended ensemble sampling in lambda - we don't
+ actually move to the new state before outputting
+ statistics, but if performing simulated tempering, we
+ do update the velocities and the tau_t. */
+
+ lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, &df_history, step, mcrng, state->v, mdatoms);
+ }
+ /* ################## START TRAJECTORY OUTPUT ################# */
+
+ /* Now we have the energies and forces corresponding to the
+ * coordinates at time t. We must output all of this before
+ * the update.
+ * for RerunMD t is read from input trajectory
+ */
+ mdof_flags = 0;
+ if (do_per_step(step, ir->nstxout))
+ {
+ mdof_flags |= MDOF_X;
+ }
+ if (do_per_step(step, ir->nstvout))
+ {
+ mdof_flags |= MDOF_V;
+ }
+ if (do_per_step(step, ir->nstfout))
+ {
+ mdof_flags |= MDOF_F;
+ }
+ if (do_per_step(step, ir->nstxtcout))
+ {
+ mdof_flags |= MDOF_XTC;
+ }
+ if (bCPT)
+ {
+ mdof_flags |= MDOF_CPT;
+ }
+ ;
+
+#if defined(GMX_FAHCORE) || defined(GMX_WRITELASTSTEP)
+ if (bLastStep)
+ {
+ /* Enforce writing positions and velocities at end of run */
+ mdof_flags |= (MDOF_X | MDOF_V);
+ }
+#endif
+#ifdef GMX_FAHCORE
+ if (MASTER(cr))
+ {
+ fcReportProgress( ir->nsteps, step );
+ }
+
+ /* sync bCPT and fc record-keeping */
+ if (bCPT && MASTER(cr))
+ {
+ fcRequestCheckPoint();
+ }
+#endif
+
+ if (mdof_flags != 0)
+ {
+ wallcycle_start(wcycle, ewcTRAJ);
+ if (bCPT)
+ {
+ if (state->flags & (1<<estLD_RNG))
+ {
+ get_stochd_state(upd, state);
+ }
+ if (state->flags & (1<<estMC_RNG))
+ {
+ get_mc_state(mcrng, state);
+ }
+ if (MASTER(cr))
+ {
+ if (bSumEkinhOld)
+ {
+ state_global->ekinstate.bUpToDate = FALSE;
+ }
+ else
+ {
+ update_ekinstate(&state_global->ekinstate, ekind);
+ state_global->ekinstate.bUpToDate = TRUE;
+ }
+ update_energyhistory(&state_global->enerhist, mdebin);
+ if (ir->efep != efepNO || ir->bSimTemp)
+ {
+ state_global->fep_state = state->fep_state; /* MRS: seems kludgy. The code should be
+ structured so this isn't necessary.
+ Note this reassignment is only necessary
+ for single threads.*/
+ copy_df_history(&state_global->dfhist, &df_history);
+ }
+ }
+ }
+ write_traj(fplog, cr, outf, mdof_flags, top_global,
+ step, t, state, state_global, f, f_global, &n_xtc, &x_xtc);
+ if (bCPT)
+ {
+ nchkpt++;
+ bCPT = FALSE;
+ }
+ debug_gmx();
+ if (bLastStep && step_rel == ir->nsteps &&
+ (Flags & MD_CONFOUT) && MASTER(cr) &&
+ !bRerunMD && !bFFscan)
+ {
+ /* x and v have been collected in write_traj,
+ * because a checkpoint file will always be written
+ * at the last step.
+ */
+ fprintf(stderr, "\nWriting final coordinates.\n");
+ if (fr->bMolPBC)
+ {
+ /* Make molecules whole only for confout writing */
+ do_pbc_mtop(fplog, ir->ePBC, state->box, top_global, state_global->x);
+ }
+ write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
+ *top_global->name, top_global,
+ state_global->x, state_global->v,
+ ir->ePBC, state->box);
+ debug_gmx();
+ }
+ wallcycle_stop(wcycle, ewcTRAJ);
+ }
+
+ /* kludge -- virial is lost with restart for NPT control. Must restart */
+ if (bStartingFromCpt && bVV)
+ {
+ copy_mat(state->svir_prev, shake_vir);
+ copy_mat(state->fvir_prev, force_vir);
+ }
+ /* ################## END TRAJECTORY OUTPUT ################ */
+
+ /* Determine the wallclock run time up till now */
+ run_time = gmx_gettime() - (double)runtime->real;
+
+ /* Check whether everything is still allright */
+ if (((int)gmx_get_stop_condition() > handled_stop_condition)
+#ifdef GMX_THREAD_MPI
+ && MASTER(cr)
+#endif
+ )
+ {
+ /* this is just make gs.sig compatible with the hack
+ of sending signals around by MPI_Reduce with together with
+ other floats */
+ if (gmx_get_stop_condition() == gmx_stop_cond_next_ns)
+ {
+ gs.sig[eglsSTOPCOND] = 1;
+ }
+ if (gmx_get_stop_condition() == gmx_stop_cond_next)
+ {
+ gs.sig[eglsSTOPCOND] = -1;
+ }
+ /* < 0 means stop at next step, > 0 means stop at next NS step */
+ if (fplog)
+ {
+ fprintf(fplog,
+ "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
+ gmx_get_signal_name(),
+ gs.sig[eglsSTOPCOND] == 1 ? "NS " : "");
+ fflush(fplog);
+ }
+ fprintf(stderr,
+ "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
+ gmx_get_signal_name(),
+ gs.sig[eglsSTOPCOND] == 1 ? "NS " : "");
+ fflush(stderr);
+ handled_stop_condition = (int)gmx_get_stop_condition();
+ }
+ else if (MASTER(cr) && (bNS || ir->nstlist <= 0) &&
+ (max_hours > 0 && run_time > max_hours*60.0*60.0*0.99) &&
+ gs.sig[eglsSTOPCOND] == 0 && gs.set[eglsSTOPCOND] == 0)
+ {
+ /* Signal to terminate the run */
+ gs.sig[eglsSTOPCOND] = 1;
+ if (fplog)
+ {
+ fprintf(fplog, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
+ }
+ fprintf(stderr, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
+ }
+
+ if (bResetCountersHalfMaxH && MASTER(cr) &&
+ run_time > max_hours*60.0*60.0*0.495)
+ {
+ 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 (MASTER(cr) && ((bGStat || !PAR(cr)) &&
+ cpt_period >= 0 &&
+ (cpt_period == 0 ||
+ run_time >= nchkpt*cpt_period*60.0)) &&
+ gs.set[eglsCHKPT] == 0)
+ {
+ gs.sig[eglsCHKPT] = 1;
+ }
+
+ /* at the start of step, randomize or scale the velocities (trotter done elsewhere) */
+ if (EI_VV(ir->eI))
+ {
+ if (!bInitStep)
+ {
+ update_tcouple(fplog, step, ir, state, ekind, wcycle, upd, &MassQ, mdatoms);
+ }
+ if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
+ {
+ gmx_bool bIfRandomize;
+ bIfRandomize = update_randomize_velocities(ir, step, mdatoms, state, upd, &top->idef, constr);
+ /* 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,
+ state, fr->bMolPBC, graph, f,
+ &top->idef, tmp_vir, NULL,
+ cr, nrnb, wcycle, upd, constr,
+ bInitStep, TRUE, bCalcVir, vetanew);
+ }
+ }
+ }
+
+ 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)
+ {
+ /* 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
+ * writing it to the energy file, so it matches the trajectory files for
+ * the same timestep above. Make a copy in a separate array.
+ */
+ copy_mat(state->box, lastbox);
+
+ bOK = TRUE;
+ dvdl_constr = 0;
+
+ 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
+ * in global_state after update, we should only do it at
+ * step % nstlist = 1 with bGStatEveryStep=FALSE.
+ */
+ }
+ else
+ {
+ update_tcouple(fplog, step, ir, state, ekind, wcycle, upd, &MassQ, mdatoms);
+ update_pcouple(fplog, step, ir, state, pcoupl_mu, M, wcycle,
+ upd, bInitStep);
+ }
+
+ if (bVV)
+ {
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+ /* velocity half-step update */
+ update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
+ bUpdateDoLR, fr->f_twin, fcd,
+ ekind, M, wcycle, upd, FALSE, etrtVELOCITY2,
+ cr, nrnb, constr, &top->idef);
+ }
+
+ /* Above, initialize just copies ekinh into ekin,
+ * it doesn't copy position (for VV),
+ * and entire integrator for MD.
+ */
+
+ if (ir->eI == eiVVAK)
+ {
+ copy_rvecn(state->x, cbuf, 0, state->natoms);
+ }
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+ update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
+ bUpdateDoLR, fr->f_twin, fcd,
+ ekind, M, wcycle, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
+ wallcycle_stop(wcycle, ewcUPDATE);
+
+ update_constraints(fplog, step, &dvdl_constr, ir, ekind, mdatoms, state,
+ fr->bMolPBC, graph, f,
+ &top->idef, shake_vir, force_vir,
+ cr, nrnb, wcycle, upd, constr,
+ bInitStep, FALSE, bCalcVir, state->veta);
+
+ if (ir->eI == eiVVAK)
+ {
+ /* erase F_EKIN and F_TEMP here? */
+ /* just compute the kinetic energy at the half step to perform a trotter step */
+ 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, NULL, FALSE, lastbox,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ cglo_flags | CGLO_TEMPERATURE
+ );
+ wallcycle_start(wcycle, ewcUPDATE);
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ4);
+ /* now we know the scaling, we can compute the positions again again */
+ copy_rvecn(cbuf, state->x, 0, state->natoms);
+
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+ update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
+ bUpdateDoLR, fr->f_twin, fcd,
+ ekind, M, wcycle, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
+ wallcycle_stop(wcycle, ewcUPDATE);
+
+ /* do we need an extra constraint here? just need to copy out of state->v to upd->xp? */
+ /* are the small terms in the shake_vir here due
+ * 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,
+ state, fr->bMolPBC, graph, f,
+ &top->idef, tmp_vir, force_vir,
+ cr, nrnb, wcycle, upd, NULL,
+ bInitStep, FALSE, bCalcVir,
+ state->veta);
+ }
+ if (!bOK && !bFFscan)
+ {
+ gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
+ }
+
+ if (fr->bSepDVDL && fplog && do_log)
+ {
+ fprintf(fplog, sepdvdlformat, "Constraint dV/dl", 0.0, dvdl_constr);
+ }
- /* only add constraint dvdl after constraints */
- enerd->term[F_DVDL_CONSTR] += dvdl_constr;
++ if (bVV)
++ {
++ /* this factor or 2 correction is necessary
++ because half of the constraint force is removed
++ in the vv step, so we have to double it. See
++ the Redmine issue #1255. It is not yet clear
++ if the factor of 2 is exact, or just a very
++ good approximation, and this will be
++ investigated. The next step is to see if this
++ can be done adding a dhdl contribution from the
++ rattle step, but this is somewhat more
++ complicated with the current code. Will be
++ investigated, hopefully for 4.6.3. However,
++ this current solution is much better than
++ having it completely wrong.
++ */
++ enerd->term[F_DVDL_CONSTR] += 2*dvdl_constr;
++ }
++ else
++ {
++ enerd->term[F_DVDL_CONSTR] += dvdl_constr;
++ }
+ }
+ else if (graph)
+ {
+ /* Need to unshift here */
+ unshift_self(graph, state->box, state->x);
+ }
+
+ if (vsite != NULL)
+ {
+ wallcycle_start(wcycle, ewcVSITECONSTR);
+ if (graph != NULL)
+ {
+ shift_self(graph, state->box, state->x);
+ }
+ construct_vsites(fplog, vsite, state->x, nrnb, ir->delta_t, state->v,
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, graph, cr, state->box);
+
+ if (graph != NULL)
+ {
+ unshift_self(graph, state->box, state->x);
+ }
+ wallcycle_stop(wcycle, ewcVSITECONSTR);
+ }
+
+ /* ############## IF NOT VV, Calculate globals HERE, also iterate constraints ############ */
+ /* With Leap-Frog we can skip compute_globals at
+ * non-communication steps, but we need to calculate
+ * the kinetic energy one step before communication.
+ */
+ 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,
+ (step_rel % gs.nstms == 0) &&
+ (multisim_nsteps < 0 || (step_rel < multisim_nsteps)),
+ lastbox,
+ top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
+ cglo_flags
+ | (!EI_VV(ir->eI) || bRerunMD ? CGLO_ENERGY : 0)
+ | (!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;
+ }
+
+ 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_dhdl(enerd, state->lambda, ir->fepvals);
+ }
+ update_box(fplog, step, ir, mdatoms, state, graph, f,
+ ir->nstlist == -1 ? &nlh.scale_tot : NULL, pcoupl_mu, nrnb, wcycle, upd, bInitStep, FALSE);
+
+ /* ################# END UPDATE STEP 2 ################# */
+ /* #### We now have r(t+dt) and v(t+dt/2) ############# */
+
+ /* The coordinates (x) were unshifted in update */
+ if (bFFscan && (shellfc == NULL || bConverged))
+ {
+ if (print_forcefield(fplog, enerd->term, mdatoms->homenr,
+ f, NULL, xcopy,
+ &(top_global->mols), mdatoms->massT, pres))
+ {
+ gmx_finalize_par();
+
+ fprintf(stderr, "\n");
+ exit(0);
+ }
+ }
+ if (!bGStat)
+ {
+ /* We will not sum ekinh_old,
+ * so signal that we still have to do it.
+ */
+ bSumEkinhOld = TRUE;
+ }
+
+ if (bTCR)
+ {
+ /* Only do GCT when the relaxation of shells (minimization) has converged,
+ * otherwise we might be coupling to bogus energies.
+ * In parallel we must always do this, because the other sims might
+ * update the FF.
+ */
+
+ /* Since this is called with the new coordinates state->x, I assume
+ * we want the new box state->box too. / EL 20040121
+ */
+ do_coupling(fplog, oenv, nfile, fnm, tcr, t, step, enerd->term, fr,
+ ir, MASTER(cr),
+ mdatoms, &(top->idef), mu_aver,
+ top_global->mols.nr, cr,
+ state->box, total_vir, pres,
+ mu_tot, state->x, f, bConverged);
+ debug_gmx();
+ }
+
+ /* ######### BEGIN PREPARING EDR OUTPUT ########### */
+
+ /* use the directly determined last velocity, not actually the averaged half steps */
+ if (bTrotter && ir->eI == eiVV)
+ {
+ enerd->term[F_EKIN] = last_ekin;
+ }
+ enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
+
+ if (bVV)
+ {
+ enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
+ }
+ else
+ {
+ enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + compute_conserved_from_auxiliary(ir, state, &MassQ);
+ }
+ /* Check for excessively large energies */
+ if (bIonize)
+ {
+#ifdef GMX_DOUBLE
+ real etot_max = 1e200;
+#else
+ real etot_max = 1e30;
+#endif
+ if (fabs(enerd->term[F_ETOT]) > etot_max)
+ {
+ fprintf(stderr, "Energy too large (%g), giving up\n",
+ enerd->term[F_ETOT]);
+ }
+ }
+ /* ######### END PREPARING EDR OUTPUT ########### */
+
+ /* Time for performance */
+ if (((step % stepout) == 0) || bLastStep)
+ {
+ runtime_upd_proc(runtime);
+ }
+
+ /* Output stuff */
+ if (MASTER(cr))
+ {
+ gmx_bool do_dr, do_or;
+
+ if (fplog && do_log && bDoExpanded)
+ {
+ /* only needed if doing expanded ensemble */
+ PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : NULL,
+ &df_history, state->fep_state, ir->nstlog, step);
+ }
+ if (!(bStartingFromCpt && (EI_VV(ir->eI))))
+ {
+ if (bCalcEner)
+ {
+ upd_mdebin(mdebin, bDoDHDL, TRUE,
+ t, mdatoms->tmass, enerd, state,
+ ir->fepvals, ir->expandedvals, lastbox,
+ shake_vir, force_vir, total_vir, pres,
+ ekind, mu_tot, constr);
+ }
+ else
+ {
+ upd_mdebin_step(mdebin);
+ }
+
+ do_dr = do_per_step(step, ir->nstdisreout);
+ do_or = do_per_step(step, ir->nstorireout);
+
+ print_ebin(outf->fp_ene, do_ene, do_dr, do_or, do_log ? fplog : NULL,
+ step, t,
+ eprNORMAL, bCompact, mdebin, fcd, groups, &(ir->opts));
+ }
+ if (ir->ePull != epullNO)
+ {
+ pull_print_output(ir->pull, step, t);
+ }
+
+ if (do_per_step(step, ir->nstlog))
+ {
+ if (fflush(fplog) != 0)
+ {
+ gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
+ }
+ }
+ }
+ if (bDoExpanded)
+ {
+ /* Have to do this part after outputting the logfile and the edr file */
+ state->fep_state = lamnew;
+ for (i = 0; i < efptNR; i++)
+ {
+ state_global->lambda[i] = ir->fepvals->all_lambda[i][lamnew];
+ }
+ }
+ /* Remaining runtime */
+ if (MULTIMASTER(cr) && (do_verbose || gmx_got_usr_signal()) && !bPMETuneRunning)
+ {
+ if (shellfc)
+ {
+ fprintf(stderr, "\n");
+ }
+ print_time(stderr, runtime, step, ir, cr);
+ }
+
+ /* Replica exchange */
+ bExchanged = FALSE;
+ if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
+ do_per_step(step, repl_ex_nst))
+ {
+ bExchanged = replica_exchange(fplog, cr, repl_ex,
+ state_global, enerd,
+ state, step, t);
+
+ if (bExchanged && DOMAINDECOMP(cr))
+ {
+ dd_partition_system(fplog, step, cr, TRUE, 1,
+ state_global, top_global, ir,
+ state, &f, mdatoms, top, fr,
+ vsite, shellfc, constr,
+ nrnb, wcycle, FALSE);
+ }
+ }
+
+ bFirstStep = FALSE;
+ bInitStep = FALSE;
+ bStartingFromCpt = FALSE;
+
+ /* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
+ /* With all integrators, except VV, we need to retain the pressure
+ * at the current step for coupling at the next step.
+ */
+ if ((state->flags & (1<<estPRES_PREV)) &&
+ (bGStatEveryStep ||
+ (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
+ {
+ /* Store the pressure in t_state for pressure coupling
+ * at the next MD step.
+ */
+ copy_mat(pres, state->pres_prev);
+ }
+
+ /* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
+
+ if ( (membed != NULL) && (!bLastStep) )
+ {
+ rescale_membed(step_rel, membed, state_global->x);
+ }
+
+ if (bRerunMD)
+ {
+ if (MASTER(cr))
+ {
+ /* read next frame from input trajectory */
+ bNotLastFrame = read_next_frame(oenv, status, &rerun_fr);
+ }
+
+ if (PAR(cr))
+ {
+ rerun_parallel_comm(cr, &rerun_fr, &bNotLastFrame);
+ }
+ }
+
+ if (!bRerunMD || !rerun_fr.bStep)
+ {
+ /* increase the MD step number */
+ step++;
+ step_rel++;
+ }
+
+ cycles = wallcycle_stop(wcycle, ewcSTEP);
+ if (DOMAINDECOMP(cr) && wcycle)
+ {
+ dd_cycles_add(cr->dd, cycles, ddCyclStep);
+ }
+
+ if (bPMETuneRunning || bPMETuneTry)
+ {
+ /* PME grid + cut-off optimization with GPUs or PME nodes */
+
+ /* Count the total cycles over the last steps */
+ cycles_pmes += cycles;
+
+ /* We can only switch cut-off at NS steps */
+ if (step % ir->nstlist == 0)
+ {
+ /* PME grid + cut-off optimization with GPUs or PME nodes */
+ if (bPMETuneTry)
+ {
+ if (DDMASTER(cr->dd))
+ {
+ /* PME node load is too high, start tuning */
+ bPMETuneRunning = (dd_pme_f_ratio(cr->dd) >= 1.05);
+ }
+ dd_bcast(cr->dd, sizeof(gmx_bool), &bPMETuneRunning);
+
+ if (bPMETuneRunning || step_rel > ir->nstlist*50)
+ {
+ bPMETuneTry = FALSE;
+ }
+ }
+ if (bPMETuneRunning)
+ {
+ /* init_step might not be a multiple of nstlist,
+ * but the first cycle is always skipped anyhow.
+ */
+ bPMETuneRunning =
+ pme_load_balance(pme_loadbal, cr,
+ (bVerbose && MASTER(cr)) ? stderr : NULL,
+ fplog,
+ ir, state, cycles_pmes,
+ fr->ic, fr->nbv, &fr->pmedata,
+ step);
+
+ /* Update constants in forcerec/inputrec to keep them in sync with fr->ic */
+ fr->ewaldcoeff = fr->ic->ewaldcoeff;
+ fr->rlist = fr->ic->rlist;
+ fr->rlistlong = fr->ic->rlistlong;
+ fr->rcoulomb = fr->ic->rcoulomb;
+ fr->rvdw = fr->ic->rvdw;
+ }
+ cycles_pmes = 0;
+ }
+ }
+
+ if (step_rel == wcycle_get_reset_counters(wcycle) ||
+ gs.set[eglsRESETCOUNTERS] != 0)
+ {
+ /* Reset all the counters related to performance over the run */
+ reset_all_counters(fplog, cr, step, &step_rel, ir, wcycle, nrnb, runtime,
+ fr->nbv != NULL && fr->nbv->bUseGPU ? fr->nbv->cu_nbv : NULL);
+ wcycle_set_reset_counters(wcycle, -1);
+ if (!(cr->duty & DUTY_PME))
+ {
+ /* Tell our PME node to reset its counters */
+ gmx_pme_send_resetcounters(cr, step);
+ }
+ /* Correct max_hours for the elapsed time */
+ max_hours -= run_time/(60.0*60.0);
+ bResetCountersHalfMaxH = FALSE;
+ gs.set[eglsRESETCOUNTERS] = 0;
+ }
+
+ }
+ /* End of main MD loop */
+ debug_gmx();
+
+ /* Stop the time */
+ runtime_end(runtime);
+
+ if (bRerunMD && MASTER(cr))
+ {
+ close_trj(status);
+ }
+
+ if (!(cr->duty & DUTY_PME))
+ {
+ /* Tell the PME only node to finish */
+ gmx_pme_send_finish(cr);
+ }
+
+ if (MASTER(cr))
+ {
+ if (ir->nstcalcenergy > 0 && !bRerunMD)
+ {
+ print_ebin(outf->fp_ene, FALSE, FALSE, FALSE, fplog, step, t,
+ eprAVER, FALSE, mdebin, fcd, groups, &(ir->opts));
+ }
+ }
+
+ 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);
+ }
+
+ if (shellfc && fplog)
+ {
+ fprintf(fplog, "Fraction of iterations that converged: %.2f %%\n",
+ (nconverged*100.0)/step_rel);
+ fprintf(fplog, "Average number of force evaluations per MD step: %.2f\n\n",
+ tcount/step_rel);
+ }
+
+ if (repl_ex_nst > 0 && MASTER(cr))
+ {
+ print_replica_exchange_statistics(fplog, repl_ex);
+ }
+
+ runtime->nsteps_done = step_rel;
+
+ return 0;
+}
--- /dev/null
- gmx_hw_opt_t *hw_opt,
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * 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 the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, 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 www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+#include <signal.h>
+#include <stdlib.h>
+#ifdef HAVE_UNISTD_H
+#include <unistd.h>
+#endif
+#include <string.h>
+#include <assert.h>
+
+#include "typedefs.h"
+#include "smalloc.h"
+#include "sysstuff.h"
+#include "statutil.h"
+#include "mdrun.h"
+#include "md_logging.h"
+#include "md_support.h"
+#include "network.h"
+#include "pull.h"
+#include "pull_rotation.h"
+#include "names.h"
+#include "disre.h"
+#include "orires.h"
+#include "pme.h"
+#include "mdatoms.h"
+#include "repl_ex.h"
+#include "qmmm.h"
+#include "domdec.h"
+#include "partdec.h"
+#include "coulomb.h"
+#include "constr.h"
+#include "mvdata.h"
+#include "checkpoint.h"
+#include "mtop_util.h"
+#include "sighandler.h"
+#include "tpxio.h"
+#include "txtdump.h"
+#include "gmx_detect_hardware.h"
+#include "gmx_omp_nthreads.h"
+#include "pull_rotation.h"
+#include "calc_verletbuf.h"
+#include "../mdlib/nbnxn_search.h"
+#include "../mdlib/nbnxn_consts.h"
+#include "gmx_fatal_collective.h"
+#include "membed.h"
+#include "macros.h"
+#include "gmx_omp.h"
+#include "gmx_thread_affinity.h"
+
+#include "gromacs/utility/gmxmpi.h"
+
+#ifdef GMX_FAHCORE
+#include "corewrap.h"
+#endif
+
+#include "gpu_utils.h"
+#include "nbnxn_cuda_data_mgmt.h"
+
+typedef struct {
+ gmx_integrator_t *func;
+} gmx_intp_t;
+
+/* The array should match the eI array in include/types/enums.h */
+const gmx_intp_t integrator[eiNR] = { {do_md}, {do_steep}, {do_cg}, {do_md}, {do_md}, {do_nm}, {do_lbfgs}, {do_tpi}, {do_tpi}, {do_md}, {do_md}, {do_md}};
+
+gmx_large_int_t deform_init_init_step_tpx;
+matrix deform_init_box_tpx;
+#ifdef GMX_THREAD_MPI
+tMPI_Thread_mutex_t deform_init_box_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+#endif
+
+
+#ifdef GMX_THREAD_MPI
+struct mdrunner_arglist
+{
+ gmx_hw_opt_t *hw_opt;
+ FILE *fplog;
+ t_commrec *cr;
+ int nfile;
+ const t_filenm *fnm;
+ output_env_t oenv;
+ gmx_bool bVerbose;
+ gmx_bool bCompact;
+ int nstglobalcomm;
+ ivec ddxyz;
+ int dd_node_order;
+ real rdd;
+ real rconstr;
+ const char *dddlb_opt;
+ real dlb_scale;
+ const char *ddcsx;
+ const char *ddcsy;
+ const char *ddcsz;
+ const char *nbpu_opt;
+ gmx_large_int_t nsteps_cmdline;
+ int nstepout;
+ int resetstep;
+ int nmultisim;
+ int repl_ex_nst;
+ int repl_ex_nex;
+ int repl_ex_seed;
+ real pforce;
+ real cpt_period;
+ real max_hours;
+ const char *deviceOptions;
+ unsigned long Flags;
+ int ret; /* return value */
+};
+
+
+/* The function used for spawning threads. Extracts the mdrunner()
+ arguments from its one argument and calls mdrunner(), after making
+ a commrec. */
+static void mdrunner_start_fn(void *arg)
+{
+ struct mdrunner_arglist *mda = (struct mdrunner_arglist*)arg;
+ struct mdrunner_arglist mc = *mda; /* copy the arg list to make sure
+ that it's thread-local. This doesn't
+ copy pointed-to items, of course,
+ but those are all const. */
+ t_commrec *cr; /* we need a local version of this */
+ FILE *fplog = NULL;
+ t_filenm *fnm;
+
+ fnm = dup_tfn(mc.nfile, mc.fnm);
+
+ cr = init_par_threads(mc.cr);
+
+ if (MASTER(cr))
+ {
+ fplog = mc.fplog;
+ }
+
+ mda->ret = mdrunner(mc.hw_opt, fplog, cr, mc.nfile, fnm, mc.oenv,
+ mc.bVerbose, mc.bCompact, mc.nstglobalcomm,
+ mc.ddxyz, mc.dd_node_order, mc.rdd,
+ mc.rconstr, mc.dddlb_opt, mc.dlb_scale,
+ mc.ddcsx, mc.ddcsy, mc.ddcsz,
+ mc.nbpu_opt,
+ mc.nsteps_cmdline, mc.nstepout, mc.resetstep,
+ mc.nmultisim, mc.repl_ex_nst, mc.repl_ex_nex, mc.repl_ex_seed, mc.pforce,
+ mc.cpt_period, mc.max_hours, mc.deviceOptions, mc.Flags);
+}
+
+/* called by mdrunner() to start a specific number of threads (including
+ the main thread) for thread-parallel runs. This in turn calls mdrunner()
+ for each thread.
+ All options besides nthreads are the same as for mdrunner(). */
+static t_commrec *mdrunner_start_threads(gmx_hw_opt_t *hw_opt,
+ FILE *fplog, t_commrec *cr, int nfile,
+ const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
+ gmx_bool bCompact, int nstglobalcomm,
+ ivec ddxyz, int dd_node_order, real rdd, real rconstr,
+ const char *dddlb_opt, real dlb_scale,
+ const char *ddcsx, const char *ddcsy, const char *ddcsz,
+ const char *nbpu_opt,
+ gmx_large_int_t nsteps_cmdline,
+ int nstepout, int resetstep,
+ int nmultisim, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
+ real pforce, real cpt_period, real max_hours,
+ const char *deviceOptions, unsigned long Flags)
+{
+ int ret;
+ struct mdrunner_arglist *mda;
+ t_commrec *crn; /* the new commrec */
+ t_filenm *fnmn;
+
+ /* first check whether we even need to start tMPI */
+ if (hw_opt->nthreads_tmpi < 2)
+ {
+ return cr;
+ }
+
+ /* a few small, one-time, almost unavoidable memory leaks: */
+ snew(mda, 1);
+ fnmn = dup_tfn(nfile, fnm);
+
+ /* fill the data structure to pass as void pointer to thread start fn */
+ mda->hw_opt = hw_opt;
+ mda->fplog = fplog;
+ mda->cr = cr;
+ mda->nfile = nfile;
+ mda->fnm = fnmn;
+ mda->oenv = oenv;
+ mda->bVerbose = bVerbose;
+ mda->bCompact = bCompact;
+ mda->nstglobalcomm = nstglobalcomm;
+ mda->ddxyz[XX] = ddxyz[XX];
+ mda->ddxyz[YY] = ddxyz[YY];
+ mda->ddxyz[ZZ] = ddxyz[ZZ];
+ mda->dd_node_order = dd_node_order;
+ mda->rdd = rdd;
+ mda->rconstr = rconstr;
+ mda->dddlb_opt = dddlb_opt;
+ mda->dlb_scale = dlb_scale;
+ mda->ddcsx = ddcsx;
+ mda->ddcsy = ddcsy;
+ mda->ddcsz = ddcsz;
+ mda->nbpu_opt = nbpu_opt;
+ mda->nsteps_cmdline = nsteps_cmdline;
+ mda->nstepout = nstepout;
+ mda->resetstep = resetstep;
+ mda->nmultisim = nmultisim;
+ mda->repl_ex_nst = repl_ex_nst;
+ mda->repl_ex_nex = repl_ex_nex;
+ mda->repl_ex_seed = repl_ex_seed;
+ mda->pforce = pforce;
+ mda->cpt_period = cpt_period;
+ mda->max_hours = max_hours;
+ mda->deviceOptions = deviceOptions;
+ mda->Flags = Flags;
+
+ /* now spawn new threads that start mdrunner_start_fn(), while
+ the main thread returns, we set thread affinity later */
+ ret = tMPI_Init_fn(TRUE, hw_opt->nthreads_tmpi, TMPI_AFFINITY_NONE,
+ mdrunner_start_fn, (void*)(mda) );
+ if (ret != TMPI_SUCCESS)
+ {
+ return NULL;
+ }
+
+ /* make a new comm_rec to reflect the new situation */
+ crn = init_par_threads(cr);
+ return crn;
+}
+
+
+static int get_tmpi_omp_thread_division(const gmx_hw_info_t *hwinfo,
+ const gmx_hw_opt_t *hw_opt,
+ int nthreads_tot,
+ int ngpu)
+{
+ int nthreads_tmpi;
+
+ /* There are no separate PME nodes here, as we ensured in
+ * check_and_update_hw_opt that nthreads_tmpi>0 with PME nodes
+ * and a conditional ensures we would not have ended up here.
+ * Note that separate PME nodes might be switched on later.
+ */
+ if (ngpu > 0)
+ {
+ nthreads_tmpi = ngpu;
+ if (nthreads_tot > 0 && nthreads_tot < nthreads_tmpi)
+ {
+ nthreads_tmpi = nthreads_tot;
+ }
+ }
+ 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);
+ }
+ else
+ {
+ /* TODO choose nthreads_omp based on hardware topology
+ when we have a hardware topology detection library */
+ /* In general, when running up to 4 threads, OpenMP should be faster.
+ * Note: on AMD Bulldozer we should avoid running OpenMP over two dies.
+ * On Intel>=Nehalem running OpenMP on a single CPU is always faster,
+ * even on two CPUs it's usually faster (but with many OpenMP threads
+ * it could be faster not to use HT, currently we always use HT).
+ * On Nehalem/Westmere we want to avoid running 16 threads over
+ * two CPUs with HT, so we need a limit<16; thus we use 12.
+ * A reasonable limit for Intel Sandy and Ivy bridge,
+ * not knowing the topology, is 16 threads.
+ */
+ 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 =
+ (gmx_cpuid_vendor(hwinfo->cpuid_info) == GMX_CPUID_VENDOR_INTEL &&
+ gmx_cpuid_family(hwinfo->cpuid_info) == 6);
+
+ if (nthreads_tot <= nthreads_omp_always_faster ||
+ (bIntel_Family6 &&
+ ((gmx_cpuid_model(hwinfo->cpuid_info) >= nthreads_omp_always_faster_Nehalem && nthreads_tot <= nthreads_omp_always_faster_Nehalem) ||
+ (gmx_cpuid_model(hwinfo->cpuid_info) >= nthreads_omp_always_faster_SandyBridge && nthreads_tot <= nthreads_omp_always_faster_SandyBridge))))
+ {
+ /* Use pure OpenMP parallelization */
+ nthreads_tmpi = 1;
+ }
+ else
+ {
+ /* Don't use OpenMP parallelization */
+ nthreads_tmpi = nthreads_tot;
+ }
+ }
+
+ return nthreads_tmpi;
+}
+
+
+/* Get the number of threads to use for thread-MPI based on how many
+ * were requested, which algorithms we're using,
+ * and how many particles there are.
+ * At the point we have already called check_and_update_hw_opt.
+ * Thus all options should be internally consistent and consistent
+ * with the hardware, except that ntmpi could be larger than #GPU.
+ */
+static int get_nthreads_mpi(gmx_hw_info_t *hwinfo,
+ gmx_hw_opt_t *hw_opt,
+ t_inputrec *inputrec, gmx_mtop_t *mtop,
+ const t_commrec *cr,
+ FILE *fplog)
+{
+ 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)
+ {
+ /* Trivial, return right away */
+ return hw_opt->nthreads_tmpi;
+ }
+
+ nthreads_hw = hwinfo->nthreads_hw_avail;
+
+ /* How many total (#tMPI*#OpenMP) threads can we start? */
+ if (hw_opt->nthreads_tot > 0)
+ {
+ nthreads_tot_max = hw_opt->nthreads_tot;
+ }
+ else
+ {
+ nthreads_tot_max = nthreads_hw;
+ }
+
+ bCanUseGPU = (inputrec->cutoff_scheme == ecutsVERLET && hwinfo->bCanUseGPU);
+ if (bCanUseGPU)
+ {
+ ngpu = hwinfo->gpu_info.ncuda_dev_use;
+ }
+ else
+ {
+ ngpu = 0;
+ }
+
+ nthreads_tmpi =
+ get_tmpi_omp_thread_division(hwinfo, hw_opt, nthreads_tot_max, ngpu);
+
+ if (inputrec->eI == eiNM || EI_TPI(inputrec->eI))
+ {
+ /* Steps are divided over the nodes iso splitting the atoms */
+ min_atoms_per_mpi_thread = 0;
+ }
+ else
+ {
+ if (bCanUseGPU)
+ {
+ min_atoms_per_mpi_thread = MIN_ATOMS_PER_GPU;
+ }
+ else
+ {
+ min_atoms_per_mpi_thread = MIN_ATOMS_PER_MPI_THREAD;
+ }
+ }
+
+ /* Check if an algorithm does not support parallel simulation. */
+ if (nthreads_tmpi != 1 &&
+ ( inputrec->eI == eiLBFGS ||
+ inputrec->coulombtype == eelEWALD ) )
+ {
+ nthreads_tmpi = 1;
+
+ md_print_warn(cr, fplog, "The integration or electrostatics algorithm doesn't support parallel runs. Using a single thread-MPI thread.\n");
+ if (hw_opt->nthreads_tmpi > nthreads_tmpi)
+ {
+ gmx_fatal(FARGS, "You asked for more than 1 thread-MPI thread, but an algorithm doesn't support that");
+ }
+ }
+ else if (mtop->natoms/nthreads_tmpi < min_atoms_per_mpi_thread)
+ {
+ /* 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);
+
+ /* Avoid partial use of Hyper-Threading */
+ if (gmx_cpuid_x86_smt(hwinfo->cpuid_info) == GMX_CPUID_X86_SMT_ENABLED &&
+ nthreads_new > nthreads_hw/2 && nthreads_new < nthreads_hw)
+ {
+ nthreads_new = nthreads_hw/2;
+ }
+
+ /* Avoid large prime numbers in the thread count */
+ if (nthreads_new >= 6)
+ {
+ /* Use only 6,8,10 with additional factors of 2 */
+ int fac;
+
+ fac = 2;
+ while (3*fac*2 <= nthreads_new)
+ {
+ fac *= 2;
+ }
+
+ nthreads_new = (nthreads_new/fac)*fac;
+ }
+ else
+ {
+ /* Avoid 5 */
+ if (nthreads_new == 5)
+ {
+ nthreads_new = 4;
+ }
+ }
+
+ nthreads_tmpi = nthreads_new;
+
+ fprintf(stderr, "\n");
+ fprintf(stderr, "NOTE: Parallelization is limited by the small number of atoms,\n");
+ fprintf(stderr, " only starting %d thread-MPI threads.\n", nthreads_tmpi);
+ fprintf(stderr, " You can use the -nt and/or -ntmpi option to optimize the number of threads.\n\n");
+ }
+
+ return nthreads_tmpi;
+}
+#endif /* GMX_THREAD_MPI */
+
+
+/* Environment variable for setting nstlist */
+static const char* NSTLIST_ENVVAR = "GMX_NSTLIST";
+/* Try to increase nstlist when using a GPU with nstlist less than this */
+static const int NSTLIST_GPU_ENOUGH = 20;
+/* Increase nstlist until the non-bonded cost increases more than this factor */
+static const float NBNXN_GPU_LIST_OK_FAC = 1.25;
+/* Don't increase nstlist beyond a non-bonded cost increases of this factor */
+static const float NBNXN_GPU_LIST_MAX_FAC = 1.40;
+
+/* Try to increase nstlist when running on a GPU */
+static void increase_nstlist(FILE *fp, t_commrec *cr,
+ t_inputrec *ir, const gmx_mtop_t *mtop, matrix box)
+{
+ char *env;
+ int nstlist_orig, nstlist_prev;
+ verletbuf_list_setup_t ls;
+ real rlist_inc, rlist_ok, rlist_max, rlist_new, rlist_prev;
+ int i;
+ t_state state_tmp;
+ gmx_bool bBox, bDD, bCont;
+ const char *nstl_fmt = "\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 *vbd_err = "Can not increase nstlist for GPU run because verlet-buffer-drift is not set or used";
+ const char *box_err = "Can not increase nstlist for GPU run because the box is too small";
+ const char *dd_err = "Can not increase nstlist for GPU run because of domain decomposition limitations";
+ char buf[STRLEN];
+
+ /* Number of + nstlist alternative values to try when switching */
+ const int nstl[] = { 20, 25, 40, 50 };
+#define NNSTL sizeof(nstl)/sizeof(nstl[0])
+
+ env = getenv(NSTLIST_ENVVAR);
+ if (env == NULL)
+ {
+ if (fp != NULL)
+ {
+ fprintf(fp, nstl_fmt, ir->nstlist);
+ }
+ }
+
+ if (ir->verletbuf_drift == 0)
+ {
+ gmx_fatal(FARGS, "You are using an old tpr file with a GPU, please generate a new tpr file with an up to date version of grompp");
+ }
+
+ if (ir->verletbuf_drift < 0)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "%s\n", vbd_err);
+ }
+ if (fp != NULL)
+ {
+ fprintf(fp, "%s\n", vbd_err);
+ }
+
+ return;
+ }
+
+ nstlist_orig = ir->nstlist;
+ if (env != NULL)
+ {
+ sprintf(buf, "Getting nstlist from environment variable GMX_NSTLIST=%s", env);
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "%s\n", buf);
+ }
+ if (fp != NULL)
+ {
+ fprintf(fp, "%s\n", buf);
+ }
+ sscanf(env, "%d", &ir->nstlist);
+ }
+
+ verletbuf_get_list_setup(TRUE, &ls);
+
+ /* Allow rlist to make the list double the size of the cut-off sphere */
+ rlist_inc = nbnxn_get_rlist_effective_inc(NBNXN_GPU_CLUSTER_SIZE, mtop->natoms/det(box));
+ rlist_ok = (max(ir->rvdw, ir->rcoulomb) + rlist_inc)*pow(NBNXN_GPU_LIST_OK_FAC, 1.0/3.0) - rlist_inc;
+ rlist_max = (max(ir->rvdw, ir->rcoulomb) + rlist_inc)*pow(NBNXN_GPU_LIST_MAX_FAC, 1.0/3.0) - rlist_inc;
+ if (debug)
+ {
+ fprintf(debug, "GPU nstlist tuning: rlist_inc %.3f rlist_max %.3f\n",
+ rlist_inc, rlist_max);
+ }
+
+ i = 0;
+ nstlist_prev = nstlist_orig;
+ rlist_prev = ir->rlist;
+ do
+ {
+ if (env == NULL)
+ {
+ ir->nstlist = nstl[i];
+ }
+
+ /* Set the pair-list buffer size in ir */
+ calc_verlet_buffer_size(mtop, det(box), ir, ir->verletbuf_drift, &ls,
+ NULL, &rlist_new);
+
+ /* Does rlist fit in the box? */
+ bBox = (sqr(rlist_new) < max_cutoff2(ir->ePBC, box));
+ bDD = TRUE;
+ if (bBox && DOMAINDECOMP(cr))
+ {
+ /* Check if rlist fits in the domain decomposition */
+ if (inputrec2nboundeddim(ir) < DIM)
+ {
+ gmx_incons("Changing nstlist with domain decomposition and unbounded dimensions is not implemented yet");
+ }
+ copy_mat(box, state_tmp.box);
+ bDD = change_dd_cutoff(cr, &state_tmp, ir, rlist_new);
+ }
+
+ bCont = FALSE;
+
+ if (env == NULL)
+ {
+ if (bBox && bDD && rlist_new <= rlist_max)
+ {
+ /* Increase nstlist */
+ nstlist_prev = ir->nstlist;
+ rlist_prev = rlist_new;
+ bCont = (i+1 < NNSTL && rlist_new < rlist_ok);
+ }
+ else
+ {
+ /* Stick with the previous nstlist */
+ ir->nstlist = nstlist_prev;
+ rlist_new = rlist_prev;
+ bBox = TRUE;
+ bDD = TRUE;
+ }
+ }
+
+ i++;
+ }
+ while (bCont);
+
+ if (!bBox || !bDD)
+ {
+ gmx_warning(!bBox ? box_err : dd_err);
+ if (fp != NULL)
+ {
+ fprintf(fp, "\n%s\n", bBox ? box_err : dd_err);
+ }
+ ir->nstlist = nstlist_orig;
+ }
+ else if (ir->nstlist != nstlist_orig || rlist_new != ir->rlist)
+ {
+ sprintf(buf, "Changing nstlist from %d to %d, rlist from %g to %g",
+ nstlist_orig, ir->nstlist,
+ ir->rlist, rlist_new);
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "%s\n\n", buf);
+ }
+ if (fp != NULL)
+ {
+ fprintf(fp, "%s\n\n", buf);
+ }
+ ir->rlist = rlist_new;
+ ir->rlistlong = rlist_new;
+ }
+}
+
+static void prepare_verlet_scheme(FILE *fplog,
+ gmx_hw_info_t *hwinfo,
+ t_commrec *cr,
- prepare_verlet_scheme(fplog, hwinfo, cr, hw_opt, nbpu_opt,
+ const char *nbpu_opt,
+ t_inputrec *ir,
+ const gmx_mtop_t *mtop,
+ matrix box,
+ gmx_bool *bUseGPU)
+{
+ /* Here we only check for GPU usage on the MPI master process,
+ * as here we don't know how many GPUs we will use yet.
+ * We check for a GPU on all processes later.
+ */
+ *bUseGPU = hwinfo->bCanUseGPU || (getenv("GMX_EMULATE_GPU") != NULL);
+
+ if (ir->verletbuf_drift > 0)
+ {
+ /* Update the Verlet buffer size for the current run setup */
+ verletbuf_list_setup_t ls;
+ real rlist_new;
+
+ /* Here we assume CPU acceleration is on. But as currently
+ * calc_verlet_buffer_size gives the same results for 4x8 and 4x4
+ * and 4x2 gives a larger buffer than 4x4, this is ok.
+ */
+ verletbuf_get_list_setup(*bUseGPU, &ls);
+
+ calc_verlet_buffer_size(mtop, det(box), ir,
+ ir->verletbuf_drift, &ls,
+ NULL, &rlist_new);
+ if (rlist_new != ir->rlist)
+ {
+ if (fplog != NULL)
+ {
+ fprintf(fplog, "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
+ ir->rlist, rlist_new,
+ ls.cluster_size_i, ls.cluster_size_j);
+ }
+ ir->rlist = rlist_new;
+ ir->rlistlong = rlist_new;
+ }
+ }
+
+ /* With GPU or emulation we should check nstlist for performance */
+ if ((EI_DYNAMICS(ir->eI) &&
+ *bUseGPU &&
+ ir->nstlist < NSTLIST_GPU_ENOUGH) ||
+ getenv(NSTLIST_ENVVAR) != NULL)
+ {
+ /* Choose a better nstlist */
+ increase_nstlist(fplog, cr, ir, mtop, box);
+ }
+}
+
+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_drift = 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 (EVDW_SWITCHED(ir->vdwtype) || EEL_SWITCHED(ir->coulombtype))
+ {
+ md_print_warn(NULL, fplog, "Converting switched or shifted interactions to a shifted potential (without force shift), this will lead to slightly different interaction potentials");
+
+ if (EVDW_SWITCHED(ir->vdwtype))
+ {
+ ir->vdwtype = evdwCUT;
+ }
+ if (EEL_SWITCHED(ir->coulombtype))
+ {
+ if (EEL_FULL(ir->coulombtype))
+ {
+ /* With full electrostatic only PME can be switched */
+ ir->coulombtype = eelPME;
+ }
+ 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;
+ }
+ }
+
+ /* We set the target energy drift 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_drift = 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, ir->verletbuf_drift, &ls,
+ NULL, &ir->rlist);
+ }
+ else
+ {
+ ir->verletbuf_drift = -1;
+ ir->rlist = 1.05*max(ir->rvdw, ir->rcoulomb);
+ }
+
+ gmx_mtop_remove_chargegroups(mtop);
+}
+
+static void check_and_update_hw_opt(gmx_hw_opt_t *hw_opt,
+ int cutoff_scheme,
+ gmx_bool bIsSimMaster)
+{
+ gmx_omp_nthreads_read_env(&hw_opt->nthreads_omp, bIsSimMaster);
+
+#ifndef GMX_THREAD_MPI
+ if (hw_opt->nthreads_tot > 0)
+ {
+ gmx_fatal(FARGS, "Setting the total number of threads is only supported with thread-MPI and Gromacs was compiled without thread-MPI");
+ }
+ if (hw_opt->nthreads_tmpi > 0)
+ {
+ gmx_fatal(FARGS, "Setting the number of thread-MPI threads is only supported with thread-MPI and Gromacs was compiled without thread-MPI");
+ }
+#endif
+
+ if (hw_opt->nthreads_tot > 0 && hw_opt->nthreads_omp_pme <= 0)
+ {
+ /* We have the same number of OpenMP threads for PP and PME processes,
+ * thus we can perform several consistency checks.
+ */
+ if (hw_opt->nthreads_tmpi > 0 &&
+ hw_opt->nthreads_omp > 0 &&
+ hw_opt->nthreads_tot != hw_opt->nthreads_tmpi*hw_opt->nthreads_omp)
+ {
+ gmx_fatal(FARGS, "The total number of threads requested (%d) does not match the thread-MPI threads (%d) times the OpenMP threads (%d) requested",
+ hw_opt->nthreads_tot, hw_opt->nthreads_tmpi, hw_opt->nthreads_omp);
+ }
+
+ if (hw_opt->nthreads_tmpi > 0 &&
+ hw_opt->nthreads_tot % hw_opt->nthreads_tmpi != 0)
+ {
+ gmx_fatal(FARGS, "The total number of threads requested (%d) is not divisible by the number of thread-MPI threads requested (%d)",
+ hw_opt->nthreads_tot, hw_opt->nthreads_tmpi);
+ }
+
+ if (hw_opt->nthreads_omp > 0 &&
+ hw_opt->nthreads_tot % hw_opt->nthreads_omp != 0)
+ {
+ gmx_fatal(FARGS, "The total number of threads requested (%d) is not divisible by the number of OpenMP threads requested (%d)",
+ hw_opt->nthreads_tot, hw_opt->nthreads_omp);
+ }
+
+ if (hw_opt->nthreads_tmpi > 0 &&
+ hw_opt->nthreads_omp <= 0)
+ {
+ hw_opt->nthreads_omp = hw_opt->nthreads_tot/hw_opt->nthreads_tmpi;
+ }
+ }
+
+#ifndef GMX_OPENMP
+ if (hw_opt->nthreads_omp > 1)
+ {
+ gmx_fatal(FARGS, "OpenMP threads are requested, but Gromacs was compiled without OpenMP support");
+ }
+#endif
+
+ if (cutoff_scheme == ecutsGROUP)
+ {
+ /* We only have OpenMP support for PME only nodes */
+ if (hw_opt->nthreads_omp > 1)
+ {
+ gmx_fatal(FARGS, "OpenMP threads have been requested with cut-off scheme %s, but these are only supported with cut-off scheme %s",
+ ecutscheme_names[cutoff_scheme],
+ ecutscheme_names[ecutsVERLET]);
+ }
+ hw_opt->nthreads_omp = 1;
+ }
+
+ if (hw_opt->nthreads_omp_pme > 0 && hw_opt->nthreads_omp <= 0)
+ {
+ gmx_fatal(FARGS, "You need to specify -ntomp in addition to -ntomp_pme");
+ }
+
+ if (hw_opt->nthreads_tot == 1)
+ {
+ hw_opt->nthreads_tmpi = 1;
+
+ if (hw_opt->nthreads_omp > 1)
+ {
+ gmx_fatal(FARGS, "You requested %d OpenMP threads with %d total threads",
+ hw_opt->nthreads_tmpi, hw_opt->nthreads_tot);
+ }
+ hw_opt->nthreads_omp = 1;
+ }
+
+ if (hw_opt->nthreads_omp_pme <= 0 && hw_opt->nthreads_omp > 0)
+ {
+ hw_opt->nthreads_omp_pme = hw_opt->nthreads_omp;
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "hw_opt: nt %d ntmpi %d ntomp %d ntomp_pme %d gpu_id '%s'\n",
+ hw_opt->nthreads_tot,
+ hw_opt->nthreads_tmpi,
+ hw_opt->nthreads_omp,
+ hw_opt->nthreads_omp_pme,
+ hw_opt->gpu_id != NULL ? hw_opt->gpu_id : "");
+
+ }
+}
+
+
+/* Override the value in inputrec with value passed on the command line (if any) */
+static void override_nsteps_cmdline(FILE *fplog,
+ gmx_large_int_t nsteps_cmdline,
+ 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];
+
+ ir->nsteps = nsteps_cmdline;
+ if (EI_DYNAMICS(ir->eI))
+ {
+ sprintf(stmp, "Overriding nsteps with value passed on the command line: %s steps, %.3f ps",
+ gmx_step_str(nsteps_cmdline, sbuf),
+ 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));
+ }
+
+ md_print_warn(cr, fplog, "%s\n", stmp);
+ }
+}
+
+/* Data structure set by SIMMASTER which needs to be passed to all nodes
+ * before the other nodes have read the tpx file and called gmx_detect_hardware.
+ */
+typedef struct {
+ int cutoff_scheme; /* The cutoff scheme from inputrec_t */
+ gmx_bool bUseGPU; /* Use GPU or GPU emulation */
+} master_inf_t;
+
+int mdrunner(gmx_hw_opt_t *hw_opt,
+ FILE *fplog, t_commrec *cr, int nfile,
+ const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
+ gmx_bool bCompact, int nstglobalcomm,
+ ivec ddxyz, int dd_node_order, real rdd, real rconstr,
+ const char *dddlb_opt, real dlb_scale,
+ const char *ddcsx, const char *ddcsy, const char *ddcsz,
+ const char *nbpu_opt,
+ gmx_large_int_t nsteps_cmdline, int nstepout, int resetstep,
+ int nmultisim, int repl_ex_nst, int repl_ex_nex,
+ int repl_ex_seed, real pforce, real cpt_period, real max_hours,
+ const char *deviceOptions, unsigned long Flags)
+{
+ gmx_bool bForceUseGPU, bTryUseGPU;
+ 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;
+ t_forcerec *fr = NULL;
+ t_fcdata *fcd = NULL;
+ real ewaldcoeff = 0;
+ gmx_pme_t *pmedata = NULL;
+ gmx_vsite_t *vsite = NULL;
+ gmx_constr_t constr;
+ int i, m, nChargePerturbed = -1, status, nalloc;
+ char *gro;
+ gmx_wallcycle_t wcycle;
+ gmx_bool bReadRNG, bReadEkin;
+ int list;
+ gmx_runtime_t runtime;
+ int rc;
+ gmx_large_int_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;
+ gmx_hw_info_t *hwinfo = NULL;
+ master_inf_t minf = {-1, FALSE};
+
+ /* CAUTION: threads may be started later on in this function, so
+ cr doesn't reflect the final parallel state right now */
+ snew(inputrec, 1);
+ snew(mtop, 1);
+
+ if (Flags & MD_APPENDFILES)
+ {
+ fplog = NULL;
+ }
+
+ bForceUseGPU = (strncmp(nbpu_opt, "gpu", 3) == 0);
+ bTryUseGPU = (strncmp(nbpu_opt, "auto", 4) == 0) || bForceUseGPU;
+
+ snew(state, 1);
+ 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));
+ }
+
+ /* Detect hardware, gather information. With tMPI only thread 0 does it
+ * and after threads are started broadcasts hwinfo around. */
+ snew(hwinfo, 1);
+ gmx_detect_hardware(fplog, hwinfo, cr,
+ bForceUseGPU, bTryUseGPU, hw_opt->gpu_id);
+
+ minf.cutoff_scheme = inputrec->cutoff_scheme;
+ minf.bUseGPU = FALSE;
+
+ if (inputrec->cutoff_scheme == ecutsVERLET)
+ {
- /* All-vs-all loops do not work with domain decomposition */
++ prepare_verlet_scheme(fplog, hwinfo, cr, nbpu_opt,
+ inputrec, mtop, state->box,
+ &minf.bUseGPU);
+ }
+ else if (hwinfo->bCanUseGPU)
+ {
+ 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");
+
+ if (bForceUseGPU)
+ {
+ gmx_fatal(FARGS, "GPU requested, but can't be used without cutoff-scheme=Verlet");
+ }
+ }
+ }
+#ifndef GMX_THREAD_MPI
+ if (PAR(cr))
+ {
+ gmx_bcast_sim(sizeof(minf), &minf, cr);
+ }
+#endif
+ if (minf.bUseGPU && cr->npmenodes == -1)
+ {
+ /* Don't automatically use PME-only nodes with GPUs */
+ cr->npmenodes = 0;
+ }
+
+ /* 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);
+
+#ifdef GMX_THREAD_MPI
+ /* With thread-MPI inputrec is only set here on the master thread */
+ if (SIMMASTER(cr))
+#endif
+ {
+ check_and_update_hw_opt(hw_opt, minf.cutoff_scheme, SIMMASTER(cr));
+
+#ifdef GMX_THREAD_MPI
+ /* Early check for externally set process affinity. Can't do over all
+ * MPI processes because hwinfo is not available everywhere, but with
+ * thread-MPI it's needed as pinning might get turned off which needs
+ * to be known before starting thread-MPI. */
+ 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)
+ {
+ gmx_fatal(FARGS, "You need to explicitly specify the number of MPI threads (-ntmpi) when using separate PME nodes");
+ }
+#endif
+
+ if (hw_opt->nthreads_omp_pme != hw_opt->nthreads_omp &&
+ cr->npmenodes <= 0)
+ {
+ gmx_fatal(FARGS, "You need to explicitly specify the number of PME nodes (-npme) when using different number of OpenMP threads for PP and PME nodes");
+ }
+ }
+
+#ifdef GMX_THREAD_MPI
+ if (SIMMASTER(cr))
+ {
+ /* NOW the threads will be started: */
+ hw_opt->nthreads_tmpi = get_nthreads_mpi(hwinfo,
+ hw_opt,
+ inputrec, mtop,
+ cr, fplog);
+ if (hw_opt->nthreads_tot > 0 && hw_opt->nthreads_omp <= 0)
+ {
+ hw_opt->nthreads_omp = hw_opt->nthreads_tot/hw_opt->nthreads_tmpi;
+ }
+
+ if (hw_opt->nthreads_tmpi > 1)
+ {
+ /* now start the threads. */
+ cr = mdrunner_start_threads(hw_opt, fplog, cr_old, nfile, fnm,
+ oenv, bVerbose, bCompact, nstglobalcomm,
+ ddxyz, dd_node_order, rdd, rconstr,
+ dddlb_opt, dlb_scale, ddcsx, ddcsy, ddcsz,
+ nbpu_opt,
+ nsteps_cmdline, nstepout, resetstep, nmultisim,
+ repl_ex_nst, repl_ex_nex, repl_ex_seed, pforce,
+ cpt_period, max_hours, deviceOptions,
+ Flags);
+ /* the main thread continues here with a new cr. We don't deallocate
+ the old cr because other threads may still be reading it. */
+ if (cr == NULL)
+ {
+ gmx_comm("Failed to spawn threads");
+ }
+ }
+ }
+#endif
+ /* END OF CAUTION: cr is now reliable */
+
+ /* g_membed initialisation *
+ * Because we change the mtop, init_membed is called before the init_parallel *
+ * (in case we ever want to make it run in parallel) */
+ if (opt2bSet("-membed", nfile, fnm))
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "Initializing membed");
+ }
+ membed = init_membed(fplog, nfile, fnm, mtop, inputrec, state, cr, &cpt_period);
+ }
+
+ if (PAR(cr))
+ {
+ /* now broadcast everything to the non-master nodes/threads: */
+ init_parallel(fplog, cr, inputrec, mtop);
+
+ /* This check needs to happen after get_nthreads_mpi() */
+ if (inputrec->cutoff_scheme == ecutsVERLET && (Flags & MD_PARTDEC))
+ {
+ gmx_fatal_collective(FARGS, cr, NULL,
+ "The Verlet cut-off scheme is not supported with particle decomposition.\n"
+ "You can achieve the same effect as particle decomposition by running in parallel using only OpenMP threads.");
+ }
+ }
+ if (fplog != NULL)
+ {
+ pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
+ }
+
+#if defined GMX_THREAD_MPI
+ /* With tMPI we detected on thread 0 and we'll just pass the hwinfo pointer
+ * to the other threads -- slightly uncool, but works fine, just need to
+ * make sure that the data doesn't get freed twice. */
+ if (cr->nnodes > 1)
+ {
+ if (!SIMMASTER(cr))
+ {
+ snew(hwinfo, 1);
+ }
+ gmx_bcast(sizeof(&hwinfo), &hwinfo, cr);
+ }
+#else
+ if (PAR(cr) && !SIMMASTER(cr))
+ {
+ /* now we have inputrec on all nodes, can run the detection */
+ /* TODO: perhaps it's better to propagate within a node instead? */
+ snew(hwinfo, 1);
+ gmx_detect_hardware(fplog, hwinfo, cr,
+ bForceUseGPU, bTryUseGPU, hw_opt->gpu_id);
+ }
+
+ /* Now do the affinity check with MPI/no-MPI (done earlier with thread-MPI). */
+ gmx_check_thread_affinity_set(fplog, cr,
+ hw_opt, hwinfo->nthreads_hw_avail, FALSE);
+#endif
+
+ /* now make sure the state is initialized and propagated */
+ set_state_entries(state, inputrec, cr->nnodes);
+
+ /* A parallel command line option consistency check that we can
+ only do after any threads have started. */
+ if (!PAR(cr) &&
+ (ddxyz[XX] > 1 || ddxyz[YY] > 1 || ddxyz[ZZ] > 1 || cr->npmenodes > 0))
+ {
+ gmx_fatal(FARGS,
+ "The -dd or -npme option request a parallel simulation, "
+#ifndef GMX_MPI
+ "but %s was compiled without threads or MPI enabled"
+#else
+#ifdef GMX_THREAD_MPI
+ "but the number of threads (option -nt) is 1"
+#else
+ "but %s was not started through mpirun/mpiexec or only one process was requested through mpirun/mpiexec"
+#endif
+#endif
+ , ShortProgram()
+ );
+ }
+
+ if ((Flags & MD_RERUN) &&
+ (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
+ {
+ gmx_fatal(FARGS, "The .mdp file specified an energy mininization or normal mode algorithm, and these are not compatible with mdrun -rerun");
+ }
+
+ if (can_use_allvsall(inputrec, mtop, TRUE, cr, fplog) && PAR(cr))
+ {
- finish_rot(fplog, inputrec->rot);
++ /* Simple neighbour searching and (also?) all-vs-all loops
++ * do not work with domain decomposition. */
+ Flags |= MD_PARTDEC;
+ }
+
+ if (!EEL_PME(inputrec->coulombtype) || (Flags & MD_PARTDEC))
+ {
+ if (cr->npmenodes > 0)
+ {
+ if (!EEL_PME(inputrec->coulombtype))
+ {
+ gmx_fatal_collective(FARGS, cr, NULL,
+ "PME nodes are requested, but the system does not use PME electrostatics");
+ }
+ if (Flags & MD_PARTDEC)
+ {
+ gmx_fatal_collective(FARGS, cr, NULL,
+ "PME nodes are requested, but particle decomposition does not support separate PME nodes");
+ }
+ }
+
+ cr->npmenodes = 0;
+ }
+
+#ifdef GMX_FAHCORE
+ fcRegisterSteps(inputrec->nsteps, inputrec->init_step);
+#endif
+
+ /* NMR restraints must be initialized before load_checkpoint,
+ * since with time averaging the history is added to t_state.
+ * For proper consistency check we therefore need to extend
+ * t_state here.
+ * So the PME-only nodes (if present) will also initialize
+ * the distance restraints.
+ */
+ snew(fcd, 1);
+
+ /* This needs to be called before read_checkpoint to extend the state */
+ init_disres(fplog, mtop, inputrec, cr, Flags & MD_PARTDEC, fcd, state, repl_ex_nst > 0);
+
+ if (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0)
+ {
+ if (PAR(cr) && !(Flags & MD_PARTDEC))
+ {
+ gmx_fatal(FARGS, "Orientation restraints do not work (yet) with domain decomposition, use particle decomposition (mdrun option -pd)");
+ }
+ /* Orientation restraints */
+ if (MASTER(cr))
+ {
+ init_orires(fplog, mtop, state->x, inputrec, cr->ms, &(fcd->orires),
+ state);
+ }
+ }
+
+ if (DEFORM(*inputrec))
+ {
+ /* Store the deform reference box before reading the checkpoint */
+ if (SIMMASTER(cr))
+ {
+ copy_mat(state->box, box);
+ }
+ if (PAR(cr))
+ {
+ gmx_bcast(sizeof(box), box, cr);
+ }
+ /* Because we do not have the update struct available yet
+ * in which the reference values should be stored,
+ * we store them temporarily in static variables.
+ * This should be thread safe, since they are only written once
+ * and with identical values.
+ */
+#ifdef GMX_THREAD_MPI
+ tMPI_Thread_mutex_lock(&deform_init_box_mutex);
+#endif
+ deform_init_init_step_tpx = inputrec->init_step;
+ copy_mat(box, deform_init_box_tpx);
+#ifdef GMX_THREAD_MPI
+ tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
+#endif
+ }
+
+ if (opt2bSet("-cpi", nfile, fnm))
+ {
+ /* Check if checkpoint file exists before doing continuation.
+ * This way we can use identical input options for the first and subsequent runs...
+ */
+ if (gmx_fexist_master(opt2fn_master("-cpi", nfile, fnm, cr), cr) )
+ {
+ load_checkpoint(opt2fn_master("-cpi", nfile, fnm, cr), &fplog,
+ cr, Flags & MD_PARTDEC, ddxyz,
+ inputrec, state, &bReadRNG, &bReadEkin,
+ (Flags & MD_APPENDFILES),
+ (Flags & MD_APPENDFILESSET));
+
+ if (bReadRNG)
+ {
+ Flags |= MD_READ_RNG;
+ }
+ if (bReadEkin)
+ {
+ Flags |= MD_READ_EKIN;
+ }
+ }
+ }
+
+ 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
+ )
+ {
+ gmx_log_open(ftp2fn(efLOG, nfile, fnm), cr, !(Flags & MD_SEPPOT),
+ Flags, &fplog);
+ }
+
+ /* override nsteps with value from cmdline */
+ override_nsteps_cmdline(fplog, nsteps_cmdline, inputrec, cr);
+
+ if (SIMMASTER(cr))
+ {
+ copy_mat(state->box, box);
+ }
+
+ if (PAR(cr))
+ {
+ gmx_bcast(sizeof(box), box, cr);
+ }
+
+ /* Essential dynamics */
+ if (opt2bSet("-ei", nfile, fnm))
+ {
+ /* Open input and output files, allocate space for ED data structure */
+ ed = ed_open(mtop->natoms, &state->edsamstate, nfile, fnm, Flags, oenv, cr);
+ }
+
+ if (PAR(cr) && !((Flags & MD_PARTDEC) ||
+ EI_TPI(inputrec->eI) ||
+ inputrec->eI == eiNM))
+ {
+ cr->dd = init_domain_decomposition(fplog, cr, Flags, ddxyz, rdd, rconstr,
+ dddlb_opt, dlb_scale,
+ ddcsx, ddcsy, ddcsz,
+ mtop, inputrec,
+ box, state->x,
+ &ddbox, &npme_major, &npme_minor);
+
+ make_dd_communicators(fplog, cr, dd_node_order);
+
+ /* Set overallocation to avoid frequent reallocation of arrays */
+ set_over_alloc_dd(TRUE);
+ }
+ else
+ {
+ /* PME, if used, is done on all nodes with 1D decomposition */
+ cr->npmenodes = 0;
+ cr->duty = (DUTY_PP | DUTY_PME);
+ npme_major = 1;
+ npme_minor = 1;
+ if (!EI_TPI(inputrec->eI))
+ {
+ npme_major = cr->nnodes;
+ }
+
+ if (inputrec->ePBC == epbcSCREW)
+ {
+ gmx_fatal(FARGS,
+ "pbc=%s is only implemented with domain decomposition",
+ epbc_names[inputrec->ePBC]);
+ }
+ }
+
+ if (PAR(cr))
+ {
+ /* After possible communicator splitting in make_dd_communicators.
+ * we can set up the intra/inter node communication.
+ */
+ gmx_setup_nodecomm(fplog, cr);
+ }
+
+ /* Initialize per-physical-node MPI process/thread ID and counters. */
+ gmx_init_intranode_counters(cr);
+
+#ifdef GMX_MPI
+ md_print_info(cr, fplog, "Using %d MPI %s\n",
+ cr->nnodes,
+#ifdef GMX_THREAD_MPI
+ cr->nnodes == 1 ? "thread" : "threads"
+#else
+ cr->nnodes == 1 ? "process" : "processes"
+#endif
+ );
+ fflush(stderr);
+#endif
+
+ gmx_omp_nthreads_init(fplog, cr,
+ hwinfo->nthreads_hw_avail,
+ hw_opt->nthreads_omp,
+ hw_opt->nthreads_omp_pme,
+ (cr->duty & DUTY_PP) == 0,
+ inputrec->cutoff_scheme == ecutsVERLET);
+
+ gmx_check_hw_runconf_consistency(fplog, hwinfo, cr, hw_opt->nthreads_tmpi, minf.bUseGPU);
+
+ /* getting number of PP/PME threads
+ PME: env variable should be read only on one node to make sure it is
+ identical everywhere;
+ */
+ /* TODO nthreads_pp is only used for pinning threads.
+ * This is a temporary solution until we have a hw topology library.
+ */
+ nthreads_pp = gmx_omp_nthreads_get(emntNonbonded);
+ nthreads_pme = gmx_omp_nthreads_get(emntPME);
+
+ wcycle = wallcycle_init(fplog, resetstep, cr, nthreads_pp, nthreads_pme);
+
+ if (PAR(cr))
+ {
+ /* Master synchronizes its value of reset_counters with all nodes
+ * including PME only nodes */
+ reset_counters = wcycle_get_reset_counters(wcycle);
+ gmx_bcast_sim(sizeof(reset_counters), &reset_counters, cr);
+ wcycle_set_reset_counters(wcycle, reset_counters);
+ }
+
+ snew(nrnb, 1);
+ if (cr->duty & DUTY_PP)
+ {
+ /* For domain decomposition we allocate dynamically
+ * in dd_partition_system.
+ */
+ if (DOMAINDECOMP(cr))
+ {
+ bcast_state_setup(cr, state);
+ }
+ else
+ {
+ if (PAR(cr))
+ {
+ bcast_state(cr, state, TRUE);
+ }
+ }
+
+ /* Initiate forcerecord */
+ fr = mk_forcerec();
+ fr->hwinfo = hwinfo;
+ init_forcerec(fplog, oenv, fr, fcd, inputrec, mtop, cr, box, FALSE,
+ opt2fn("-table", nfile, fnm),
+ opt2fn("-tabletf", nfile, fnm),
+ opt2fn("-tablep", nfile, fnm),
+ opt2fn("-tableb", nfile, fnm),
+ nbpu_opt,
+ FALSE, pforce);
+
+ /* version for PCA_NOT_READ_NODE (see md.c) */
+ /*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)
+ {
+ init_QMMMrec(cr, box, mtop, inputrec, fr);
+ }
+
+ /* Initialize the mdatoms structure.
+ * mdatoms is not filled with atom data,
+ * as this can not be done now with domain decomposition.
+ */
+ mdatoms = init_mdatoms(fplog, mtop, inputrec->efep != efepNO);
+
+ if (mdatoms->nPerturbed > 0 && inputrec->cutoff_scheme == ecutsVERLET)
+ {
+ gmx_fatal(FARGS, "The Verlet cut-off scheme does not (yet) support free-energy calculations with perturbed atoms, only perturbed interactions. This will be implemented soon. Use the group scheme for now.");
+ }
+
+ /* Initialize the virtual site communication */
+ vsite = init_vsite(mtop, cr, FALSE);
+
+ calc_shifts(box, fr->shift_vec);
+
+ /* With periodic molecules the charge groups should be whole at start up
+ * and the virtual sites should not be far from their proper positions.
+ */
+ if (!inputrec->bContinuation && MASTER(cr) &&
+ !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols))
+ {
+ /* Make molecules whole at start of run */
+ if (fr->ePBC != epbcNONE)
+ {
+ do_pbc_first_mtop(fplog, inputrec->ePBC, box, mtop, state->x);
+ }
+ if (vsite)
+ {
+ /* Correct initial vsite positions are required
+ * for the initial distribution in the domain decomposition
+ * and for the initial shell prediction.
+ */
+ construct_vsites_mtop(fplog, vsite, mtop, state->x);
+ }
+ }
+
+ if (EEL_PME(fr->eeltype))
+ {
+ ewaldcoeff = fr->ewaldcoeff;
+ pmedata = &fr->pmedata;
+ }
+ else
+ {
+ pmedata = NULL;
+ }
+ }
+ else
+ {
+ /* This is a PME only node */
+
+ /* We don't need the state */
+ done_state(state);
+
+ ewaldcoeff = calc_ewaldcoeff(inputrec->rcoulomb, inputrec->ewald_rtol);
+ snew(pmedata, 1);
+ }
+
+ if (hw_opt->thread_affinity != threadaffOFF)
+ {
+ /* Before setting affinity, check whether the affinity has changed
+ * - which indicates that probably the OpenMP library has changed it
+ * since we first checked).
+ */
+ gmx_check_thread_affinity_set(fplog, cr,
+ hw_opt, hwinfo->nthreads_hw_avail, TRUE);
+
+ /* Set the CPU affinity */
+ gmx_set_thread_affinity(fplog, cr, hw_opt, nthreads_pme, hwinfo, inputrec);
+ }
+
+ /* Initiate PME if necessary,
+ * either on all nodes or on dedicated PME nodes only. */
+ if (EEL_PME(inputrec->coulombtype))
+ {
+ if (mdatoms)
+ {
+ nChargePerturbed = mdatoms->nChargePerturbed;
+ }
+ if (cr->npmenodes > 0)
+ {
+ /* The PME only nodes need to know nChargePerturbed */
+ gmx_bcast_sim(sizeof(nChargePerturbed), &nChargePerturbed, cr);
+ }
+
+ if (cr->duty & DUTY_PME)
+ {
+ status = gmx_pme_init(pmedata, cr, npme_major, npme_minor, inputrec,
+ mtop ? mtop->natoms : 0, nChargePerturbed,
+ (Flags & MD_REPRODUCIBLE), nthreads_pme);
+ if (status != 0)
+ {
+ gmx_fatal(FARGS, "Error %d initializing PME", status);
+ }
+ }
+ }
+
+
+ if (integrator[inputrec->eI].func == do_md)
+ {
+ /* Turn on signal handling on all nodes */
+ /*
+ * (A user signal from the PME nodes (if any)
+ * is communicated to the PP nodes.
+ */
+ signal_handler_install();
+ }
+
+ if (cr->duty & DUTY_PP)
+ {
+ if (inputrec->ePull != epullNO)
+ {
+ /* Initialize pull code */
+ init_pull(fplog, inputrec, nfile, fnm, mtop, cr, oenv, inputrec->fepvals->init_lambda,
+ EI_DYNAMICS(inputrec->eI) && MASTER(cr), Flags);
+ }
+
+ if (inputrec->bRot)
+ {
+ /* Initialize enforced rotation code */
+ init_rot(fplog, inputrec, nfile, fnm, cr, state->x, box, mtop, oenv,
+ bVerbose, Flags);
+ }
+
+ constr = init_constraints(fplog, mtop, inputrec, ed, state, cr);
+
+ if (DOMAINDECOMP(cr))
+ {
+ dd_init_bondeds(fplog, cr->dd, mtop, vsite, constr, inputrec,
+ Flags & MD_DDBONDCHECK, fr->cginfo_mb);
+
+ set_dd_parameters(fplog, cr->dd, dlb_scale, inputrec, fr, &ddbox);
+
+ setup_dd_grid(fplog, cr->dd);
+ }
+
+ /* Now do whatever the user wants us to do (how flexible...) */
+ integrator[inputrec->eI].func(fplog, cr, nfile, fnm,
+ oenv, bVerbose, bCompact,
+ nstglobalcomm,
+ vsite, constr,
+ nstepout, inputrec, mtop,
+ fcd, state,
+ mdatoms, nrnb, wcycle, ed, fr,
+ repl_ex_nst, repl_ex_nex, repl_ex_seed,
+ membed,
+ cpt_period, max_hours,
+ deviceOptions,
+ Flags,
+ &runtime);
+
+ if (inputrec->ePull != epullNO)
+ {
+ finish_pull(fplog, inputrec->pull);
+ }
+
+ if (inputrec->bRot)
+ {
++ finish_rot(inputrec->rot);
+ }
+
+ }
+ else
+ {
+ /* do PME only */
+ gmx_pmeonly(*pmedata, cr, nrnb, wcycle, ewaldcoeff, FALSE, inputrec);
+ }
+
+ if (EI_DYNAMICS(inputrec->eI) || EI_TPI(inputrec->eI))
+ {
+ /* Some timing stats */
+ if (SIMMASTER(cr))
+ {
+ if (runtime.proc == 0)
+ {
+ runtime.proc = runtime.real;
+ }
+ }
+ else
+ {
+ runtime.real = 0;
+ }
+ }
+
+ wallcycle_stop(wcycle, ewcRUN);
+
+ /* Finish up, write some stuff
+ * if rerunMD, don't write last frame again
+ */
+ finish_run(fplog, cr, ftp2fn(efSTO, nfile, fnm),
+ inputrec, nrnb, wcycle, &runtime,
+ fr != NULL && fr->nbv != NULL && fr->nbv->bUseGPU ?
+ nbnxn_cuda_get_timings(fr->nbv->cu_nbv) : NULL,
+ nthreads_pp,
+ EI_DYNAMICS(inputrec->eI) && !MULTISIM(cr));
+
+ if ((cr->duty & DUTY_PP) && fr->nbv != NULL && fr->nbv->bUseGPU)
+ {
+ char gpu_err_str[STRLEN];
+
+ /* free GPU memory and uninitialize GPU (by destroying the context) */
+ nbnxn_cuda_free(fplog, fr->nbv->cu_nbv);
+
+ if (!free_gpu(gpu_err_str))
+ {
+ gmx_warning("On node %d failed to free GPU #%d: %s",
+ cr->nodeid, get_current_gpu_device_id(), gpu_err_str);
+ }
+ }
+
+ if (opt2bSet("-membed", nfile, fnm))
+ {
+ sfree(membed);
+ }
+
+#ifdef GMX_THREAD_MPI
+ if (PAR(cr) && SIMMASTER(cr))
+#endif
+ {
+ gmx_hardware_info_free(hwinfo);
+ }
+
+ /* Does what it says */
+ print_date_and_time(fplog, cr->nodeid, "Finished mdrun", &runtime);
+
+ /* Close logfile already here if we were appending to it */
+ if (MASTER(cr) && (Flags & MD_APPENDFILES))
+ {
+ gmx_log_close(fplog);
+ }
+
+ rc = (int)gmx_get_stop_condition();
+
+#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
+ wait for that. */
+ if (PAR(cr) && MASTER(cr))
+ {
+ tMPI_Finalize();
+ }
+#endif
+
+ return rc;
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff